PiHelper: an open source framework for drug-target and antibody-target data. - Bülent Arman Aksoy; Jianjiong Gao; Gideon Dresdner; Weiqing Wang; Alex Root; Xiaohong Jing; Ethan G. Cerami; Chris Sander (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)

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. - Bülent Arman Aksoy; Emek Demir; Özgün Babur; Weiqing Wang; Xiaohong Jing; Nikolaus Schultz; Chris Sander (Bioinform., 2014)

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

PaxtoolsR: pathway analysis in R using Pathway Commons. - Augustin Luna; Özgün Babur; Bülent Arman Aksoy; Emek Demir; Chris Sander (Bioinform., 2016)

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data. - Dan Vanderkam; Bülent Arman Aksoy; Isaac Hodes; Jaclyn Perrone; Jeff Hammerbacher (Bioinform., 2016)

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. - Bülent Arman Aksoy; Vlado Dancík; Kenneth Smith 001; Jessica N. Mazerik; Zhou Ji; Benjamin E. Gross; Olga Nikolova; Nadia Jaber; Andrea Califano; Stuart L. Schreiber; Daniela S. Gerhard; Leandro Hermida; et al. (Database J. Biol. Databases Curation, 2017)

Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging. - Eric Czech; Bülent Arman Aksoy; Pinar Aksoy; Jeff Hammerbacher (BMC Bioinform., 2019)

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)