Genome Biology

official impact factor 6.89

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Osprey: a network visualization system

Bobby-Joe Breitkreutz, Chris Stark and Mike Tyers*

Genome Biology 2003, 4:R22-0012.6 doi:10.1186/gb-2003-4-3-r22

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BioMed Central: 33 citations

Technical Note   Open Access

Medusa: A tool for exploring and clustering biological networks

Georgios A Pavlopoulos, Sean D Hooper, Alejandro Sifrim, Reinhard Schneider, Jan Aerts BMC Research Notes 2011, 4:384 (6 October 2011)

Software   Open Access Highly Accessed

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 (22 July 2011)

Software   Open Access Highly Accessed

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 (17 February 2010)

Review   Open Access

Construction and analysis of protein–protein interaction networks

Karthik Raman Automated Experimentation 2010, 2:2 (15 February 2010)

Software   Open Access Highly Accessed

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 (27 January 2010)

Software   Open Access Highly Accessed

Graphle: Interactive exploration of large, dense graphs

Curtis Huttenhower, Sajid O Mehmood, Olga G Troyanskaya BMC Bioinformatics 2009, 10:417 (14 December 2009)

Research article   Open Access Highly Accessed

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 Neuroscience 2009, 10:98 (19 August 2009)

Research   Open Access Highly Accessed

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 (19 May 2009)

Software   Open Access

FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data

Jussi Paananen, Garry Wong BMC Systems Biology 2009, 3:26 (24 February 2009)

Software   Open Access Highly Accessed

GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments

Andreas Keller, Christina Backes, Maher Al-Awadhi, Andreas Gerasch, Jan Küntzer, Oliver Kohlbacher, Michael Kaufmann, Hans-Peter Lenhof BMC Bioinformatics 2008, 9:552 (22 December 2008)

Review   Open Access Highly Accessed

A survey of visualization tools for biological network analysis

Georgios A Pavlopoulos, Anna-Lynn Wegener, Reinhard Schneider BioData Mining 2008, 1:12 (28 November 2008)

Software   Open Access Highly Accessed

Arena3D: visualization of biological networks in 3D

Georgios A Pavlopoulos, Seán I O'Donoghue, Venkata P Satagopam, Theodoros G Soldatos, Evangelos Pafilis, Reinhard Schneider BMC Systems Biology 2008, 2:104 (28 November 2008)

Research   Open Access

A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection

Amanda Greenall, Guiyuan Lei, Daniel C Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J Wilkinson, David Lydall Genome Biology 2008, 9:R146 (1 October 2008)

NAD+ metabolism may be linked to telomere end protection in yeast.

Research article   Open Access

A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining

Bor-Sen Chen, Shih-Kuang Yang, Chung-Yu Lan, Yung-Jen Chuang BMC Medical Genomics 2008, 1:46 (30 September 2008)

Software   Open Access Highly Accessed

NetGrep: fast network schema searches in interactomes

Eric Banks, Elena Nabieva, Ryan Peterson, Mona Singh Genome Biology 2008, 9:R138 (18 September 2008)

NetGrep is a system for searching protein interaction networks for matches to user-supplied network schemas.

Research   Open Access

Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors

Thomas J Lukas, Haixi Miao, Lin Chen, Sean M Riordan, Wenjun Li, Andrea M Crabb, Alexandria Wise, Pan Du, Simon M Lin, M Rosario Hernandez Genome Biology 2008, 9:R111 (9 July 2008)

Comparison of gene expression in normal and glaucomatous eyes from Caucasian American and African American donors reveals differences that might reflect different susceptibility to glaucoma.

Research article   Open Access Highly Accessed

Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets

Liang-Hui Chu, Bor-Sen Chen BMC Systems Biology 2008, 2:56 (30 June 2008)

Research article   Open Access

Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions

José F Rodríguez-Quiñones, Rafael A Irizarry, Nitza L Díaz-Blanco, Félix E Rivera-Molina, Diana Gómez-Garzón, José R Rodríguez-Medina BMC Genomics 2008, 9:34 (23 January 2008)

Research article   Open Access Highly Accessed

Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells

Roger A Barthelson, Georgina M Lambert, Cheryl Vanier, Ronald M Lynch, David W Galbraith BMC Genomics 2007, 8:340 (25 September 2007)

Methodology article   Open Access Highly Accessed

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

Brian J Holden, John W Pinney, Simon C Lovell, Grigoris D Amoutzias, David L Robertson BMC Bioinformatics 2007, 8:289 (6 August 2007)

Research   Open Access Highly Accessed

Functional coordination of alternative splicing in the mammalian central nervous system

Matthew Fagnani, Yoseph Barash, Joanna Y Ip, Christine Misquitta, Qun Pan, Arneet L Saltzman, Ofer Shai, Leo Lee, Aviad Rozenhek, Naveed Mohammad, Sandrine Willaime-Morawek, Tomas Babak, Wen Zhang, Timothy R Hughes, Derek van der Kooy, Brendan J Frey, Benjamin J Blencowe Genome Biology 2007, 8:R108 (12 June 2007)

A microarray analysis provides new evidence suggesting that specific cellular processes in the mammalian CNS are coordinated at the level of alternative splicing, and that a complex splicing code underlies CNS-specific alternative splicing regulation.

Proceedings   Open Access Highly Accessed

An evaluation of human protein-protein interaction data in the public domain

Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, YL Ramachandra, Akhilesh Pandey BMC Bioinformatics 2006, 7(Suppl 5):S19 (18 December 2006)

Proceedings   Open Access

Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology

Chung-Yen Lin, Shu-Hwa Chen, Chi-Shiang Cho, Chia-Ling Chen, Fan-Kai Lin, Chieh-Hua Lin, Pao-Yang Chen, Chen-Zen Lo, Chao A Hsiung BMC Bioinformatics 2006, 7(Suppl 5):S18 (18 December 2006)

Research article   Open Access Highly Accessed

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 Journal of Biology 2006, 5:11 (8 June 2006)

A new literature-based yeast database documents over 33,000 biological interactions, manually curated from the primary literature, and provides an invaluable resource to benchmark high-throughput methods in the study of complex networks.

Research article   Open Access

Differential evolutionary conservation of motif modes in the yeast protein interaction network

Wei-Po Lee, Bing-Chiang Jeng, Tun-Wen Pai, Chin-Pei Tsai, Chang-Yung Yu, Wen-Shyong Tzou BMC Genomics 2006, 7:89 (25 April 2006)

Database   Open Access

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila

Svetlana Pacifico, Guozhen Liu, Stephen Guest, Jodi R Parrish, Farshad Fotouhi, Russell L Finley BMC Bioinformatics 2006, 7:195 (7 April 2006)

Software   Open Access Highly Accessed

VANTED: A system for advanced data analysis and visualization in the context of biological networks

Björn H Junker, Christian Klukas, Falk Schreiber BMC Bioinformatics 2006, 7:109 (6 March 2006)

Software   Open Access

iVici: Interrelational Visualization and Correlation Interface

Kirill Tarassov, Stephen W Michnick Genome Biology 2005, 6:R115 (30 December 2005)

iVici, a new tool for the simultaneous visualization and correlation of multiple datasets, allows the analysis and comparison of different types of networks.

Software   Open Access

Ulysses - an application for the projection of molecular interactions across species

Danielle Kemmer, Yong Huang, Sohrab P Shah, Jonathan Lim, Jochen Brumm, Macaire MS Yuen, John Ling, Tao Xu, Wyeth W Wasserman, BF Francis Ouellette Genome Biology 2005, 6:R106 (2 December 2005)

Ulysses, a new software for the parallel analysis and display of protein interactions detected in various species, is described.

Research article   Open Access

HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms

Maria Persico, Arnaud Ceol, Caius Gavrila, Robert Hoffmann, Arnaldo Florio, Gianni Cesareni BMC Bioinformatics 2005, 6(Suppl 4):S21 (1 December 2005)

Methodology article   Open Access Highly Accessed

The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks

Ruth Dunn, Frank Dudbridge, Christopher M Sanderson BMC Bioinformatics 2005, 6:39 (1 March 2005)

Software   Open Access

MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states

Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq, Stéphane Vialette BMC Bioinformatics 2004, 5:20 (3 March 2004)

Methodology article   Open Access Highly Accessed

VisANT: an online visualization and analysis tool for biological interaction data

Zhenjun Hu, Joseph Mellor, Jie Wu, Charles DeLisi BMC Bioinformatics 2004, 5:17 (19 February 2004)