Analysis of the position dependent amino acid probabilities and its application to the search for remote homologues. - Shamil R. Sunyaev; Igor V. Rodchenkov; Frank Eisenhaber; Eugene N. Kuznetsov (RECOMB, 1998)

Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information. - Igor V. Tetko; Igor V. Rodchenkov; Mathias C. Walter; Thomas Rattei; Hans-Werner Mewes (Bioinform., 2008)

CCancer: a bird's eye view on gene lists reported in cancer-related studies. - Sabine Dietmann; Wanseon Lee; Philip Wong; Igor V. Rodchenkov; Alexey V. Antonov (Nucleic Acids Res., 2010)

Pathway Commons, a web resource for biological pathway data. - Ethan G. Cerami; Benjamin E. Gross; Emek Demir; Igor V. Rodchenkov; Özgün Babur; Nadia Anwar; Nikolaus Schultz; Gary D. Bader; Chris Sander (Nucleic Acids Res., 2011)

The BioPAX Validator. - Igor V. Rodchenkov; Emek Demir; Chris Sander; Gary D. Bader (Bioinform., 2013)

Using Biological Pathway Data with Paxtools. - Emek Demir; Özgün Babur; Igor V. Rodchenkov; Bülent Arman Aksoy; Ken I. Fukuda; Benjamin E. Gross; Selçuk Onur Sümer; Gary D. Bader; Chris Sander (PLoS Comput. Biol., 2013)

Pattern search in BioPAX models. - Özgün Babur; Bülent Arman Aksoy; Igor V. Rodchenkov; Selçuk Onur Sümer; Chris Sander; Emek Demir (Bioinform., 2014)

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. - Igor V. Rodchenkov; Ozgun Babur; Augustin Luna; Bülent Arman Aksoy; Jeffrey V. Wong; Dylan Fong; Max Franz; Metin Can Siper; Manfred Cheung; Michael Wrana; Harsh Mistry; Logan Mosier; et al. (Nucleic Acids Res., 2020)