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Validation and refinement of gene-regulatory pathways on a network of physical interactions
Chen-Hsiang Yeang, H Craig Mak, Scott McCuine, Christopher Workman, Tommi Jaakkola, Trey Ideker
Genome Biol. 2005; 6(7): R62. Published online 2005 July 1. doi: 10.1186/gb-2005-6-7-r62
PMCID:
PMC1175993
Abstract Full Text PDF–482K Supplementary Material

Is Cited by the Following 23 Articles in this Archive:

Unveiling Protein Functions through the Dynamics of the Interaction Network
Irene Sendiña–Nadal, Yanay Ofran, Juan A. Almendral, Javier M. Buldú, Inmaculada Leyva, Daqing Li, Shlomo Havlin, Stefano Boccaletti
PLoS One. 2011; 6(3): e17679. Published online 2011 March 9. doi: 10.1371/journal.pone.0017679
PMCID:
PMC3052369
Abstract Full Text PDF–725K Supplementary Material
TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information
Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai, Lu Xie
BMC Bioinformatics. 2010; 11(Suppl 11): S5. Published online 2010 December 14. doi: 10.1186/1471-2105-11-S11-S5
PMCID:
PMC3024863
Abstract Full Text PDF–710K Supplementary Material
Characterizing regulatory path motifs in integrated networks using perturbational data
Anagha Joshi, Thomas Van Parys, Yves Van de Peer, Tom Michoel
Genome Biol. 2010; 11(3): R32. Published online 2010 March 11. doi: 10.1186/gb-2010-11-3-r32
PMCID:
PMC2864572
Abstract Full Text PDF–1.4M Supplementary Material
How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens
Florian Markowetz
PLoS Comput Biol. 2010 February; 6(2): e1000655. Published online 2010 February 26. doi: 10.1371/journal.pcbi.1000655
PMCID:
PMC2829042
Full Text PDF–323K
Toward the dynamic interactome: it's about time
Teresa M. Przytycka, Mona Singh, Donna K. Slonim
Brief Bioinform. 2010 January; 11(1): 15–29. Published online 2010 January 8. doi: 10.1093/bib/bbp057
PMCID:
PMC2810115
Abstract Full Text PDF–151K
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments
Ewa Szczurek, Irit Gat-Viks, Jerzy Tiuryn, Martin Vingron
Mol Syst Biol. 2009; 5: 287. Published online 2009 July 7. doi: 10.1038/msb.2009.45
PMCID:
PMC2724975
Abstract Full Text PDF–6.5M Supplementary Material
Backup in gene regulatory networks explains differences between binding and knockout results
Anthony Gitter, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo Oliva, Itamar Simon, Ziv Bar-Joseph
Mol Syst Biol. 2009; 5: 276. Published online 2009 June 16. doi: 10.1038/msb.2009.33
PMCID:
PMC2710864
Abstract Full Text PDF–989K Supplementary Material
A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, Joshua M. Stuart
PLoS Comput Biol. 2009 January; 5(1): e1000274. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000274
PMCID:
PMC2613752
Abstract Full Text PDF–579K Supplementary Material
A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast
Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina Leslie
PLoS Comput Biol. 2008 November; 4(11): e1000224. Published online 2008 November 14. doi: 10.1371/journal.pcbi.1000224
PMCID:
PMC2573020
Abstract Full Text PDF–1.5M Supplementary Material
Gene network dynamics controlling keratinocyte migration
Hauke Busch, David Camacho-Trullio, Zbigniew Rogon, Kai Breuhahn, Peter Angel, Roland Eils, Axel Szabowski
Mol Syst Biol. 2008; 4: 199. Published online 2008 July 1. doi: 10.1038/msb.2008.36
PMCID:
PMC2516358
Abstract Full Text PDF–2.0M Supplementary Material
Inferring the role of transcription factors in regulatory networks
Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel
BMC Bioinformatics. 2008; 9: 228. Published online 2008 May 6. doi: 10.1186/1471-2105-9-228
PMCID:
PMC2422845
Abstract Full Text PDF–705K
Characterization of the proneural gene regulatory network during mouse telencephalon development
Julia M Gohlke, Olivier Armant, Frederick M Parham, Marjolein V Smith, Celine Zimmer, Diogo S Castro, Laurent Nguyen, Joel S Parker, Gerard Gradwohl, Christopher J Portier, François Guillemot
BMC Biol. 2008; 6: 15. Published online 2008 March 31. doi: 10.1186/1741-7007-6-15
PMCID:
PMC2330019
Abstract Full Text PDF–1.7M Supplementary Material
A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response
Kai Tan, Hoda Feizi, Colin Luo, Stephanie H. Fan, Timothy Ravasi, Trey G. Ideker
Proc Natl Acad Sci U S A. 2008 February 26; 105(8): 2934–2939. Published online 2008 February 19. doi: 10.1073/pnas.0708670105
PMCID:
PMC2268563
Abstract Full Text PDF–398K Supplementary Material
Inferring cellular networks – a review
Florian Markowetz, Rainer Spang
BMC Bioinformatics. 2007; 8(Suppl 6): S5. Published online 2007 September 27. doi: 10.1186/1471-2105-8-S6-S5
PMCID:
PMC1995541
Abstract Full Text PDF–502K
Integrating physical and genetic maps: from genomes to interaction networks
Andreas Beyer, Sourav Bandyopadhyay, Trey Ideker
Nat Rev Genet. Author manuscript; available in PMC 2010 January 25.
Published in final edited form as: Nat Rev Genet. 2007 September; 8(9): 699–710. doi: 10.1038/nrg2144
PMCID:
PMC2811081
Abstract Full Text PDF–1.7M
A Three Stage Integrative Pathway Search (TIPS©) framework to identify toxicity relevant genes and pathways
Zheng Li, Shireesh Srivastava, Sheenu Mittal, Xuerui Yang, Lufang Sheng, Christina Chan
BMC Bioinformatics. 2007; 8: 202. Published online 2007 June 14. doi: 10.1186/1471-2105-8-202
PMCID:
PMC1906836
Abstract Full Text PDF–746K Supplementary Material
Network-based prediction of protein function
Roded Sharan, Igor Ulitsky, Ron Shamir
Mol Syst Biol. 2007; 3: 88. Published online 2007 March 13. doi: 10.1038/msb4100129
PMCID:
PMC1847944
Abstract Full Text PDF–353K
Refinement and expansion of signaling pathways: The osmotic response network in yeast
Irit Gat-Viks, Ron Shamir
Genome Res. 2007 March; 17(3): 358–367. doi: 10.1101/gr.5750507
PMCID:
PMC1800927
Abstract Full Text PDF–962K
A network biology approach to prostate cancer
Ayla Ergün, Carolyn A Lawrence, Michael A Kohanski, Timothy A Brennan, James J Collins
Mol Syst Biol. 2007; 3: 82. Published online 2007 February 13. doi: 10.1038/msb4100125
PMCID:
PMC1828752
Abstract Full Text PDF–162K Supplementary Material
Transcriptional regulation of protein complexes within and across species
Kai Tan, Tomer Shlomi, Hoda Feizi, Trey Ideker, Roded Sharan
Proc Natl Acad Sci U S A. 2007 January 23; 104(4): 1283–1288. Published online 2007 January 16. doi: 10.1073/pnas.0606914104
PMCID:
PMC1783126
Abstract Full Text PDF–1.0M Supplementary Material
CellCircuits: a database of protein network models
H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker
Nucleic Acids Res. 2007 January; 35(Database issue): D538–D545. Published online 2006 November 29. doi: 10.1093/nar/gkl937
PMCID:
PMC1751555
Abstract Full Text PDF–606K
Integrated Assessment and Prediction of Transcription Factor Binding
Andreas Beyer, Christopher Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker
PLoS Comput Biol. 2006 June; 2(6): e70. Prepublished online 2006 May 8. Published online 2006 June 16. doi: 10.1371/journal.pcbi.0020070
PMCID:
PMC1479087
Abstract Full Text PDF–609K Supplementary Material
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach
Christian L Barrett, Bernhard O Palsson
PLoS Comput Biol. 2006 May; 2(5): e52. Prepublished online 2006 April 5. Published online 2006 May 19. doi: 10.1371/journal.pcbi.0020052
PMCID:
PMC1463018
Abstract Full Text PDF–259K Supplementary Material
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