From: Charles Plessy Date: Thu, 18 Jan 2018 03:59:49 +0000 (+0900) Subject: Old X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=140bbfe108e913107f6d0f4664d6bb78ad079857;p=source.git Old --- diff --git a/biblio/15372033.mdwn b/biblio/15372033.mdwn new file mode 100644 index 00000000..5f639d5a --- /dev/null +++ b/biblio/15372033.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Nature. 2004 Sep 16;431(7006):308-12."]] +[[!tag network]] + +Nature. 2004 Sep 16;431(7006):308-12 doi:10.1038/nature02782 + +Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. + +Genomic analysis of regulatory network dynamics reveals large topological changes. + +[[!pmid 15372033 desc="Primary paper for SANDY. Distinguishes "endogenous" from "exogenous" networks, and introduces transient hubs."]] diff --git a/biblio/To_Do b/biblio/To_Do index 86859b00..e68f2e59 100644 --- a/biblio/To_Do +++ b/biblio/To_Do @@ -189,9 +189,6 @@ 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. @@ -220,9 +217,6 @@ 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. @@ -247,9 +241,6 @@ 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. @@ -382,9 +373,6 @@ Two mouse/fugu conserved regions (-66kb, -62kb), only one has an enhancer activi 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. @@ -415,9 +403,6 @@ 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. - 16024824 [enhancers] The ultraconserved elements in the Irx clusters are transcription enhancers. @@ -448,9 +433,6 @@ Supports the idea that the only function of some RNA is to have been transcribed 16094371 [networks] Functional validation. -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.