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Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
Lan V Zhang, Oliver D King, Sharyl L Wong, Debra S Goldberg, Amy HY Tong, Guillaume Lesage, Brenda Andrews, Howard Bussey, Charles Boone, Frederick P Roth
J Biol. 2005; 4(2): 6. Published online 2005 June 1. doi: 10.1186/jbiol23
PMCID:
PMC1175995
Abstract Full Text PDF–190K Supplementary Material

Is Cited by the Following 47 Articles in this Archive:

Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy
Seyed Yahya Anvar, Allan Tucker, Veronica Vinciotti, Andrea Venema, Gert-Jan B. van Ommen, Silvere M. van der Maarel, Vered Raz, Peter A. C. ‘t Hoen
PLoS Comput Biol. 2011 November; 7(11): e1002258. Published online 2011 November 3. doi: 10.1371/journal.pcbi.1002258
Correction in:
PLoS Comput Biol. 2011 November; 7(11): 10.1371/annotation/fc0b4192-6427-4fb3-b347-c66651adf855.
PMCID:
PMC3207951
Abstract Full Text PDF–1.7M Supplementary Material Correction
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs
Fergal Casey, Nevan Krogan, Denis C Shields, Gerard Cagney
BMC Syst Biol. 2011; 5: 133. Published online 2011 August 22. doi: 10.1186/1752-0509-5-133
PMCID:
PMC3176491
Abstract Full Text PDF–1.5M Supplementary Material
Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi
Elin Axelsson, Thomas Sandmann, Thomas Horn, Michael Boutros, Wolfgang Huber , Bernd Fischer
BMC Bioinformatics. 2011; 12: 342. Published online 2011 August 17. doi: 10.1186/1471-2105-12-342
PMCID:
PMC3230910
Abstract Full Text PDF–580K Supplementary Material
Retrieval, alignment, and clustering of computational models based on semantic annotations
Marvin Schulz, Falko Krause, Nicolas Le Novère, Edda Klipp, Wolfram Liebermeister
Mol Syst Biol. 2011; 7: 512. Published online 2011 July 19. doi: 10.1038/msb.2011.41
PMCID:
PMC3159965
Abstract Full Text PDF–3.4M Supplementary Material
Failure Tolerance of Motif Structure in Biological Networks
Baharan Mirzasoleiman, Mahdi Jalili
PLoS One. 2011; 6(5): e20512. Published online 2011 May 26. doi: 10.1371/journal.pone.0020512
PMCID:
PMC3102726
Abstract Full Text PDF–555K
Interactome Networks and Human Disease
Marc Vidal, Michael E. Cusick, Albert-László Barabási
Cell. Author manuscript; available in PMC 2012 March 18.
Published in final edited form as: Cell. 2011 March 18; 144(6): 986–998. doi: 10.1016/j.cell.2011.02.016
PMCID:
PMC3102045
Abstract Full Text PDF–300K
Discovering conditional co-regulated protein complexes by integrating diverse data sources
Fei Luo, Juan Liu, Jinyan Li
BMC Syst Biol. 2010; 4(Suppl 2): S4. Published online 2010 September 13. doi: 10.1186/1752-0509-4-S2-S4
PMCID:
PMC2982691
Abstract Full Text PDF–1.0M Supplementary Material
Genome-Wide Scoring of Positive and Negative Epistasis through Decomposition of Quantitative Genetic Interaction Fitness Matrices
Ville-Pekka Eronen, Rolf O. Lindén, Anna Lindroos, Mirella Kanerva, Tero Aittokallio
PLoS One. 2010; 5(7): e11611. Published online 2010 July 15. doi: 10.1371/journal.pone.0011611
PMCID:
PMC2904709
Abstract Full Text PDF–841K Supplementary Material
Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test
Chao Wu, Fan Zhang, Xia Li, Shihua Zhang, Jiang Li, Fei Su, Kongning Li, Yuqing Yan
BMC Syst Biol. 2010; 4: 82. Published online 2010 June 10. doi: 10.1186/1752-0509-4-82
PMCID:
PMC2901225
Abstract Full Text PDF–2.9M 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
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae
Chris Stark, Ting-Cheng Su, Ashton Breitkreutz, Pedro Lourenco, Matthew Dahabieh, Bobby-Joe Breitkreutz, Mike Tyers, Ivan Sadowski
Database (Oxford) 2010; 2010: bap026. Published online 2010 January 28. doi: 10.1093/database/bap026
PMCID:
PMC2860897
Abstract Full Text PDF–633K
Towards accurate imputation of quantitative genetic interactions
Igor Ulitsky, Nevan J Krogan, Ron Shamir
Genome Biol. 2009; 10(12): R140. Published online 2009 December 10. doi: 10.1186/gb-2009-10-12-r140
PMCID:
PMC2812947
Abstract Full Text PDF–1.5M Supplementary Material
The capacity for multistability in small gene regulatory networks
Dan Siegal-Gaskins, Erich Grotewold, Gregory D Smith
BMC Syst Biol. 2009; 3: 96. Published online 2009 September 21. doi: 10.1186/1752-0509-3-96
PMCID:
PMC2759935
Abstract Full Text PDF–1.5M Supplementary Material
Automatic Parameter Learning for Multiple Local Network Alignment
Jason Flannick, Antal Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou
J Comput Biol. 2009 August; 16(8): 1001–1022. doi: 10.1089/cmb.2009.0099
PMCID:
PMC3154456
Abstract Full Text PDF–868K
Triangle network motifs predict complexes by complementing high-error interactomes with structural information
Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder
BMC Bioinformatics. 2009; 10: 196. Published online 2009 June 27. doi: 10.1186/1471-2105-10-196
PMCID:
PMC2714575
Abstract Full Text PDF–3.0M Supplementary Material
Maximal Extraction of Biological Information from Genetic Interaction Data
Gregory W. Carter, David J. Galas, Timothy Galitski
PLoS Comput Biol. 2009 April; 5(4): e1000347. Published online 2009 April 3. doi: 10.1371/journal.pcbi.1000347
PMCID:
PMC2659753
Abstract Full Text PDF–712K Supplementary Material
Regulation by transcription factors in bacteria: beyond description
Enrique Balleza, Lucia N López-Bojorquez, Agustino Martínez-Antonio, Osbaldo Resendis-Antonio, Irma Lozada-Chávez, Yalbi I Balderas-Martínez, Sergio Encarnación, Julio Collado-Vides
FEMS Microbiol Rev. 2009 January; 33(1): 133–151. Published online 2008 December. doi: 10.1111/j.1574-6976.2008.00145.x
PMCID:
PMC2704942
Abstract Full Text PDF–615K
Shortest-Path Network Analysis Is a Useful Approach toward Identifying Genetic Determinants of Longevity
J. R. Managbanag, Tarynn M. Witten, Danail Bonchev, Lindsay A. Fox, Mitsuhiro Tsuchiya, Brian K. Kennedy, Matt Kaeberlein
PLoS ONE. 2008; 3(11): e3802. Published online 2008 November 25. doi: 10.1371/journal.pone.0003802
PMCID:
PMC2583956
Abstract Full Text PDF–528K Supplementary Material
Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network
Gal Chechik, Eugene Oh, Oliver Rando, Jonathan Weissman, Aviv Regev, Daphne Koller
Nat Biotechnol. Author manuscript; available in PMC 2009 March 5.
Published in final edited form as: Nat Biotechnol. 2008 November; 26(11): 1251–1259. doi: 10.1038/nbt.1499
PMCID:
PMC2651818
Abstract Full Text PDF–1.9M Supplementary Material
Combination chemical genetics
Joseph Lehár, Brent R Stockwell, Guri Giaever, Corey Nislow
Nat Chem Biol. Author manuscript; available in PMC 2009 July 20.
Published in final edited form as: Nat Chem Biol. 2008 November; 4(11): 674–681. doi: 10.1038/nchembio.120
PMCID:
PMC2712875
Abstract Full Text PDF–1.6M
Organization of Physical Interactomes as Uncovered by Network Schemas
Eric Banks, Elena Nabieva, Bernard Chazelle, Mona Singh
PLoS Comput Biol. 2008 October; 4(10): e1000203. Published online 2008 October 24. doi: 10.1371/journal.pcbi.1000203
PMCID:
PMC2561054
Abstract Full Text PDF–1.2M Supplementary Material
NetGrep: fast network schema searches in interactomes
Eric Banks, Elena Nabieva, Ryan Peterson, Mona Singh
Genome Biol. 2008; 9(9): R138. Published online 2008 September 18. doi: 10.1186/gb-2008-9-9-r138
PMCID:
PMC2592716
Abstract Full Text PDF–1.8M Supplementary Material
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions
Igor Ulitsky, Tomer Shlomi, Martin Kupiec, Ron Shamir
Mol Syst Biol. 2008; 4: 209. Published online 2008 July 15. doi: 10.1038/msb.2008.42
PMCID:
PMC2516364
Abstract Full Text PDF–6.9M Supplementary Material
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
Sara Mostafavi, Debajyoti Ray, David Warde-Farley, Chris Grouios, Quaid Morris
Genome Biol. 2008; 9(Suppl 1): S4. Published online 2008 June 27. doi: 10.1186/gb-2008-9-s1-s4
PMCID:
PMC2447538
Abstract Full Text PDF–332K Supplementary Material
VisANT: an integrative framework for networks in systems biology
Zhenjun Hu, Evan S. Snitkin, Charles DeLisi
Brief Bioinform. Author manuscript; available in PMC 2009 September 14.
Published in final edited form as: Brief Bioinform. 2008 July; 9(4): 317–325. Published online 2008 May 7. doi: 10.1093/bib/bbn020
PMCID:
PMC2743399
Abstract Full Text PDF–946K
Genome-wide Expression Profiling, In Vivo DNA Binding Analysis, and Probabilistic Motif Prediction Reveal Novel Abf1 Target Genes during Fermentation, Respiration, and Sporulation in Yeast
Ulrich Schlecht, Ionas Erb, Philippe Demougin, Nicolas Robine, Valérie Borde, Erik van Nimwegen, Alain Nicolas, Michael Primig
Mol Biol Cell. 2008 May; 19(5): 2193–2207. doi: 10.1091/mbc.E07-12-1242
PMCID:
PMC2366881
Abstract Full Text PDF–2.4M Supplementary Material
Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data
Sourav Bandyopadhyay, Ryan Kelley, Nevan J. Krogan, Trey Ideker
PLoS Comput Biol. 2008 April; 4(4): e1000065. Published online 2008 April 18. doi: 10.1371/journal.pcbi.1000065
PMCID:
PMC2289880
Abstract Full Text PDF–551K Supplementary Material
A map of human cancer signaling
Qinghua Cui, Yun Ma, Maria Jaramillo, Hamza Bari, Arif Awan, Song Yang, Simo Zhang, Lixue Liu, Meng Lu, Maureen O'Connor-McCourt, Enrico O Purisima, Edwin Wang
Mol Syst Biol. 2007; 3: 152. Published online 2007 December 18. doi: 10.1038/msb4100200
PMCID:
PMC2174632
Abstract Full Text PDF–3.0M Supplementary Material
Network Inference, Analysis, and Modeling in Systems Biology
Réka Albert
Plant Cell. 2007 November; 19(11): 3327–3338. doi: 10.1105/tpc.107.054700
PMCID:
PMC2174897
Full Text PDF–279K
Regulation of gene expression by small non-coding RNAs: a quantitative view
Yishai Shimoni, Gilgi Friedlander, Guy Hetzroni, Gali Niv, Shoshy Altuvia, Ofer Biham, Hanah Margalit
Mol Syst Biol. 2007; 3: 138. Published online 2007 September 25. doi: 10.1038/msb4100181
PMCID:
PMC2013925
Abstract Full Text PDF–300K Supplementary Material
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