Genome Biology

official impact factor 6.89

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Reactome: a knowledge base of biologic pathways and processes

Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney and Lincoln Stein*

Genome Biology 2007, 8:R39 doi:10.1186/gb-2007-8-3-r39

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Database   Open Access Highly Accessed

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

Akhil Kumar, Patrick F Suthers, Costas D Maranas BMC Bioinformatics 2012, 13:6 (10 January 2012)

Database   Open Access Highly Accessed

The representation of protein complexes in the Protein Ontology (PRO)

Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A Blake, Cathy Wu BMC Bioinformatics 2011, 12:371 (19 September 2011)

ProComp is a component of the Protein Ontology (PRO) database for implementing a logical and consistent representation of protein complexes, and facilitates robust annotation of variations in composition and function contexts within and between species

Research article   Open Access

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data

Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemysław Biecek, Jerzy Tiuryn, Martin Vingron BMC Bioinformatics 2011, 12:249 (21 June 2011)

Research   Open Access

Concept and application of a computational vaccinology workflow

Johannes Söllner, Andreas Heinzel, Georg Summer, Raul Fechete, Laszlo Stipkovits, Susan Szathmary, Bernd Mayer Immunome Research 2010, 6(Suppl 2):S7 (3 November 2010)

Software   Open Access Highly Accessed

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

Kris Laukens, Jens Hollunder, Thanh Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren, Koenraad Van Leemput BMC Bioinformatics 2010, 11:360 (1 July 2010)

Research   Open Access Highly Accessed

A human functional protein interaction network and its application to cancer data analysis

Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010)

A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.

Research article   Open Access Highly Accessed

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

Sobia Raza, Neil McDerment, Paul A Lacaze, Kevin Robertson, Steven Watterson, Ying Chen, Michael Chisholm, George Eleftheriadis, Stephanie Monk, Maire O'Sullivan, Arran Turnbull, Douglas Roy, Athanasios Theocharidis, Peter Ghazal, Tom C Freeman BMC Systems Biology 2010, 4:63 (14 May 2010)

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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)

Method   Open Access Highly Accessed

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

Bolan Linghu, Evan S Snitkin, Zhenjun Hu, Yu Xia, Charles DeLisi Genome Biology 2009, 10:R91 (3 September 2009)

An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes

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MouseCyc: a curated biochemical pathways database for the laboratory mouse

Alexei V Evsikov, Mary E Dolan, Michael P Genrich, Emily Patek, Carol J Bult Genome Biology 2009, 10:R84 (14 August 2009)

MouseCyc is a database of curated metabolic pathways for the laboratory mouse.

Database   Open Access

DDEC: Dragon database of genes implicated in esophageal cancer

Magbubah Essack, Aleksandar Radovanovic, Ulf Schaefer, Sebastian Schmeier, Sundararajan V Seshadri, Alan Christoffels, Mandeep Kaur, Vladimir B Bajic BMC Cancer 2009, 9:219 (6 July 2009)

Methodology article   Open Access Highly Accessed

BowTieBuilder: modeling signal transduction pathways

Jochen Supper, Lucía Spangenberg, Hannes Planatscher, Andreas Dräger, Adrian Schröder, Andreas Zell BMC Systems Biology 2009, 3:67 (30 June 2009)

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The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process

Erick Antezana, Mikel Egaña, Ward Blondé, Aitzol Illarramendi, Iñaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov, Martin Kuiper Genome Biology 2009, 10:R58 (29 May 2009)

A software resource for the analysis of cell cycle related molecular networks.

Proceedings   Open Access

TGF-beta signaling proteins and the Protein Ontology

Cecilia N Arighi, Hongfang Liu, Darren A Natale, Winona C Barker, Harold Drabkin, Judith A Blake, Barry Smith, Cathy H Wu BMC Bioinformatics 2009, 10(Suppl 5):S3 (6 May 2009)

Research article   Open Access

Gene set internal coherence in the context of functional profiling

David Montaner, Pablo Minguez, Fátima Al-Shahrour, Joaquín Dopazo BMC Genomics 2009, 10:197 (27 April 2009)

Correction   Free

Correction: Reactome: a knowledge base of biologic pathways and processes

Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein Genome Biology 2009, 10:402 (4 February 2009)

Research article   Open Access Highly Accessed

Emergence, development and diversification of the TGF-β signalling pathway within the animal kingdom

Lukasz Huminiecki, Leon Goldovsky, Shiri Freilich, Aristidis Moustakas, Christos Ouzounis, Carl-Henrik Heldin BMC Evolutionary Biology 2009, 9:28 (3 February 2009)

Research   Open Access

Knowledge driven decomposition of tumor expression profiles

Martin H van Vliet, Lodewyk FA Wessels, Marcel JT Reinders BMC Bioinformatics 2009, 10(Suppl 1):S20 (30 January 2009)

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BioMart – biological queries made easy

Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk BMC Genomics 2009, 10:22 (14 January 2009)

Research article   Open Access Highly Accessed

Complex nature of SNP genotype effects on gene expression in primary human leucocytes

Graham A Heap, Gosia Trynka, Ritsert C Jansen, Marcel Bruinenberg, Morris A Swertz, Lotte C Dinesen, Karen A Hunt, Cisca Wijmenga, David A vanHeel, Lude Franke BMC Medical Genomics 2009, 2:1 (7 January 2009)

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)

Research article   Open Access

Prediction of evolutionarily conserved interologs in Mus musculus

Sailu Yellaboina, Dawood B Dudekula, Minoru SH Ko BMC Genomics 2008, 9:465 (8 October 2008)

Database   Open Access

DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions

Jingkai Yu, Svetlana Pacifico, Guozhen Liu, Russell L Finley BMC Genomics 2008, 9:461 (7 October 2008)

Research article   Open Access Highly Accessed

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

Intawat Nookaew, Michael C Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana BMC Systems Biology 2008, 2:71 (7 August 2008)

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T2D-Db: An integrated platform to study the molecular basis of Type 2 diabetes

Shipra Agrawal, Nevenka Dimitrova, Prasanthi Nathan, K Udayakumar, S Sai Lakshmi, S Sriram, N Manjusha, Urmi Sengupta BMC Genomics 2008, 9:320 (7 July 2008)

Research   Open Access

RDFScape: Semantic Web meets Systems Biology

Andrea Splendiani BMC Bioinformatics 2008, 9(Suppl 4):S6 (25 April 2008)

Research article   Open Access Highly Accessed

How many human genes can be defined as housekeeping with current expression data?

Jiang Zhu, Fuhong He, Shuhui Song, Jing Wang, Jun Yu BMC Genomics 2008, 9:172 (16 April 2008)

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MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data

Igor Ulitsky, Irit Gat-Viks, Ron Shamir Genome Biology 2008, 9:R1 (2 January 2008)

A new computational tool is presented that allows the integration of high-throughput experimental results with the probabilistic modeling of previously obtained information about cellular systems. The tool (MetaReg) is demonstrated on the leucine biosynthesis system in S.cerevisiae.

Commentary   Open Access Highly Accessed

microRNAs in viral oncogenesis

Vinod Scaria, Vaibhav Jadhav Retrovirology 2007, 4:82 (24 November 2007)

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A data integration approach for cell cycle analysis oriented to model simulation in systems biology

Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi BMC Systems Biology 2007, 1:35 (1 August 2007)

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GenMAPP 2: new features and resources for pathway analysis

Nathan Salomonis, Kristina Hanspers, Alexander C Zambon, Karen Vranizan, Steven C Lawlor, Kam D Dahlquist, Scott W Doniger, Josh Stuart, Bruce R Conklin, Alexander R Pico BMC Bioinformatics 2007, 8:217 (24 June 2007)