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
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
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
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers: e1004765
Senbabaoglu, Yasin, Sümer, Selçuk Onur, Sánchez-Vega, Francisco, Bemis, Debra, Ciriello, Giovanni, Schultz, Nikolaus, Sander, Chris
Published in PLoS computational biology (01.02.2016)
Published in PLoS computational biology (01.02.2016)
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Journal Article
3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets
Gao, Jianjiong, Chang, Matthew T, Johnsen, Hannah C, Gao, Sizhi Paul, Sylvester, Brooke E, Sumer, Selcuk Onur, Zhang, Hongxin, Solit, David B, Taylor, Barry S, Schultz, Nikolaus, Sander, Chris
Published in Genome medicine (23.01.2017)
Published in Genome medicine (23.01.2017)
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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
Using Biological Pathway Data with Paxtools: e1003194
Demir, Emek, Babur, Özgün, 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
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
Accelerating Discovery of Functional Mutant Alleles in Cancer
Chang, Matthew T, Bhattarai, Tripti Shrestha, Schram, Alison M, Bielski, Craig M, Donoghue, Mark T A, Jonsson, Philip, Chakravarty, Debyani, Phillips, Sarah, Kandoth, Cyriac, Penson, Alexander, Gorelick, Alexander, Shamu, Tambudzai, Patel, Swati, Harris, Christopher, Gao, JianJiong, Sumer, Selcuk Onur, Kundra, Ritika, Razavi, Pedram, Li, Bob T, Reales, Dalicia N, Socci, Nicholas D, Jayakumaran, Gowtham, Zehir, Ahmet, Benayed, Ryma, Arcila, Maria E, Chandarlapaty, Sarat, Ladanyi, Marc, Schultz, Nikolaus, Baselga, José, Berger, Michael F, Rosen, Neal, Solit, David B, Hyman, David M, Taylor, Barry S
Published in Cancer discovery (01.02.2018)
Published in Cancer discovery (01.02.2018)
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Journal Article
The context-specific role of germline pathogenicity in tumorigenesis
Srinivasan, Preethi, Bandlamudi, Chaitanya, Jonsson, Philip, Kemel, Yelena, Chavan, Shweta S, Richards, Allison L, Penson, Alexander V, Bielski, Craig M, Fong, Christopher, Syed, Aijazuddin, Jayakumaran, Gowtham, Prasad, Meera, Hwee, Jason, Sumer, Selcuk Onur, de Bruijn, Ino, Li, Xiang, Gao, JianJiong, Schultz, Nikolaus, Cambria, Roy, Galle, Jesse, Mukherjee, Semanti, Vijai, Joseph, Cadoo, Karen A, Carlo, Maria I, Walsh, Michael F, Mandelker, Diana, Ceyhan-Birsoy, Ozge, Shia, Jinru, Zehir, Ahmet, Ladanyi, Marc, Hyman, David M, Zhang, Liying, Offit, Kenneth, Robson, Mark E, Solit, David B, Stadler, Zsofia K, Berger, Michael F, Taylor, Barry S
Published in Nature genetics (01.11.2021)
Published in Nature genetics (01.11.2021)
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Journal Article
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer
de Bruijn, Ino, Li, Xiang, Sumer, Selcuk Onur, Gross, Benjamin, Sheridan, Robert, Ochoa, Angelica, Wilson, Manda, Wang, Avery, Zhang, Hongxin, Lisman, Aaron, Abeshouse, Adam, Zhang, Emily, Thum, Alice, Sadagopan, Ananthan, Heins, Zachary, Kandoth, Cyriac, Rodenburg, Sander, Tan, Sander, Lukasse, Pieter, van Hagen, Sjoerd, Fijneman, Remond J A, Meijer, Gerrit A, Schultz, Nikolaus, Gao, Jianjiong
Published in JCO clinical cancer informatics (01.02.2022)
Published in JCO clinical cancer informatics (01.02.2022)
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Journal Article
Abstract 1249: cBioPortal for Cancer Genomics
Mazor, Tali, de Bruijn, Ino, AlHamad, Rima, Chennault, Calla, Dubin, Corey, Easton-Marks, Jeremy, Fu, Zhaoyuan, Gross, Benjamin, Haynes, Charles, Higgins, David M., Hwee, Jason, Jagannathan, Prasanna K., Kalafati, Mirella, Kalletla, Karthik, Ko, James, Kuijpers, Tim, Kumar, Sowmiyaa, Kumari, Priti, Kundra, Ritika, Lai, Bryan, Li, Xiang, Lindsay, James, Lisman, Aaron, Lu, Qi-Xuan, Madupuri, Ramyasree, Ochoa, Angelica, Özgül, Yusuf Z., Plantalech, Oleguer, Pon, Matthijs N., Satravada, Baby A., Singh, Jessica, Sumer, Selcuk Onur, van Nierop, Pim, Vleugels, Floris, Wang, Avery, Wilson, Manda, Zhang, Hongxin, Zhao, Gaofei, Dogrusoz, Ugur, Heath, Allison, Resnick, Adam, Pugh, Trevor J., Sander, Chris, Cerami, Ethan, Gao, Jianjiong, Schultz, Nikolaus
Published in Cancer research (Chicago, Ill.) (22.03.2024)
Published in Cancer research (Chicago, Ill.) (22.03.2024)
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Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement
de Bruijn, Ino, Nikolov, Milen, Lau, Clarisse, Clayton, Ashley, Gibbs, David L, Mitraka, Elvira, Pozhidayeva, Dar’ya, Lash, Alex, Sumer, Selcuk Onur, Altreuter, Jennifer, Anton, Kristen, DeFelice, Mialy, Li, Xiang, Lisman, Aaron, R Longabaugh, William J, Muhlich, Jeremy, Santagata, Sandro, Nandakumar, Subhiksha, Sorger, Peter K, Suver, Christine, Schultz, Nikolaus, Taylor, Adam J, Thorsson, Vésteinn, Cerami, Ethan, Eddy, James A
Published in bioRxiv (30.06.2024)
Published in bioRxiv (30.06.2024)
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