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+[[!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 86859b008c386851afd87c86b2650a7fbe7a18f3..e68f2e591e995aef066b4ae9b656aaac02d7f646 100644 (file)
--- 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.