Discovering modulators of gene expression
Babur, Özgün, Demir, Emek, Gönen, Mithat, Sander, Chris, Dogrusoz, Ugur
Published in Nucleic acids research (01.09.2010)
Published in Nucleic acids research (01.09.2010)
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Journal Article
The BioPAX community standard for pathway data sharing
Bader, Gary D, Demir, Emek, Cary, Michael P, Paley, Suzanne, Fukuda, Ken, Lemer, Christian, Vastrik, Imre, Wu, Guanming, D'Eustachio, Peter, Schaefer, Carl, Luciano, Joanne, Schacherer, Frank, Martinez-Flores, Irma, Hu, Zhenjun, Jimenez-Jacinto, Veronica, Joshi-Tope, Geeta, Kandasamy, Kumaran, Lopez-Fuentes, Alejandra C, Mi, Huaiyu, Pichler, Elgar, Rodchenkov, Igor, Splendiani, Andrea, Tkachev, Sasha, Zucker, Jeremy, Gopinath, Gopal, Rajasimha, Harsha, Ramakrishnan, Ranjani, Shah, Imran, Syed, Mustafa, Anwar, Nadia, Babur, Özgün, Blinov, Michael, Brauner, Erik, Corwin, Dan, Donaldson, Sylva, Gibbons, Frank, Goldberg, Robert, Hornbeck, Peter, Luna, Augustin, Murray-Rust, Peter, Neumann, Eric, Reubenacker, Oliver, Samwald, Matthias, van Iersel, Martijn, Wimalaratne, Sarala, Allen, Keith, Braun, Burk, Whirl-Carrillo, Michelle, Cheung, Kei-Hoi, Dahlquist, Kam, Finney, Andrew, Gillespie, Marc, Glass, Elizabeth, Gong, Li, Haw, Robin, Honig, Michael, Hubaut, Olivier, Kane, David, Krupa, Shiva, Kutmon, Martina, Leonard, Julie, Marks, Debbie, Merberg, David, Petri, Victoria, Pico, Alex, Ravenscroft, Dean, Ren, Liya, Shah, Nigam, Sunshine, Margot, Tang, Rebecca, Whaley, Ryan, Letovksy, Stan, Buetow, Kenneth H, Rzhetsky, Andrey, Schachter, Vincent, Sobral, Bruno S, Dogrusoz, Ugur, McWeeney, Shannon, Aladjem, Mirit, Birney, Ewan, Collado-Vides, Julio, Goto, Susumu, Hucka, Michael, Novère, Nicolas Le, Maltsev, Natalia, Pandey, Akhilesh, Thomas, Paul, Wingender, Edgar, Karp, Peter D, Sander, Chris
Published in Nature biotechnology (01.09.2010)
Published in Nature biotechnology (01.09.2010)
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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
A proteogenomic portrait of lung squamous cell carcinoma
Satpathy, Shankha, Krug, Karsten, Jean Beltran, Pierre M, Savage, Sara R, Petralia, Francesca, Kumar-Sinha, Chandan, Dou, Yongchao, Reva, Boris, Kane, M Harry, Avanessian, Shayan C, Vasaikar, Suhas V, Krek, Azra, Lei, Jonathan T, Jaehnig, Eric J, Omelchenko, Tatiana, Geffen, Yifat, Bergstrom, Erik J, Stathias, Vasileios, Christianson, Karen E, Heiman, David I, Cieslik, Marcin P, Cao, Song, Song, Xiaoyu, Ji, Jiayi, Liu, Wenke, Li, Kai, Wen, Bo, Li, Yize, Gümüş, Zeynep H, Selvan, Myvizhi Esai, Soundararajan, Rama, Visal, Tanvi H, Raso, Maria G, Parra, Edwin Roger, Babur, Özgün, Vats, Pankaj, Anand, Shankara, Schraink, Tobias, Cornwell, MacIntosh, Rodrigues, Fernanda Martins, Zhu, Houxiang, Mo, Chia-Kuei, Zhang, Yuping, da Veiga Leprevost, Felipe, Huang, Chen, Chinnaiyan, Arul M, Wyczalkowski, Matthew A, Omenn, Gilbert S, Newton, Chelsea J, Schurer, Stephan, Ruggles, Kelly V, Fenyö, David, Jewell, Scott D, Thiagarajan, Mathangi, Mesri, Mehdi, Rodriguez, Henry, Mani, Sendurai A, Udeshi, Namrata D, Getz, Gad, Suh, James, Li, Qing Kay, Hostetter, Galen, Paik, Paul K, Dhanasekaran, Saravana M, Govindan, Ramaswamy, Ding, Li, Robles, Ana I, Clauser, Karl R, Nesvizhskii, Alexey I, Wang, Pei, Carr, Steven A, Zhang, Bing, Mani, D R, Gillette, Michael A
Published in Cell (05.08.2021)
Published in Cell (05.08.2021)
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Journal Article
PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data
Bahceci, Istemi, Dogrusoz, Ugur, La, Konnor C, Babur, Özgün, Gao, Jianjiong, Schultz, Nikolaus
Published in Bioinformatics (Oxford, England) (15.07.2017)
Published in Bioinformatics (Oxford, England) (15.07.2017)
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Journal Article
Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas
Donehower, Lawrence A., Soussi, Thierry, Korkut, Anil, Liu, Yuexin, Schultz, Andre, Cardenas, Maria, Li, Xubin, Babur, Ozgun, Hsu, Teng-Kuei, Lichtarge, Olivier, Weinstein, John N., Akbani, Rehan, Wheeler, David A.
Published in Cell reports (Cambridge) (30.07.2019)
Published in Cell reports (Cambridge) (30.07.2019)
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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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Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps
Balci, Hasan, Siper, Metin Can, Saleh, Nasim, Safarli, Ilkin, Roy, Ludovic, Kilicarslan, Merve, Ozaydin, Rumeysa, Mazein, Alexander, Auffray, Charles, Babur, Özgün, Demir, Emek, Dogrusoz, Ugur
Published in Bioinformatics (16.06.2021)
Published in Bioinformatics (16.06.2021)
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Journal Article
Pathway Commons, a web resource for biological pathway data
Cerami, Ethan G, Gross, Benjamin E, Demir, Emek, Rodchenkov, Igor, Babur, Ozgün, Anwar, Nadia, Schultz, Nikolaus, Bader, Gary D, Sander, Chris
Published in Nucleic acids research (01.01.2011)
Published in Nucleic acids research (01.01.2011)
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Journal Article
A framework for considering prior information in network‐based approaches to omics data analysis
Somers, Julia, Fenner, Madeleine, Kong, Garth, Thirumalaisamy, Dharani, Yashar, William M., Thapa, Kisan, Kinali, Meric, Nikolova, Olga, Babur, Özgün, Demir, Emek
Published in Proteomics (Weinheim) (01.11.2023)
Published in Proteomics (Weinheim) (01.11.2023)
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Journal Article
Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs
Babur, Özgün, Melrose, Alexander R., Cunliffe, Jennifer M., Klimek, John, Pang, Jiaqing, Sepp, Anna-Liisa I., Zilberman-Rudenko, Jevgenia, Tassi Yunga, Samuel, Zheng, Tony, Parra-Izquierdo, Iván, Minnier, Jessica, McCarty, Owen J.T., Demir, Emek, Reddy, Ashok P., Wilmarth, Phillip A., David, Larry L., Aslan, Joseph E.
Published in Blood (12.11.2020)
Published in Blood (12.11.2020)
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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
Aging-related alterations in mechanistic target of rapamycin signaling promote platelet hyperreactivity and thrombosis
Portier, Irina, Manne, Bhanu Kanth, Kosaka, Yasuhiro, Tolley, Neal D., Denorme, Frederik, Babur, Özgün, Reddy, Ashok P., Wilmarth, Phillip A., Aslan, Joseph E., Weyrich, Andrew S., Rondina, Matthew T., Campbell, Robert A.
Published in Journal of thrombosis and haemostasis (01.09.2024)
Published in Journal of thrombosis and haemostasis (01.09.2024)
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Journal Article
Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas
Donehower, Lawrence A., Soussi, Thierry, Korkut, Anil, Liu, Yuexin, Schultz, Andre, Cardenas, Maria, Li, Xubin, Babur, Ozgun, Hsu, Teng-Kuei, Lichtarge, Olivier, Weinstein, John N., Akbani, Rehan, Wheeler, David A.
Published in Cell reports (Cambridge) (10.09.2019)
Published in Cell reports (Cambridge) (10.09.2019)
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Journal Article
Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses
Onken, Michael D., Erdmann-Gilmore, Petra, Zhang, Qiang, Thapa, Kisan, King, Emily, Kaltenbronn, Kevin M., Noda, Sarah E., Makepeace, Carol M., Goldfarb, Dennis, Babur, Özgün, Townsend, R. Reid, Blumer, Kendall J.
Published in Molecular & cellular proteomics (01.11.2023)
Published in Molecular & cellular proteomics (01.11.2023)
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Journal Article
Large-scale automated machine reading discovers new cancer-driving mechanisms
Valenzuela-Escárcega, Marco A, Babur, Özgün, Hahn-Powell, Gus, Bell, Dane, Hicks, Thomas, Noriega-Atala, Enrique, Wang, Xia, Surdeanu, Mihai, Demir, Emek, Morrison, Clayton T
Published in Database : the journal of biological databases and curation (01.01.2018)
Published in Database : the journal of biological databases and curation (01.01.2018)
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Journal Article
Author-sourced capture of pathway knowledge in computable form using Biofactoid
Wong, Jeffrey V, Franz, Max, Siper, Metin Can, Fong, Dylan, Durupinar, Funda, Dallago, Christian, Luna, Augustin, Giorgi, John, Rodchenkov, Igor, Babur, Özgün, Bachman, John A, Gyori, Benjamin M, Demir, Emek, Bader, Gary D, Sander, Chris
Published in eLife (03.12.2021)
Published in eLife (03.12.2021)
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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
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
Predicting transcription factor activity using prior biological information
Yashar, William M., Estabrook, Joseph, Holly, Hannah D., Somers, Julia, Nikolova, Olga, Babur, Özgün, Braun, Theodore P., Demir, Emek
Published in iScience (15.03.2024)
Published in iScience (15.03.2024)
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