Genome Biology

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Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

Arun K Ramani, Razvan C Bunescu, Raymond J Mooney* and Edward M Marcotte*

Genome Biology 2005, 6:R40 doi:10.1186/gb-2005-6-5-r40

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Proceedings   Open Access

Sensitive detection of pathway perturbations in cancers

Corban G Rivera, Brett M Tyler, TM Murali BMC Bioinformatics 2012, 13(Suppl 3):S9 (21 March 2012)

Proceedings   Open Access

Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection

Dukyong Yoon, Hyosil Kim, Haeyoung Suh-Kim, Rae Woong Park, KiYoung Lee BMC Systems Biology 2011, 5(Suppl 2):S1 (14 December 2011)

Research article   Open Access

Differential C3NET reveals disease networks of direct physical interactions

Gökmen Altay, Mohammad Asim, Florian Markowetz, David E Neal BMC Bioinformatics 2011, 12:296 (21 July 2011)

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.

Proceedings   Open Access

HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features

Richard Tsai, Po-Ting Lai, Hong-Jie Dai, Chi-Hsin Huang, Yue-Yang Bow, Yen-Ching Chang, Wen-Harn Pan, Wen-Lian Hsu BMC Bioinformatics 2009, 10(Suppl 15):S9 (3 December 2009)

Research   Open Access

HAPPI: an online database of comprehensive human annotated and predicted protein interactions

Jake Chen, SudhaRani Mamidipalli, Tianxiao Huan BMC Genomics 2009, 10(Suppl 1):S16 (7 July 2009)

Research   Open Access

Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies

Erdahl T Teber, Jason Y Liu, Sara Ballouz, Diane Fatkin, Merridee A Wouters BMC Bioinformatics 2009, 10(Suppl 1):S69 (30 January 2009)

Research article   Open Access Highly Accessed

Extraction of semantic biomedical relations from text using conditional random fields

Markus Bundschus, Mathaeus Dejori, Martin Stetter, Volker Tresp, Hans-Peter Kriegel BMC Bioinformatics 2008, 9:207 (23 April 2008)

Research article   Open Access Highly Accessed

Improving protein function prediction methods with integrated literature data

Aaron P Gabow, Sonia M Leach, William A Baumgartner, Lawrence E Hunter, Debra S Goldberg BMC Bioinformatics 2008, 9:198 (15 April 2008)

Method   Open Access Highly Accessed

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes

Kriston L McGary, Insuk Lee, Edward M Marcotte Genome Biology 2007, 8:R258 (5 December 2007)

Loss-of-function phenotypes of yeast genes can be predicted from the loss-of-function phenotypes of their neighbours in functional gene networks. This could potentially be applied to the prediction of human disease genes.

Research article   Open Access

Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining

Xochitl C Morgan, Shulin Ni, Daniel P Miranker, Vishwanath R Iyer BMC Bioinformatics 2007, 8:445 (15 November 2007)

Research article   Open Access

BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features

Richard Tsai, Wen-Chi Chou, Ying-Shan Su, Yu-Chun Lin, Cheng-Lung Sung, Hong-Jie Dai, Irene Yeh, Wei Ku, Ting-Yi Sung, Wen-Lian Hsu BMC Bioinformatics 2007, 8:325 (1 September 2007)

Research article   Open Access Highly Accessed

Probabilistic prediction and ranking of human protein-protein interactions

Michelle S Scott, Geoffrey J Barton BMC Bioinformatics 2007, 8:239 (5 July 2007)

Methodology article   Open Access Highly Accessed

Reconstruction of human protein interolog network using evolutionary conserved network

Tao-Wei Huang, Chung-Yen Lin, Cheng-Yan Kao BMC Bioinformatics 2007, 8:152 (10 May 2007)

Software   Open Access Highly Accessed

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, Lincoln Stein Genome Biology 2007, 8:R39 (16 March 2007)

Reactome, an online curated resource for human pathway data, can be used to infer equivalent reactions in non-human species and as a tool to aid in the interpretation of microarrays and other high-throughput data sets.

Opinion   Free

How complete are current yeast and human protein-interaction networks?

G Traver Hart, Arun K Ramani, Edward M Marcotte Genome Biology 2006, 7:120 (1 December 2006)

How can protein-interaction networks can be made more complete?

Database   Open Access Highly Accessed

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model

Kai Xia, Dong Dong, Jing-Dong J Han BMC Bioinformatics 2006, 7:508 (18 November 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   Open Access

Similarity searches in genome-wide numerical data sets

Galina Glazko, Michael Coleman, Arcady Mushegian Biology Direct 2006, 1:13 (30 May 2006)

Research article   Open Access

Topology and weights in a protein domain interaction network – a novel way to predict protein interactions

Stefan Wuchty BMC Genomics 2006, 7:122 (23 May 2006)