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Osprey: a network visualization system
Bobby-Joe Breitkreutz, Chris Stark, Mike Tyers
Genome Biol. 2003; 4(3): R22. Published online 2003 February 27.
PMCID:
PMC153462
Abstract Full Text PDF–960K
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 Is Cited by the Following 89 Articles in this Archive:
Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters
Thadeous Kacmarczyk, Peter Waltman, Ashley Bate, Patrick Eichenberger, Richard Bonneau
PLoS Comput Biol. 2011 December; 7(12): e1002228. Published online 2011 December 1. doi: 10.1371/journal.pcbi.1002228
PMCID:
PMC3228777
Abstract Full Text PDF–4.3M Supplementary Material
Medusa: A tool for exploring and clustering biological networks
Georgios A Pavlopoulos, Sean D Hooper, Alejandro Sifrim, Reinhard Schneider, Jan Aerts
BMC Res Notes. 2011; 4: 384. Published online 2011 October 6. doi: 10.1186/1756-0500-4-384
PMCID:
PMC3197509
Abstract Full Text PDF–418K
Novel Interactions between Actin and the Proteasome Revealed by Complex Haploinsufficiency
Brian Haarer, Dimitra Aggeli, Susan Viggiano, Daniel J. Burke, David C. Amberg
PLoS Genet. 2011 September; 7(9): e1002288. Published online 2011 September 22. doi: 10.1371/journal.pgen.1002288
PMCID:
PMC3178594
Abstract Full Text PDF–2.7M
Transcriptome Analysis of Potato Leaves Expressing the Trehalose-6-Phosphate Synthase 1 Gene of Yeast
Mihály Kondrák, Ferenc Marincs, Balázs Kalapos, Zsófia Juhász, Zsófia Bánfalvi
PLoS One. 2011; 6(8): e23466. Published online 2011 August 16. doi: 10.1371/journal.pone.0023466
PMCID:
PMC3156770
Abstract Full Text PDF–625K Supplementary Material
GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data
Marie E Fahey, Melanie J Bennett, Cathal Mahon, Stefanie Jäger, Lars Pache, Dhiraj Kumar, Alex Shapiro, Kanury Rao, Sumit K Chanda, Charles S Craik, Alan D Frankel, Nevan J Krogan
BMC Bioinformatics. 2011; 12: 298. Published online 2011 July 22. doi: 10.1186/1471-2105-12-298
PMCID:
PMC3213248
Abstract Full Text PDF–3.1M Supplementary Material
Knowledge management for systems biology a general and visually driven framework applied to translational medicine
Dieter Maier, Wenzel Kalus, Martin Wolff, Susana G Kalko, Josep Roca, Igor Marin de Mas, Nil Turan, Marta Cascante, Francesco Falciani, Miguel Hernandez, Jordi Villà-Freixa, Sascha Losko
BMC Syst Biol. 2011; 5: 38. Published online 2011 March 5. doi: 10.1186/1752-0509-5-38
PMCID:
PMC3060864
Abstract Full Text PDF–1.6M Supplementary Material
Post-transcriptional regulation in the myo1Δ mutant of Saccharomyces cerevisiae
Marielis E Rivera-Ruiz, José F Rodríguez-Quiñones, Pearl Akamine, José R Rodríguez-Medina
BMC Genomics. 2010; 11: 690. Published online 2010 December 2. doi: 10.1186/1471-2164-11-690
PMCID:
PMC3017085
Abstract Full Text PDF–982K Supplementary Material
The BioGRID Interaction Database: 2011 update
Chris Stark, Bobby-Joe Breitkreutz, Andrew Chatr-aryamontri, Lorrie Boucher, Rose Oughtred, Michael S. Livstone, Julie Nixon, Kimberly Van Auken, Xiaodong Wang, Xiaoqi Shi, Teresa Reguly, Jennifer M. Rust, Andrew Winter, Kara Dolinski, Mike Tyers
Nucleic Acids Res. 2011 January; 39(Database issue): D698–D704. Published online 2010 November 11. doi: 10.1093/nar/gkq1116
PMCID:
PMC3013707
Abstract Full Text PDF–4.4M
Functional Gene Expression Profiling in Yeast Implicates Translational Dysfunction in Mutant Huntingtin Toxicity
Eran Tauber, Leonor Miller-Fleming, Robert P. Mason, Wanda Kwan, Jannine Clapp, Nicola J. Butler, Tiago F. Outeiro, Paul J. Muchowski, Flaviano Giorgini
J Biol Chem. 2011 January 7; 286(1): 410–419. Published online 2010 November 2. doi: 10.1074/jbc.M110.101527
PMCID:
PMC3012999
Abstract Full Text Supplementary Material
Reconstitution and Protein Composition Analysis of Endocytic Actin Patches
Alphée Michelot, Michael Costanzo, Ali Sarkeshik, Charles Boone, John R. Yates, III, David G. Drubin
Curr Biol. Author manuscript; available in PMC 2011 November 9.
Published in final edited form as: Curr Biol. 2010 November 9; 20(21): 1890–1899. Published online 2010 October 28. doi: 10.1016/j.cub.2010.10.016
PMCID:
PMC2998891
Abstract Full Text PDF–2.6M Supplementary Material
A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data
Willy Aucher, Emmanuelle Becker, Emilie Ma, Simona Miron, Arnaud Martel, Françoise Ochsenbein, Marie-Claude Marsolier-Kergoat, Raphaël Guerois
Mol Cell Proteomics. 2010 December; 9(12): 2745–2759. Published online 2010 September 10. doi: 10.1074/mcp.M110.003319
PMCID:
PMC3101860
Abstract Full Text Supplementary Material
The Protein Network Surrounding the Human Telomere Repeat Binding Factors TRF1, TRF2, and POT1
Richard J. Giannone, Hayes W. McDonald, Gregory B. Hurst, Rong-Fong Shen, Yisong Wang, Yie Liu
PLoS One. 2010; 5(8): e12407. Published online 2010 August 25. doi: 10.1371/journal.pone.0012407
PMCID:
PMC2928292
Abstract Full Text PDF–1.3M Supplementary Material
The Nucleosome Remodeling Factor ISWI Functionally Interacts With an Evolutionarily Conserved Network of Cellular Factors
Walter Arancio, Maria C. Onorati, Giosalba Burgio, Marianna Collesano, Antonia M. R. Ingrassia, Swonild I. Genovese, Manolis Fanto, Davide F. V. Corona
Genetics. 2010 May; 185(1): 129–140. doi: 10.1534/genetics.110.114256
PMCID:
PMC2870949
Abstract Full Text PDF–8.6M
A systems biology approach to understanding atherosclerosis
Stephen A. Ramsey, Elizabeth S. Gold, Alan Aderem
EMBO Mol Med. Author manuscript; available in PMC 2010 November 27.
Published in final edited form as: EMBO Mol Med. 2010 March; 2(3): 79–89. doi: 10.1002/emmm.201000063
PMCID:
PMC2992755
Abstract Full Text PDF–1.2M
BisoGenet: a new tool for gene network building, visualization and analysis
Alexander Martin, Maria E Ochagavia, Laya C Rabasa, Jamilet Miranda, Jorge Fernandez-de-Cossio, Ricardo Bringas
BMC Bioinformatics. 2010; 11: 91. Published online 2010 February 17. doi: 10.1186/1471-2105-11-91
PMCID:
PMC3098113
Abstract Full Text PDF–1.8M
Construction and analysis of protein–protein interaction networks
Karthik Raman
Autom Exp. 2010; 2: 2. Published online 2010 February 15. doi: 10.1186/1759-4499-2-2
PMCID:
PMC2834675
Abstract Full Text PDF–440K
VirtualPlant: A Software Platform to Support Systems Biology Research
Manpreet S. Katari, Steve D. Nowicki, Felipe F. Aceituno, Damion Nero, Jonathan Kelfer, Lee Parnell Thompson, Juan M. Cabello, Rebecca S. Davidson, Arthur P. Goldberg, Dennis E. Shasha, Gloria M. Coruzzi, Rodrigo A. Gutiérrez
Plant Physiol. 2010 February; 152(2): 500–515. doi: 10.1104/pp.109.147025
PMCID:
PMC2815851
Abstract Full Text PDF–2.2M 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
Biana: a software framework for compiling biological interactions and analyzing networks
Javier Garcia-Garcia, Emre Guney, Ramon Aragues, Joan Planas-Iglesias, Baldo Oliva
BMC Bioinformatics. 2010; 11: 56. Published online 2010 January 27. doi: 10.1186/1471-2105-11-56
PMCID:
PMC3098100
Abstract Full Text PDF–1.2M
Graphle: Interactive exploration of large, dense graphs
Curtis Huttenhower, Sajid O Mehmood, Olga G Troyanskaya
BMC Bioinformatics. 2009; 10: 417. Published online 2009 December 14. doi: 10.1186/1471-2105-10-417
PMCID:
PMC2803856
Abstract Full Text PDF–526K
A yeast killer toxin screen provides insights into A/B toxin entry, trafficking and killing mechanisms
Susheela Y. Carroll, Peter C. Stirling, Helen E. M. Stimpson, Esther Gießelmann, Manfred J. Schmitt, David G. Drubin
Dev Cell. Author manuscript; available in PMC 2010 October 20.
Published in final edited form as: Dev Cell. 2009 October 20; 17(4): 552–560. doi: 10.1016/j.devcel.2009.08.006
PMCID:
PMC2768656
Abstract Full Text PDF–2.8M Supplementary Material
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto
Kevin R. Brown, David Otasek, Muhammad Ali, Michael J. McGuffin, Wing Xie, Baiju Devani, Ian Lawson van Toch, Igor Jurisica
Bioinformatics. 2009 December 15; 25(24): 3327–3329. Published online 2009 October 16. doi: 10.1093/bioinformatics/btp595
PMCID:
PMC2788933
Abstract Full Text PDF–426K Supplementary Material
Disease Progression And Solid Tumor Survival: A Transcriptome Decoherence Model
Adrian E. Platts, Claudia Lalancette, Benjamin R. Emery, Douglas T. Carrell, Stephen A. Krawetz
Mol Cell Probes. Author manuscript; available in PMC 2011 February 1.
Published in final edited form as: Mol Cell Probes. 2010 February; 24(1): 53. Published online 2009 October 14. doi: 10.1016/j.mcp.2009.09.005
PMCID:
PMC2818311
Abstract Full Text PDF–2.8M Supplementary Material
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data
Yong Wang, Xiang-Sun Zhang, Yu Xia
Nucleic Acids Res. 2009 October; 37(18): 5943–5958. Published online 2009 October. doi: 10.1093/nar/gkp625
PMCID:
PMC2764433
Abstract Full Text PDF–3.1M Supplementary Material
Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis
Joseph A Nielsen, Pierre Lau, Dragan Maric, Jeffery L Barker, Lynn D Hudson
BMC Neurosci. 2009; 10: 98. Published online 2009 August 19. doi: 10.1186/1471-2202-10-98
PMCID:
PMC2736963
Abstract Full Text PDF–4.7M Supplementary Material
Proteomic Analysis of Microtubule-associated Proteins during Macrophage Activation
Prerna C. Patel, Katherine H. Fisher, Eric C. C. Yang, Charlotte M. Deane, Rene E. Harrison
Mol Cell Proteomics. 2009 November; 8(11): 2500–2514. Published online 2009 August 2. doi: 10.1074/mcp.M900190-MCP200
PMCID:
PMC2773717
Abstract Full Text Supplementary Material
Local Network Topology in Human Protein Interaction Data Predicts Functional Association
Hua Li, Shoudan Liang
PLoS One. 2009; 4(7): e6410. Published online 2009 July 29. doi: 10.1371/journal.pone.0006410
PMCID:
PMC2713831
Abstract Full Text PDF–800K Supplementary Material
PathBuilder—open source software for annotating and developing pathway resources
Kumaran Kandasamy, Shivakumar Keerthikumar, Rajesh Raju, T. S. Keshava Prasad, Y. L. Ramachandra, Sujatha Mohan, Akhilesh Pandey
Bioinformatics. 2009 November 1; 25(21): 2860–2862. Published online 2009 July 23. doi: 10.1093/bioinformatics/btp453
PMCID:
PMC2781757
Abstract Full Text PDF–146K Supplementary Material
Genomewide Analysis Reveals Novel Pathways Affecting Endoplasmic Reticulum Homeostasis, Protein Modification and Quality Control
Alenka Čopič, Mariana Dorrington, Silvere Pagant, Justine Barry, Marcus C. S. Lee, Indira Singh, John L. Hartman, IV, Elizabeth A. Miller
Genetics. 2009 July; 182(3): 757–769. doi: 10.1534/genetics.109.101105
PMCID:
PMC2710157
Abstract Full Text PDF–1.7M
In vitro nuclear interactome of the HIV-1 Tat protein
Virginie W Gautier, Lili Gu, Niaobh O'Donoghue, Stephen Pennington, Noreen Sheehy, William W Hall
Retrovirology. 2009; 6: 47. Published online 2009 May 19. doi: 10.1186/1742-4690-6-47
PMCID:
PMC2702331
Abstract Full Text PDF–2.6M Supplementary Material
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