Search Results - "Sumer, Selcuk Onur"

Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells by 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

“…Resistance to targeted cancer therapies is an important clinical problem. The discovery of anti-resistance drug combinations is challenging as resistance can…”
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The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data by 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

“…The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets,…”
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3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets by 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

“…Many mutations in cancer are of unknown functional significance. Standard methods use statistically significant recurrence of mutations in tumor samples as an…”
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SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps by Sari, Mecit, Bahceci, Istemi, Dogrusoz, Ugur, Sumer, Selcuk Onur, Aksoy, Bülent Arman, Babur, Özgün, Demir, Emek

“…Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN…”
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Pattern search in BioPAX models by Babur, Özgün, Aksoy, Bülent Arman, Rodchenkov, Igor, Sümer, Selçuk Onur, Sander, Chris, Demir, Emek

“…BioPAX is a standard language for representing complex cellular processes, including metabolic networks, signal transduction and gene regulation. Owing to the…”
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A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers by Şenbabaoğlu, Yasin, Sümer, Selçuk Onur, Sánchez-Vega, Francisco, Bemis, Debra, Ciriello, Giovanni, Schultz, Nikolaus, Sander, Chris

“…Protein expression and post-translational modification levels are tightly regulated in neoplastic cells to maintain cellular processes known as 'cancer…”
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Using biological pathway data with paxtools by Demir, Emek, Babur, Ozgün, Rodchenkov, Igor, Aksoy, Bülent Arman, Fukuda, Ken I, Gross, Benjamin, Sümer, Onur Selçuk, Bader, Gary D, Sander, Chris

“…A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial…”
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Accelerating Discovery of Functional Mutant Alleles in Cancer by 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

“…Most mutations in cancer are rare, which complicates the identification of therapeutically significant mutations and thus limits the clinical impact of genomic…”
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The context-specific role of germline pathogenicity in tumorigenesis by 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.

“…Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152…”
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MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer by Gauthier, Nicholas Paul, Reznik, Ed, Gao, Jianjiong, Sumer, Selcuk Onur, Schultz, Nikolaus, Sander, Chris, Miller, Martin L

“…The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in…”
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Abstract 5140: Individual patient cancer profiles in the cBio Cancer Genomic Portal by Gao, Jianjiong, Sumer, Selcuk Onur, Dresdner, Gideon, Aksoy, Bülent Arman, Sander, Chris, Schultz, Nikolaus

“…Abstract The most prominent or most interesting genomic alteration events from an individual tumor sample can now be browsed and analyzed in the cBio Cancer…”
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Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer by 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

“…Interpretation of genomic variants in tumor samples still presents a challenge in research and the clinical setting. A major issue is that information for…”
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Abstract 1249: cBioPortal for Cancer Genomics by 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

“…Abstract cBioPortal for Cancer Genomics is an open-source platform for interactive, exploratory analysis of large-scale clinico-genomic data. cBioPortal…”
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A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers: e1004765 by Senbabaoglu, Yasin, Sümer, Selçuk Onur, Sánchez-Vega, Francisco, Bemis, Debra, Ciriello, Giovanni, Schultz, Nikolaus, Sander, Chris

“…Protein expression and post-translational modification levels are tightly regulated in neoplastic cells to maintain cellular processes known as 'cancer…”
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Using Biological Pathway Data with Paxtools: e1003194 by Demir, Emek, Babur, Özgün, Rodchenkov, Igor, Aksoy, Bülent Arman, Fukuda, Ken I, Gross, Benjamin, Sümer, Onur Selçuk, Bader, Gary D, Sander, Chris

“…A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial…”
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Chisio Web: A Web-Based Framework for Customizable Visualization of Relational Information by Sümer, Selçuk Onur

“…Graphs are widely used to represent complex relational information. Graph visualization is crucial for effective analysis of information. In simple graphs,…”
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