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Results: 1 to 20 of 28

References for PMC Articles for PubMed (Select 23016513)

1.

HiNO: an approach for inferring hierarchical organization from regulatory networks.

Hartsperger ML, Strache R, Stümpflen V.

PLoS One. 2010 Nov 4;5(11):e13698. doi: 10.1371/journal.pone.0013698.

2.

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105. doi: 10.1093/nar/gkq1110. Epub 2010 Nov 4.

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.

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.

Bhardwaj N, Yan KK, Gerstein MB.

Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6841-6. doi: 10.1073/pnas.0910867107. Epub 2010 Mar 29.

5.

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture.

Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM.

Mol Syst Biol. 2009;5:294. doi: 10.1038/msb.2009.52. Epub 2009 Aug 18.

6.

A molecular function map of Ewing's sarcoma.

Kauer M, Ban J, Kofler R, Walker B, Davis S, Meltzer P, Kovar H.

PLoS One. 2009;4(4):e5415. doi: 10.1371/journal.pone.0005415. Epub 2009 Apr 30.

7.

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes.

Zhang R, Lin Y.

Nucleic Acids Res. 2009 Jan;37(Database issue):D455-8. doi: 10.1093/nar/gkn858. Epub 2008 Oct 30.

8.

EWS/FLI mediates transcriptional repression via NKX2.2 during oncogenic transformation in Ewing's sarcoma.

Owen LA, Kowalewski AA, Lessnick SL.

PLoS One. 2008 Apr 16;3(4):e1965. doi: 10.1371/journal.pone.0001965.

9.

The Biology of Ewing sarcoma.

Riggi N, Stamenkovic I.

Cancer Lett. 2007 Aug 28;254(1):1-10. Epub 2007 Jan 23. Review.

PMID:
17250957
10.

TRED: a transcriptional regulatory element database, new entries and other development.

Jiang C, Xuan Z, Zhao F, Zhang MQ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D137-40.

11.

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.

12.

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.

Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L.

J Mol Biol. 2006 Jun 30;360(1):213-27. Epub 2006 May 3.

PMID:
16762362
13.

Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks.

Balaji S, Iyer LM, Aravind L, Babu MM.

J Mol Biol. 2006 Jun 30;360(1):204-12. Epub 2006 Apr 27.

PMID:
16730024
14.

Bayesian error analysis model for reconstructing transcriptional regulatory networks.

Sun N, Carroll RJ, Zhao H.

Proc Natl Acad Sci U S A. 2006 May 23;103(21):7988-93. Epub 2006 May 15.

15.

Genomic analysis of regulatory network dynamics reveals large topological changes.

Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M.

Nature. 2004 Sep 16;431(7006):308-12.

16.

Transcriptional regulatory code of a eukaryotic genome.

Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA.

Nature. 2004 Sep 2;431(7004):99-104.

17.

Cellular and genetic analysis of wound healing in Drosophila larvae.

Galko MJ, Krasnow MA.

PLoS Biol. 2004 Aug;2(8):E239. Epub 2004 Jul 20.

18.

Gene regulatory network growth by duplication.

Teichmann SA, Babu MM.

Nat Genet. 2004 May;36(5):492-6. Epub 2004 Apr 11.

PMID:
15107850
19.

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.

Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M.

Genes Dev. 2002 Dec 1;16(23):3017-33.

20.

Transcriptional regulatory networks in Saccharomyces cerevisiae.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA.

Science. 2002 Oct 25;298(5594):799-804.

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