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Items: 1 to 20 of 31

1.

The Gene Ontology: enhancements for 2011.

Gene Ontology Consortium..

Nucleic Acids Res. 2012 Jan;40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. Epub 2011 Nov 18.

2.

The BioGRID Interaction Database: 2011 update.

Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704. doi: 10.1093/nar/gkq1116. Epub 2010 Nov 11.

3.

Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators.

Bhardwaj N, Kim PM, Gerstein MB.

Sci Signal. 2010 Nov 2;3(146):ra79. doi: 10.1126/scisignal.2001014.

4.

Global coordination of transcriptional control and mRNA decay during cellular differentiation.

Amorim MJ, Cotobal C, Duncan C, Mata J.

Mol Syst Biol. 2010 Jun 8;6:380. doi: 10.1038/msb.2010.38.

5.

Integrated assessment of genomic correlates of protein evolutionary rate.

Xia Y, Franzosa EA, Gerstein MB.

PLoS Comput Biol. 2009 Jun;5(6):e1000413. doi: 10.1371/journal.pcbi.1000413. Epub 2009 Jun 12.

6.

Evolutionary rates and centrality in the yeast gene regulatory network.

Jovelin R, Phillips PC.

Genome Biol. 2009;10(4):R35. doi: 10.1186/gb-2009-10-4-r35. Epub 2009 Apr 9.

7.

Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.

Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ.

PLoS One. 2008 Sep 3;3(9):e3112. doi: 10.1371/journal.pone.0003112.

8.

Topological comparison of methods for predicting transcriptional cooperativity in yeast.

Aguilar D, Oliva B.

BMC Genomics. 2008 Mar 25;9:137. doi: 10.1186/1471-2164-9-137.

9.

Global variation in copy number in the human genome.

Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME.

Nature. 2006 Nov 23;444(7118):444-54.

10.

Genomic analysis of the hierarchical structure of regulatory networks.

Yu H, Gerstein M.

Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14724-31. Epub 2006 Sep 26.

11.

Identification of transcription factor cooperativity via stochastic system model.

Chang YH, Wang YC, Chen BS.

Bioinformatics. 2006 Sep 15;22(18):2276-82. Epub 2006 Jul 14.

PMID:
16844711
12.

Integrated assessment and prediction of transcription factor binding.

Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T.

PLoS Comput Biol. 2006 Jun 16;2(6):e70. Epub 2006 Jun 16.

13.

Why highly expressed proteins evolve slowly.

Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH.

Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14338-43. Epub 2005 Sep 21.

14.

Statistical methods for identifying yeast cell cycle transcription factors.

Tsai HK, Lu HH, Li WH.

Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13532-7. Epub 2005 Sep 12.

15.

Identifying cooperative transcriptional regulations using protein-protein interactions.

Nagamine N, Kawada Y, Sakakibara Y.

Nucleic Acids Res. 2005 Aug 26;33(15):4828-37. Print 2005.

16.

The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.

Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Güldener U, Mannhaupt G, Münsterkötter M, Mewes HW.

Nucleic Acids Res. 2004 Oct 14;32(18):5539-45. Print 2004.

17.

Combinatorial control of gene expression.

Reményi A, Schöler HR, Wilmanns M.

Nat Struct Mol Biol. 2004 Sep;11(9):812-5. Review.

PMID:
15332082
18.

Identifying cooperativity among transcription factors controlling the cell cycle in yeast.

Banerjee N, Zhang MQ.

Nucleic Acids Res. 2003 Dec 1;31(23):7024-31.

19.

Collaborative competition mechanism for gene activation in vivo.

Miller JA, Widom J.

Mol Cell Biol. 2003 Mar;23(5):1623-32.

20.

Highly expressed genes in yeast evolve slowly.

Pál C, Papp B, Hurst LD.

Genetics. 2001 Jun;158(2):927-31. No abstract available.

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