From: Charles Plessy Date: Sun, 9 Jan 2011 13:59:27 +0000 (+0900) Subject: # Bibliographic entries X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=198b8aac6fbb005b292085b16a3ebb244c2b92be;p=source%2F.git # Bibliographic entries --- diff --git a/biblio.mdwn b/biblio.mdwn new file mode 100644 index 00000000..2008f340 --- /dev/null +++ b/biblio.mdwn @@ -0,0 +1,2 @@ +[[!pagestats pages="biblio/tags/*"]] +[[!inline pages="biblio/* and !biblio/tags/* and !biblio/template*"]] diff --git a/biblio/10037822.mdwn b/biblio/10037822.mdwn new file mode 100644 index 00000000..222e5c0c --- /dev/null +++ b/biblio/10037822.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Amplification of cDNA ends based on template-switching effect and step-out PCR."]] +[[!tag amplification]] +[[!pmid 10037822 desc="Uses PCR-Suppression effect to limit background in 5'RACE, due to "non specific" template switching."]] diff --git a/biblio/10378372.mdwn b/biblio/10378372.mdwn new file mode 100644 index 00000000..3239a596 --- /dev/null +++ b/biblio/10378372.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Quantitative analysis of NF1 and OMGP gene transcripts in sporadic gliomas, sporadic meningiomas and neurofibromatosis type 1-associated plexiform neurofibromas."]] +[[!tag normaisation qPCR]] +[[!pmid 10378372 desc="GAPD can vary strongly between samples. Normalising on the quantity of input mRNA may be wiser."]] diff --git a/biblio/10445153.mdwn b/biblio/10445153.mdwn new file mode 100644 index 00000000..617d9a08 --- /dev/null +++ b/biblio/10445153.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Nuclear snRNA and nuclear function (discovery of 5' cap structures in RNA)."]] +[[!tag cap review]] +[[!pmid 10445153 desc="Comprehensive review about caps."]] diff --git a/biblio/10518626.mdwn b/biblio/10518626.mdwn new file mode 100644 index 00000000..f7702e42 --- /dev/null +++ b/biblio/10518626.mdwn @@ -0,0 +1,3 @@ +[[!meta title="CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs."]] +[[!tag cap methods enzyme]] +[[!pmid 10518626 desc="In presence of the 5' cap and Mn2+, the SuperScriptII enzyme adds 3-4 extra dC residues to the first strand cDNA."]] diff --git a/biblio/10573121.mdwn b/biblio/10573121.mdwn new file mode 100644 index 00000000..702aabfc --- /dev/null +++ b/biblio/10573121.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Aberrant mRNAs with extended 3’ UTRs are substrates for rapid degradation by mRNA surveillance."]] +[[!tag 3′UTR]] +[[!pmid 10573121 desc="“Abnormally 3’-extended mRNAs are degraded by the same machinery that degrades mRNAs with premature nonsense codons”"]] diff --git a/biblio/10657981.mdwn b/biblio/10657981.mdwn new file mode 100644 index 00000000..3506a921 --- /dev/null +++ b/biblio/10657981.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells."]] +[[!tag transcription non-coding]] +[[!pmid 10657981 desc="Provides essential references about nuclear non-coding RNAs."]] diff --git a/biblio/10748532.mdwn b/biblio/10748532.mdwn new file mode 100644 index 00000000..6ab3a03a --- /dev/null +++ b/biblio/10748532.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-fidelity mRNA amplification for gene profiling."]] +[[!tag amplification]] +[[!pmid 10748532 desc="Combines template switch with aRNA amplification"]] diff --git a/biblio/10985772.mdwn b/biblio/10985772.mdwn new file mode 100644 index 00000000..e3377081 --- /dev/null +++ b/biblio/10985772.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes."]] +[[!tag hybridisation oligonucleotides]] +[[!pmid 10985772 desc="Some DNA/RNA mismatches are less unstable than some DNA/DNA mismatches."]] diff --git a/biblio/11063259.mdwn b/biblio/11063259.mdwn new file mode 100644 index 00000000..7e7c3555 --- /dev/null +++ b/biblio/11063259.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The olfactory receptor gene superfamily: data mining, classification, and nomenclature."]] +[[!tag olfaction nomenclature]] +[[!pmid 11063259 desc="Does not seem to be followed anymore."]] diff --git a/biblio/11071950.mdwn b/biblio/11071950.mdwn new file mode 100644 index 00000000..4310d57a --- /dev/null +++ b/biblio/11071950.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A simple and reliable 5'-RACE approach."]] +[[!tag amplification]] +[[!pmid 11071950 desc="Removes the primer artefacts by physical separation on beads."]] diff --git a/biblio/11170746.mdwn b/biblio/11170746.mdwn new file mode 100644 index 00000000..fda3aa4e --- /dev/null +++ b/biblio/11170746.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Mouse-human orthology relationships in an olfactory receptor gene cluster."]] +[[!tag olfaction]] +[[!pmid 11170746 desc="Found Ikaros motifs near promoters of olfactory receptors."]] diff --git a/biblio/11416212.mdwn b/biblio/11416212.mdwn new file mode 100644 index 00000000..f1992fc3 --- /dev/null +++ b/biblio/11416212.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genomic analysis of orthologous mouse and human olfactory receptor loci."]] +[[!tag olfaction]] +[[!pmid 11416212 desc="Found Ikaros motifs."]] diff --git a/biblio/11464524.mdwn b/biblio/11464524.mdwn new file mode 100644 index 00000000..3994d208 --- /dev/null +++ b/biblio/11464524.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Increased yield of PCR products by addition of T4 gene 32 protein to the SMART PCR cDNA synthesis system."]] +[[!tag enzyme methods amplification template_switching]] +[[!pmid 11464524 desc="The T4gp32 protein is directly added to the RNA."]] diff --git a/biblio/11553460.mdwn b/biblio/11553460.mdwn new file mode 100644 index 00000000..c7f37cbf --- /dev/null +++ b/biblio/11553460.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Molecular recognition of DNA by small molecules."]] +[[!tag review method promoter silencing]] +[[!pmid 11553460 desc="A review on the discovery of sequence-specific non-nucleotidic inhibitors that bind the minor groove."]] diff --git a/biblio/11713326.mdwn b/biblio/11713326.mdwn new file mode 100644 index 00000000..5fe30d03 --- /dev/null +++ b/biblio/11713326.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Detection of the 5'-cap structure of messenger RNAs with the use of the cap-jumping approach."]] +[[!tag cap methods]] +[[!pmid 11713326 desc="Binds an oligonucleotide to the cap using its free diol group, and integrates its sequence to the full-length cDNA using template-switching."]] diff --git a/biblio/11779833.mdwn b/biblio/11779833.mdwn new file mode 100644 index 00000000..527512f1 --- /dev/null +++ b/biblio/11779833.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor alpha/delta loci."]] +[[!tag olfaction]] +[[!pmid 11779833 desc="No evidence for recombination (ORs and TCRs are chromosomal neighbours)."]] diff --git a/biblio/11802173.mdwn b/biblio/11802173.mdwn new file mode 100644 index 00000000..193db7e0 --- /dev/null +++ b/biblio/11802173.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The olfactory receptor gene superfamily of the mouse."]] +[[!tag olfaction superfamily]] +[[!pmid 11802173 desc="Primary paper for the classified predicted ORFs AY072961–AY074256."]] diff --git a/biblio/11814287.mdwn b/biblio/11814287.mdwn new file mode 100644 index 00000000..82f18834 --- /dev/null +++ b/biblio/11814287.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A highly efficient method for long-chain cDNA synthesis using trehalose and betaine."]] +[[!tag thermo-enhancement method enzyme betaine]] +[[!pmid 11814287 desc="Effects of trehalose and betaine on reverse-transcriptase are additive."]] diff --git a/biblio/12019793.mdwn b/biblio/12019793.mdwn new file mode 100644 index 00000000..ab72b02f --- /dev/null +++ b/biblio/12019793.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Extra-long first-strand cDNA synthesis."]] +[[!tag thermo-enhancement libraries]] +[[!pmid 12019793 desc="First publication of our laboratory using a mixture of trehalose and sorbitol. T4gp32 does not seem to improve trehalose-enhanced protocols at standard concentrations."]] diff --git a/biblio/12368261.mdwn b/biblio/12368261.mdwn new file mode 100644 index 00000000..a6f6e334 --- /dev/null +++ b/biblio/12368261.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins."]] +[[!tag small_RNA ribosome]] +[[!pmid 12368261 desc="One more article challenging the concept of house-keeping gene."]] diff --git a/biblio/12397315.mdwn b/biblio/12397315.mdwn new file mode 100644 index 00000000..da3c1cea --- /dev/null +++ b/biblio/12397315.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Super-enzyme patents get their day in court."]] +[[!tag intellectual-property patent]] +[[!pmid 12397315 desc="Some commercial kits contain dangerous clauses about the property of the products made with them."]] diff --git a/biblio/12462399.mdwn b/biblio/12462399.mdwn new file mode 100644 index 00000000..1b2ad8a5 --- /dev/null +++ b/biblio/12462399.mdwn @@ -0,0 +1,3 @@ +[[!meta title="RNA Amplification in Brain Tissues."]] +[[!tag template_switching]] +[[!pmid 12462399 desc="Comparison of template swithching oligos ending in -AAA, -CCC, -GGG or -TTT. No qualitative difference for the CCC and GGG variants were reported."]] diff --git a/biblio/12637542.mdwn b/biblio/12637542.mdwn new file mode 100644 index 00000000..9a0208d5 --- /dev/null +++ b/biblio/12637542.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Complex transcription and splicing of odorant receptor genes."]] +[[!tag olfaction promoters]] +[[!pmid 12637542 desc="Cases of multiple promoters, shortened CDS and truncated transcripts detected by RACE-PCR."]] diff --git a/biblio/12661155.mdwn b/biblio/12661155.mdwn new file mode 100644 index 00000000..43d50b07 --- /dev/null +++ b/biblio/12661155.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Mapping of transcription start sites by direct sequencing of SMART RACE products."]] +[[!tag methods transcription cap]] +[[!pmid 12661155 desc="Notes that the detected five prime end is frequently off for one or two bases, and supposes that the presence of the cap interferes with the proper recognition of the terminal nucleotides."]] diff --git a/biblio/12730373.mdwn b/biblio/12730373.mdwn new file mode 100644 index 00000000..9bae749c --- /dev/null +++ b/biblio/12730373.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Digital genotyping and haplotyping with polymerase colonies."]] +[[!tag polony genetics]] +[[!pmid 12730373 desc="SNP are read using single base extension, and haplotype reconstituted according to the overlapping SBE colonies."]] diff --git a/biblio/12895469.mdwn b/biblio/12895469.mdwn new file mode 100644 index 00000000..9d1459ae --- /dev/null +++ b/biblio/12895469.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Fluorescent in situ sequencing on polymerase colonies."]] +[[!tag polony]] +[[!pmid 12895469 desc="Trapping polymerase in the gel ensures that there is no dephasing. Rate-limiting primer concentration during amplification reduces the overlap of polonies through mutual growth inihibition."]] diff --git a/biblio/13115372.mdwn b/biblio/13115372.mdwn new file mode 100644 index 00000000..25509017 --- /dev/null +++ b/biblio/13115372.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The bases of the nucleic acids of some bacterial and animal viruses: the occurrence of 5-hydroxymethylcytosine."]] +[[!tag biochemistry nucleotides]] +[[!pmid 13115372 desc="Discovery of HMC viruses like phage T4."]] diff --git a/biblio/1324170.mdwn b/biblio/1324170.mdwn new file mode 100644 index 00000000..128035d9 --- /dev/null +++ b/biblio/1324170.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Human beta-globin mRNAs that harbor a nonsense codon are degraded in murine erythroid tissues to intermediates lacking regions of exon I or exons I and II that have a cap-like structure at the 5' termini."]] +[[!tag cap]] +[[!pmid 1324170 desc="The capped products appear together with the full length mRNA, and are found in the cytoplasmic compartment. Their expression ratios with the full length are differents in different tissues."]] diff --git a/biblio/14076688.mdwn b/biblio/14076688.mdwn new file mode 100644 index 00000000..1c478dcc --- /dev/null +++ b/biblio/14076688.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Use of alkyltrimethylammonium bromides for the isolation of ribo- and desoxyribo-nucleic acids."]] +[[!tag methods purification]] +[[!pmid 14076688 desc="Shows the concentration-dependant solubility of CTAB-DNA salts in NaCl."]] diff --git a/biblio/14611657.mdwn b/biblio/14611657.mdwn new file mode 100644 index 00000000..cc928a25 --- /dev/null +++ b/biblio/14611657.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Odorant receptor expressed sequence tags demonstrate olfactory expression of over 400 genes, extensive alternate splicing and unequal expression levels."]] +[[!tag olfaction cDNA]] +[[!pmid 14611657 desc="1264 full length cDNAs, using common and alternative promoters, expressed at different levels. Class I is particularly low-expressed."]] diff --git a/biblio/15028277.mdwn b/biblio/15028277.mdwn new file mode 100644 index 00000000..829aa676 --- /dev/null +++ b/biblio/15028277.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-accuracy amplification of nanogram total RNA amounts for gene profiling."]] +[[!tag enzyme ssbp]] +[[!pmid 15028277 desc="Augment temperature, lower primer concentration, and add T4gp32 to enhance reverse transcription."]] diff --git a/biblio/15035624.mdwn b/biblio/15035624.mdwn new file mode 100644 index 00000000..5d5006be --- /dev/null +++ b/biblio/15035624.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures."]] +[[!tag oligonucleotides hybridisation]] +[[!pmid 15035624 desc="Has a table of melting temperatures for 92 oligos at 5 different sodium concentrations."]] diff --git a/biblio/15155949.mdwn b/biblio/15155949.mdwn new file mode 100644 index 00000000..6486115c --- /dev/null +++ b/biblio/15155949.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genetic structure of the purebred domestic dog."]] +[[!tag dog]] +[[!pmid 15155949 desc="Most of the modern dog breeds are more related than expected."]] diff --git a/biblio/15198809.mdwn b/biblio/15198809.mdwn new file mode 100644 index 00000000..dae019cf --- /dev/null +++ b/biblio/15198809.mdwn @@ -0,0 +1,3 @@ +[[!meta title="SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones."]] +[[!tag amplification fractionation]] +[[!pmid 15198809 desc="Size fractionnation using 2D agarose gel."]] diff --git a/biblio/15223348.mdwn b/biblio/15223348.mdwn new file mode 100644 index 00000000..a7c14649 --- /dev/null +++ b/biblio/15223348.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Separable enhancer sequences regulate the expression of the neural bHLH transcription factor neurogenin 1."]] +[[!tag neurogenin]] +[[!pmid 15223348 desc="Characterisation of a mouse dorsal neural tube enhancer, homologous to the zebrafish LATE element."]] diff --git a/biblio/15289471.mdwn b/biblio/15289471.mdwn new file mode 100644 index 00000000..eb06082b --- /dev/null +++ b/biblio/15289471.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Regional patterns of gene expression in human and chimpanzee brains."]] +[[!tag chimpanzee brain visual-cortex variability]] +[[!pmid 15289471 desc="Individual variations are stronger than regional variations in cortex. Developmental genes are implicated in inter-reigonal, but not inter-species variations. Differential interspecific variation correlates with recent chromosomal duplications."]] diff --git a/biblio/15314641.mdwn b/biblio/15314641.mdwn new file mode 100644 index 00000000..8898d444 --- /dev/null +++ b/biblio/15314641.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Gene loops juxtapose promoters and terminators in yeast."]] +[[!tag chromatin 5′UTR 3′UTR]] +[[!pmid 15314641 desc="Uses run-on, ChIP, and 3C to demonstrate the existence of a loop structure in the FMP27 gene (and ChIP for the SEN1 gene)."]] diff --git a/biblio/15353588.mdwn b/biblio/15353588.mdwn new file mode 100644 index 00000000..77e93dce --- /dev/null +++ b/biblio/15353588.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Molecular basis for catecholaminergic neuron diversity."]] +[[!tag catecholaminergic rat laser-capture microarray]] +[[!pmid 15353588 desc="Rat cDNA microarray analysis with laser-capture microdissected cells identify markers for subpopulations."]] diff --git a/biblio/15377787.mdwn b/biblio/15377787.mdwn new file mode 100644 index 00000000..1be26eca --- /dev/null +++ b/biblio/15377787.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-throughput microarray detection of olfactory receptor gene expression in the mouse."]] +[[!tag olfaction microarray]] +[[!pmid 15377787 desc="Microarray with custom 3’ probes. Developmental profile of olfactory receptors. Some olfactory receptors that are mostly expressed in the same zone cluster on the genome."]] diff --git a/biblio/15469847.mdwn b/biblio/15469847.mdwn new file mode 100644 index 00000000..307a01cd --- /dev/null +++ b/biblio/15469847.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos."]] +[[!tag promoter repeats embryo]] +[[!pmid 15469847 desc="Transcription initiation start sites in transposons can be alternative promoters for many genes in the mouse oocytes."]] diff --git a/biblio/1549778.mdwn b/biblio/1549778.mdwn new file mode 100644 index 00000000..5c98b6bb --- /dev/null +++ b/biblio/1549778.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Cyclic 2',3'-phosphates and nontemplated nucleotides at the 3' end of spliceosomal U6 small nuclear RNA's."]] +[[!tag misc]] +[[!pmid 1549778 desc="Can we capture this with specialised tRNA ligases?"]] diff --git a/biblio/15500255.mdwn b/biblio/15500255.mdwn new file mode 100644 index 00000000..abe68a21 --- /dev/null +++ b/biblio/15500255.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Determination of the capped site sequence of mRNA based on the detection of cap-dependent nucleotide addition using an anchor ligation method."]] +[[!tag cap enzyme]] +[[!pmid 15500255 desc="ADP cap templates extra T in the first strand cDNA."]] diff --git a/biblio/15520289.mdwn b/biblio/15520289.mdwn new file mode 100644 index 00000000..4544374d --- /dev/null +++ b/biblio/15520289.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity."]] +[[!tag cap enzyme]] +[[!pmid 15520289 desc="The presence of an extra G in pseudogenes suggests that many reverse-transcriptases can reverse transcribe the cap."]] diff --git a/biblio/15556860.mdwn b/biblio/15556860.mdwn new file mode 100644 index 00000000..91847555 --- /dev/null +++ b/biblio/15556860.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa."]] +[[!tag cap small_RNA]] +[[!pmid 15556860 desc="Some metazoan C'/D' snoRNAs are capped"]] diff --git a/biblio/15574958.mdwn b/biblio/15574958.mdwn new file mode 100644 index 00000000..b299c217 --- /dev/null +++ b/biblio/15574958.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Reevaluation and reduction of a PCR bias caused by reannealing of templates."]] +[[!tag PCR amplification bias]] +[[!pmid 15574958 desc="Slow ramp time from melting to annealing normalises concentrations towards 1:1 ratio at high cycles."]] diff --git a/biblio/15611301.mdwn b/biblio/15611301.mdwn new file mode 100644 index 00000000..4750b6e3 --- /dev/null +++ b/biblio/15611301.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Structure-function analysis of the yeast NAD+-dependent tRNA 2'-phosphotransferase Tpt1."]] +[[!tag enzyme]] +[[!pmid 15611301 desc="Could it be used to 2' kinate RNA oligos?"]] diff --git a/biblio/15690449.mdwn b/biblio/15690449.mdwn new file mode 100644 index 00000000..8b9a709d --- /dev/null +++ b/biblio/15690449.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures."]] +[[!tag methods biotin]] +[[!pmid 15690449 desc="One second at seventy degrees separates biotin from streptavidin."]] diff --git a/biblio/15750340.mdwn b/biblio/15750340.mdwn new file mode 100644 index 00000000..60d1eb64 --- /dev/null +++ b/biblio/15750340.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Identification of a deoxyribonuclease I inhibitor from a phage-peptide library."]] +[[!tag enzyme]] +[[!pmid 15750340 desc="These peptides can compete with monomeric actin, which is also a DNAse I inhibitor."]] diff --git a/biblio/15888489.mdwn b/biblio/15888489.mdwn new file mode 100644 index 00000000..d78388b2 --- /dev/null +++ b/biblio/15888489.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Cell type-specific gene expression of midbrain dopaminergic neurons reveals molecules involved in their vulnerability and protection."]] +[[!tag catecholaminergic microarray laser-capture]] +[[!pmid 15888489 desc="Only 100 genes show a differential expression between A10 and A9 neurons."]] diff --git a/biblio/16026759.mdwn b/biblio/16026759.mdwn new file mode 100644 index 00000000..2fbf05dd --- /dev/null +++ b/biblio/16026759.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I--usefulness in SAGE."]] +[[!tag enzyme products methods sequence_tags]] +[[!pmid 16026759 desc="Sinefungin promotes cleavage of the DNA molecules even if they contain only one EcoP15I site."]] diff --git a/biblio/16056220.mdwn b/biblio/16056220.mdwn new file mode 100644 index 00000000..a54a5bc7 --- /dev/null +++ b/biblio/16056220.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genome sequencing in microfabricated high-density picolitre reactors."]] +[[!tag emulsion sequencing]] +[[!pmid 16056220 desc="Primary reference for “454” sequencing."]] diff --git a/biblio/16081699.mdwn b/biblio/16081699.mdwn new file mode 100644 index 00000000..eef5b622 --- /dev/null +++ b/biblio/16081699.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Accurate multiplex polony sequencing of an evolved bacterial genome."]] +[[!tag polony sequencing]] +[[!pmid 16081699 desc="Estimated a cost of $0.11 per kilobase."]] diff --git a/biblio/16169976.mdwn b/biblio/16169976.mdwn new file mode 100644 index 00000000..8094f413 --- /dev/null +++ b/biblio/16169976.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The solution to the streptavidin-biotin paradox: the influence of history on the strength of single molecular bonds."]] +[[!tag methods biotin]] +[[!pmid 16169976 desc="The strenght of the bond between biotin and streptavidin takes time to reach its maximum."]] diff --git a/biblio/16175253.mdwn b/biblio/16175253.mdwn new file mode 100644 index 00000000..f68730c9 --- /dev/null +++ b/biblio/16175253.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Coating of poly(dimethylsiloxane) with n-dodecyl-beta-D-maltoside to minimize nonspecific protein adsorption."]] +[[!tag lab-chip methods]] +[[!pmid 16175253 desc="Continuous washing is necessary for efficient DDM coating."]] diff --git a/biblio/16204448.mdwn b/biblio/16204448.mdwn new file mode 100644 index 00000000..5a65ab00 --- /dev/null +++ b/biblio/16204448.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Expressible molecular colonies."]] +[[!tag polony]] +[[!pmid 16204448 desc="PCR reaction mix is inhibitory for in vitro translation. Washing in saline alcohol allows coupled in vitro translation on the polonies."]] diff --git a/biblio/16220265.mdwn b/biblio/16220265.mdwn new file mode 100644 index 00000000..fc2892bc --- /dev/null +++ b/biblio/16220265.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Vertebrate neurogenin evolution: long-term maintenance of redundant duplicates."]] +[[!tag neurogenin]] +[[!pmid 16220265 desc="Phylogentic hypothesis on the origin of the neurogenin paralogs."]] diff --git a/biblio/16264087.mdwn b/biblio/16264087.mdwn new file mode 100644 index 00000000..86359976 --- /dev/null +++ b/biblio/16264087.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes."]] +[[!tag oligonucleotides hybridisation]] +[[!pmid 16264087 desc="I:C > I:A > I:T > I:G > I:I, but sequence context also matters."]] diff --git a/biblio/16325480.mdwn b/biblio/16325480.mdwn new file mode 100644 index 00000000..804f1051 --- /dev/null +++ b/biblio/16325480.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Sexually dimorphic expression of the X-linked gene Eif2s3x mRNA but not protein in mouse brain."]] +[[!tag sex brain mouse]] +[[!pmid 16325480 desc="Useful marker do doublecheck sample’s sex."]] diff --git a/biblio/16357227.mdwn b/biblio/16357227.mdwn new file mode 100644 index 00000000..b913a473 --- /dev/null +++ b/biblio/16357227.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C."]] +[[!tag snoRNA small_RNA non-coding]] +[[!pmid 16357227 desc="Example of snoRNA modifying a mRNA."]] diff --git a/biblio/16448564.mdwn b/biblio/16448564.mdwn new file mode 100644 index 00000000..c916d41d --- /dev/null +++ b/biblio/16448564.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The RIN: an RNA integrity number for assigning integrity values to RNA measurements."]] +[[!tag method product RNA]] +[[!pmid 16448564 desc="Primary reference for RINs"]] diff --git a/biblio/16493423.mdwn b/biblio/16493423.mdwn new file mode 100644 index 00000000..ae3ad1d1 --- /dev/null +++ b/biblio/16493423.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Long-range polony haplotyping of individual human chromosome molecules."]] +[[!tag polony genetics]] +[[!pmid 16493423 desc="Chromosomes are frozen, thawn and digested by proteinase before embedding in gels. Haplotypes were determined over more than 150 megabases."]] diff --git a/biblio/1651093.mdwn b/biblio/1651093.mdwn new file mode 100644 index 00000000..6f6f9998 --- /dev/null +++ b/biblio/1651093.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Sequencing the termini of capped viral RNA by 5′-3′ ligation and PCR."]] +[[!tag not_read method cap]] +[[!pmid 1651093 desc="First use of TAP to decap before ligation?"]] diff --git a/biblio/16535713.mdwn b/biblio/16535713.mdwn new file mode 100644 index 00000000..8ddbf976 --- /dev/null +++ b/biblio/16535713.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Stabilization of Enzymes against Thermal Stress and Freeze-Drying by Mannosylglycerate."]] +[[!tag thermo-enhancement]] +[[!pmid 16535713 desc="However, thremoactivation is not assessed…"]] diff --git a/biblio/16547197.mdwn b/biblio/16547197.mdwn new file mode 100644 index 00000000..ae4114d3 --- /dev/null +++ b/biblio/16547197.mdwn @@ -0,0 +1,3 @@ +[[!meta title="An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis."]] +[[!tag amplification]] +[[!pmid 16547197 desc="RNA is reverse-transcribed with oligo dT primers carrying a viral RNA pol. promoter, the first strand cDNAs are A-tailed, the second-strand cDNAs are synthethised with oligo dT primers carrying another viral promoter, and after PCR amplification probes are synthethised by in vitro transcription."]] diff --git a/biblio/16582906.mdwn b/biblio/16582906.mdwn new file mode 100644 index 00000000..b6bea860 --- /dev/null +++ b/biblio/16582906.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Effects of visual experience on activity-dependent gene regulation in cortex."]] +[[!tag microarray visual-cortex]] +[[!pmid 16582906 desc="Pinpoints immediate-early genes."]] diff --git a/biblio/16600568.mdwn b/biblio/16600568.mdwn new file mode 100644 index 00000000..578b0abf --- /dev/null +++ b/biblio/16600568.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Differentially expressed transcripts from phenotypically identified olfactory sensory neurons."]] +[[!tag olfaction promoters gene-structure]] +[[!pmid 15682396 desc="Related OR genes can have a different intron-exon structure and even share promoters."]] diff --git a/biblio/16633343.mdwn b/biblio/16633343.mdwn new file mode 100644 index 00000000..e7b20c46 --- /dev/null +++ b/biblio/16633343.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex."]] +[[!tag visual-cortex microarray]] +[[!pmid 16633343 desc="Microarray analsysis of monocular deprivation and dark rearing."]] diff --git a/biblio/16642997.mdwn b/biblio/16642997.mdwn new file mode 100644 index 00000000..60280045 --- /dev/null +++ b/biblio/16642997.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Microfluidic single-cell mRNA isolation and analysis."]] +[[!tag microfluidics single-cell]] +[[!pmid 16642997 desc="The RNA are manipulated with magnetic beads which carry oliognuclotides serving as support and as RT primers."]] diff --git a/biblio/16708285.mdwn b/biblio/16708285.mdwn new file mode 100644 index 00000000..95500786 --- /dev/null +++ b/biblio/16708285.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Transcriptional regulation of neurogenesis in the olfactory epithelium."]] +[[!tag olfaction review]] +[[!pmid 16708285 desc="Reviews important transcription factors for the development of olfactory neurons."]] diff --git a/biblio/16708763.mdwn b/biblio/16708763.mdwn new file mode 100644 index 00000000..6aa14b65 --- /dev/null +++ b/biblio/16708763.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA."]] +[[!tag protocols cDNA oligonucleotides hybridisation]] +[[!pmid 16708763 desc="Almost 100% of the RNA molecules are primed (using massive amounts of oligonucleotides)."]] diff --git a/biblio/16731615.mdwn b/biblio/16731615.mdwn new file mode 100644 index 00000000..0423a495 --- /dev/null +++ b/biblio/16731615.mdwn @@ -0,0 +1,3 @@ +[[!meta title="tRNAHis guanylyltransferase catalyzes a 3′-5′ polymerization reaction that is distinct from G₋₁ addition."]] +[[!tag enzyme]] +[[!pmid 16731615 desc="Can incorporate dGTP as well."]] diff --git a/biblio/16791213.mdwn b/biblio/16791213.mdwn new file mode 100644 index 00000000..0b2900de --- /dev/null +++ b/biblio/16791213.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Amplification of complex gene libraries by emulsion PCR."]] +[[!tag ]] +[[!pmid 16791213 desc="Protects the templates frome size bias by isolating them from each other."]] diff --git a/biblio/16791214.mdwn b/biblio/16791214.mdwn new file mode 100644 index 00000000..437bfcfb --- /dev/null +++ b/biblio/16791214.mdwn @@ -0,0 +1,3 @@ +[[!meta title="BEAMing: single-molecule PCR on microparticles in water-in-oil emulsion."]] +[[!tag emulsion biotin]] +[[!pmid 16791214 desc="Recommends (in Box 1) a double-biotin to avoid breaking the complexes at high temperatures."]] diff --git a/biblio/16791215.mdwn b/biblio/16791215.mdwn new file mode 100644 index 00000000..791dd70d --- /dev/null +++ b/biblio/16791215.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Directed evolution by in vitro compartmentalization."]] +[[!tag emulsion]] +[[!pmid 16791215 desc="Method for water in oil in water emulsion (w/o/w)."]] diff --git a/biblio/16845422.mdwn b/biblio/16845422.mdwn new file mode 100644 index 00000000..4d96e7df --- /dev/null +++ b/biblio/16845422.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Organization and mobility of water in amorphous and crystalline trehalose."]] +[[!tag methods]] +[[!pmid 16845422 desc="A structural explanation of the protective properties of trehalose."]] diff --git a/biblio/16873069.mdwn b/biblio/16873069.mdwn new file mode 100644 index 00000000..47e30581 --- /dev/null +++ b/biblio/16873069.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Interchromosomal interactions and olfactory receptor choice."]] +[[!tag olfaction]] +[[!pmid 16873069 desc="The H region can associate with OR genes on other chromosomes."]] diff --git a/biblio/1689846.mdwn b/biblio/1689846.mdwn new file mode 100644 index 00000000..58ee7b95 --- /dev/null +++ b/biblio/1689846.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Amplified RNA synthesized from limited quantities of heterogeneous cDNA."]] +[[!tag amplification]] +[[!pmid 1689846 desc="Primary paper for aRNA."]] diff --git a/biblio/16902085.mdwn b/biblio/16902085.mdwn new file mode 100644 index 00000000..757fc3d1 --- /dev/null +++ b/biblio/16902085.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Identification of potential regulatory motifs in odorant receptor genes by analysis of promoter sequences."]] +[[!tag olfaction]] +[[!pmid 16902085 desc="RACE-PCR to get 198 additional OR gene promoters."]] diff --git a/biblio/16963776.mdwn b/biblio/16963776.mdwn new file mode 100644 index 00000000..7ec0dcc2 --- /dev/null +++ b/biblio/16963776.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Dynamic assembly of primers on nucleic acid templates."]] +[[!tag enzyme]] +[[!pmid 16963776 desc="MMuLV reverse-transcriptase can not use 5′ NH₂ 8-mers for DNA-dependant DNA polymerisation."]] diff --git a/biblio/17071717.mdwn b/biblio/17071717.mdwn new file mode 100644 index 00000000..8558a030 --- /dev/null +++ b/biblio/17071717.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Gene expression profiling of single cells on large-scale oligonucleotide arrays."]] +[[!tag single-cell amplification oligonucleotides]] +[[!pmid 17071717 desc="High concentration of a dT and random primers mix in reverse transcription."]] diff --git a/biblio/17135571.mdwn b/biblio/17135571.mdwn new file mode 100644 index 00000000..aa89ed7b --- /dev/null +++ b/biblio/17135571.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines."]] +[[!tag sequence_tags template_switching small_samples]] +[[!pmid 17135571 desc="SMART amplification with less than 50 ng material, but primes with oligo dT."]] diff --git a/biblio/17194496.mdwn b/biblio/17194496.mdwn new file mode 100644 index 00000000..0b068de4 --- /dev/null +++ b/biblio/17194496.mdwn @@ -0,0 +1,3 @@ +[[!meta title="PCR-suppression effect: kinetic analysis and application to representative or long-molecule biased PCR-based amplification of complex samples."]] +[[!tag template_switching]] +[[!pmid 17194496 desc="Uses a 3′ phosphate to prevent the template switching oligonucleotide to prime a first strand cDNA."]] diff --git a/biblio/17204646.mdwn b/biblio/17204646.mdwn new file mode 100644 index 00000000..646c6d09 --- /dev/null +++ b/biblio/17204646.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Counting low-copy number proteins in a single cell."]] +[[!tag lab-chip methods]] +[[!pmid 17204646 desc="Uses n-dodecyl beta-D-maltose for cell lysis."]] diff --git a/biblio/17284461.mdwn b/biblio/17284461.mdwn new file mode 100644 index 00000000..c93f6a46 --- /dev/null +++ b/biblio/17284461.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Biochemical and genetic analysis of RNA cap guanine-N2 methyltransferases from Giardia lamblia and Schizosaccharomyces pombe."]] +[[!tag cap]] +[[!pmid 17284461 desc="S. pombe and G. lamblia can grow in absence of trimethylated caps, like S. cerevisae."]] diff --git a/biblio/17350283.mdwn b/biblio/17350283.mdwn new file mode 100644 index 00000000..d1332385 --- /dev/null +++ b/biblio/17350283.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Differential impact of Lhx2 deficiency on expression of class I and class II odorant receptor genes in mouse."]] +[[!tag olfaction]] +[[!pmid 17350283 desc="Lhx2 is transcribed but not necessary in neurons expressing class I OR genes."]] diff --git a/biblio/17373481.mdwn b/biblio/17373481.mdwn new file mode 100644 index 00000000..ce7e81d8 --- /dev/null +++ b/biblio/17373481.mdwn @@ -0,0 +1,3 @@ +[[!meta title="5′-tailed sequencing primers improve sequencing quality of PCR products."]] +[[!tag sanger sequencing]] +[[!pmid 17373481 desc="A long tail (40 bp, for instance) increases the size of the fragments to separate on gel, and therefore resolution in 5′"]] diff --git a/biblio/17412960.mdwn b/biblio/17412960.mdwn new file mode 100644 index 00000000..0ed669f6 --- /dev/null +++ b/biblio/17412960.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A single IGF1 allele is a major determinant of small size in dogs."]] +[[!tag dog QTL]] +[[!pmid 17412960 desc="First analysis within a breed, then second analysis comparing small and giant breeds."]] diff --git a/biblio/17478416.mdwn b/biblio/17478416.mdwn new file mode 100644 index 00000000..fdf56cfb --- /dev/null +++ b/biblio/17478416.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Differential gene expression between sensory neocortical areas: potential roles for Ten_m3 and Bcl6 in patterning visual and somatosensory pathways."]] +[[!tag microarray visual-cortex]] +[[!pmid 17478416 desc="A comparison with somatosensory cortex show ~120 differentially expressed genes out of ~30,000. However dramatic changes of expression pattern between P0 and adult stages were observed."]] diff --git a/biblio/17509148.mdwn b/biblio/17509148.mdwn new file mode 100644 index 00000000..86ca98d4 --- /dev/null +++ b/biblio/17509148.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray."]] +[[!tag olfaction]] +[[!pmid 17509148 desc="Many human olfactory pseudogenes are expressed."]] diff --git a/biblio/17530926.mdwn b/biblio/17530926.mdwn new file mode 100644 index 00000000..e8bc1765 --- /dev/null +++ b/biblio/17530926.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs."]] +[[!tag dog]] +[[!pmid 17530926 desc="Similar mutations are found in several mammalian species."]] diff --git a/biblio/17556586.mdwn b/biblio/17556586.mdwn new file mode 100644 index 00000000..6558b01b --- /dev/null +++ b/biblio/17556586.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy."]] +[[!tag sequence_tags polony]] +[[!pmid 17556586 desc="14-bp tags. 2,000,000 reads translate into 70,000 unique sequences, for 20,000 different genes."]] diff --git a/biblio/17656108.mdwn b/biblio/17656108.mdwn new file mode 100644 index 00000000..1faf732d --- /dev/null +++ b/biblio/17656108.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Promotor elements governing the clustered expression pattern of odorant receptor genes."]] +[[!tag olfaction]] +[[!pmid 17656108 desc="Conserved elements in the promoters of the family mOR262 on the chromosome 4."]] diff --git a/biblio/17852196.mdwn b/biblio/17852196.mdwn new file mode 100644 index 00000000..42bc04a4 --- /dev/null +++ b/biblio/17852196.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Screening of genes associated with termination of the critical period of visual cortex plasticity in rats."]] +[[!tag visual-cortex library]] +[[!pmid 17852196 desc="Substractive analysis show that MBP is downregulated in dark reared animals. A recovery is observed after 7 days of exposure to light."]] diff --git a/biblio/17920026.mdwn b/biblio/17920026.mdwn new file mode 100644 index 00000000..eb9f0b45 --- /dev/null +++ b/biblio/17920026.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Artifactual detection of biotin on histones by streptavidin."]] +[[!tag biotin]] +[[!pmid 17920026 desc="“Radiolabeled biotin was readily detectable on carboxylases but not on histones, implying very low levels of biotin in the nucleus attached to histone proteins (< 0.03% biotinylation).”"]] diff --git a/biblio/17965236.mdwn b/biblio/17965236.mdwn new file mode 100644 index 00000000..4eb918c4 --- /dev/null +++ b/biblio/17965236.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genomic analysis of human microRNA transcripts."]] +[[!tag small_RNA promoter]] +[[!pmid 17965236 desc="Prediction of the primary transcripts for intergenic miRNAs"]] diff --git a/biblio/18007592.mdwn b/biblio/18007592.mdwn new file mode 100644 index 00000000..ac17bd7f --- /dev/null +++ b/biblio/18007592.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Neurogenin and NeuroD direct transcriptional targets and their regulatory enhancers."]] +[[!tag neurogenin tfbs]] +[[!pmid 18007592 desc="ChIP on chip and sequence analysis identify CAg[a/c]TG as the binding site for ngn/NeuroD."]] diff --git a/biblio/18045541.mdwn b/biblio/18045541.mdwn new file mode 100644 index 00000000..e32f45e7 --- /dev/null +++ b/biblio/18045541.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Prominent roles for odorant receptor coding sequences in allelic exclusion."]] +[[!tag olfaction]] +[[!pmid 18045541 desc="Early expression of an olfactory receptor with an unrelated promoter leads to its exclusive expression in a large fraction of olfactory neurons, at the expense of the engogenous repertoire."]] diff --git a/biblio/18077433.mdwn b/biblio/18077433.mdwn new file mode 100644 index 00000000..bae150bf --- /dev/null +++ b/biblio/18077433.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Deletion of the core-H region in mice abolishes the expression of three proximal odorant receptor genes in cis."]] +[[!tag olfaction]] +[[!pmid 18077433 desc="A H region supplied in trans in mutant background could not rescue the phenotype."]] diff --git a/biblio/18232016.mdwn b/biblio/18232016.mdwn new file mode 100644 index 00000000..6878ec6c --- /dev/null +++ b/biblio/18232016.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The olfactory vector hypothesis of neurodegenerative disease: is it viable?"]] +[[!tag olfaction review parkinson]] +[[!pmid 18232016 desc="Discusses the possibility that Parkinson and Alzheimer diseases can be caused by harmful agents penetrating the brain through the nose."]] diff --git a/biblio/18388294.mdwn b/biblio/18388294.mdwn new file mode 100644 index 00000000..4c1f6803 --- /dev/null +++ b/biblio/18388294.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Single-molecule DNA sequencing of a viral genome."]] +[[!tag sequencing]] +[[!pmid 18388294 desc="Primary paper for Helicos sequencing."]] diff --git a/biblio/18410131.mdwn b/biblio/18410131.mdwn new file mode 100644 index 00000000..fd9e53a8 --- /dev/null +++ b/biblio/18410131.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-throughput single copy DNA amplification and cell analysis in engineered nanoliter droplets."]] +[[!tag emulsion microfluidics]] +[[!pmid 18410131 desc="Preparation of emulsions on microfluidic chips."]] diff --git a/biblio/18519653.mdwn b/biblio/18519653.mdwn new file mode 100644 index 00000000..eecc3a32 --- /dev/null +++ b/biblio/18519653.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The new paradigm of flow cell sequencing."]] +[[!tag sequencing review]] +[[!pmid 18519653 desc="Summarises 454, Solexa and SOLiD."]] diff --git a/biblio/18562465.mdwn b/biblio/18562465.mdwn new file mode 100644 index 00000000..e832cd91 --- /dev/null +++ b/biblio/18562465.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotyping."]] +[[!tag emulsion 96-wells]] +[[!pmid 18562465 desc="Emulsions are prepared in 96-well plates by vortexing with tungsten beads."]] diff --git a/biblio/18603591.mdwn b/biblio/18603591.mdwn new file mode 100644 index 00000000..872d0fdb --- /dev/null +++ b/biblio/18603591.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Chum-RNA allows preparation of a high-quality cDNA library from a single-cell quantity of mRNA without PCR amplification."]] +[[!tag amplification]] +[[!pmid 18603591 desc="Addition of unrelated, but distinguishible RNA to a sample can raise the overall concentration and stimulate the reaction."]] diff --git a/biblio/18611170.mdwn b/biblio/18611170.mdwn new file mode 100644 index 00000000..88f7ad34 --- /dev/null +++ b/biblio/18611170.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing."]] +[[!tag sequence_tags RNA-seq template_switching]] +[[!pmid 18611170 desc="Tempate switching and RT with random hexamers, followed by sonication, adapter ligation, size fractionnation, amplification and sequencing."]] diff --git a/biblio/18674909.mdwn b/biblio/18674909.mdwn new file mode 100644 index 00000000..c9c73adf --- /dev/null +++ b/biblio/18674909.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Sponge genes provide new insight into the evolutionary origin of the neurogenic circuit."]] +[[!tag neurogenin]] +[[!pmid 18674909 desc="AmqbHLH1 is the sponge precursor of neurog and many other bHLH genes."]] diff --git a/biblio/18676813.mdwn b/biblio/18676813.mdwn new file mode 100644 index 00000000..7999ef79 --- /dev/null +++ b/biblio/18676813.mdwn @@ -0,0 +1,3 @@ +[[!meta title="PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element."]] +[[!tag chromatin loops antisense enhancer]] +[[!pmid 18676813 desc="Transcriptioni of sense and anti-sense RNAs made parallel by chromatin loops."]] diff --git a/biblio/18700840.mdwn b/biblio/18700840.mdwn new file mode 100644 index 00000000..85628188 --- /dev/null +++ b/biblio/18700840.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genetic control of experience-dependent plasticity in the visual cortex."]] +[[!tag visual-cortex genetics]] +[[!pmid 18700840 desc="A plasticity-defective strain opens the way to genetic analysis."]] diff --git a/biblio/18708127.mdwn b/biblio/18708127.mdwn new file mode 100644 index 00000000..bfeda331 --- /dev/null +++ b/biblio/18708127.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Visual experience regulates Kv3.1b and Kv3.2 expression in developing rat visual cortex."]] +[[!tag visual-cortex]] +[[!pmid 18708127 desc="Dark rearing from birth neither prevented nor delayed the upregulation of Kv3.1b and Kv3.2."]] diff --git a/biblio/18725631.mdwn b/biblio/18725631.mdwn new file mode 100644 index 00000000..63c407b5 --- /dev/null +++ b/biblio/18725631.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Global alignment of multiple protein interaction networks with application to functional orthology detection."]] +[[!tag networks data-analysis]] +[[!pmid 18725631 desc="Introduces the IsoRank algorithm."]] diff --git a/biblio/18791030.mdwn b/biblio/18791030.mdwn new file mode 100644 index 00000000..d8c583a6 --- /dev/null +++ b/biblio/18791030.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Unique substrate spectrum and PCR application of Nanoarchaeum equitans family B DNA polymerase."]] +[[!tag enzyme amplification]] +[[!pmid 18791030 desc="Capable to use dUTP and to a lower extent, dITP."]] diff --git a/biblio/18820678.mdwn b/biblio/18820678.mdwn new file mode 100644 index 00000000..df3a7eab --- /dev/null +++ b/biblio/18820678.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs."]] +[[!tag non-coding chromatin yeast]] +[[!pmid 18820678 desc="The passage of RNA polymerase II through an upstream UAS site in necessary for the binding of a transactivator and the induction of the downstream gene."]] diff --git a/biblio/18832167.mdwn b/biblio/18832167.mdwn new file mode 100644 index 00000000..a26d6b22 --- /dev/null +++ b/biblio/18832167.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A procedure for highly specific, sensitive, and unbiased whole-genome amplification."]] +[[!tag thermo-enhancement methods]] +[[!pmid 18832167 desc="Locus bias was suppressed for concentrations higher than 0.3 M."]] diff --git a/biblio/18838674.mdwn b/biblio/18838674.mdwn new file mode 100644 index 00000000..8e485211 --- /dev/null +++ b/biblio/18838674.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood."]] +[[!tag sequencing microfluidics]] +[[!pmid 18838674 desc="Uses microfluidic digital PCR for validation."]] diff --git a/biblio/18839960.mdwn b/biblio/18839960.mdwn new file mode 100644 index 00000000..2497626a --- /dev/null +++ b/biblio/18839960.mdwn @@ -0,0 +1,3 @@ +[[!meta title="DcpS as a therapeutic target for spinal muscular atrophy."]] +[[!tag cap]] +[[!pmid 18839960 desc="D156844 is an inhibitor of DcpS – an enzyme implicated in decaping and degradation of m7GDP."]] diff --git a/biblio/18940872.mdwn b/biblio/18940872.mdwn new file mode 100644 index 00000000..1033425c --- /dev/null +++ b/biblio/18940872.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase."]] +[[!tag enzyme]] +[[!pmid 18940872 desc="Manganese stimulates enzyme by destabilising them."]] diff --git a/biblio/18940923.mdwn b/biblio/18940923.mdwn new file mode 100644 index 00000000..42f1114a --- /dev/null +++ b/biblio/18940923.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Delayed plasticity of inhibitory neurons in developing visual cortex."]] +[[!tag visual-cortex]] +[[!pmid 18940923 desc="A very good reason to analyse cell types separately."]] diff --git a/biblio/18953341.mdwn b/biblio/18953341.mdwn new file mode 100644 index 00000000..4bf4a123 --- /dev/null +++ b/biblio/18953341.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans."]] +[[!tag complex-loci]] +[[!pmid 18953341 desc="LRTOMT is apparently the fusion of two neighbouring genes in other lineages, Lrrc51 and Tomt."]] diff --git a/biblio/18957701.mdwn b/biblio/18957701.mdwn new file mode 100644 index 00000000..046a8f7c --- /dev/null +++ b/biblio/18957701.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries."]] +[[!tag enhancer]] +[[!pmid 18957701 desc="Proposes a role for ultraconserved elements in dosage compensation."]] diff --git a/biblio/18978772.mdwn b/biblio/18978772.mdwn new file mode 100644 index 00000000..dbd997af --- /dev/null +++ b/biblio/18978772.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Alternative isoform regulation in human tissue transcriptomes."]] +[[!tag splicing]] +[[!pmid 18978772 desc="92–94% of human genes undergo alternative splicing, ~86% with a minor isoform frequency of 15% or more."]] diff --git a/biblio/18987734.mdwn b/biblio/18987734.mdwn new file mode 100644 index 00000000..822b21e8 --- /dev/null +++ b/biblio/18987734.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Accurate whole human genome sequencing using reversible terminator chemistry."]] +[[!tag methods sequencing sequence_tags]] +[[!pmid 18987734 desc="Primary paper for Illumina-Solexa technology. The supplemental information contains the sequence of the oligonucleotides used on the flow cells."]] diff --git a/biblio/18992237.mdwn b/biblio/18992237.mdwn new file mode 100644 index 00000000..82f92501 --- /dev/null +++ b/biblio/18992237.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A novel conserved evx1 enhancer links spinal interneuron morphology and cis-regulation from fish to mammals."]] +[[!tag enhancer]] +[[!pmid 18992237 desc="Deletion analysis shows a repressor function for the conserved sequences."]] diff --git a/biblio/19012738.mdwn b/biblio/19012738.mdwn new file mode 100644 index 00000000..d7fb7cb7 --- /dev/null +++ b/biblio/19012738.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Odorant receptor (OR) gene choice is biased and non-clonal in two olfactory placode cell lines, and OR RNA is nuclear prior to differentiation of these lines."]] +[[!tag olfaction nucleus RNA localisation]] +[[!pmid 19012738 desc="“Monogenic OR expression is established in undifferentiated cells and persists through differentiation, but OR gene choice is not a clonal property of either cell line.”"]] diff --git a/biblio/19019041.mdwn b/biblio/19019041.mdwn new file mode 100644 index 00000000..18519a7e --- /dev/null +++ b/biblio/19019041.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A novel, enigmatic histone modification: biotinylation of histones by holocarboxylase synthetase."]] +[[!tag biotin epigenetics]] +[[!pmid 19019041 desc="One should better carefully design negative controls when playing with histones and streptavidin."]] diff --git a/biblio/19050060.mdwn b/biblio/19050060.mdwn new file mode 100644 index 00000000..bc444740 --- /dev/null +++ b/biblio/19050060.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Regulation of neural macroRNAs by the transcriptional repressor REST."]] +[[!tag ncRNAs]] +[[!pmid 19050060 desc="Evidence for repression: activation by a dominant-negative construct."]] diff --git a/biblio/19052148.mdwn b/biblio/19052148.mdwn new file mode 100644 index 00000000..69592fa3 --- /dev/null +++ b/biblio/19052148.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Large number of ultraconserved elements were already present in the jawed vertebrate ancestor."]] +[[!tag enhancer]] +[[!pmid 19052148 desc="Shark genome sequence suggests that conserved enhancer diverged quicker in teleosts."]] diff --git a/biblio/19056821.mdwn b/biblio/19056821.mdwn new file mode 100644 index 00000000..c2451f86 --- /dev/null +++ b/biblio/19056821.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Novel mutations in Moloney Murine Leukemia Virus reverse transcriptase increase thermostability through tighter binding to template-primer."]] +[[!tag enzyme]] +[[!pmid 19056821 desc="From Agilent/Stratagene."]] diff --git a/biblio/19056895.mdwn b/biblio/19056895.mdwn new file mode 100644 index 00000000..9bf6b450 --- /dev/null +++ b/biblio/19056895.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Chromatin structure analyses identify miRNA promoters."]] +[[!tag miRNA promoter]] +[[!pmid 19056895 desc="“One-third of intronic miRNAs have transcription initiation regions independent from their host promoters.”"]] diff --git a/biblio/19060310.mdwn b/biblio/19060310.mdwn new file mode 100644 index 00000000..d103d319 --- /dev/null +++ b/biblio/19060310.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Characterization of Moloney Murine Leukaemia Virus/Avian Myeloblastosis Virus Chimeric Reverse Transcriptases."]] +[[!tag enzyme]] +[[!pmid 19060310 desc="Unfortunately for biotechnology, the chimers' activity is less than 0.1% of that of MMLV RT."]] diff --git a/biblio/19074369.mdwn b/biblio/19074369.mdwn new file mode 100644 index 00000000..7873c803 --- /dev/null +++ b/biblio/19074369.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE."]] +[[!tag sequence_tags data-analysis]] +[[!pmid 19074369 desc="Do not say “tissue speficic”, say “preferentially expressed”."]] diff --git a/biblio/19084513.mdwn b/biblio/19084513.mdwn new file mode 100644 index 00000000..56dd093f --- /dev/null +++ b/biblio/19084513.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Functional analysis of the evolutionarily conserved cis-regulatory elements on the sox17 gene in zebrafish."]] +[[!tag enhancer]] +[[!pmid 19084513 desc="Transgenic analysis of multiple modules in sox17."]] diff --git a/biblio/19097946.mdwn b/biblio/19097946.mdwn new file mode 100644 index 00000000..e820f077 --- /dev/null +++ b/biblio/19097946.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription."]] +[[!tag enhancer]] +[[!pmid 19097946 desc="Evidence for physical ssociation between the ssh locus and one of its distal enhancer in the cells where this enhancer is required for expression."]] diff --git a/biblio/19129761.mdwn b/biblio/19129761.mdwn new file mode 100644 index 00000000..e364965c --- /dev/null +++ b/biblio/19129761.mdwn @@ -0,0 +1,3 @@ +[[!meta title="One for all? A viral protein supplants the mRNA cap-binding complex."]] +[[!tag cap]] +[[!pmid 19129761 desc="This protein may be useful to purify capped molecules."]] diff --git a/biblio/19136549.mdwn b/biblio/19136549.mdwn new file mode 100644 index 00000000..da1f56de --- /dev/null +++ b/biblio/19136549.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Profiling model T-cell metagenomes with short reads."]] +[[!tag TCR CDR3 assembly software]] +[[!pmid 19136549 desc="In silico proof of principle aimed at short (35–50 bp) reads."]] diff --git a/biblio/19136965.mdwn b/biblio/19136965.mdwn new file mode 100644 index 00000000..5f5acdfd --- /dev/null +++ b/biblio/19136965.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb."]] +[[!tag iPS]] +[[!pmid 19136965 desc="Induction of pluripotent stem cells with Oct4, Sox2 and Esrrb."]] diff --git a/biblio/19151709.mdwn b/biblio/19151709.mdwn new file mode 100644 index 00000000..4f000ddc --- /dev/null +++ b/biblio/19151709.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Precision and diversity in an odor map on the olfactory bulb."]] +[[!tag olfaction]] +[[!pmid 19151709 desc="Intraspecific precision of the arrangement is of about 1 glomerulus, but interspecific is about 5."]] diff --git a/biblio/19155324.mdwn b/biblio/19155324.mdwn new file mode 100644 index 00000000..8d76e83b --- /dev/null +++ b/biblio/19155324.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus."]] +[[!tag enzyme]] +[[!pmid 19155324 desc="GTP hydrolysis is not necessary, and GTPγS enhanced the ligation activity."]] diff --git a/biblio/19169241.mdwn b/biblio/19169241.mdwn new file mode 100644 index 00000000..9a72a46e --- /dev/null +++ b/biblio/19169241.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs."]] +[[!tag cap promoters ncRNAs]] +[[!pmid 19169241 desc="Uses an antibody against m3/m7G to demonstrate the capping of exonic small RNAs."]] diff --git a/biblio/19171886.mdwn b/biblio/19171886.mdwn new file mode 100644 index 00000000..5fdbec7c --- /dev/null +++ b/biblio/19171886.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Design of 240,000 orthogonal 25mer DNA barcode probes."]] +[[!tag oligonucleotides hybridisation]] +[[!pmid 19171886 desc="CCCC stacks tend to cross-hybridise."]] diff --git a/biblio/19182800.mdwn b/biblio/19182800.mdwn new file mode 100644 index 00000000..d95da5b7 --- /dev/null +++ b/biblio/19182800.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Biological basis for restriction of microRNA targets to the 3' untranslated region in mammalian mRNAs."]] +[[!tag miRNA]] +[[!pmid 19182800 desc="miRNA translation inhibition is more efficient when bound in untranslated region."]] diff --git a/biblio/19186165.mdwn b/biblio/19186165.mdwn new file mode 100644 index 00000000..48866733 --- /dev/null +++ b/biblio/19186165.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Mapping of class I and class II odorant receptors to glomerular domains by two distinct types of olfactory sensory neurons in the mouse."]] +[[!tag olfaction]] +[[!pmid 19186165 desc="Axons segregate in the olfactory nerve according to the class, and in the bulb according to the receptor."]] diff --git a/biblio/19194492.mdwn b/biblio/19194492.mdwn new file mode 100644 index 00000000..cfc698af --- /dev/null +++ b/biblio/19194492.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Reduced responsiveness to long-term monocular deprivation of parvalbumin neurons assessed by c-Fos staining in rat visual cortex."]] +[[!tag visual-cortex]] +[[!pmid 19194492 desc="Visual induction of c-Fos in rat PV cells is unaffected by monocular deprivation."]] diff --git a/biblio/19197024.mdwn b/biblio/19197024.mdwn new file mode 100644 index 00000000..f8b73e0a --- /dev/null +++ b/biblio/19197024.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Molecular and evolutionary history of melanism in North American gray wolves."]] +[[!tag dog]] +[[!pmid 19197024 desc="Evidence for hybridisation between dogs and wild wolves."]] diff --git a/biblio/19208638.mdwn b/biblio/19208638.mdwn new file mode 100644 index 00000000..5bfa600e --- /dev/null +++ b/biblio/19208638.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A synthetic snRNA m3G-CAP enhances nuclear delivery of exogenous proteins and nucleic acids."]] +[[!tag cap methods]] +[[!pmid 19208638 desc="The m3G CAP is a signal of nuclear import for the U snRNP."]] diff --git a/biblio/19213877.mdwn b/biblio/19213877.mdwn new file mode 100644 index 00000000..0e68fadd --- /dev/null +++ b/biblio/19213877.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genome-Wide Analysis In Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling."]] +[[!tag sequence_tags methods]] +[[!pmid 19213877 desc="Also detects the small “upstream open reading frames” (uORFs). Uses circularisation by ssDNA ligase to avoid the bias of the RNA ligase classicaly used to clone small RNAs."]] diff --git a/biblio/19223322.mdwn b/biblio/19223322.mdwn new file mode 100644 index 00000000..3fcea59a --- /dev/null +++ b/biblio/19223322.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing."]] +[[!tag library methods]] +[[!pmid 19223322 desc="5S and tRNAs are removed by exposing to complementary DNA oligonucletides and RNAse H, that degrades DNA/RNA hybrids."]] diff --git a/biblio/19223470.mdwn b/biblio/19223470.mdwn new file mode 100644 index 00000000..07219984 --- /dev/null +++ b/biblio/19223470.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Identification of a cytoplasmic complex that adds a cap onto 5'-monophosphate RNA."]] +[[!tag cap]] +[[!pmid 19223470 desc="Does not exclude that the caps could be trimethylated."]] diff --git a/biblio/19234473.mdwn b/biblio/19234473.mdwn new file mode 100644 index 00000000..d6e9b9ae --- /dev/null +++ b/biblio/19234473.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence."]] +[[!tag enhancer]] +[[!pmid 19234473 desc="Point mutation in a SOX9 conserved element that has an enhancer activity caused congenital malformation."]] diff --git a/biblio/19237398.mdwn b/biblio/19237398.mdwn new file mode 100644 index 00000000..fbe09d35 --- /dev/null +++ b/biblio/19237398.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Massive transcriptional start site analysis of human genes in hypoxia cells."]] +[[!tag promoters]] +[[!pmid 19237398 desc="Uses random-priming and oligo-capping on very large (200 µg) amounts of total RNA. 5' ends were sequenced after size fractionation on polyacrylamide gel."]] diff --git a/biblio/19250940.mdwn b/biblio/19250940.mdwn new file mode 100644 index 00000000..7ef8a9a2 --- /dev/null +++ b/biblio/19250940.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two Sites in the DNA Target."]] +[[!tag enzyme products sequence_tags]] +[[!pmid 19250940 desc="“Adenine stretches on the 5' or 3' side of CAGCAG led to preferred cleavage of this site.”"]] diff --git a/biblio/19251760.mdwn b/biblio/19251760.mdwn new file mode 100644 index 00000000..22f49f7a --- /dev/null +++ b/biblio/19251760.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A library-based method to rapidly analyse chromatin accessibility at multiple genomic regions."]] +[[!tag biotin library methods DNase-hypersensitivity]] +[[!pmid 19251760 desc="Includes a smart step to make sure that PCR templates have a different linker at each end."]] diff --git a/biblio/19270062.mdwn b/biblio/19270062.mdwn new file mode 100644 index 00000000..ea8089eb --- /dev/null +++ b/biblio/19270062.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Long 3’-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae."]] +[[!tag 3′UTR ]] +[[!pmid 19270062 desc="“replacement of the natural, long 3’-UTR from wild-type PGA1 mRNA, which encodes a protein that is important for cell wall biosynthesis, with a short 3’-UTR renders it immune to NMD.”"]] diff --git a/biblio/19275900.mdwn b/biblio/19275900.mdwn new file mode 100644 index 00000000..4aa3659f --- /dev/null +++ b/biblio/19275900.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Conserved recoding RNA editing of vertebrate C1q-related factor C1QL1."]] +[[!tag editing SNP ]] +[[!pmid 19275900 desc="Case of editing wrongly annotated as genomic SNP."]] diff --git a/biblio/19282448.mdwn b/biblio/19282448.mdwn new file mode 100644 index 00000000..2e7752a2 --- /dev/null +++ b/biblio/19282448.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Novel method for high-throughput colony PCR screening in nanoliter-reactors."]] +[[!tag methods]] +[[!pmid 19282448 desc="Uses alginate gel droplets to perform PCR on isolated colonies."]] diff --git a/biblio/19317658.mdwn b/biblio/19317658.mdwn new file mode 100644 index 00000000..0cb54241 --- /dev/null +++ b/biblio/19317658.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-throughput verification of transcriptional starting sites by Deep-RACE."]] +[[!tag sequence_tags promoters high-throughput methods]] +[[!pmid 19317658 desc="Sequencing of 5' RACE PCR products with second generation sequencers."]] diff --git a/biblio/19359275.mdwn b/biblio/19359275.mdwn new file mode 100644 index 00000000..26a59bfb --- /dev/null +++ b/biblio/19359275.mdwn @@ -0,0 +1,3 @@ +[[!meta title="RNA transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: new candidates for the pathophysiology of facioscapulohumeral dystrophy."]] +[[!tag non-coding miRNA journal-club]] +[[!pmid 19359275 desc="This locus accumulates many exceptions to the rule"]] diff --git a/biblio/19363473.mdwn b/biblio/19363473.mdwn new file mode 100644 index 00000000..20cd88fe --- /dev/null +++ b/biblio/19363473.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis."]] +[[!tag single-cell]] +[[!pmid 19363473 desc="“Protein state is transmitted from mother to daughter, giving rise to transient heritability in fate, but protein synthesis promotes rapid divergence so that sister cells soon become no more similar to each other than pairs of cells chosen at random.”"]] diff --git a/biblio/19369540.mdwn b/biblio/19369540.mdwn new file mode 100644 index 00000000..1fd98c2a --- /dev/null +++ b/biblio/19369540.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Axonal mRNA in uninjured and regenerating cortical mammalian axons."]] +[[!tag microfluidics compartment]] +[[!pmid 19369540 desc="Cells are in one chamber and axons are attracted in a harvest chamber where cell bodies can not enter."]] diff --git a/biblio/19372383.mdwn b/biblio/19372383.mdwn new file mode 100644 index 00000000..803bc14a --- /dev/null +++ b/biblio/19372383.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Progressive lengthening of 3’ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development."]] +[[!tag 3′UTR]] +[[!pmid 19372383 desc="Based on SAGE, EST and microarray analysis."]] diff --git a/biblio/19372391.mdwn b/biblio/19372391.mdwn new file mode 100644 index 00000000..0cf07b07 --- /dev/null +++ b/biblio/19372391.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by the MLL Fusion Partner TET1."]] +[[!tag epigenetics nucleotides]] +[[!pmid 19372391 desc="Detection of hmC in mouse ES cells."]] diff --git a/biblio/19372393.mdwn b/biblio/19372393.mdwn new file mode 100644 index 00000000..d45202cd --- /dev/null +++ b/biblio/19372393.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain."]] +[[!tag epigenetics nucleotides purkinje]] +[[!pmid 19372393 desc="hmC is enriched in the brain."]] diff --git a/biblio/19375315.mdwn b/biblio/19375315.mdwn new file mode 100644 index 00000000..bb843a15 --- /dev/null +++ b/biblio/19375315.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Redefining microRNA targets."]] +[[!tag miRNAs theory]] +[[!pmid 19375315 desc="Disscusses the possibility that the function of the miRNA binding sites in some transcripts is to inhibit the miRNA, as hypomorphic miRNA mutants can be rescued by the removal of some of their targets."]] diff --git a/biblio/19380378.mdwn b/biblio/19380378.mdwn new file mode 100644 index 00000000..f8a7a698 --- /dev/null +++ b/biblio/19380378.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Kinetics and thermodynamics of DNA hybridization on gold nanoparticles."]] +[[!tag hybridation]] +[[!pmid 19380378 desc="DNA melting temperature is lower on gold particles, except for hairpins."]] diff --git a/biblio/19387439.mdwn b/biblio/19387439.mdwn new file mode 100644 index 00000000..fe999c12 --- /dev/null +++ b/biblio/19387439.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Formyl peptide receptor-like proteins are a novel family of vomeronasal chemosensors."]] +[[!tag olfaction]] +[[!pmid 19387439 desc="Reports that Fpr-rs1, 3, 4, 6, 7 are restricted to the vomeronasal organ, while FPR1 and FPR2 have a broad expression pattern."]] diff --git a/biblio/19417902.mdwn b/biblio/19417902.mdwn new file mode 100644 index 00000000..56b73001 --- /dev/null +++ b/biblio/19417902.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Automated microfluidic chromatin immunoprecipitation from 2,000 cells."]] +[[!tag epigenetics microfluidics]] +[[!pmid 19417902 desc="ChIP on chip, but without microarray."]] diff --git a/biblio/19423829.mdwn b/biblio/19423829.mdwn new file mode 100644 index 00000000..fdd3c84e --- /dev/null +++ b/biblio/19423829.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-throughput sequencing of the zebrafish antibody repertoire."]] +[[!tag sequencing zebrafish BCR CDR3]] +[[!pmid 19423829 desc="In vivo proof of principle."]] diff --git a/biblio/19443781.mdwn b/biblio/19443781.mdwn new file mode 100644 index 00000000..e383a4c8 --- /dev/null +++ b/biblio/19443781.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Direct detection of abortive RNA transcripts in vivo."]] +[[!tag transcription small_RNA]] +[[!pmid 19443781 desc="Detected in bacteria."]] diff --git a/biblio/19444217.mdwn b/biblio/19444217.mdwn new file mode 100644 index 00000000..44d3fa62 --- /dev/null +++ b/biblio/19444217.mdwn @@ -0,0 +1,3 @@ +[[!meta title="qiRNA is a new type of small interfering RNA induced by DNA damage."]] +[[!tag small_RNA]] +[[!pmid 19444217 desc="“qiRNA are about 20–21 nucleotides long (several nucleotides shorter than Neurospora siRNAs), with a strong preference for uridine at the 5’ end, and originate mostly from the ribosomal DNA locus”"]] diff --git a/biblio/19448611.mdwn b/biblio/19448611.mdwn new file mode 100644 index 00000000..d002506b --- /dev/null +++ b/biblio/19448611.mdwn @@ -0,0 +1,3 @@ +[[!meta title="dUTP incorporation into genomic DNA is linked to transcription in yeast."]] +[[!tag transcription mutation]] +[[!pmid 19448611 desc="dUTP could originate from locally high UTP concentrations."]] diff --git a/biblio/19470483.mdwn b/biblio/19470483.mdwn new file mode 100644 index 00000000..6e48eded --- /dev/null +++ b/biblio/19470483.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Essential role for a long-term depression mechanism in ocular dominance plasticity."]] +[[!tag visual-cortex plasticity ocular-dominance]] +[[!pmid 19470483 desc="Blockage of AMPA receptor internalization by the G2CT peptide (interacting with GluR2) inhibits ocular dominance shift after monocular deprivation."]] diff --git a/biblio/19474147.mdwn b/biblio/19474147.mdwn new file mode 100644 index 00000000..7c349eeb --- /dev/null +++ b/biblio/19474147.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Small RNAs derived from snoRNAs."]] +[[!tag snoRNA]] +[[!pmid 19474147 desc="SdRNAs derived from C/D snoRNAs show a bimodal size distribution at approximately 17-19 nt and >27 nt and predominantly originate from the 5’ end"]] diff --git a/biblio/19474302.mdwn b/biblio/19474302.mdwn new file mode 100644 index 00000000..0ff870da --- /dev/null +++ b/biblio/19474302.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Chemically inducible inactivation of protein synthesis in genetically targeted neurons."]] +[[!tag methods plasticity]] +[[!pmid 19474302 desc="Combines the inhibitory function of PKR with a drug-inducible dimerisation domain."]] diff --git a/biblio/19474331.mdwn b/biblio/19474331.mdwn new file mode 100644 index 00000000..022ebddc --- /dev/null +++ b/biblio/19474331.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Transcriptional and electrophysiological maturation of neocortical fast-spiking GABAergic interneurons."]] +[[!tag plasticity microarray]] +[[!pmid 19474331 desc="G42-GFP cells from the somatosensory cortex."]] diff --git a/biblio/19487571.mdwn b/biblio/19487571.mdwn new file mode 100644 index 00000000..19b2b4c2 --- /dev/null +++ b/biblio/19487571.mdwn @@ -0,0 +1,3 @@ +[[!meta title="L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism."]] +[[!tag transposons RNA-inheritance]] +[[!pmid 19487571 desc="L1 RNA carried over from germ cells is detected until preimplementation stages but not at E10.5, and is able to retrotranspose."]] diff --git a/biblio/19497865.mdwn b/biblio/19497865.mdwn new file mode 100644 index 00000000..a998501f --- /dev/null +++ b/biblio/19497865.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ."]] +[[!tag olfaction]] +[[!pmid 19497865 desc="Fpr1 and Fpr-rs2 are expressed in both the olfactory epithelium and the vomeronasal organ."]] diff --git a/biblio/19515973.mdwn b/biblio/19515973.mdwn new file mode 100644 index 00000000..60339ff5 --- /dev/null +++ b/biblio/19515973.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Stalled Hox promoters as chromosomal boundaries."]] +[[!tag promoters expression repression]] +[[!pmid 19515973 desc="“The stalled Pol II along with the NELF and DSIF complex may interact with putative insulator sequences, as seen for the Abd-B promoter (stalled) and the Fab7 (insulator).”"]] diff --git a/biblio/19528076.mdwn b/biblio/19528076.mdwn new file mode 100644 index 00000000..72ea0288 --- /dev/null +++ b/biblio/19528076.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq."]] +[[!tag SNP sequencing]] +[[!pmid 19528076 desc="Does not use quality values, and recommends to discard redundant reads."]] diff --git a/biblio/19534766.mdwn b/biblio/19534766.mdwn new file mode 100644 index 00000000..d40ada65 --- /dev/null +++ b/biblio/19534766.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Definition, conservation and epigenetics of housekeeping and tissue-enriched genes."]] +[[!tag normalisation]] +[[!pmid 19534766 desc="Provides a list of potential house-keeping genes with the coefficient of variation of their expression over 42 human tissues."]] diff --git a/biblio/19535462.mdwn b/biblio/19535462.mdwn new file mode 100644 index 00000000..2905b331 --- /dev/null +++ b/biblio/19535462.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Efficient oligonucleotide-mediated degradation of nuclear noncoding RNAs in mammalian cultured cells."]] +[[!tag ncRNA method]] +[[!pmid 19535462 desc="Antisense chimeric oligonucleotides are nucleofected and degrade target ncRNAs, maybe with a through RNaseH."]] diff --git a/biblio/19541912.mdwn b/biblio/19541912.mdwn new file mode 100644 index 00000000..cc3cf594 --- /dev/null +++ b/biblio/19541912.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing."]] +[[!tag TCR sequencing]] +[[!pmid 19541912 desc="Uses the Illumina Genome Analyzer to acheive high coverage, and compensates short read length with a shearing and assembly approach."]] diff --git a/biblio/19556463.mdwn b/biblio/19556463.mdwn new file mode 100644 index 00000000..2b9bf55e --- /dev/null +++ b/biblio/19556463.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A gene network regulating lysosomal biogenesis and function."]] +[[!tag network TFBS]] +[[!pmid 19556463 desc="A striking example of a very flat network centered on one transcription factor."]] diff --git a/biblio/19559618.mdwn b/biblio/19559618.mdwn new file mode 100644 index 00000000..da82b18c --- /dev/null +++ b/biblio/19559618.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Allelic Polymorphism within the TAS1R3 Promoter Is Associated with Human Taste Sensitivity to Sucrose."]] +[[!tag SNP enhancer]] +[[!pmid 19559618 desc="A SNP in an upstream repressor that is not conserved with rodents explains increased gene activity."]] diff --git a/biblio/19571010.mdwn b/biblio/19571010.mdwn new file mode 100644 index 00000000..fa9246f7 --- /dev/null +++ b/biblio/19571010.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression."]] +[[!tag non-coding]] +[[!pmid 19571010 desc="Experimental evidence obtained by immunoprecipitating protein-RNA complexes and identifying the RNAs on a custom microarray."]] diff --git a/biblio/19578066.mdwn b/biblio/19578066.mdwn new file mode 100644 index 00000000..d49ef300 --- /dev/null +++ b/biblio/19578066.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection."]] +[[!tag enzyme sequence_tags]] +[[!pmid 19578066 desc="Proposes a new class for the MmeI family, IIL."]] diff --git a/biblio/19589965.mdwn b/biblio/19589965.mdwn new file mode 100644 index 00000000..44121e19 --- /dev/null +++ b/biblio/19589965.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Dependence of mouse embryonic stem cells on threonine catabolism."]] +[[!tag stem-cells metabolism]] +[[!pmid 19589965 desc="Another example that “house keeping” genes can have cell-specific functions."]] diff --git a/biblio/19620212.mdwn b/biblio/19620212.mdwn new file mode 100644 index 00000000..673d50f4 --- /dev/null +++ b/biblio/19620212.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Transcriptome analysis by strand-specific sequencing of complementary DNA."]] +[[!tag sequence_tags RNA-seq]] +[[!pmid 19620212 desc="Directional RNA-seq protocol based on incorporation of dUTP during second strand synthesis."]] diff --git a/biblio/19620975.mdwn b/biblio/19620975.mdwn new file mode 100644 index 00000000..04070927 --- /dev/null +++ b/biblio/19620975.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry."]] +[[!tag non-coding knock-out]] +[[!pmid 19620975 desc="Transcription of an enhancer blocked by the insertion of a triple polyadenylation signal."]] diff --git a/biblio/19622793.mdwn b/biblio/19622793.mdwn new file mode 100644 index 00000000..82faf026 --- /dev/null +++ b/biblio/19622793.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Quantitative phenotyping via deep barcode sequencing."]] +[[!tag sequencing application]] +[[!pmid 19622793 desc="Genomics barcodes were amplified with PCR primers that were themselves barcoded, allowing multiplex analysis."]] diff --git a/biblio/19631370.mdwn b/biblio/19631370.mdwn new file mode 100644 index 00000000..a02bc59c --- /dev/null +++ b/biblio/19631370.mdwn @@ -0,0 +1,3 @@ +[[!meta title="RNA Polymerase III Detects Cytosolic DNA and Induces Type I Interferons through the RIG-I Pathway."]] +[[!tag polymerase cytoplasm cap]] +[[!pmid 19631370 desc="The RNA produced is probably 5’ triphosphate."]] diff --git a/biblio/19651612.mdwn b/biblio/19651612.mdwn new file mode 100644 index 00000000..ede98a7b --- /dev/null +++ b/biblio/19651612.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Inclusion formation and neuronal cell death through neuron-to-neuron transmission of α-synuclein."]] +[[!tag prion parkinson]] +[[!pmid 19651612 desc="Opens the possibility that the Parkinson disease is a prion disease."]] diff --git a/biblio/19666595.mdwn b/biblio/19666595.mdwn new file mode 100644 index 00000000..45aede78 --- /dev/null +++ b/biblio/19666595.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Conservation of enhancer location in divergent insects."]] +[[!tag enhancer]] +[[!pmid 19666595 desc="Analysis in Drosophila, Anopheles and Tribolium."]] diff --git a/biblio/19668204.mdwn b/biblio/19668204.mdwn new file mode 100644 index 00000000..ba18c55d --- /dev/null +++ b/biblio/19668204.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Digital transcriptome profiling using selective hexamer priming for cDNA synthesis."]] +[[!tag method reverse-transcription oligonucleotides]] +[[!pmid 19668204 desc="Because of reduced complexity, many 5′ ends are difficult to cover."]] diff --git a/biblio/19684116.mdwn b/biblio/19684116.mdwn new file mode 100644 index 00000000..ee244b98 --- /dev/null +++ b/biblio/19684116.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs."]] +[[!tag small_RNA immune-system]] +[[!pmid 19684116 desc="Detected with Cy3 labels."]] diff --git a/biblio/19692348.mdwn b/biblio/19692348.mdwn new file mode 100644 index 00000000..8f505383 --- /dev/null +++ b/biblio/19692348.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits."]] +[[!tag genetics eQTL microarray monkey]] +[[!pmid 19692348 desc="Selected genes whose expression level is highly heritable by focusion on inter-individual differences, filtered those whose expression level is correlated in brain and blood, and performed an eQTL analysis on blood samples using these genes, in the goal of extrapolating to brain."]] diff --git a/biblio/19696078.mdwn b/biblio/19696078.mdwn new file mode 100644 index 00000000..2c2b40d6 --- /dev/null +++ b/biblio/19696078.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Zip Nucleic Acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription."]] +[[!tag PCR oligonucleotides method]] +[[!pmid 19696078 desc="Useful for who wants to force a higher annealing temperature."]] diff --git a/biblio/19710321.mdwn b/biblio/19710321.mdwn new file mode 100644 index 00000000..f373ee49 --- /dev/null +++ b/biblio/19710321.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Regionalized loss of parvalbumin interneurons in the cerebral cortex of mice with deficits in GFRalpha1 signaling."]] +[[!tag parvalbumin visual-cortex]] +[[!pmid 19710321 desc="Neuronal loss in the visual cortex is stronger when it is deprived of input."]] diff --git a/biblio/19750007.mdwn b/biblio/19750007.mdwn new file mode 100644 index 00000000..b8ea8660 --- /dev/null +++ b/biblio/19750007.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Identification of gemin5 as a novel 7-methylguanosine cap-binding protein."]] +[[!tag cap]] +[[!pmid 19750007 desc="Some residues are necessary for both binding caps and U1/U4 snRNAs."]] diff --git a/biblio/19751533.mdwn b/biblio/19751533.mdwn new file mode 100644 index 00000000..7bd96bf8 --- /dev/null +++ b/biblio/19751533.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species."]] +[[!tag olfaction]] +[[!pmid 19751533 desc="Evidence for expression of vomeronasal receptors type 1 in the goat olfactory epithelium."]] diff --git a/biblio/197518.mdwn b/biblio/197518.mdwn new file mode 100644 index 00000000..da139cdb --- /dev/null +++ b/biblio/197518.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Importance of 5′-terminal blocking structure to stabilize mRNA in eukaryotic protein synthesis."]] +[[!tag enzyme buffer pyrophosphatase]] +[[!pmid 197518 desc="In this study, TAP is used in 0.1 M NaAc (pH 5.5), 5 mM EDTA, during 90 min at 30℃."]] diff --git a/biblio/19766623.mdwn b/biblio/19766623.mdwn new file mode 100644 index 00000000..2ab0421e --- /dev/null +++ b/biblio/19766623.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Flexibility of transcription factor target site position in conserved cis-regulatory modules."]] +[[!tag enhancer]] +[[!pmid 19766623 desc="“The most invariably conserved features, as seen also in other systems, were pairs of target sites that are immediately adjacent to one another.”"]] diff --git a/biblio/19767758.mdwn b/biblio/19767758.mdwn new file mode 100644 index 00000000..7a8a61d5 --- /dev/null +++ b/biblio/19767758.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms."]] +[[!tag sequencing genetics method]] +[[!pmid 19767758 desc="Under- or over-representation of insertion points in the sequenced library indicate if the insertion was deleterious or advantageous."]] diff --git a/biblio/19770080.mdwn b/biblio/19770080.mdwn new file mode 100644 index 00000000..d7637956 --- /dev/null +++ b/biblio/19770080.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Biotin is not a natural histone modification."]] +[[!tag biotin]] +[[!pmid 19770080 desc="Western blot and mass spectrometry analysis argue against histone biotinylation in vivo."]] diff --git a/biblio/19782672.mdwn b/biblio/19782672.mdwn new file mode 100644 index 00000000..dc846be8 --- /dev/null +++ b/biblio/19782672.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split."]] +[[!tag enhancer zebrafish]] +[[!pmid 19782672 desc="Conserved enhancers of fgf8."]] diff --git a/biblio/19805129.mdwn b/biblio/19805129.mdwn new file mode 100644 index 00000000..bde974e6 --- /dev/null +++ b/biblio/19805129.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast."]] +[[!tag non-coding epigenetics not-read]] +[[!pmid 19805129 desc="ncRNAs implicated in variegation"]] diff --git a/biblio/19820114.mdwn b/biblio/19820114.mdwn new file mode 100644 index 00000000..c9e46162 --- /dev/null +++ b/biblio/19820114.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High DNA melting temperature predicts transcription start site location in human and mouse."]] +[[!tag promoter genome]] +[[!pmid 19820114 desc="Correlation between CAGE promoters and regions of high melting temperature."]] diff --git a/biblio/19820686.mdwn b/biblio/19820686.mdwn new file mode 100644 index 00000000..f6c1287e --- /dev/null +++ b/biblio/19820686.mdwn @@ -0,0 +1,3 @@ +[[!meta title="RNA polymerase II-TFIIB structure and mechanism of transcription initiation."]] +[[!tag transcription promoter]] +[[!pmid 19820686 desc="Mutation of the adenine base in -8 strongly suppresses transcription initiation."]] diff --git a/biblio/19825846.mdwn b/biblio/19825846.mdwn new file mode 100644 index 00000000..51f1038c --- /dev/null +++ b/biblio/19825846.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing."]] +[[!tag sequencing genetics RNA-seq SNP]] +[[!pmid 19825846 desc="Basecalled RNA-seq reads to find SNPs and study allelic imbalance."]] diff --git a/biblio/19837043.mdwn b/biblio/19837043.mdwn new file mode 100644 index 00000000..32875d48 --- /dev/null +++ b/biblio/19837043.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A guide for in-house design of template-switch-based 5′ rapid amplification of cDNA ends systems."]] +[[!tag method template_switching]] +[[!pmid 19837043 desc="Uses desoxyriboguanosine tails for template switching (but the last one is blocked by a propyl group (C3 spacer)."]] diff --git a/biblio/19852763.mdwn b/biblio/19852763.mdwn new file mode 100644 index 00000000..f6d8bfa7 --- /dev/null +++ b/biblio/19852763.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Enhanced amplification of GC-rich DNA with two organic reagents."]] +[[!tag method amplification betaine]] +[[!pmid 19852763 desc="“Ethylene glycol and 1,2-propanediol were found to be more effective than betaine.”"]] diff --git a/biblio/19879328.mdwn b/biblio/19879328.mdwn new file mode 100644 index 00000000..06c12da3 --- /dev/null +++ b/biblio/19879328.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genetic analysis of the NEUROG2 gene in patients with Parkinson's disease."]] +[[!tag neurogenin Parkinson]] +[[!pmid 19879328 desc="Neurog2 does not seem to be implicated in Parkinson’s disease."]] diff --git a/biblio/19881494.mdwn b/biblio/19881494.mdwn new file mode 100644 index 00000000..e199eb4c --- /dev/null +++ b/biblio/19881494.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Microdroplet-based PCR enrichment for large-scale targeted sequencing."]] +[[!tag emulsion microfluidics]] +[[!pmid 19881494 desc="A library of droplets containing each a single pair of primers is fused with droplets containing genomic DNA."]] diff --git a/biblio/19895802.mdwn b/biblio/19895802.mdwn new file mode 100644 index 00000000..5ef57da0 --- /dev/null +++ b/biblio/19895802.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis."]] +[[!tag enhancer zebrafish]] +[[!pmid 19895802 desc="Evolutionary conserved enhancer in an apparently structural gene."]] diff --git a/biblio/19915551.mdwn b/biblio/19915551.mdwn new file mode 100644 index 00000000..c83de6b3 --- /dev/null +++ b/biblio/19915551.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis."]] +[[!tag barcode sequencing promoter mutant]] +[[!pmid 19915551 desc="Uses six barcodes per subject."]] diff --git a/biblio/19915615.mdwn b/biblio/19915615.mdwn new file mode 100644 index 00000000..31c125e4 --- /dev/null +++ b/biblio/19915615.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Enhanced mRNA cap methylation increases Cyclin D1 expression and promotes cell transformation."]] +[[!tag cap]] +[[!pmid 19915615 desc="Some mRNAs in mammalian cells have unmethylated caps."]] diff --git a/biblio/19922870.mdwn b/biblio/19922870.mdwn new file mode 100644 index 00000000..a8df4e3c --- /dev/null +++ b/biblio/19922870.mdwn @@ -0,0 +1,3 @@ +[[!meta title="MOR23 Promotes Muscle Regeneration and Regulates Cell Adhesion and Migration."]] +[[!tag olfaction]] +[[!pmid 19922870 desc="New function for an olfactory receptor outside the nose."]] diff --git a/biblio/19933106.mdwn b/biblio/19933106.mdwn new file mode 100644 index 00000000..59f13e95 --- /dev/null +++ b/biblio/19933106.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A Simple Cipher Governs DNA Recognition by TAL Effectors."]] +[[!tag TFBS Biotechnology]] +[[!pmid 19933106 desc="Opens the possibility to design very sequence-specific DNA binding sites."]] diff --git a/biblio/19933107.mdwn b/biblio/19933107.mdwn new file mode 100644 index 00000000..8025f82f --- /dev/null +++ b/biblio/19933107.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Breaking the Code of DNA-Binding Specificity of TAL-Type III Effectors."]] +[[!tag TFBS Biotechnology]] +[[!pmid 19933107 desc="Opens the possibility to design very sequence-specific DNA binding sites."]] diff --git a/biblio/19935646.mdwn b/biblio/19935646.mdwn new file mode 100644 index 00000000..b41f990a --- /dev/null +++ b/biblio/19935646.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Cancer-associated IDH1 mutations produce 2-hydroxyglutarate."]] +[[!tag cancer SNP]] +[[!pmid 19935646 desc="A gain of function responsible for the production of a cancerigenic metabolite."]] diff --git a/biblio/19945389.mdwn b/biblio/19945389.mdwn new file mode 100644 index 00000000..9dc7f3c6 --- /dev/null +++ b/biblio/19945389.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Classical MHCI molecules regulate retinogeniculate refinement and limit ocular dominance plasticity."]] +[[!tag visual-cortex MHC mouse knock-out plasticity]] +[[!pmid 19945389 desc="Impairment of the refinement of the neuronal projections by knocking out Class I MHC genes enhance ocular dominance plasticity."]] diff --git a/biblio/19952141.mdwn b/biblio/19952141.mdwn new file mode 100644 index 00000000..536911c8 --- /dev/null +++ b/biblio/19952141.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Extreme variability among mammalian V1R gene families."]] +[[!tag pheromones olfaction]] +[[!pmid 19952141 desc="V1R repertoires for most mammals are “semi-private”."]] diff --git a/biblio/19962179.mdwn b/biblio/19962179.mdwn new file mode 100644 index 00000000..c287899f --- /dev/null +++ b/biblio/19962179.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Nuclear Receptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer."]] +[[!tag cancer transolcation mechanism]] +[[!pmid 19962179 desc="A complex pathway comprising the androgen receptor (AR), LINE-1 ORF2 endonuclease, activation-induced cytidine deaminase (AID), uracil-DNA glycosylase (UNG), and PIWIL1 is responsible for some translocations commonly observed in prostate cancer. (Does this happen in all “transcription factories”?)"]] diff --git a/biblio/20005806.mdwn b/biblio/20005806.mdwn new file mode 100644 index 00000000..d682ef9f --- /dev/null +++ b/biblio/20005806.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Somatic sex reprogramming of adult ovaries to testes by FOXL2 ablation."]] +[[!tag mouse differenciation]] +[[!pmid 20005806 desc="Repressor gene necessary to maintain an embryonnary differenciation choice in the adult."]] diff --git a/biblio/20015970.mdwn b/biblio/20015970.mdwn new file mode 100644 index 00000000..1ae4ec6e --- /dev/null +++ b/biblio/20015970.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants."]] +[[!tag software format sequencing]] +[[!pmid 20015970 desc="Documents and clarifies the differences."]] diff --git a/biblio/20016068.mdwn b/biblio/20016068.mdwn new file mode 100644 index 00000000..c9b684f0 --- /dev/null +++ b/biblio/20016068.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays."]] +[[!tag snoRNA compartments imprinting]] +[[!pmid 20016068 desc="snoRNA host transcripts that are compartmentalized and retained in the vicinity of their transcription sites."]] diff --git a/biblio/20080596.mdwn b/biblio/20080596.mdwn new file mode 100644 index 00000000..5113f109 --- /dev/null +++ b/biblio/20080596.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Rate, molecular spectrum, and consequences of human mutation."]] +[[!tag genetics SNP mutation]] +[[!pmid 20080596 desc="“Proliferative cells (such as those in intestinal epithelium and the epidermis) at this age [60 years old] could very well contain 4,000 to 40,000 mutations.”"]] diff --git a/biblio/20080641.mdwn b/biblio/20080641.mdwn new file mode 100644 index 00000000..e978bee0 --- /dev/null +++ b/biblio/20080641.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets."]] +[[!tag sequencing human TCR CDR3 SRA]] +[[!pmid 20080641 desc="454 sequencing of α and β TCRs."]] diff --git a/biblio/20080942.mdwn b/biblio/20080942.mdwn new file mode 100644 index 00000000..21d029cd --- /dev/null +++ b/biblio/20080942.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Alternative splicing produces high levels of noncoding isoforms of bHLH transcription factors during development."]] +[[!tag splicing bHLH non-coding neurogenin.]] +[[!pmid 20080942 desc="The coding sequence of Math5 is entirely skipped in the major splicing form. Ngn3, thought to be a single exon gene, contains an intron that introduces a premature stop codon with a frame shift."]] diff --git a/biblio/20081206.mdwn b/biblio/20081206.mdwn new file mode 100644 index 00000000..bdaa5ed2 --- /dev/null +++ b/biblio/20081206.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli."]] +[[!tag cap small_RNA plant]] +[[!pmid 20081206 desc="Capped and non-capped were cloned and sequenced separately in this study."]] diff --git a/biblio/20081834.mdwn b/biblio/20081834.mdwn new file mode 100644 index 00000000..9e68b3c8 --- /dev/null +++ b/biblio/20081834.mdwn @@ -0,0 +1,3 @@ +[[!meta title="FRT-seq: amplification-free, strand-specific transcriptome sequencing."]] +[[!tag sequence_tags method sequencing]] +[[!pmid 20081834 desc="Uses 250 ng of polyadenlyated RNA."]] diff --git a/biblio/20110323.mdwn b/biblio/20110323.mdwn new file mode 100644 index 00000000..edf4c71f --- /dev/null +++ b/biblio/20110323.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Digital nature of the immediate-early transcriptional response."]] +[[!tag single-cell transcription]] +[[!pmid 20110323 desc="Dictyostelium slugs stimulated with cAMP and DIF show a dose-dependent mosaic response."]] diff --git a/biblio/20124551.mdwn b/biblio/20124551.mdwn new file mode 100644 index 00000000..8070e6e5 --- /dev/null +++ b/biblio/20124551.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor."]] +[[!tag non-coding]] +[[!pmid 20124551 desc="Acts by “competing with DNA GREs for binding to the GR”"]] diff --git a/biblio/20133332.mdwn b/biblio/20133332.mdwn new file mode 100644 index 00000000..1a631f12 --- /dev/null +++ b/biblio/20133332.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Digital transcriptome profiling from attomole-level RNA samples."]] +[[!tag heliscope RNA-seq transcriptome]] +[[!pmid desc="90–94% of the signal matches ribosomal RNA when using standard random hexamers."]] diff --git a/biblio/20133776.mdwn b/biblio/20133776.mdwn new file mode 100644 index 00000000..0d6d6011 --- /dev/null +++ b/biblio/20133776.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Synthetic design of strong promoters."]] +[[!tag promoter synthethic oligonucleotides method]] +[[!pmid 20133776 desc="The sequence library was created by printing oligonucleotides with restriction sites on a microarray, and releasing them by cleavage."]] diff --git a/biblio/20139302.mdwn b/biblio/20139302.mdwn new file mode 100644 index 00000000..3a9be506 --- /dev/null +++ b/biblio/20139302.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Close association of RNA polymerase II and many transcription factors with Pol III genes."]] +[[!tag transcription]] +[[!pmid 20139302 desc="ChIP analysis shows Pol III binding many known Pol II genes and vice-versa."]] diff --git a/biblio/20142503.mdwn b/biblio/20142503.mdwn new file mode 100644 index 00000000..3f96b31d --- /dev/null +++ b/biblio/20142503.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Histidine-mediated RNA transfer to GDP for unique mRNA capping by vesicular stomatitis virus RNA polymerase."]] +[[!tag cap]] +[[!pmid 20142503 desc="A different capping pathway in viruses."]] diff --git a/biblio/20164839.mdwn b/biblio/20164839.mdwn new file mode 100644 index 00000000..e334de89 --- /dev/null +++ b/biblio/20164839.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The primary transcriptome of the major human pathogen Helicobacter pylori."]] +[[!tag sequence_tags RNA-seq bacteria]] +[[!pmid 20164839 desc="dRNA-seq, a method to capture the TSS of 5′PPP mRNAS (frequent in prokaryotes)."]] diff --git a/biblio/20188178.mdwn b/biblio/20188178.mdwn new file mode 100644 index 00000000..060902a0 --- /dev/null +++ b/biblio/20188178.mdwn @@ -0,0 +1,3 @@ +[[!meta title="MBD2 and MeCP2 Regulate Distinct Transitions in the Stage-Specific Differentiation of Olfactory Receptor Neurons."]] +[[!tag olfaction methylation]] +[[!pmid 20188178 desc="Could it be that MeCP2 has a role in monoallelic OR expression?"]] diff --git a/biblio/20192178.mdwn b/biblio/20192178.mdwn new file mode 100644 index 00000000..883e3abb --- /dev/null +++ b/biblio/20192178.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-Performance Single Cell Genetic Analysis Using Microfluidic Emulsion Generator Arrays."]] +[[!tag microfluidics PCR]] +[[!pmid 20192178 desc="Cells are encapsulated in droplets and PCR on beads follows lysis."]] diff --git a/biblio/20203190.mdwn b/biblio/20203190.mdwn new file mode 100644 index 00000000..8395e982 --- /dev/null +++ b/biblio/20203190.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Critical Period for Inhibitory Plasticity in RodentBinocular V1."]] +[[!tag visual-cortex plasticity]] +[[!pmid 20203190 desc="“Depression of inhibitory synapses onto pyramidal neurons is induced when rats are monocularly deprived for 2 d at the end of the third postnatal week (pre-CP), whereas potentiation is induced if the monocular deprivation is started in the fourth postnatal week (CP).”"]] diff --git a/biblio/2020552.mdwn b/biblio/2020552.mdwn new file mode 100644 index 00000000..9dcb4cd8 --- /dev/null +++ b/biblio/2020552.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products."]] +[[!tag method libraries cloning enzyme]] +[[!pmid 2020552 desc="Can also be used to produce A-inserts."]] diff --git a/biblio/20211140.mdwn b/biblio/20211140.mdwn new file mode 100644 index 00000000..b06060a8 --- /dev/null +++ b/biblio/20211140.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The lta4h Locus Modulates Susceptibility to Mycobacterial Infection in Zebrafish and Humans."]] +[[!tag genetics]] +[[!pmid 20211140 desc="Selection pressure to keep a locus heterozygote."]] diff --git a/biblio/20228806.mdwn b/biblio/20228806.mdwn new file mode 100644 index 00000000..b5a2492f --- /dev/null +++ b/biblio/20228806.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Loss of Arc renders the visual cortex impervious to the effects of sensory experience or deprivation."]] +[[!tag visual-cortex plasticity]] +[[!pmid 20228806 desc="“Although Arc(-/-) mice exhibited normal visual acuity, baseline ocular dominance was abnormal and resembled that observed after dark-rearing.”"]] diff --git a/biblio/202926.mdwn b/biblio/202926.mdwn new file mode 100644 index 00000000..51605f87 --- /dev/null +++ b/biblio/202926.mdwn @@ -0,0 +1,3 @@ +[[!meta title="End labeling of enzymatically decapped mRNA."]] +[[!tag enzyme buffer pyrophosphatase phosphatase]] +[[!pmid 202926 desc="TAP can be assayed by degrading gamma 32P ATP. 250 mM phosphate inhibits TAP. 10 mM phosphate inhibits BAP."]] diff --git a/biblio/20359321.mdwn b/biblio/20359321.mdwn new file mode 100644 index 00000000..bf1543a7 --- /dev/null +++ b/biblio/20359321.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Optimized design and data analysis of tag-based cytosine methylation assays."]] +[[!tag sequence_tags methylation method]] +[[!pmid 20359321 desc="Uses EcoP15I."]] diff --git a/biblio/20363979.mdwn b/biblio/20363979.mdwn new file mode 100644 index 00000000..a471562d --- /dev/null +++ b/biblio/20363979.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers."]] +[[!tag enhancer promoter TFBS]] +[[!pmid 20363979 desc="Used “known binding motifs for vertebrate TFs and a hidden Markov model-based approach to detect HCTs in the human, mouse, chicken, and fugu genomes”"]] diff --git a/biblio/20368444.mdwn b/biblio/20368444.mdwn new file mode 100644 index 00000000..3442d770 --- /dev/null +++ b/biblio/20368444.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Addition of poly(A) and poly(A)-rich tails during RNA degradation in the cytoplasm of human cells."]] +[[!tag degradation poly-A]] +[[!pmid 20368444 desc="“RNAi-mediated silencing of the major RNA decay machinery of the cell resulted in the accumulation of these polyadenylated RNA fragments, indicating that they are degradation intermediates.”"]] diff --git a/biblio/20392962.mdwn b/biblio/20392962.mdwn new file mode 100644 index 00000000..a9bc9120 --- /dev/null +++ b/biblio/20392962.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Neuronal pentraxins mediate silent synapse conversion in the developing visual system."]] +[[!tag visual-cortex knock-out]] +[[!pmid 20392962 desc="Suggests “a novel role for NP1/2 in silent synapse conversion during a discrete developmental period when visual circuit connections are undergoing eye-specific refinement”"]] diff --git a/biblio/20393465.mdwn b/biblio/20393465.mdwn new file mode 100644 index 00000000..4dbb9129 --- /dev/null +++ b/biblio/20393465.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Widespread transcription at neuronal activity-regulated enhancers."]] +[[!tag enhancer]] +[[!pmid 20393465 desc="Enhancers were defined by the binding of CBP."]] diff --git a/biblio/20400770.mdwn b/biblio/20400770.mdwn new file mode 100644 index 00000000..b765e02d --- /dev/null +++ b/biblio/20400770.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer."]] +[[!tag cap sequence_tags oligo-capping rna-seq cytomplasm]] +[[!pmid 20400770 desc="Dual oligo-capping / RNA-seq analysis that finds that the “non-RefSeq-linked” TSS correspond to RNAs preferrentially located in the cytoplasm."]] diff --git a/biblio/20485488.mdwn b/biblio/20485488.mdwn new file mode 100644 index 00000000..008894f7 --- /dev/null +++ b/biblio/20485488.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A large fraction of extragenic RNA pol II transcription sites overlap enhancers."]] +[[!tag enhancer promoter ChIP]] +[[!pmid 20485488 desc="Co-localisation of ChIP-seq signals for promoters and enhancers."]] diff --git a/biblio/20495556.mdwn b/biblio/20495556.mdwn new file mode 100644 index 00000000..e80a1306 --- /dev/null +++ b/biblio/20495556.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A paired-end sequencing strategy to map the complex landscape of transcription initiation."]] +[[!tag sequence_tags cap]] +[[!pmid 20495556 desc="Based on oligo capping. Used 150 µg of total RNA as starting material."]] diff --git a/biblio/20507918.mdwn b/biblio/20507918.mdwn new file mode 100644 index 00000000..95fd37e2 --- /dev/null +++ b/biblio/20507918.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Tiny abortive initiation transcripts exert antitermination activity on an RNA hairpin-dependent intrinsic terminator."]] +[[!tag not-read small_RNA transcription hairpin]] +[[!pmid 20507918 desc="The tiny RNAs inhibit the formation of a terminal hairpin, in a sequence-specific manner."]] diff --git a/biblio/20522740.mdwn b/biblio/20522740.mdwn new file mode 100644 index 00000000..ad223d9b --- /dev/null +++ b/biblio/20522740.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The Landscape of C. elegans 3'UTRs."]] +[[!tag 3′UTR]] +[[!pmid 20522740 desc="Short length. Poly-A tails detected on histon genes."]] diff --git a/biblio/20543846.mdwn b/biblio/20543846.mdwn new file mode 100644 index 00000000..e7bbeb16 --- /dev/null +++ b/biblio/20543846.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan."]] +[[!tag sequence_tags cap]] +[[!pmid 20543846 desc="nanoCAGE and CAGEscan with read length of 36 bases."]] diff --git a/biblio/20571086.mdwn b/biblio/20571086.mdwn new file mode 100644 index 00000000..ae368559 --- /dev/null +++ b/biblio/20571086.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A flexible and efficient template format for circular consensus sequencing and SNP detection."]] +[[!tag missing-method]] +[[!pmid 20571086 desc="Does not disclose which enzymes are used for phosphorylation and tailing."]] diff --git a/biblio/20581822.mdwn b/biblio/20581822.mdwn new file mode 100644 index 00000000..06b688ab --- /dev/null +++ b/biblio/20581822.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Transcriptional regulation by small RNAs at sequences downstream from 3' gene termini."]] +[[!tag small_RNA chromatin UTR non-coding]] +[[!pmid 20581822 desc="3′ non-coding RNA regulate progesterone receptor through small RNAs and chromatin."]] diff --git a/biblio/20613842.mdwn b/biblio/20613842.mdwn new file mode 100644 index 00000000..4caf2de8 --- /dev/null +++ b/biblio/20613842.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Conserved role of intragenic DNA methylation in regulating alternative promoters."]] +[[!tag methylation promoters CAGE RNA-seq CpG]] +[[!pmid 20613842 desc="Show “intragenic” promoters that create shorter proteins."]] diff --git a/biblio/20615941.mdwn b/biblio/20615941.mdwn new file mode 100644 index 00000000..694c505a --- /dev/null +++ b/biblio/20615941.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Global analysis of trans-splicing in Drosophila."]] +[[!tag drosophila trans-splicing]] +[[!pmid 20615941 desc="Hybrid experiment found cases of trans-splicing, but few."]] diff --git a/biblio/20616232.mdwn b/biblio/20616232.mdwn new file mode 100644 index 00000000..be08e4c0 --- /dev/null +++ b/biblio/20616232.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-resolution analysis of parent-of-origin allelic expression in the mouse brain."]] +[[!tag RNA-seq SNP]] +[[!pmid 20616232 desc="SNP analysed with custom R and Perl scripts."]] diff --git a/biblio/20616235.mdwn b/biblio/20616235.mdwn new file mode 100644 index 00000000..46b7e958 --- /dev/null +++ b/biblio/20616235.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Long noncoding RNA as modular scaffold of histone modification complexes."]] +[[!tag non-coding lincRNA RNA-protein]] +[[!pmid 20616235 desc="Interaction between HOTAIR, PRC2 and LSD1."]] diff --git a/biblio/20627890.mdwn b/biblio/20627890.mdwn new file mode 100644 index 00000000..a6e96847 --- /dev/null +++ b/biblio/20627890.mdwn @@ -0,0 +1,3 @@ +[[!meta title="TATA is a modular component of synthetic promoters."]] +[[!tag promoter TATA]] +[[!pmid 20627890 desc="TATA box as an amplifier."]] diff --git a/biblio/20631301.mdwn b/biblio/20631301.mdwn new file mode 100644 index 00000000..51463e49 --- /dev/null +++ b/biblio/20631301.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Sirtuin 1 regulation of developmental genes during differentiation of stem cells."]] +[[!tag enhancer ]] +[[!pmid 20631301 desc="The ChIP was analysed on a promoter microarray…"]] diff --git a/biblio/20668191.mdwn b/biblio/20668191.mdwn new file mode 100644 index 00000000..c7973858 --- /dev/null +++ b/biblio/20668191.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Chromosomal location-dependent nonstochastic onset of odor receptor expression."]] +[[!tag olfaction]] +[[!pmid 20668191 desc="Expression monitored from E9 to E17, and from E15 to P550."]] diff --git a/biblio/20671709.mdwn b/biblio/20671709.mdwn new file mode 100644 index 00000000..64ef0471 --- /dev/null +++ b/biblio/20671709.mdwn @@ -0,0 +1,3 @@ +[[!meta title="New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism."]] +[[!tag small_RNA heliscope antisense]] +[[!pmid 20671709 desc="5′-polyuridylated RNAs."]] diff --git a/biblio/20679221.mdwn b/biblio/20679221.mdwn new file mode 100644 index 00000000..4485d4f1 --- /dev/null +++ b/biblio/20679221.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Trimethylguanosine capping selectively promotes expression of Rev-dependent HIV-1 RNAs."]] +[[!tag cap HIV]] +[[!pmid 20679221 desc="‘The methyltransferase responsible for TMG modification of HIV-1 RNAs is the human PIMT (peroxisome proliferator-activated receptor-interacting protein with methyltransferase) protein’"]] diff --git a/biblio/20699384.mdwn b/biblio/20699384.mdwn new file mode 100644 index 00000000..d0a43bcf --- /dev/null +++ b/biblio/20699384.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis."]] +[[!tag miRNA]] +[[!pmid 20699384 desc="Drosha cleavage product directly processed by Ago2."]] diff --git a/biblio/20702422.mdwn b/biblio/20702422.mdwn new file mode 100644 index 00000000..857b3f23 --- /dev/null +++ b/biblio/20702422.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Sequence-specific cleavage of RNA by Type II restriction enzymes."]] +[[!tag enzyme RNA]] +[[!pmid 20702422 desc="AvaII, AvrII, BanI, HaeIII, HinfI and TaqI catalyze robust and specific cleavage of both RNA and DNA strands of RNA–DNA heteroduplex oligonucleotide substrates."]] diff --git a/biblio/20702565.mdwn b/biblio/20702565.mdwn new file mode 100644 index 00000000..d2df7242 --- /dev/null +++ b/biblio/20702565.mdwn @@ -0,0 +1,3 @@ +[[!meta title="An SNP in an ultraconserved regulatory element affects Dlx5/Dlx6 regulation in the forebrain."]] +[[!tag ultraconserved mouse SNP]] +[[!pmid 20702565 desc="Transgenic reporter and EMSA experiments"]] diff --git a/biblio/20703300.mdwn b/biblio/20703300.mdwn new file mode 100644 index 00000000..311a3359 --- /dev/null +++ b/biblio/20703300.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Mammalian microRNAs predominantly act to decrease target mRNA levels."]] +[[!tag miRNA sequence_tags]] +[[!pmid 20703300 desc="No changes in the ribosome profiling."]] diff --git a/biblio/20713044.mdwn b/biblio/20713044.mdwn new file mode 100644 index 00000000..efd187ac --- /dev/null +++ b/biblio/20713044.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Experience-dependent reactivation of ocular dominance plasticity in the adult visual cortex."]] +[[!tag visual-cortex plasticity]] +[[!pmid 20713044 desc="Has the treatment also an impact on the epigenome?"]] diff --git a/biblio/20724440.mdwn b/biblio/20724440.mdwn new file mode 100644 index 00000000..57e2df13 --- /dev/null +++ b/biblio/20724440.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE."]] +[[!tag sequence_tags CAGE siRNA TFBS]] +[[!pmid 20724440 desc="Inferring transcription factor binding sites from knock-down experiments and CAGE."]] diff --git a/biblio/20729808.mdwn b/biblio/20729808.mdwn new file mode 100644 index 00000000..efa2e3a1 --- /dev/null +++ b/biblio/20729808.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression."]] +[[!tag non-coding not_read synapse microarray]] +[[!pmid 20729808 desc="“DNA microarray analysis in Malat1-depleted neuroblastoma cells indicates that Malat1 controls the expression of genes involved not only in nuclear processes, but also in synapse function”"]] diff --git a/biblio/20729851.mdwn b/biblio/20729851.mdwn new file mode 100644 index 00000000..9b7a178d --- /dev/null +++ b/biblio/20729851.mdwn @@ -0,0 +1,3 @@ +[[!meta title="ChIP-Seq identification of weakly conserved heart enhancer."]] +[[!tag heart enhancer ChIP sequencing]] +[[!pmid 20729851 desc="Most enhancer bound by P300 in the mouse embryonnic heart at E11.5 are not strongly conserved."]] diff --git a/biblio/20733072.mdwn b/biblio/20733072.mdwn new file mode 100644 index 00000000..d433bfe8 --- /dev/null +++ b/biblio/20733072.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Distinct 3'UTRs differentially regulate activity-dependent translation of brain-derived neurotrophic factor (BDNF)."]] +[[!tag translation 3′UTR]] +[[!pmid 20733072 desc="A long 3′ UTR that functions as a signal-dependant translational repressor."]] diff --git a/biblio/20801935.mdwn b/biblio/20801935.mdwn new file mode 100644 index 00000000..cbf9de30 --- /dev/null +++ b/biblio/20801935.mdwn @@ -0,0 +1,3 @@ +[[!meta title="The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery."]] +[[!tag promoter motif Drosophila ribosome]] +[[!pmid 20801935 desc="“A specialized TCT-based transcription system that is directed toward the synthesis of ribosomal proteins.”"]] diff --git a/biblio/20802495.mdwn b/biblio/20802495.mdwn new file mode 100644 index 00000000..146377cd --- /dev/null +++ b/biblio/20802495.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells."]] +[[!tag sequencing mouse BCR CDR3]] +[[!pmid 20802495 desc="78 % of the recombinant antibodies generated from the most abundant sequences were antigen-specific."]] diff --git a/biblio/20811459.mdwn b/biblio/20811459.mdwn new file mode 100644 index 00000000..bf40a173 --- /dev/null +++ b/biblio/20811459.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Genome-wide measurement of RNA secondary structure in yeast."]] +[[!tag sequence_tags RNA structure yeast]] +[[!pmid 20811459 desc="An intriguing three-nucleotide periodicity of secondary structure across coding regions."]] diff --git a/biblio/20823260.mdwn b/biblio/20823260.mdwn new file mode 100644 index 00000000..8f556f6f --- /dev/null +++ b/biblio/20823260.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Selective cell death mediated by small conditional RNAs."]] +[[!tag small_RNA PKR patented]] +[[!pmid 20823260 desc="Conditional activation of the PKR pathway by exogenous small RNAs kills cell expressing marker sequence."]] diff --git a/biblio/20837552.mdwn b/biblio/20837552.mdwn new file mode 100644 index 00000000..72384c84 --- /dev/null +++ b/biblio/20837552.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Branchiostoma floridae has separate healing and sealing enzymes for 5'-phosphate RNA ligation."]] +[[!tag enzyme ligase RNA]] +[[!pmid 20837552 desc="B. floridae RNA Ligase Forms a 2′-Phosphomonoester-3′,5′-Phosphodiester Junction."]] diff --git a/biblio/20849957.mdwn b/biblio/20849957.mdwn new file mode 100644 index 00000000..ab983a27 --- /dev/null +++ b/biblio/20849957.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Foxa2 regulates the expression of Nato3 in the floor plate by a novel evolutionarily-conserved promoter."]] +[[!tag not-read conserved-enhancer floor-plate mouse chicken]] +[[!pmid 20849957 desc="“Evolutionarily-conserved 204bp genomic region, which is necessary and sufficient to drive expression to the chick FP.”"]] diff --git a/biblio/20868489.mdwn b/biblio/20868489.mdwn new file mode 100644 index 00000000..096fdae8 --- /dev/null +++ b/biblio/20868489.mdwn @@ -0,0 +1,3 @@ +[[!meta title="An arthropod cis-regulatory element functioning in sensory organ precursor development dates back to the Cambrian."]] +[[!tag enhancer sequence-conservation drosophila]] +[[!pmid 20868489 desc="The atonal sensory organ precursor enhancer (SOPE)"]] diff --git a/biblio/20876732.mdwn b/biblio/20876732.mdwn new file mode 100644 index 00000000..05629aec --- /dev/null +++ b/biblio/20876732.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins."]] +[[!tag Olf-1 structure]] +[[!pmid 20876732 desc="‘The encirclement of DNA […] most likely does not allow Ebf1 to bind its recognition motif in the context of nucleosome-wrapped DNA.’"]] diff --git a/biblio/20937878.mdwn b/biblio/20937878.mdwn new file mode 100644 index 00000000..c66e29a9 --- /dev/null +++ b/biblio/20937878.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Cell-permeable Foxp3 protein alleviates autoimmune disease associated with inflammatory bowel disease and allergic airway inflammation."]] +[[!tag lymphocyte FoxP3 Treg therapy]] +[[!pmid 20937878 desc=""]] diff --git a/biblio/20964636.mdwn b/biblio/20964636.mdwn new file mode 100644 index 00000000..fb69d7f8 --- /dev/null +++ b/biblio/20964636.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing."]] +[[!tag library small_RNA LNA OSC]] +[[!pmid 20964636 desc="The dimer eliminator overlaps the ligation site between the 5′ and 3′ adapters."]] diff --git a/biblio/21030656.mdwn b/biblio/21030656.mdwn new file mode 100644 index 00000000..17acfc05 --- /dev/null +++ b/biblio/21030656.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Fitness correlates of heritable variation in antibody responsiveness in a wild mammal."]] +[[!tag auto_immunity natural_selection]] +[[!pmid 21030656 desc="‘in females, the presence of self-reactive antibodies was positively associated with adult survival during harsh winters.’"]] diff --git a/biblio/21034732.mdwn b/biblio/21034732.mdwn new file mode 100644 index 00000000..a2fa94de --- /dev/null +++ b/biblio/21034732.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A cluster of non-redundant Ngn1 binding sites is required for regulation of deltaA expression in zebrafish."]] +[[!tag neurogenin zebrafish enhancer TFBS]] +[[!pmid 21034732 desc="“Regulation of deltaA […] requires three clustered E-box binding sites that act in a non-redundant manner.”"]] diff --git a/biblio/21041477.mdwn b/biblio/21041477.mdwn new file mode 100644 index 00000000..c5bcffa8 --- /dev/null +++ b/biblio/21041477.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Epigenetic control of retrotransposon expression in human embryonic stem cells."]] +[[!tag repeats embryo not_read]] +[[!pmid 21041477 desc="‘expressed Alu elements are enriched in the youngest subfamily Y, and that expressed L1s are mostly located within genes, suggesting an epigenetic control of retrotransposon expression in hESCs’"]] diff --git a/biblio/21045082.mdwn b/biblio/21045082.mdwn new file mode 100644 index 00000000..6d1d90f7 --- /dev/null +++ b/biblio/21045082.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome."]] +[[!tag sequence_tags exon_painting CAGE cap cytoplasm]] +[[!pmid 21045082 desc="Comparison with 5′SAGE, PARE, small RNA and ChIP libraries."]] diff --git a/biblio/21119779.mdwn b/biblio/21119779.mdwn new file mode 100644 index 00000000..c842413f --- /dev/null +++ b/biblio/21119779.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Correlated Levels of mRNA and Soma Size in Single Identified Neurons: Evidence for Compartment-specific Regulation of Gene Expression."]] +[[!tag single_cell PCR ]] +[[!pmid 21119779 desc="18S, EF1-α, GAPDH, but not actin nor tubulin correlate well with neuronal soma size."]] diff --git a/biblio/21169561.mdwn b/biblio/21169561.mdwn new file mode 100644 index 00000000..cf19335d --- /dev/null +++ b/biblio/21169561.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Role of Pax3 acetylation in the regulation of Hes1 and Neurog2."]] +[[!tag not_read neurogenin post_translational_modification transcription_factor]] +[[!pmid 21169561 desc="“suggest that Pax3 acetylation results in decreased Hes1 and increased Neurog2 activity”"]] diff --git a/biblio/236548.mdwn b/biblio/236548.mdwn new file mode 100644 index 00000000..7d35f0f8 --- /dev/null +++ b/biblio/236548.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Size fractionation of double-stranded DNA by precipitation with polyethylene glycol."]] +[[!tag methods purification]] +[[!pmid 236548 desc="At lower concentrations, PEG does not preciptiate smaller DNA molecules."]] diff --git a/biblio/2440339.mdwn b/biblio/2440339.mdwn new file mode 100644 index 00000000..537ef06e --- /dev/null +++ b/biblio/2440339.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction."]] +[[!tag method rna purification]] +[[!pmid 2440339 desc="Original protocol, covered by US patent 4,843,155."]] diff --git a/biblio/2531075.mdwn b/biblio/2531075.mdwn new file mode 100644 index 00000000..64902ee9 --- /dev/null +++ b/biblio/2531075.mdwn @@ -0,0 +1,3 @@ +[[!meta title="U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus."]] +[[!tag snoRNA cap]] +[[!pmid 2531075 desc="U8 (SNORD118) is precipitated by anti-trimethylcap antibodies."]] diff --git a/biblio/2813391.mdwn b/biblio/2813391.mdwn new file mode 100644 index 00000000..50b1c7c6 --- /dev/null +++ b/biblio/2813391.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Gamma-monomethyl phosphate: a cap structure in spliceosomal U6 small nuclear RNA."]] +[[!tag cap]] +[[!pmid 2813391 desc="Sequence-specific capping, with the information being in the 25 first bases of the snRNA."]] diff --git a/biblio/4874239.mdwn b/biblio/4874239.mdwn new file mode 100644 index 00000000..79ddec4b --- /dev/null +++ b/biblio/4874239.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms."]] +[[!tag hybridisation repeats]] +[[!pmid 4874239 desc="C0t"]] diff --git a/biblio/4913914.mdwn b/biblio/4913914.mdwn new file mode 100644 index 00000000..f02772d8 --- /dev/null +++ b/biblio/4913914.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Central dogma of molecular biology."]] +[[!tag Crick]] +[[!pmid 4913914 desc="No sequence information goes back from protein to nucleic acid."]] diff --git a/biblio/6117828.mdwn b/biblio/6117828.mdwn new file mode 100644 index 00000000..721e42c2 --- /dev/null +++ b/biblio/6117828.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Polypeptides encoded by polyadenylated and non-polyadenylated messenger RNAs from normal and heat shocked HeLa cells."]] +[[!tag mRNA non-polyadenylated protein-coding]] +[[!pmid 6117828 desc="Evidence from translation of non-polyA RNA from control and heat shocked cells in rabbit reticulocyte cell-free system. Lists additional genes (actin, histons, myosin heavy chain, albumin) in the discussion."]] diff --git a/biblio/7518525.mdwn b/biblio/7518525.mdwn new file mode 100644 index 00000000..c54eb8f8 --- /dev/null +++ b/biblio/7518525.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Strand displacement synthesis capability of Moloney murine leukemia virus reverse transcriptase."]] +[[!tag enzyme]] +[[!pmid 7518525 desc="RNAse H activity is not strictly necessary for strand displacement by reverse-transcriptase. This activity is encoded in the C-terminal region."]] diff --git a/biblio/7685078.mdwn b/biblio/7685078.mdwn new file mode 100644 index 00000000..87086b00 --- /dev/null +++ b/biblio/7685078.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Cloning of RNA molecules in vitro."]] +[[!tag polony]] +[[!pmid 7685078 desc="Exponential amplification between a thin-layer gel containing Qbeta replicase, and a nylon membrane soaked in substrates and templates."]] diff --git a/biblio/7937132.mdwn b/biblio/7937132.mdwn new file mode 100644 index 00000000..9541ffbb --- /dev/null +++ b/biblio/7937132.mdwn @@ -0,0 +1,3 @@ +[[!meta title="U21, a novel small nucleolar RNA with a 13 nt. complementarity to 28S rRNA, is encoded in an intron of ribosomal protein L5 gene in chicken and mammals."]] +[[!tag snoRNA cap]] +[[!pmid 7937132 desc="U21 (SNORD21) is not capped."]] diff --git a/biblio/8321284.mdwn b/biblio/8321284.mdwn new file mode 100644 index 00000000..7340b7da --- /dev/null +++ b/biblio/8321284.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast."]] +[[!tag Olf-1]] +[[!pmid 8321284 desc="Cloning of Olf-1/EBF1 by one-hybrid screen."]] diff --git a/biblio/8335005.mdwn b/biblio/8335005.mdwn new file mode 100644 index 00000000..6a61f8bc --- /dev/null +++ b/biblio/8335005.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Small nucleolar RNAs encoded by introns of the human cell cycle regulatory gene RCC1."]] +[[!tag snoRNA cap]] +[[!pmid 8335005 desc="U17a and U17b (SNORNA37A and SNORNA37B) are not capped."]] diff --git a/biblio/8346046.mdwn b/biblio/8346046.mdwn new file mode 100644 index 00000000..a4c8180d --- /dev/null +++ b/biblio/8346046.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Determination of messenger RNA 5'-ends by reverse transcription of the cap structure."]] +[[!tag cap enzyme]] +[[!pmid 8346046 desc="The mRNA cap can template an extra C in the first strand cDNA."]] diff --git a/biblio/8938445.mdwn b/biblio/8938445.mdwn new file mode 100644 index 00000000..02913ccc --- /dev/null +++ b/biblio/8938445.mdwn @@ -0,0 +1,3 @@ +[[!meta title="High-efficiency full-length cDNA cloning by biotinylated CAP trapper."]] +[[!tag cap method]] +[[!pmid 8938445 desc="Primary reference for CAP trapper."]] diff --git a/biblio/9288755.mdwn b/biblio/9288755.mdwn new file mode 100644 index 00000000..95f0da0b --- /dev/null +++ b/biblio/9288755.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A novel family of putative pheromone receptors in mammals with a topographically organized and sexually dimorphic distribution."]] +[[!tag olfaction]] +[[!pmid 9288755 desc="Discovery of the type 2 vomeronasal receptors"]] diff --git a/biblio/9288756.mdwn b/biblio/9288756.mdwn new file mode 100644 index 00000000..2ed398b1 --- /dev/null +++ b/biblio/9288756.mdwn @@ -0,0 +1,3 @@ +[[!meta title="A multigene family encoding a diverse array of putative pheromone receptors in mammals."]] +[[!tag olfaction]] +[[!pmid 9288756 desc="Discovery of the type 2 vomeronasal receptors"]] diff --git a/biblio/9435224.mdwn b/biblio/9435224.mdwn new file mode 100644 index 00000000..f2b7ba31 --- /dev/null +++ b/biblio/9435224.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Thermostabilization and thermoactivation of thermolabile enzyme by trehalose and its application for the synthesis of full length cDNA."]] +[[!tag thermo-enhancement enzyme methods]] +[[!pmid 9435224 desc="“Thermoactivated reverse transcriptase displays full activity even at 60 degrees ℃”"]] diff --git a/biblio/9545343.mdwn b/biblio/9545343.mdwn new file mode 100644 index 00000000..73177ca2 --- /dev/null +++ b/biblio/9545343.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Characterization of RNA strand displacement synthesis by Moloney murine leukemia virus reverse transcriptase."]] +[[!tag enzyme]] +[[!pmid 9545343 desc="RNAse H activity generate nicks that enhance strand-displacement."]] diff --git a/biblio/9973624.mdwn b/biblio/9973624.mdwn new file mode 100644 index 00000000..9e4cd3fc --- /dev/null +++ b/biblio/9973624.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display."]] +[[!tag thermo-enhancement enzyme]] +[[!pmid 9973624 desc="Reverse transcriptase can prime when the last two bases mismatch."]] diff --git a/biblio/LNwXAAAAEBAJ.mdwn b/biblio/LNwXAAAAEBAJ.mdwn new file mode 100644 index 00000000..56ca1410 --- /dev/null +++ b/biblio/LNwXAAAAEBAJ.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Methods and compositions for full-length cDNA Cloning using a template-switching oligonucleotide."]] +[[!tag patent cap]] +[[!gpatent LNwXAAAAEBAJ desc="The Clontech patent for 5'RACE. See also its obsolete counterpart, 5,962,271."]] diff --git a/biblio/MOUNAAAAEBAJ.mdwn b/biblio/MOUNAAAAEBAJ.mdwn new file mode 100644 index 00000000..ae75c7fd --- /dev/null +++ b/biblio/MOUNAAAAEBAJ.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Method for the 5’-cap-dependent amplification of cDNAs."]] +[[!tag cap patent]] +[[!gpatent MOUNAAAAEBAJ desc="Only RNAseH-minus reverse transcriptases will add more cap-templated nucleotides to the first strand cDNA in presence of manganese."]] diff --git a/biblio/To_Do b/biblio/To_Do new file mode 100644 index 00000000..3393792b --- /dev/null +++ b/biblio/To_Do @@ -0,0 +1,1504 @@ + +15131266 +Ultraconserved elements are stretches > 200 bp 100 % conserved from mouse to human. One can sort them in three classes exonic, non-exonic, unknown. Non exonic are preferentially found around devlopmental genes and transcription factors. +15028117 + +12917688 [enhancers] +Human-fish comparisons miss most non-coding homologies in CFTR locus. + + +Nature 430, 85 - 88 (01 July 2004); doi:10.1038/nature02698 +Evolutionary changes in cis and trans gene regulation +PATRICIA J. WITTKOPP, BELINDA K. HAERUM & ANDREW G. CLARK + + +Nature 411, 41 - 42 (03 May 2001); doi:10.1038/35075138 +Lethality and centrality in protein networks +The most highly connected proteins in the cell are the most important for its survival. + + +Nature \ 430, 88 - 93 (01 July 2004); doi:10.1038/nature02555 +Nature AOP, published online 9 June 2004 +Evidence for dynamically organized modularity in the yeast proteinprotein interaction network +JING-DONG J. HAN1, NICOLAS BERTIN1, TONG HAO1, DEBRA S. GOLDBERG2, GABRIEL F. BERRIZ2, LAN V. ZHANG2, DENIS DUPUY1, ALBERTHA J. M. WALHOUT1,*, MICHAEL E. CUSICK1, FREDERICK P. ROTH2 & MARC VIDAL1 + + +1557406 +Adds a second round of amplification + +11687821 +Review citing the 2 upper articles + +12089562 [amplification] +* Incorporates aminoallyl-dUTP instead of cy3/5dUTP +* uses priming hexamers with a amino C6dT in 5' +This allows to reduce by 10 folds the quantity of RNA as a starting material. +* Presence of amplification products of t/rRNAs is not a problem when «optimal» quantities of total RNA are used. + +12172558 +* Says that exponential (65+25 cycles) is more faithful than linear. +* Limits [dNTP] to produce only 3' cDNA that are a few hundrer base pairs long. + +10471753 +Amplify preferentially long PCR product with a single +primer. Shorter molecules have a higher probability of undergoing +inhibitory intramolecular interactions. + +http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371%2Fjournal.pbio.0020178 +ggcacgcga/cc => C-box for dro hairy. + +10537171 +Full in situ random priming cDNA synthesis + +12399449 [single cell] +Single cell cDNA library construction. 5' poly A added by terminal transferase. + +12636919 [single cell] +Single cell PCR with 2x poly T. + +9883850 [amplification] +3 rounds of T7 RNA amplification (aRNA). + +12593794 [general] +Noise due to RNA extraction is 40 times greater than noise due to replicate hybridisation + +12595569 [amplificaiton] +Aminoallyl UTP to labal cRNAs. In contrast to cDNAs, DMSO is required for subsequent cyanine labelling. + +11955710 [visual cortex] +Cat visual cortex cDNAs hybridized to human macroarrays to study critical period mechanism + +12636919 [single cell] +Single cell PCR, using 5'poly1-tagged cDNAs. + +11222780 [amplification] +T7 pol generates aberrant template-unrelated products. This is fixed by reducing the concentration of oligo dT primers, and of enzymes. Under these conditions, 2 rounds of RNA linear amplification is not generatng too much bias. Small-volume protocol. T4gp32, a single stranded protein, increases RT processivity. + +12161654 [misc] +Fluorescent bar-coded oligos to monitor transcription in vivo. + +12613261 [amplification] +Uses T3N9 random nonamer amplification rounds (up to 5), after an initial T7dT RT. + +10499525 [single cell] +Single cell RT-PCR. + +15047890 [single cell] +Uses SMART7, PCR, and multiple aRNA rounds. + +12711698 [amplification] [tracked] +Uses T3N9 instead of T7dT during all the RT reactions. No 3' bias. Efficient on degraded RNA. Independant of polyadenylation (useful for non-polyA genes, like histones). + +12188181 [libraries] +Nuclear integrity preserved during tissue grinding. + +12560512 [amplification] [tracked] +«Semi-linear» Taq polymerase amplification used on the cDNA sample at the labelling step. + +14602935 [amplification] [tracked] +Performs SMART, then exponential PCR, then random-primed klenow labelling. + +11414214 [libraries] +Alternative to homopolymeric priming: the use of GN5 3' overhanging oligls as a template for second strand cDNA synthesis. + +12398200 [amplification] +Advocates a systematic round of RNA amplificatin, becaus it reduces interarray variability. + +15205470 [libraries] [tracked] +T4 RNA ligase reaction efficiency improved by PEG and pre-adenylation. +direct labelling method for big quantities: RNA fragmentation, then T4 RNA ligation of biotinylated oligos. + +3978074 [enzymes] +Adenylated RNA is a better substrate for T4 RNA ligase. + +3299268 [enzymes] +Synthesis of adenylated RNA + +12503310 [enzymes] +De-adenylation of T4 RNA ligase is required prior using adenylated substrates. Incubating with pyrophosphate during some purification steps does the job. Commercial T4 usually contains mostly de-adenylated enzyme. Mesuring reaction efficiency without ATP gives adenylation levels. + +9373199 [libraries] +Oligo-capping to build 5' ou FL cDNA libraries. + +11337467 [libraries] +Oligo-capping to study transcription initiation genomewide. + +11375929 [libraries] +Oligo-capping to fine-map transcription start sites. + +14606961 [libraries] +The nuclease activity of T7 RNA pol could also show some transcript specificity. + +12736331 [single cell] +Proof of concept and method, from Johnson & Johnson, Acturus, and OmniViz. + +14704353 [libraries] [tracked] +T4 DNA ligase used to ligate a double stranded cap-tag. + +12703294 [single cells] +Improvement of TPEA method. Gets rid of the nucleus by centrifugation. + +11730011 [libraries] +Type IIS restriction digest followed py 3'primer ligation, to rempve the poly A from cDNA. + + +3799962 [enzymes] +Optimal : Donor/acceptor 5:1; hexammine cobalt chloride 5.0 mM, PEG8000 25%; ATP 100µM. Inhibitors: ATP > 100 µM, MN 2+ > 5mM, NaCl > 20 mM. + +15247329 [libraries] [tracked] +Ligation of cDNA and methylated oligos, in presence of methy-sensitive restriction enzymes, eliminates the cDNA dimer product du to mass action. + +14513556 [libraries] +Hybridises single-stranded tester plasmid and driver PCR product, then purified single strand molecules out of duplexes using hydroxyapatite. + +12202777 [single cells] [tracked] +Single cell precipitation protocol, becausr Reverse Transcriptase from the cDNA mixture inhibits PCR. + +12161758 [amplification] +A method to amplify two distinguishable substrates in the same PCR tube, so that they are subjected to the same biases. + +12582258 [misc] +Direct labeling of 10µg total RNA. + +15272081 [libraries] +81% of the 5'/3' tag pairs could be used to amplify a cDNA by RT-PCR. + +14973331 [libraries] +cDNAs substracted by their former templates. DNS cleaves DNA from DNA/RNA duplexes, leaving RNA molecules intact. This would suggest the strong reduction of abundant transcripts. + +8125298 [libraries] +Oligo capping primary paper. + +11042159 [libraries] +Biotin-labeled RNA to remove hybridizing cDNA. + +12902159 [networks] +Correlating subnetwork topology, correlation or inverse collrelation, and phase. + +10611672 [misc] [review] +Describes the general attractions of the RNA world theme park to be built. + +14707170 [genome] +Functionnal validaiton. + +9520387 [libraries] +Engeneered T7 used to generate dye-terminated amplification products. + +15271495 [single cell] +Review + +9742245 [single cell] [tracked] +Nucleus removed by spinning. 1st PCR with poly-T and random primer. 2nd PCR nested and gene specific. + +15070753 [libraries] +Library of DNAseI ends, to map hypersensitive sites. Substrraction with a HS-depleted tester. + +15256515 [genome] [tracked] +Analysis of the distribution of all possible 8-mers in human proximal promoters. Identifiers 9 clusters of sequence. TATA found only in 2.6% of the promoters. + +9925643 [misc] [tracked] +Using in vitro cell extracts, demonstrate a role for the ELAV family, ARE binding, HuR protein in mRNA stabilisation. + +15153998 [enhancers] [review] +Discusses the intests of comparing close species to detect positive selection, and distant species for negative selection. + +12547512 [enhancers] +Differential distribution of TEs in the promoters. In 4.5% of the studied genes, TE sequences contain expermientally validated TransFac binding sites. + +15215383 [networks] +1) Defines coregulated groups. TFs from these groups are proposed regulators of the group. 2) Analyses the predicted promoters with transfac or jaspar. 3) Builds a network from the results of 1) and 2). + +10632582 [single cell] [tracked] +Accute dissociatin of slices before cell isolation. Variablility between RT lots? Evaluation of mRNA abundance through a serial dillution and callibration approach. + +12934013 [networks] [tracked] +Defines metagenes as a set of genes from different organisms, that are each other's reciprocal best blast hit. Focuces on the highly clustered components of a metagene coexpression network. + +9409673 [neurogenin] +Primary paper for zebrafish. + +15079056 [networks] [tracked] +Combines protein-protein, and transcriptional interactions. Identifies "motifs", subnetworks with 2, 3, or 4 nodes, that are over-represented. Most 4-node motifs are the combination of 3-node motifs. + +11418835 [Crick] +Discussees unconscious"online systems" ("zombies"), and wonder whether they use the same networks as consciousness, and whether what differenciates them is the level of firing synchrony. + +15297624 [misc] +siRNA need to access the nucleus in order to trigger transcriptional gene silencing. + +13063483 [Crick] +Wow, the GC pair had only 2 hydrogen bonds at that time! + +13272717 [Crick] + +13013241 [Crick] +Says that alpha-keratin is more likely to have coiled-coiled structure, rather that a straight alpha-helix structure, because coil-coil allows a better packing, and would better fit the structural data. + +15280214 [misc] [tracked] +Apical localisation increases the robustness of development (more segmenatal defects in egl hypomorphs). It could prevent mRNA dillution in the blastoderm of Drosophila. + +15380082 [misc] [review] +A common feature of sex-determination loci is X/Y crossing-over inhibition, followed by divergence, and accumulation of transposons and other junks in the Y locus. + +14732405 [promoters] +Pax6 has at least two transcription start sites. + +15345244 [visual cortex] +Differential display. Age-dependant variations account for 6.5% of the variations. + +15196954 [enhancers] [review] +Gene networks. + +15379890 [alternative promoters] +RLM-RACE to identify variants. CHIP to confirm TBP on TATA-less promoters. Luciferase assays to confirm new promoters. + +14593172 [genome] +Dual strategy using full length cDNAs and whole genome tiling arrays to annotate the Arabidopsis genome. + +15001784 [networks] [tracked] +Distribution of triads and tetrads in networks can cluster them in functional classes. + +15295028 [visual cortex] [tracked] +Synaptic changes in dark-reared animals stimulated by 6 hours of light before sacrifice. + +15208707 [networks] + +4599081 [crick] +Comments on his discovery, 20 years later. + +13054692 [crick] +The double helix paper. + +7366731 [crick] +A more dynamic view of "junk DNA" + +4920018 [crick] +He was a Genius. + +13309339 [crick] +Cristallographical arguments supporting the existence of two main classes of plant viruses: helicoidal ans icosaedral. + +15190252 [networks] +Date hubs vs. Party hubs. + +11333967 [networks] +Hubs of the yeast protein network are more frequently encoded by essential genes than other nodes. + +6866101 [crick] +Reverse learning hypothesis. + +4599081 [crick] +Comment on the double helix discovery, 20 years later + +15358733 [enhancer] [tracked] [review] +Reviews conserved enhancers and their mutations. + +12615002 [genome] +MARs could account for 10% of the "Homologous Intergenic Tracts" (HITs). + +15475268 [enhancers] +Defines a criterion to predict whether a human-mouse conserved non-coding sequence will also be conserved in Fugu. + +14563999 [enhancers] +DACH enhancers, scattered and unrearranged over > 500 kbp, detected by mouse-fugu conservation. + +8901419 [enhancers] [review] +Search for conserved enhancers started with developmental genes. + +15496438 [neurogenin] [tracked] +The LATE ngn1 enhancer is active in mouse telencephalon, but not in fish, because the Pax6 expression domain expanded in mouse. + +12453456 [enhancers] +The zebrafish netrin1 floor plate enhancer functions in mouse, but its sequence does not seem conserved. + +15496924 [enhancers] +The two studied gene deserts do not contain mouse-fish conserved elements. + +15496914 [genome] +Evidence for a whole genome duplication in teleosts. + +12555104 [crick] +Competinc cellular assemblies could provide a neural correlate of conciousness. + +15289483 [networks] +Monitoring 20-min intervals over 8-h and 16-h. + +15372033 [networks] +Primary paper for SANDY. Distinguishes "endogenous" from "exogenous" networks, and introduces transient hubs. + +15229602 [genome] +Uses a hybrid melanogaster / simulans approach, to demonstrate that interspecific variations in gene expression mostly originate from modification of cis-regulation. + +15496913 [genome] +Quality good enough to discuss segmental duplications. + + +15496912 [genome] +Shotgun drafts lack a lot of duplicated regions. + +15472078 [misc] +A novel virus family ? + +14960301 [genome] +CAGE & ESTs to express all microarray results in TPM (Transcripts per million). + +15297624 [miRNA] +5' siRNAs induce transcriptinal silencing when targeted to the nucleus. + +15489326 [library] [tracked] +Enrichement for large size flcDNA by size fractionation. + +15372072 [miRNA] +It is necessary to inactivate the drosha RNase to detect the capped precursors correctly. + +14967495 [enzymes] +One more tool in the box? + +12228725 [enzymes] +Investigates ATP, Mg2+, Mn2+, and pH. + +12611899 [enzymes] +Investigates pH and ATP concentration. + +15339661 [genome] +Open chromatin fibers contain both active and inactive genes. + +15314228 [genome] +Codon usage has been preserved during human-mouse evolution. + +15343339 [networks] +Defines "condition invariant", "condition enabled", "condition expanded", and "condition altered" transcription factor binding behaviour. + +15328367 [alternative promoters] +Alternative promoters which transcribe variants with different translational efficiencies. + +14663149 [libraries] [tracked] +5' 20mers to map transcription start sites, and mesaure their usage. + +11768647 [single cell] +Lysis in Dynabeads buffer, followed by first strand synthesis from poly-A. + +15342556 [genome] +These blocks contain most validated and predicted transcription factor binding sites. + +15084599 [enzymes] +Further characterisation of the enzyme. + +15509747 [visual cortex] +Another slightly different critical period, and another PV:GFP transgene. + +15849325 [genome] +Proteomics to demonstrate that some short ORFs are translated. + +15197164 [genome] +RT-PCR on putative 5'-3' EST pairs. + +14530453 [networks] [tracked] +Matrix representation of networks to detect regulatory circuits. + +11099257 [mining] [review] +Summarises a lot of clustering algorithms. + +15239836 [mining] +To take into account the discrete distributin of SAGE tags. + +15598746 [networking] +Two types of subgraphs are distinguished. Type I are abundant and form giant componants. Type II are rare and form clusters. The belonging to class I and II depend on global network propertiesm and vice-versa. + +15588312 [mining] +Trains learning machines with a GO categor, and interrogates a 40 000 genes x 55 tissues matrix of microarray results. + +15560142 [amplification] +Presentation of the Ribo-SPIA kit, which can replace T7 in vitro translation for linear amplification. + +7732590 [misc] [review] +Reminds that in some organisms, most transcripts share their 5' end. + +15642699 [enzymes] +Preference for circularisation. Optimum : 65-70ºC, 25µM ATP, pH 7.5-8, 10x more efficient than commercial ones. + +15590943 [genome] +Distinguishes "stable" from "variable" deserts. Stable deserts contain more evolutionary conserved regions, compared to variable deserts. + +12538257 [misc] +To create publication-quality figures, or on-the-fly graphics for a dynamic webpage. + +15647503 [genome] +Alternative polyadenylation sites are more frequent in nuclear and RNA-binding protein coding genes than in membrane proteins. + +15653639 [enzymes] +Ligates 2'-3'P molecules to 5'OH. Has a broad substrate range. + +15620361 [genome] +SACO is a serial analysis of chromatin occupancy, based on chromatin immunoprecipitation and sequencing of genomic sequence tags. + +15341601 [misc] +Magnetic beads to capture dissociated cells. BDNF and KCl-triggered depolarisations to induce parvalbumin expression. + +12559493 [neurogenin] +Lateral stripe and anterior neural plate elements delineated. Primary paper for -8.4, -3.4 and -3.1:GFP transgenic lines, and for -8.4:nRFP. + +15574821 [alternative promoters] +Proposes a RACE-PCR investigation of the 6000 genescan loci that are unsupported by ESTs or cDNAs. + +15499019 [misc] +Correlation of SNP haplotypes with phenotypes. + +15647298 [alternative promoters] +Example of alternative 5' exons which modify protein sequence (this is not the case with alternative TSS in the same 5' exon). + +15539566 [genome] +Oligonucleotide chips discover 10,595 novel transcribed sequences. + +11181992 [genome] +Defines RIDGEs : Regions of IncreaseD Gens Expression. SAGE-based study demonstrating low expression in chromosomes 4, 13, 18, 21. + +15572134 [misc] +Uses the fact that some enhancers are transcribed to analyse chromatin looping by flurorescent in situ hybridisation. + +15572454 [enhancers] +Finds the "developmental bias" in human-mouse comparisons by analysing 8kbp upstream sequences. + +15664173 [misc] +1-30,000 cells sorted to compare homogeneoous populations, and identify subtype-specific markers. + +15677727 [enhancers] [not read] +KO of a mouse-medaka conserved enhancer with expected phenotype. + +15528436 [misc] +The poly-U tract could be implicated in decapping and 5' degradation of the 5' product of the cleavage of mRNA by miRNA. + +12538875 [networks] +Distances between nodes are computed and used to cluster the nodes. Modules are inferred from this cluster. + +15674285 [networks] +Introduces a box-based renormalisation procedure, to demonstrate the link between scale-invariance and self-similarity. + +15729348 [networks] +New method to partition networks in modules. Defines provincial hubs and non-hub connectors, the latter being more conserved in evolution. + +15297301 [networks] +graph, Rgraphviz, and RBGL packages. + +15735639 [genome] +3' conserved 8-mers led to identificationo of putative miRNAs. + +15668391 [tags] +MPSS singletons are particularly noisy. + +15685193 [miRNA] +microRNAs target a large number of transcripts through a short 5' recognition sequence. + +11597334 [mining] +Template matching approach on expression vectors. + +10581018 [genome] +55 highly expressed transcripts make 18% of the RNA mass. 25 % of the RNA mass comprises 92% of the expressed transcriptome, at a copy number of 5 or less. + +15785770 [misc] +Future Nobel prize ? Maybe an explanation for the conservation of dev. enhancers. + +15786810 [libraries] +High size is preserved by ligating a 5'adapter before each amplification. + +15778292 [genome] +2n species covered 1x would be more efficient than n covered 2x for the discovery of conserved elements, but the resulting genome assemblies would be of a much poorer qualities. + +15781865 [tags] +Not tested on a large scale. Ditags without a spacer, separated by a 4-cutter (TalI) + +15564293 [misc] +[not read] Normalisations based on uni/multivariate models, rather than substraction of the mean followed by divisoin by sd, are much more effective at detecting covariations. + +15705831 [networks] +The proportion of regulators increases with the size of the network. + +15788456 [not read] +Implicates a atpxyz gene in a neurodevelopmental function. + +11988575 [networks] +"The hub node and its immediate surroundings tend to separate from other hubs" : highly connected nodes have low-connected partners in the protein and transcriptional networks. + +15690032 [enhancers] +Coordinated expression of e and y is necessary for spot formation. Ancestral patterning mechanisms provide possible pigmentation patterns through transcription factors recruitement. + +15282333 [networks] +CDS, 3'UTRs, but not 5'UTRs of highly connected genes of the human and mouse coexpression networks evolve more slowly + +15009647 [visual cortex] +Identifies immediate early genes that are upregulated in visual cortex after monocular enucleation. + +15860629 [networks] +Model of network growth which takes into account the propension to link to newcommers or to good old friends. + +15833122 [networks] +Five well-documented example to question the relevance of network motifs. + +15894530 [misc] +M. leprae has a lot of pseudogenes, but its clonality suggest that they appeared before its spread. + +15897470 [networks] +A representative-committee network is projected into a committee network, which is subsequently clustered using single-linkage approach. + +15905473 [tags] +Tags are also frequently found in the CDS, but rarely in the 3'UTR. Tag number is correlated with transcript length. + +15893974 [enhancers] [not read] +vent2 and id3 regulator elements identified by xenopus-human comparisons. + +12060727 [networks] +Delineates "communauties" by removing one by one the edges having the higest "betweenness". (computer intensive) + +15923379 [enzymes] +50 residues were mutated and tested for complementation in a Trl1 null yeast strain. + +15782219 [miRNA] +Small RNA viruses and retroviruses do not seem to encode miRNAs. Some viral miRNAs are transcribed through a polIII tRNA promoter. + +15815676 [misc] +A badly writtem MTA can be worse than non MTA at all. + +12933796 [enzymes] [not read] +Trl1 can be separated in three funcionnal polypeptides : a cyclic phosphodiesterase, a A/GTP-dependant polynucleotide kinase, and an ATP-dependant 3'OH 2'P - 5'P ligase. + +15937218 [miRNA] +Repeat Associated siRNA (rasiRNA) were detected in zebrafish. + +15939778 [single cells] +The cells were pulled out from midly digested ganglia with glass microelectrodes. + +15371555 [tags] +Semi-random priming: the 5' oligo is N6-NlaIII. + +15901564 [visual cortex] +OBCAM RNA and protein levels are higher juvenile and dark reared adults, compared to light reared adults. + +15911778 [networks] +The muticommunauty structure of the air transortation network explains why some cities with a high centrality are not hubs. + +15944709 [miRNA] +A polII transcription factor implicated in the regulation of a human miRNA cluster. + +11159306 [tags] +Predicts the false negative rate of the chi square test for different sequencing dephts in combination with different expression levels. + +15933178 [misc] +Shows how ornithology is modern in its way of implicating lay citizens in research. + +15913596 [enhancers] [not read] +HB9 mouse enhancer similar with fish. + +15885503 [enhancers] [not read] +The Dc2 element from DACH1 is necessary but not sufficient for directing lacZ expression in the brain of mouse transgenics. There is a paralogous Dc2' in the first intron of the DACH2 gene. + +15939571 [enhancers] +Tests more conserved elements in the (surprisingly large) syntenic region containing shh. + +15859353 [enhancers] +Two mouse/fugu conserved regions (-66kb, -62kb), only one has an enhancer activity. + +15990270 [enhancers] [not read] +Conserved in mammals but not in chicken. + +15603590 [networks] +Based on a transcriptional regulatory network which contains only 20% of the E. coli genes. Shows that there is no feedback loop at a purely transcriptional level. As a consequence, eht network can be represented by five hierarchical layers. + +15967424 [enhancers] [not read] +This one is conserved between human and mouse. Not tested in ZF. + +15913596 [enhancers] [not read] +A ~300 bp element conserved in mammal-fugu, but not ZF has no activity, and a neighbouring ~125 element conserved in mammals and fishes (duplicated in ZF) has enhancing activity. + +15987774 [enhancers] [not read] +Conserved in human, mouse and oppossum. What about fish ? + +15998913 [tags] +99% of the tags are excluded from the analysis. + +15919954 [miRNA] +Very sharp expression patterns. + +15897197 [enzymes] +These activities depend on Mn2+, and could be used to generate a 3'rNOH or 3'rNp oligo. + +15979195 [enhancers] +A 5' GC-rich / AT-rich, and a conversely 3' AT-rich / GC-rich motifs were discovered. The change in nucleotide composition seems to delinate the boundaries of the enhancers. + +14962393 [enzymes] +Primary paper for Rnl2(1-249) which ligates AppRNA in abscence of ATP, ten times faster than the full length enzyme. + +15778709 [networks] +The resulting networks allow non-transcription factors to regulate a gene. The direct neighborhood of Myc is enriched in its direct targets. + +15908506 [networks] +Defines origons as subnetworks originating from a single TF (in their model - a directed regulatory network - there is no strong component). + +15861189 [mining] +Uses "compare plots" + +2657738 [enzymes] +Isocitrate used to buffer Mn2+ ions. + +15740627 [amplification] +Introduces a T3 promoter during the second strand synthesis. Very nice introduction. + +10672035 [enzymes] +Primary paper for antarctic phosphatase. Says that it is strongly inhibited by Zn2+ and EDTA, but this apparently false for Zn2+ + +11589698 [enzymes] +The buffer contains 1mM Zn2+ + +15741315 [enhancers] [not read] +Transcribed enhancers in Drosophila. + +15961632 [genome] +A lot of proximal promoters are histone-free. This includes genes which are inactive, but are ready to react. + +15598744 [networks] +Uses Self-Organising Maps to aggregate the transcriptome of B cells into 12 megamodules. + +14654700 [enzymes] +Optimal pH between 6 and 7. Enhanced by 25% PEG 6000 and 1mM HCC. + +4342972 [enzymes] +0.1 mM PPi inhibits RNL1. Polypurines concatenate better than polypyrimidines. Primary paper for the RNA ligase assay. + +10446205 [enzymes] +L. tar mitochondrial RNA ligase performs 100x better on nicked dsRNA than T4RNL1. + +320212 [enzymes] +Activation of donors requires 3'OH acceptors. Acceptors can be exchanged. + +16024824 [enhancers] +The ultraconserved elements in the Irx clusters are transcription enhancers. + +15037782 [enzymes] +The adenylation of RNA by T4 RNL1 is enhanced when they are annealed to a DNA oligos, leaving 3-4 protruding 5'ribonucleotides. + +7796821 [enzymes] +Protein bound to the DNA between the EcoP15I interfer negatively with cleavage. + +14676315 [tags] +Uses the class III enzyme EcoP15I to get longer tags. + +15899965 [enhancers] +Out of 126 ultraconserved elements in a melanogaster / A. Gambiae comparison, only 1 is intergenic, the other being mostly ncRNA and exons. + +7082652 [enzymes] +T4RNL1 & AMP can remove or exchange 3' pNp from RNA molecles. + +4609429 [enzymes] +(pA)8 is the smallet substrate, and the reaction is most efficient with (pA)10. The ligation efficicency then decreas with substrate length. + +173425 [enzymes] +The distance between the EcoP15I sites can be as much as a few kilobasepairs. + +12429865 [tags] +Provides an easy access to various statistical tests. + +1116099 [tags] +The distribution of the R statistic is exponential in randomized datasets. This could be used to determine a threshold. + +9331369 [tags] +Bayesian approach to identify differentially expressed genes in pairwise comparison. + +16059932 [enhancers] [not read] +Small human-fugu conserved sequences (max 24 bp) in the promoter and intron 1 of a non-TF gene. + +15339345 [tags] +Usage of "Bayes Error Rate" instead of a cutoff on p-values. R packaged available under GPL. + +16103215 [misc] +Supports the idea that the only function of some RNA is to have been transcribed. + +16107646 [visual cortex] +Substracted library spotted on microarrays. + +16094371 [networks] +Functional validation. + +16141072 [genome] +62.5 % of the mouse genome is transcribed. + +15608232 [networks] +Comprehensive database featuring coexpression, co-occurence in the litterature, genomic neighbourhood in addition to high-throughput informations as protein-protein interaction. + +16077029 [misc] +Suppressive PCR allows the use of one gene-specific primer, and one random primer. Asymetric cloning is the second safeguard against background. + +16049110 [enhancers] +The minimal promoter used here is from GATA2 and may cause a bias towards enhancers of developmental regulators. + +10037822 [libraries] +To counter internal template swiching. + +16179648 [enhancers] +Neighbour genes of clusters of NCECR are enriched in Transcription Factor ontologies. 16 NCECR were experimentally investigated (10/16 are positive), but the gene names are not given. + +16024824 [enhancers] +Sequence surrounding UCRs might regulate negatively their activity. + +16141073 [genome] +S/AS pairs usually show positive correlation of their expression. + +16195464 [visual cortex] +Loss of function delays the closure of the critical period. + +16168087 [networks] +Different collaboration network in different research consortiums. + +16120967 [enzymes] +Apparently, only one of the two head-to-head sites is cut... + +2020554 [libraries] +Uses terminal transferase. + +16046619 [mining] +When a group of TFs have more than one Transfac entry, only the most over-represented is taken into account to build the network. + +11842121 [mining] +Normalisation between print tips. + +16204192 [single cells] +Geometric mean can be more relevant than arithmetic mean when the expression follows a lognormal distribution. + +16141248 [networks] +Primary paper for the GeneNT R library. Clustering using direct and shortest-path distances. + +16227618 [mirna] +The intergenic transcripts do not seem to be polymerised by pol IV + +16199517 [mining] +Assessed wether some gene sets based on common function, cytogenetic location, predicted regulators, ... are enriched in differentially expressed genes. + +16214800 [emulsion] +The composition of the mixture has been modified so that it stays stable in a PCR of 55 cycles of 10 minutes. + +16233792 [emulsion] +The emulsion is destroyed by centrifugation after 13 cycles, and then the PCR is restarted for 30 cycles. + +15737411 [misc] +Single-tube nested PCR using two different annealing temperatures. + +8663453 [enzymes] +Uracil RNA does not have the same inhibiting effect on PCR. + +11782527 [enzymes] +dTTP is deaminated to dUTP during PCR, which causes the synthesis of uracil-containing DNA, a potent inhibitor of archeal DNA polymerases. + +11574151 [neurogenin] +Unlike mouse ngn3, zebrafish ngn3 is not expressed in the pancreas (but zebrafish ngn1 is). + +16280998 [patents] +Perpetual-motion machines are not patentable. + +99661199 [emulsion] +Only the constructs encoding methylases escape degradation. + +10471784 [emulsion] +The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded. + +15522920 [emulsion] +A methyl transferase fusion protein which binds covalently 5-fluorodesoxycytosine, gets linked to the constructs in which it is encoded. + +12482612 [emulsion] +As tyramide is converted to a free radical which reacts with neighbouring proteins, only beads displaying the epitope become fluorescent. + +12433997 [emulsion] +Random primers were used to introduce mutations. + +16242713 [emulsion] +With their Kd of 3pM, zinc finger protein fusions could be used instead of streptavitin or M.HaeIII to bind the DNA molecule in which they are encoded. + +16131588 [emulsion] +During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead in no excess of biotin is added. + +11274352 [emulsion] +No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density. + +16260754 [emulsion] +Small molecules mixed with EtOH or DMSO were added by vortexing. + +15644201 [emulsion] +Selection pressure can be increased by reducing the volume of the spheres. + +14990785 [emulsion] +Abil EM90 oil is inert enough to allow protein experssion in the RRL system. + +14985532 [emulsion] +Uses 16% glycerol to promote star activity. + +12697388 [emulsion] +Uses the Triton X-100 contained in the PCR buffer as a surfactant. + +14715296 [emulsion] +Oil droplets containing water droplets can be FACS sorted. + +14500846 [emulsion] +Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR. + +15247328 [emulsion] +The cleaved DNA molecules are selected by filling of their ends with biotin-dUTP + +15156154 [emulsion] +Polymerases selected on the ability to amplify their gene despite a 3' mismach in the primers were shown to be able to incorporate a broad range of nucleotide analogs. + +7760832 [libraries] +An eIF-4E fusion protein is used to bind the caps of RNA/DNA duplexes. RNase A cuts single stranded RNAs, thus separating the complexes from the cDNA if they are not full length. + +16314311 [enzymes] +Phenol / Chloroform / Isoamyl alcohol (PCI) treatment followed by ethanol precipitation strongly decreases Ct as well as increases the consistencies of the comparisons between different dillutions of the same samples. + +16308152 [amplification] +Detailed protocol for Terminal Continuation (TC). + +16224006 [IP] +20 % of the human coding genome is patented. + +16344560 [promoters] [oligo-capping] +Estimates as 88% the frequency of full length cDNA produced by the oligo-capping method + +16299470 [enzymes] +The T4 DNA ligase can join 5'p to 2'OH 3'p or 2'p 3'OH nucleotides. The Taq polymerase can elongate across up to three ribonucleotides. + +16251272 [misc] +Transcriptional repressor involved in splicing. + +1180897 [protocols] +Precipitation of RNA in 240 mM NH4OAc. + +16418487 [enhancers] +Not read. Deletion of an enhancer conserved in mouse and chicken and its phenotype. + +14701942 [enhancers] +Not read. A pdx-1 enhancer conserved in human, mouse and chicken. + +10408598 [visual cortex] +Not read. egr1 is down-regulated in dark-reared rats. + +11739581 [visual cortex] +Not read. Phenotype of the egr1 KO for the activity-dependant plasticity in the visual cortex. + +8656291 [visual cortex] +not read. Nuclear extracts from dark reared rats have a lesser binding activity to an egr1 probe. + +16314298 [protocols] +Adding gold in PCR tubes enhances the yield when the cycling is quick. + +16400149 [networks] +In this changing network, most parameters except the clustering coefficient depend on the width of the smoothing window. + +15899964 [promoters] +ChIP on chip focused on the preinitiation complexes of the ENCODE regions. + +10471753 [amplification] +Single-primer PCR with a moderate suppressive effect can be used to regulate the product size. + +16407397 [enhancers] +Idenification of conserved enhancers of shh hundreds of kp far of the coding sequence. + +16141076 [miRNA] +Not read. A liver miRNA which facilitates the replication of a virus. + +16365385 [enhancers] +Not read. Transposon-free regions are enriched with developmental regulators. + +16380714 [enhancers] +There are statistically significantly less SNPs in the conserved non coding regions of the human genome. This difference is weakest in the elements located more than 10 kbp upstream of the promoter. + +16369481 [amplification] +At least 30 cells are needed to acheive a good reproducibility + +10911985 [protocols] +Primers to amplify histone h4. + +16432206 [genome] +Using pseudogenes as cDNAs, the authors analyse splice variants and alternative promoters. + +16421516 [miRNA] +This miRNA is localised with its target in the synapto-dendritic compartment. + +16458883 [enhancers] +The first enhancer conserved from insects to vertebrates. + +16465154 [IP] +In the US, one can not be inventor on a patent if he has not made an intellectual contribution. + +16408288 [enhancers] +Not read. Sox 2 enhancers conserved in vertebrates. + +16185862 [enhancers] +Review. Looking for a function. + +1643220 [promoters] +The genes controled by the two classes differ by their ontologies and broadness of expression. + +15326340 [IP] +Proposing a distributed research system similar to distributed computing, and discussing it in the context of intellectual property. + +16336043 [misc] +The human faeces might be a vector of infections plant RNA viruses. + +16141074 [miRNA] +Many small RNAs match transposons or intergenic regions. + +16489339 [tags] +Protocol with random primers + +16495311 [enhancers] +Not read. Enhancers of Krox-20, conserved between chicken and mouse. + +16527264 [enhancers] +Not read. An enhancer of Rpx/Hesx1 conserved between mouse and xenopus. + +16540572 [visual cortex] +Not read. Monocular deprivation can lead to shifts in ocular dominance in adults if they are deprived of visual stumuli 10 days before the experiment... + +16540077 [misc] +The PPi produced during the PCR can be removed with the pyrosequencing enzymes themselves. The antarctic phosphatase from NEB was not very efficient at this task. + +16461948 [protocols] +T4gp32 increases the yield of the smallest cDNAs by 10 %. + +2326177 [protocols] +More inert than glycogen. + +12448877 [protocols] +Ligating a DNA adaptor 3' to the FScDNA using T4RNA ligase. + +7479050 [protocols] +HCC protects DNA and enhances ligation at 1 mM. HCC is thought to condense DNA, similarly to spermine and spermidine. + +4000951 [protocols] +HCC (1 mM) promotes intermolecular ligation. This effect is countered by monovalent cations. + +386284 [protocols] +A low ATP concentration contributes to the attainment of high yields. ATP regenerating systems allow to work at sub-stoechiometric concentrations. Rnase A can be used as a SSBP. Spermine enhances yield. + +724498 [enzymes] +Optimal temperature between 0 and 15 degrees. 15-20 % DMSO enhance the reaction. pCp is easily ligated to the 3' end of tRNAs, but the 5' end of tRNAs is difficult to ligate to pCp if it is engaged in a double helix. + +9380524 [protocols] +Concentrations as high as 1 M or 2.5 M can strongly improve the yield. + +16533910 [enhancers] +The directionality of the CNEs is often conserved beween paralogous loci. + +16629394 [single cells] +50 % success on B cells to amplify the Ig variable region with polyG tailing and nested PCR. + +16682450 [misc] +The structure of the genetic code favours secondary structures in coding RNA. + +16707659 [enzymes] +By weakening the DNA-protein interaction, the authors acheived the suppression of the non-temlated products in rolling circle amplification. + +16618967 [enzymes] +The combined use of a complementary DNA oligo and DNA ligase suppresses the artifacts seen in RNA ligase adenylation. + +16709670 [visual cortex] +Weakening the extracellular matrix influences the plasticity process. + +16723524 [visual cortex] +Publicly available cell-type-specific expression patterns were used to analyse the results of whole-tissue microarray experiments. + +16344560 [alternative promoters] +Detected an average of 3.1 promoters per gene. + +16728472 [enhancers] [not read] +Conserved between mouse and human. + +16569696 [enhancers] +Identifies conserved motifs whose mutation lead to the abolition of the expression in certain locations. Some of the motifs overlap with coding sequences. + +16766680 [small RNAs] +They are not found in other cell types. + +16751343 [non-coding RNA] +Few of them overlap FANTOM3 transcripts, but 32/36 can be detected by RT-PCR. + +16542485 [amplification] +SMART has a much lower false discovery rate (FDR), but compresses the expression ratios. + +16751773 [small RNAs] +The mutation was found by quantitative trait locus (QTL) and single nucleotide polymorphism (SNP) analysis. + +16723398 [networks] +Iterative division method with rules for stopping. Uses a "modularity matrix". + +16751776 [small RNAs] +Loci encoding piRNAs are conserved, but not the piRNA themselves. + +16778019 [small RNAs] +The piRNA were copurified with proteins having ATPase and helicase activity. + +16769978 [enhancers] +As the highest conservations scores in close species comparison usually correspond to conserved regions in distant species, sequence comparisons with distance species are not necessary to identify funcitonal elements. + +16809489 [small RNAs] +rasiRNA, the drosophila piRNA, are 5'P and one of their 2' or 3' is not OH. They are processed independantly from Dicer1 and Dicer2. + +16778056 [small RNAs] +Its neighbors got pseudogenized too in humans. + +16790564 [protocols] +Generates primers by MmeI cleavage of cDNA extremities, and inactivates those which are complementary to the driver library by extending them with ddNTP. + +16822854 [protocols] +The fluorophore and the quencher are separated by the strand-displacement activity of the enzyme. + +16862119 [genome] +The position of nucleosomes is encoded by AA/TT/TA and GC dinucleotides with a period of 10 bp and opposite phases. + +16806968 [enhancers] +Some fish and frog orthologous enhancers differ in their expression pattern when inserted in the same construct. + +16917059 [emulsions] +Not read. This could be useful to prepare reversible emulsion microreactors. + +16915236 [non-coding] +No northern blot? + +17012272 [tags] +EST analysis by oligo-capping and 454-sequencing unravelled 5'polyA tails in maize. + +17008526 [mining] +Uses GSEA to mine a database of transcriptional profiles of cell clutures exposed to > 150 different chemicals. Hierachical clustering identified mostly batch effects. + +16998490 [enhancers] +A model in which heterozyogcity is deleterious suggests an explanation for the ultraconservation. An alternative model is based on local enhanced repair. + +16964265 [genome] +The AA/TT Nucleosome Positionning Pattern is conserved across evolution in Yeast. + +16951679 [genome] +Not read. 85 % of the fly genome is transcribed, and 30 % contributes to mature transcripts. + +16930954 [enhancers] +Not read. Human-mouse conserved enhancer in fgf15. + +17003135 [networks] +Breadth-first search: organises a network in a layered hierarchy. Highest nodes tend to be influencial, middle to have a high betweenness, and lowest to be essential. + +16893951 [amplification] +Combined use of T7 polymerase and helicase, strong strand displacement, and branched rolling circle isothermal amplification. + +15084599 [enzymes] +Complete Appylation by RNL2 is possible in absence of Mg2+, but is slower. + +16964210 [amplification] +Apparently, DNA - RNA hybridisation is very tolerant to mismatches. + +17024178 [enzymes] +This enzyme is dependant on Mn2+ and does not require a primer. + +16971463 [enzymes] +Degrades single-strand DNA, not RNA nor double strand DNA. + +16964207 [misc] +Reommends to use only dbSNP entries which have a phred score higher than 40. + +15693942 [mining] +Uses a highly replicated experimental desigh to show that metabolic genes vary in their expresison between tissues, individuals and populations. + +10400927 [protocol] +0.3 mM MnCl2 + 1:1 MnCit in absence of EDTA is optimal. + +17018278 [enzymes] +Not Read + +16698958 [enhancers] +Defines the concept of "maximal N-mers". + +17053078 [misc] +The bigger the weapon, the smaller the testis. + +17067785 [enhancers] +Not read. Mouse-Fish conservation in Gbx + +16872493 [misc] +[not read] 18S is a much better control than gapdh in non-small cell lung cancer. + +17066168 [nanotech] +[not read] Celles are trapped on a chip which looks like a building with many balconies. + +17028099 [tags] +SAGE libraries sequenced wiht 454 technology. + +17095694 [genome] +Tiling arrays were designed with draft genome sequence; 11~13,000 genes detected. + +11410683 [tags] +Small changes in handling temperature can melt AT-rich tags and deplete them from the library. + +16630818 [enhancers] +Not read. Conserved developmental enhancers acting as silencers in ES cells. + +17086198 [enhancers] +61% of ultraconserved human-fugu non coding elements have an enhancing activity. + +17098862 [nanotechnologies] +The reactions produce fluorecent molecules and are performed on a PDMS slide which is scanned. + +17067785 [enhancers] +[not read] Mouse-fish conserved enhancers in gbx2. + +16873663 [misc] +Most mispaired residues are hydrolysed by the penultimate nucleotide in RTases. + +16397291 [protocols] +Using Chelex to purify ChIPed DNA faster. + +17202257 [misc] +[not read] Oscillation of the concentration of the Notch mRNA in a binary cell system. + +17135569 [enhancers] +[not read] histone acetylation islands frequently overlap mouse-fugu conserved regions. + +17185593 [enhancers] +The regulatory regions of the teleosts may have diverged faster than the ones of cartilaginaeous fishes. + +17204650 [miRNA] +This sequence does not confer the cell cycle properties of mir-29b to siRNAs. + +16175253 [nanotechnologies] +Continuous washing is necessary for efficient DDM coating. + +17185604 [networks] +Mutually exclusive interactions defined by distinguishing interfaces on the nodes. + +17159156 [enhancers] +Function of an enhancer lost in teleosts transferred to another one. + +15020752 [tags] +Rescures circularised concatemers by partial digestion. + +17124291 [miRNA] +5'ppp RNAs cloned using a "ligation independant" protocol. + +17158288 [miRNA] +Small RNA cloned by 3' polyadenylation and 5' RACE. + +17159153 [nanotechnologies] +Glass / PDMS mixed system + +17038566 [enhancers] [not read] +A RP score based on mammal-mammal conservation and presence of GATA-1 sites correlates with enhancer activity. + +15815687 [misc] +Normalisation genes in qPCR should be validated in the particular systems studied. + +17189378 [genetics] [not read] [patent] +Whole-genome analysis of sequences flanking restriction sites, some of which being polymorphic. + +17299583 [libraries] +There is a bias that might be caused by some sequence-specificity of the DNA ligase. + +15884678 [misc] +Intronic LNA 14-mer to inhibit the gene-specific amplification of genomic DNA during RT-PCR. + +17290226 [enzymes] +Requres the Ku heterodimer. + +17267814 [tags] +The novel transcripts have an average of 0.84 copies per cell. + +17274809 [enhancers] +[Not read] + +17376869 [genome] +Human-chimp comparisons. + +17406439 [tags] [not read] +ChIp, then extraction of tags. + +17409112 [enhancers] +[Not read] A transcription factor binding site in a conserved enhancer. + +17369403 [enhancers] +[Not read] Some ultraconserved exons surprisingly contain stop codons in all three frames. + +17361132 [enhancers] +[Not read] Some ultraconserved exons surprisingly contain stop codons in all three frames. + +15582152 [misc] +No correlation between in situ expression pattern and gene ontology in the brain. + +17470793 [networks] +[not read] Reshaping of networks to a tree-like structure using renormalisation. + +17405768 [microfluidics] +Cycling 100 times (94°C for 30 s, 55°C for 30 s, and 72°C for 60 s) in 0.1% DDM, x1 Pfu Buffer before use improves product yield. + +17488851 [enzymes] +In presence of Co²⁺, can extend an oligonucleotide on a template using rNTPs. + +17488852 [enzymes] +Useful to prepare 2' phosphate ends, which are substrate for the yeast tRNA ligase. + +17606638 [enzymes] +Coud be useful in molecular biology of siRNA. + +17412892 [tags] +Strand-swichin method, with oligo dT primers and 3000 cells. + +17620602 [microfluidics] +Isolation, lysis and isothermal amplification in a PDMS chip. + +17632057 [promoters] +Transcription of 5' fragments was detected on promoters of genes which produce less than one full-length transcript per cell. + +11328886 [pcr] +Method of normalisation taking PCR efficiency into account. + +17609372 [networks] +Disease network. + +17550599 [enhancers] +35 % of conserved Drosophila enhancers are transcribed (as detected by tiling arrays). + +17646654 [enzymes] +Mechanistic insights with fast-scanning atomic force microscopy. + +17609390 [QTL] +Identifies Affymetrix probes overlapping a SNP by chance. + +17339210 [QTL] +eQTL approach using bayesian statistics and Markoc chains. + +12671682 [normalisation] +Global normalisation does not allow to survey broad increases or decreases of the total transcriptional activity. This method is more suited when this happens. + +17656717 [networks] +Derives a product network from per-country export data, and analyses how the countries evolve in time within this network. + +17703193 [promoters] +Some genes are up-regulated by the loss of TBP. + +1017013 [transcription] +Estimates the number of mRNA molecules per cell to 300,000. + +17586543 [mining] +Faster than Pearson correlation ? + +17823314 [amplification] +RT with a tailed random octamer, RNaseH digestion, and then 2nd strand synthesis with the same primer at a low temperature for the first cycles. + +17804464 [enzymes] +Digests single-stranded 5' phosphorylated DNA or RNA molecules + +14999098 [mining] +[not read] Power law in microarray data. + +12136033 [tags] +The distribution of the SAGE tags follow a power law. + +17897965 [protocols] +Adding actinomycin D suppresse self-priming. + +17936740 [enhancers] +Another conserved enhancer in a developmental regulator that is not a transcription factor. + +17301169 [olfactory] +[not read] If a OR gene is inactivated by a reporter transgene, only neighbour receptors are chosen in the cells in which the transgene is activated. (or is it the reverse?) + +17881408 [tags] +Provides a R library + +15682396 [olfactory] +List of enriched genes, obtained by substraction. + +9151732 [olfactory] +[not read] Primary paper for O/E-2 and O/E-3 and their binding capacities. + +14656972 [olfactory] +[not read] Six promoters from a OR gene family, the analysis of conserved motifs, bandshifts and yeast one-hybrid. + +15550249 [olfactory] +[not read] SAGE library made from single olfactory neurons. + +8474458 [olfactory] +[not read] "The Olf-1-binding motif consensus sequence was defined as TCCCC(A/T)NGGAG." + +10395892 [misc] +[not read] Review on the "Kozak" sequence. + +18032727 [tags] +Primary paper for paraclu + +17010214 [olfactory] +Primary paper for CLICs (clusters in conservation). + +17284453 [misc] +[not read] The 3' end of RefSeq protein-coding genes is enriched in putative binding sites (the 5' as well). + +17510325 [transcriptome] +Small RNAs were directly labelled with pCpBiotin. + +18024554 [tags] +A sort of Superverylong 3'SAGE. + +18171944 [misc] +Identifies specific genes of neurons, astrocytes and oligodendrocytes. + +18195365 [misc] +After 10 weeks, elevated DNA strand break levels are detected in the sperm DNA of mice raised near a highway or a steel factory, but not in controls breezing the same but filtered air. + +16902134 [networks] +Behavioral graph coloring + +16432518 [emulsions] +RCA amplification of DNA coupled to beads, followed by single-base extension and flow sorting. + +16449203 [enzymes] +2'OMe RNAs can not be polyadenylated in vitro. + +7682819 [misc] +[not read] Studies teh strength of the biotin-streptavidin bond. + +15649321 [misc] +The buffer is dried on the lid of the tube, and one cell is deposited in a small volume of liquid with a capillary. + +17412706 [enzymes] +An interesting protein that condensates DNA. + +15944704 [networks] +Adjascent k-clique communities can share nodes while staying distinct. This allows to create networks of communitiest. + +15289330 [pcr] +A method for selecting normalisation genes. + +16705037 [enhancers] +Did not find FANTOM3 CAGE tags. + +18292225 [non-coding] +[not read] Links antisense transcription and hypermutation. + +18339674 [enhancers] +[not read] Conserved sequence very near the ATG. + +17412960 [qtl] +First analysis within a breed, then second analysis comparing small and giant breeds. + +16105897 [mining] +Two genes of opposite expression profiles define a "top scoring pair", and are used to sort the other genes. + +18369765 [microfluidics] +Another implementation of the revese-transcription on beads. + +18362361 [networks] +[not read] Algorithm to transform a time serie into a graph. + +18417536 [enhancers] +First report of a conserved enhancer in a coding sequence ? + +18367472 [promoters] +This method tends to predict functional TFBFS in the [-200,100] promoter. + +18417536 [enhancers] +Necessary but not sufficient. + +18156157 [enhancers] +In a transgenic context, mutating some neighboring bases had a much smaller effect despite their similar level of conservation. + +12169536 [mining] +Uses arcsinh (argsinh in French) as a substitude of log scale (to cope with the zero values). + +18579682 [enhancers] +Deletion of the enhancer has an effect on bone size. + +18606989 [tags] +The forumlas were successfully applied to MPSS data. + +18487259 [tags] +Includes a comparative promoter analysis of three genes with either vector-capping or oligo-capping. + +10637631 [cDNA] +RefSeq takes the longest 5'end that maintians the integrity of the coding sequence. + +18511537 [enzymes] +Thermostable ligase that can circularise even at 95 °C. + +18493018 [genetics] +Repeats may be the cause of the rearrangements that gave rise to the coat color allelles in sheep. + +18676817 [enhancers] +A conserved element essential for repression. + +18606121 [misc] +Striking example of mRNAs having been multiple times retrotranscribed in the genome. (As revealed by the presence of vestigial splice leader sequences). + +17353264 [enzymes] +Useful for U-tailing ? + +18697905 [enhancers] +Conserved enhancer in Gbx2, with Dlx binding sites. + +14656972 [olfactory] +6 promoters that bind O/E-2, but do not display strong consensus sequences. + +18542052 [tags] +Ligation on a 5' adaptor to cleavage products that are naturally 5'-phosphorylated. + +18728187 [misc] +neurons have cilia! + +18787168 [enzymes] +Could be useful to specifically degrade miRNAs ? + +18773071 [enhancers] +A Sox10 enhancer contains a Sox dimer binding site. + +18754010 [misc] +Another histone modification to take into account. + +527589 [transcription] +Evidence for complex polyA minus mRNA. + +18829718 [enzymes] +Optimal at 65 ℃, inactivated at 75 ℃, and mostly adenylylating at 37 ℃. + +18836037 [misc] +[not read] Having a binding site is not always essential. + +18829718 [enzymes] +[not read]De-adenylates at 35 ℃, and circularises at 65 ℃. + +18988746 [genome] +[not read] Many chromosomal aberrations in ES cells. + +18981420 [enzymes] +[not read] RNA ligase inhibitor. + +18931376 [enzymes] +MmeI needs two sites but one can be provided in trans by short duplexes. + +18948291 [3'UTR] +Detached 3'UTRs that stay associated with the polysomes. + +18993075 [5'UTR] [mapping] +A good reason to map with indels. + +17439302 [non-coding] +Example of a putatively non-coding RNA that polycistronically expresses small peptides. + +18818370 [enhancers] +[not read] Among all the sequences bound by GATA1, the evolutionary conserved ones are the most likely to bear the WGATAR motif. + +14647400 [library] [template switching] +Templates switching with an oligonucleotide ending in a mixture of Gs and Cs. + +19038026 [miRNAs] +77, 58 and 47 human, mouse and rat pre-miRNAs respectively. + +19029911 [misc] [miRNA] +This might be used to cut RNA during library construction? + +6247631 [5' end] [review] +[not read] Much more comprehensive than any textbook. + +19161242 [neurogenin] +Seems to forget about Ngr1-b + +19059995 [RNA] +I suppose somebody will make a deep-sequencing version of it some day. diff --git a/biblio/US5759822.mdwn b/biblio/US5759822.mdwn new file mode 100644 index 00000000..eff3b18f --- /dev/null +++ b/biblio/US5759822.mdwn @@ -0,0 +1,4 @@ +[[!meta title="Method for suppressing DNA fragment amplification during PCR."]] +[[!tag patent amplification]] +[[!gpatent Ak0jAAAAEBAJ desc="Suppressive PCR."]] +See also patent [[!gpatent L-ccAAAAEBAJ desc="5565340"]]. diff --git a/biblio/US6372437.mdwn b/biblio/US6372437.mdwn new file mode 100644 index 00000000..96aa5dab --- /dev/null +++ b/biblio/US6372437.mdwn @@ -0,0 +1,4 @@ +[[!meta title="Method for improving heat stability of RNA."]] +[[!tag patent libraries]] +[[!gpatent LbkKAAAAEBAJ desc="Describes the use of chaproning agents to protect the RT, of moderate excess of dNTPs to protect RNA from magnesium, and even of very small quantities of detergents to further increase the rate of full-length transcription."]] +See also patents [[!gpatent DCEGAAAAEBAJ desc="6221599"]] and [[!gpatent y-cAAAAAEBAJ desc="6013488"]]. diff --git a/biblio/epicentre_SCCE0610.mdwn b/biblio/epicentre_SCCE0610.mdwn new file mode 100644 index 00000000..b07896b3 --- /dev/null +++ b/biblio/epicentre_SCCE0610.mdwn @@ -0,0 +1,3 @@ +[[!meta title="ScriptCap™ m7G Capping System."]] +[[!tag cap product enzyme epicentre]] +Available from [EPICENTRE](http://www.epibio.com/item.asp?ID=498) under cat. № SCCE0610 and SCCE0625. In Japan, avaliable from [ARB-LS](http://www.arb-ls.com/products/scriptcap_m7g_capping_system/). diff --git a/biblio/template b/biblio/template new file mode 100644 index 00000000..50b0d986 --- /dev/null +++ b/biblio/template @@ -0,0 +1,3 @@ +[[!meta title=""]] +[[!tag ]] +[[!pmid desc=""]] diff --git a/biblio/y9YNAAAAEBAJ.mdwn b/biblio/y9YNAAAAEBAJ.mdwn new file mode 100644 index 00000000..7bdbaf3d --- /dev/null +++ b/biblio/y9YNAAAAEBAJ.mdwn @@ -0,0 +1,3 @@ +[[!meta title="Process for selective amplification of a full-length cDNA involving an anchor nucleic acid."]] +[[!tag patent cap]] +[[!gpatent y9YNAAAAEBAJ desc="Based on ligation, but using the polyC tail."]]