Emerging landscape of oncogenic signatures across human cancers
Ciriello, Giovanni, Miller, Martin L, Aksoy, Bülent Arman, Senbabaoglu, Yasin, Schultz, Nikolaus, Sander, Chris
Published in Nature genetics (01.10.2013)
Published in Nature genetics (01.10.2013)
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Journal Article
Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
Babur, Özgün, Gönen, Mithat, Aksoy, Bülent Arman, Schultz, Nikolaus, Ciriello, Giovanni, Sander, Chris, Demir, Emek
Published in Genome Biology (26.02.2015)
Published in Genome Biology (26.02.2015)
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Journal Article
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal
Gao, Jianjiong, Aksoy, Bülent Arman, Dogrusoz, Ugur, Dresdner, Gideon, Gross, Benjamin, Sumer, S Onur, Sun, Yichao, Jacobsen, Anders, Sinha, Rileen, Larsson, Erik, Cerami, Ethan, Sander, Chris, Schultz, Nikolaus
Published in Science signaling (02.04.2013)
Published in Science signaling (02.04.2013)
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Journal Article
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data
Cerami, Ethan, Gao, Jianjiong, Dogrusoz, Ugur, Gross, Benjamin E, Sumer, Selcuk Onur, Aksoy, Bülent Arman, Jacobsen, Anders, Byrne, Caitlin J, Heuer, Michael L, Larsson, Erik, Antipin, Yevgeniy, Reva, Boris, Goldberg, Arthur P, Sander, Chris, Schultz, Nikolaus
Published in Cancer discovery (01.05.2012)
Published in Cancer discovery (01.05.2012)
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Journal Article
Pan-Cancer Analysis of Mutation Hotspots in Protein Domains
Miller, Martin L., Reznik, Ed, Gauthier, Nicholas P., Aksoy, Bülent Arman, Korkut, Anil, Gao, Jianjiong, Ciriello, Giovanni, Schultz, Nikolaus, Sander, Chris
Published in Cell systems (23.09.2015)
Published in Cell systems (23.09.2015)
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Journal Article
A Landscape of Metabolic Variation across Tumor Types
Reznik, Ed, Luna, Augustin, Aksoy, Bülent Arman, Liu, Eric Minwei, La, Konnor, Ostrovnaya, Irina, Creighton, Chad J., Hakimi, A. Ari, Sander, Chris
Published in Cell systems (28.03.2018)
Published in Cell systems (28.03.2018)
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Journal Article
Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis
Vedanayagam, Jeffrey, Chatila, Walid K., Aksoy, Bülent Arman, Majumdar, Sonali, Skanderup, Anders Jacobsen, Demir, Emek, Schultz, Nikolaus, Sander, Chris, Lai, Eric C.
Published in Nature communications (15.08.2019)
Published in Nature communications (15.08.2019)
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Journal Article
Chemotherapy resistance in diffuse type gastric adenocarcinoma is mediated by RhoA activation in cancer stem-like cells
Yoon, Changhwan, Cho, Soo-Jeong, Aksoy, Bülent Arman, Park, Do Joong, Schultz, Nikolaus, Ryeom, Sandra W., Yoon, Sam S.
Published in Clinical cancer research (15.02.2016)
Published in Clinical cancer research (15.02.2016)
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Journal Article
PaxtoolsR: pathway analysis in R using Pathway Commons
Luna, Augustin, Babur, Özgün, Aksoy, Bülent Arman, Demir, Emek, Sander, Chris
Published in Bioinformatics (15.04.2016)
Published in Bioinformatics (15.04.2016)
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Journal Article
SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps
Sari, Mecit, Bahceci, Istemi, Dogrusoz, Ugur, Sumer, Selcuk Onur, Aksoy, Bülent Arman, Babur, Özgün, Demir, Emek
Published in PloS one (01.06.2015)
Published in PloS one (01.06.2015)
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Journal Article
Pattern search in BioPAX models
Babur, Özgün, Aksoy, Bülent Arman, Rodchenkov, Igor, Sümer, Selçuk Onur, Sander, Chris, Demir, Emek
Published in Bioinformatics (01.01.2014)
Published in Bioinformatics (01.01.2014)
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Journal Article
KMT2C Mutations in Diffuse-Type Gastric Adenocarcinoma Promote Epithelial-to-Mesenchymal Transition
Cho, Soo-Jeong, Yoon, Changhwan, Lee, Jun Ho, Chang, Kevin K, Lin, Jian-Xian, Kim, Young-Ho, Kook, Myeong-Cherl, Aksoy, Bülent Arman, Park, Do Joong, Ashktorab, Hassan, Smoot, Duane T, Schultz, Nikolaus, Yoon, Sam S
Published in Clinical cancer research (15.12.2018)
Published in Clinical cancer research (15.12.2018)
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Journal Article
Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging
Czech, Eric, Aksoy, Bulent Arman, Aksoy, Pinar, Hammerbacher, Jeff
Published in BMC bioinformatics (02.09.2019)
Published in BMC bioinformatics (02.09.2019)
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Journal Article
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
Rodchenkov, Igor, Babur, Ozgun, Luna, Augustin, Aksoy, Bulent Arman, Wong, Jeffrey V, Fong, Dylan, Franz, Max, Siper, Metin Can, Cheung, Manfred, Wrana, Michael, Mistry, Harsh, Mosier, Logan, Dlin, Jonah, Wen, Qizhi, O’Callaghan, Caitlin, Li, Wanxin, Elder, Geoffrey, Smith, Peter T, Dallago, Christian, Cerami, Ethan, Gross, Benjamin, Dogrusoz, Ugur, Demir, Emek, Bader, Gary D, Sander, Chris
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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Journal Article
Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis
Snyder, Alexandra, Nathanson, Tavi, Funt, Samuel A, Ahuja, Arun, Buros Novik, Jacqueline, Hellmann, Matthew D, Chang, Eliza, Aksoy, Bulent Arman, Al-Ahmadie, Hikmat, Yusko, Erik, Vignali, Marissa, Benzeno, Sharon, Boyd, Mariel, Moran, Meredith, Iyer, Gopa, Robins, Harlan S, Mardis, Elaine R, Merghoub, Taha, Hammerbacher, Jeff, Rosenberg, Jonathan E, Bajorin, Dean F
Published in PLoS medicine (26.05.2017)
Published in PLoS medicine (26.05.2017)
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Journal Article
Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells
Korkut, Anil, Wang, Weiqing, Demir, Emek, Aksoy, Bülent Arman, Jing, Xiaohong, Molinelli, Evan J, Babur, Özgün, Bemis, Debra L, Onur Sumer, Selcuk, Solit, David B, Pratilas, Christine A, Sander, Chris
Published in eLife (18.08.2015)
Published in eLife (18.08.2015)
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Journal Article
Coral: Clear and Customizable Visualization of Human Kinome Data
Metz, Kathleen S., Deoudes, Erika M., Berginski, Matthew E., Jimenez-Ruiz, Ivan, Aksoy, Bulent Arman, Hammerbacher, Jeff, Gomez, Shawn M., Phanstiel, Douglas H.
Published in Cell systems (26.09.2018)
Published in Cell systems (26.09.2018)
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Journal Article
Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial
Rubinsteyn, Alex, Kodysh, Julia, Hodes, Isaac, Mondet, Sebastien, Aksoy, Bulent Arman, Finnigan, John P, Bhardwaj, Nina, Hammerbacher, Jeffrey
Published in Frontiers in immunology (18.01.2018)
Published in Frontiers in immunology (18.01.2018)
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Journal Article
Using biological pathway data with paxtools
Demir, Emek, Babur, Ozgün, Rodchenkov, Igor, Aksoy, Bülent Arman, Fukuda, Ken I, Gross, Benjamin, Sümer, Onur Selçuk, Bader, Gary D, Sander, Chris
Published in PLoS computational biology (01.09.2013)
Published in PLoS computational biology (01.09.2013)
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Journal Article
PI3Kδ Inhibition Enhances the Antitumor Fitness of Adoptively Transferred CD8 + T Cells
Bowers, Jacob S, Majchrzak, Kinga, Nelson, Michelle H, Aksoy, Bulent Arman, Wyatt, Megan M, Smith, Aubrey S, Bailey, Stefanie R, Neal, Lillian R, Hammerbacher, Jeffrey E, Paulos, Chrystal M
Published in Frontiers in immunology (29.09.2017)
Published in Frontiers in immunology (29.09.2017)
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