My NCBISign In
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga G Troyanskya, Trey Ideker, Kara Dolinski, Nizar N Batada, Mike Tyers
J Biol. 2006; 5(4): 11. Published online 2006 June 8. doi: 10.1186/jbiol36
PMCID:
PMC1561585
Abstract Full Text PDF–1.7M Supplementary Material

Is Cited by the Following 88 Articles in this Archive:

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization
Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S Nevalainen, Tero Aittokallio
BioData Min. 2012; 5: 2. Published online 2012 March 26. doi: 10.1186/1756-0381-5-2
PMCID:
PMC3342218
Abstract Full Text PDF–2.9M Supplementary Material
Crosstalk between transcription factors and microRNAs in human protein interaction network
Chen-Ching Lin, Ya-Jen Chen, Cho-Yi Chen, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang
BMC Syst Biol. 2012; 6: 18. Published online 2012 March 13. doi: 10.1186/1752-0509-6-18
PMCID:
PMC3337275
Abstract Full Text PDF–3.3M Supplementary Material
Epistasis for Growth Rate and Total Metabolic Flux in Yeast
Agata Jakubowska, Ryszard Korona
PLoS One. 2012; 7(3): e33132. Published online 2012 March 6. doi: 10.1371/journal.pone.0033132
PMCID:
PMC3295780
Abstract Full Text PDF–343K Supplementary Material
Homology Inference of Protein-Protein Interactions via Conserved Binding Sites
Manoj Tyagi, Ratna R. Thangudu, Dachuan Zhang, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko
PLoS One. 2012; 7(1): e28896. Published online 2012 January 31. doi: 10.1371/journal.pone.0028896
PMCID:
PMC3269416
Abstract Full Text PDF–421K Supplementary Material
Network-based functional enrichment
Christopher L Poirel, Clifford C Owens, III, Murali
BMC Bioinformatics. 2011; 12(Suppl 13): S14. Published online 2011 November 30. doi: 10.1186/1471-2105-12-S13-S14
PMCID:
PMC3278830
Abstract Full Text PDF–408K
A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria
Suzanne Hoppins, Sean R. Collins, Ann Cassidy-Stone, Eric Hummel, Rachel M. DeVay, Laura L. Lackner, Benedikt Westermann, Maya Schuldiner, Jonathan S. Weissman, Jodi Nunnari
J Cell Biol. 2011 October 17; 195(2): 323–340. doi: 10.1083/jcb.201107053
PMCID:
PMC3198156
Abstract Full Text PDF–4.1M Supplementary Material
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases
Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers
BMC Bioinformatics. 2011; 12(Suppl 8): S8. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S8
PMCID:
PMC3269943
Abstract Full Text PDF–480K
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme
George D Kritikos, Charalampos Moschopoulos, Michalis Vazirgiannis, Sophia Kossida
BMC Bioinformatics. 2011; 12: 239. Published online 2011 June 16. doi: 10.1186/1471-2105-12-239
PMCID:
PMC3230908
Abstract Full Text PDF–853K
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning
Edoardo M. Airoldi, Katherine A. Heller, Ricardo Silva
Bioinformatics. 2011 July 1; 27(13): i374–i382. Published online 2011 June 14. doi: 10.1093/bioinformatics/btr236
PMCID:
PMC3117334
Abstract Full Text
Generative probabilistic models for protein–protein interaction networks—the biclique perspective
Regev Schweiger, Michal Linial, Nathan Linial
Bioinformatics. 2011 July 1; 27(13): i142–i148. Published online 2011 June 14. doi: 10.1093/bioinformatics/btr201
PMCID:
PMC3117378
Abstract Full Text Supplementary Material
Improved functional overview of protein complexes using inferred epistatic relationships
Colm Ryan, Derek Greene, Aude Guénolé, Haico van Attikum, Nevan J Krogan, Pádraig Cunningham, Gerard Cagney
BMC Syst Biol. 2011; 5: 80. Published online 2011 May 23. doi: 10.1186/1752-0509-5-80
PMCID:
PMC3117733
Abstract Full Text PDF–1.4M Supplementary Material
Shared Molecular Strategies of the Malaria Parasite P. falciparum and the Human Virus HIV-1
Stefan Wuchty, Geoffrey H. Siwo, Michael T. Ferdig
Mol Cell Proteomics. 2011 October; 10(10): M111.009035. Published online 2011 May 17. doi: 10.1074/mcp.M111.009035
PMCID:
PMC3205867
Free in PMC on 2012/10/01
Processes of Fungal Proteome Evolution and Gain of Function: Gene Duplication and Domain Rearrangement
Inbar Cohen-Gihon, Roded Sharan, Ruth Nussinov
Phys Biol. Author manuscript; available in PMC 2012 June 1.
Published in final edited form as: Phys Biol. 2011 June; 8(3): 035009. Published online 2011 May 13. doi: 10.1088/1478-3975/8/3/035009
PMCID:
PMC3140765
Free in PMC on 2012/06/01
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID
Andrew G. Winter, Jan Wildenhain, Mike Tyers
Bioinformatics. 2011 April 1; 27(7): 1043–1044. Published online 2011 February 7. doi: 10.1093/bioinformatics/btr062
PMCID:
PMC3065694
Abstract Full Text PDF–197K Supplementary Material
Understanding protein evolutionary rate by integrating gene co-expression with protein interactions
Kaifang Pang, Chao Cheng, Zhenyu Xuan, Huanye Sheng, Xiaotu Ma
BMC Syst Biol. 2010; 4: 179. Published online 2010 December 30. doi: 10.1186/1752-0509-4-179
PMCID:
PMC3022652
Abstract Full Text PDF–1.7M Supplementary Material
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size
Laure Sambourg, Nicolas Thierry-Mieg
BMC Bioinformatics. 2010; 11: 605. Published online 2010 December 21. doi: 10.1186/1471-2105-11-605
PMCID:
PMC3023808
Abstract Full Text PDF–486K Supplementary Material
Difference in gene duplicability may explain the difference in overall structure of protein-protein interaction networks among eukaryotes
Takeshi Hase, Yoshihito Niimura, Hiroshi Tanaka
BMC Evol Biol. 2010; 10: 358. Published online 2010 November 18. doi: 10.1186/1471-2148-10-358
PMCID:
PMC2994879
Abstract Full Text PDF–1.9M Supplementary Material
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins
William P Kelly, Michael PH Stumpf
BMC Bioinformatics. 2010; 11: 470. Published online 2010 September 20. doi: 10.1186/1471-2105-11-470
PMCID:
PMC2955699
Abstract Full Text PDF–1.5M Supplementary Material
Viral Organization of Human Proteins
Stefan Wuchty, Geoffrey Siwo, Michael T. Ferdig
PLoS One. 2010; 5(8): e11796. Published online 2010 August 25. doi: 10.1371/journal.pone.0011796
PMCID:
PMC2932736
Abstract Full Text PDF–579K Supplementary Material
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation
Subir K Nandy, Paula Jouhten, Jens Nielsen
BMC Syst Biol. 2010; 4: 68. Published online 2010 May 25. doi: 10.1186/1752-0509-4-68
PMCID:
PMC2889877
Abstract Full Text PDF–3.7M Supplementary Material
Modularity and anti-modularity in networks with arbitrary degree distribution
Arend Hintze, Christoph Adami
Biol Direct. 2010; 5: 32. Published online 2010 May 6. doi: 10.1186/1745-6150-5-32
PMCID:
PMC2881120
Abstract Full Text PDF–2.5M
Incomplete and noisy network data as a percolation process
Michael P. H. Stumpf, Carsten Wiuf
J R Soc Interface. 2010 October 6; 7(51): 1411–1419. Published online 2010 April 8. doi: 10.1098/rsif.2010.0044
PMCID:
PMC2935600
Abstract Full Text PDF–874K
Revealing strengths and weaknesses of methods for gene network inference
Daniel Marbach, Robert J. Prill, Thomas Schaffter, Claudio Mattiussi, Dario Floreano, Gustavo Stolovitzky
Proc Natl Acad Sci U S A. 2010 April 6; 107(14): 6286–6291. Published online 2010 March 22. doi: 10.1073/pnas.0913357107
PMCID:
PMC2851985
Abstract Full Text PDF–453K 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
Improved network performance via antagonism: From synthetic rescues to multi-drug combinations
Adilson E Motter
Bioessays. 2010 March; 32(3): 236–245. doi: 10.1002/bies.200900128
PMCID:
PMC2841822
Abstract Full Text PDF–405K
Reply to Robert et al.: Model criticism informs model choice and model comparison
Oliver Ratmann, Christophe Andrieu, Carsten Wiuf, Sylvia Richardson
Proc Natl Acad Sci U S A. 2010 January 19; 107(3): E6–E7. Published online 2010 January 14. doi: 10.1073/pnas.0912887107
PMCID:
PMC2824293
Full Text PDF–574K
Reconstructing ancestral gene content by coevolution
Tamir Tuller, Hadas Birin, Uri Gophna, Martin Kupiec, Eytan Ruppin
Genome Res. 2010 January; 20(1): 122–132. doi: 10.1101/gr.096115.109
PMCID:
PMC2798824
Abstract Full Text PDF–937K
Phylogeny-guided interaction mapping in seven eukaryotes
Janusz Dutkowski, Jerzy Tiuryn
BMC Bioinformatics. 2009; 10: 393. Published online 2009 November 30. doi: 10.1186/1471-2105-10-393
PMCID:
PMC2793266
Abstract Full Text PDF–3.3M Supplementary Material
From evidence to inference: probing the evolution of protein interaction networks
Oliver Ratmann, Carsten Wiuf, John W. Pinney
HFSP J. 2009 October; 3(5): 290–306. Published online 2009 October 19. doi: 10.2976/1.3167215
PMCID:
PMC2801530
Abstract Full Text PDF–380K
The Modular Organization of Protein Interactions in Escherichia coli
José M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, John Parkinson
PLoS Comput Biol. 2009 October; 5(10): e1000523. Published online 2009 October 2. doi: 10.1371/journal.pcbi.1000523
PMCID:
PMC2739439
Abstract Full Text PDF–1.0M Supplementary Material
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