Search Results - Emek Demir

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  1. 1
    Crosstalk between Signaling Pathways Provided by Single and Multiple Protein Phosphorylation Sites

    Crosstalk between Signaling Pathways Provided by Single and Multiple Protein Phosphorylation Sites by Hafumi Nishi, Emek Demir, Anna R. Panchenko

    Published 2014
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  2. 2
    ChiBE: interactive visualization and manipulation of BioPAX pathway models

    ChiBE: interactive visualization and manipulation of BioPAX pathway models by Özgün Babur, Uḡur Doḡrusöz, Emek Demir, Chris Sander

    Published 2009
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  3. 3
    Automated Network Analysis Identifies Core Pathways in Glioblastoma

    Automated Network Analysis Identifies Core Pathways in Glioblastoma by Ethan Cerami, Emek Demir, Nikolaus Schultz, Barry S. Taylor, Chris Sander

    Published 2010
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  4. 4
    Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

    Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations by Özgün Babur, Mithat Gönen, Bülent Arman Aksoy, Nikolaus Schultz, Giovanni Ciriello, Chris Sander, Emek Demir

    Published 2015
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  5. 5
    Pathway Commons, a web resource for biological pathway data

    Pathway Commons, a web resource for biological pathway data by Ethan Cerami, Benjamin Groß, Emek Demir, Igor Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Chris Sander

    Published 2010
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  6. 6
    Using Biological Pathway Data with Paxtools

    Using Biological Pathway Data with Paxtools by Emek Demir, Özgün Babur, Igor Rodchenkov, Bülent Arman Aksoy, Ken Fukuda, Benjamin Groß, Onur Sumer, Gary D. Bader, Chris Sander

    Published 2013
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  7. 7
    Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

    Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 by Huaiyu Mi, Falk Schreiber, Stuart Moodie, Tobias Czauderna, Emek Demir, Robin Haw, Augustin Luna, Nicolas Le Novère, Anatoly Sorokin, Alice Villéger

    Published 2015
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  8. 8
    Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis

    Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis by Jeffrey Vedanayagam, Walid K. Chatila, Bülent Arman Aksoy, Sonali Majumdar, Anders J. Skanderup, Emek Demir, Nikolaus Schultz, Chris Sander, Eric C. Lai

    Published 2019
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  9. 9
    Large-scale automated machine reading discovers new cancer-driving mechanisms

    Large-scale automated machine reading discovers new cancer-driving mechanisms by Marco A. Valenzuela-Escárcega, Özgün Babur, Gus Hahn-Powell, Dane Bell, Thomas Hicks, Enrique Noriega-Atala, Xia Wang, Mihai Surdeanu, Emek Demir, Clayton T. Morrison

    Published 2018
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  10. 10
    Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps

    Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps by Hasan Balcı, Metin Can Siper, Nasim Saleh, Ilkin Safarli, Ludovic Roy, Merve Kilicarslan, Rumeysa Ozaydin, Alexander Mazein, Charles Auffray, Özgün Babur, Emek Demir, Uḡur Doḡrusöz

    Published 2020
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  11. 11
    Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells

    Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells by Anil Korkut, Weiqing Wang, Emek Demir, Bülent Arman Aksoy, Xiaohong Jing, Evan Molinelli, Özgün Babur, Debra L. Bemis, S. Onur Sumer, David B. Solit, Christine A. Pratilas, Chris Sander

    Published 2015
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  12. 12
    Causal interactions from proteomic profiles: Molecular data meet pathway knowledge

    Causal interactions from proteomic profiles: Molecular data meet pathway knowledge by Özgün Babur, Augustin Luna, Anil Korkut, Funda Durupınar, Metin Can Siper, Uḡur Doḡrusöz, Alvaro Sebastian Vaca Jacome, Ryan Peckner, Karen E. Christianson, Jacob D. Jaffe, Paul T. Spellman, Joseph E. Aslan, Chris Sander, Emek Demir

    Published 2021
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  13. 13
    Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

    Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0 by Adrien Rougny, Vasundra Touré, Stuart Moodie, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Uḡur Doḡrusöz, Alexander Mazein, Andreas Dräger, Michael L. Blinov, Alice Villéger, Robin Haw, Emek Demir, Huaiyu Mi, Anatoly Sorokin, Falk Schreiber, Augustin Luna

    Published 2019
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  14. 14
    Software support for SBGN maps: SBGN-ML and LibSBGN

    Software support for SBGN maps: SBGN-ML and LibSBGN by Martijn van Iersel, Alice C. Villéger, Tobias Czauderna, Sarah Boyd, Frank Bergmann, Augustin Luna, Emek Demir, Anatoly Sorokin, Uḡur Doḡrusöz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart Moodie, Hiroaki Kitano, Nicolas Le Novère, Falk Schreiber

    Published 2012
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  15. 15
    Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs

    Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs by Özgün Babur, Alexander R. Melrose, Jennifer M. Cunliffe, John Klimek, Jiaqing Pang, Anna-Liisa I. Sepp, Jevgenia Zilberman‐Rudenko, Samuel Tassi Yunga, Tony J. Zheng, Iván Parra‐Izquierdo, Jessica Minnier, Owen J. T. McCarty, Emek Demir, Ashok P. Reddy, Phillip A. Wilmarth, Larry L. David, Joseph E. Aslan

    Published 2020
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  16. 16
    Ribavirin shows antiviral activity against SARS-CoV-2 and downregulates the activity of TMPRSS2 and the expression of ACE2 in vitro

    Ribavirin shows antiviral activity against SARS-CoV-2 and downregulates the activity of TMPRSS2 and the expression of ACE2 in vitro by Mehmet Altay Ünal, Ceylan Verda Bitirim, Gökçe Yağmur Summak, Sidar Bereketoğlu, İnci Cevher Zeytin, Ömür Beşbinar, Cansu Gürcan, Dunya Aydos, Ezgi Göksoy, Ebru Kocakaya, Zeynep Eran, Merve Murat, Nil Demir, Zeynep Büşra Aksoy, Julia Somers, Emek Demir, Hasan Nazır, Síbel A. Özkan, Aykut Özkul, Alpay Azap, Açelya Yılmazer, Kamil Can Akçalı

    Published 2021
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  17. 17
    Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

    Pathway Commons 2019 Update: integration, analysis and exploration of pathway data by Igor Rodchenkov, Özgün Babur, Augustin Luna, Bülent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O’Callaghan, Wanxin Li, G Domingues Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Groß, Uḡur Doḡrusöz, Emek Demir, Gary D. Bader, Chris Sander

    Published 2019
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  18. 18
    The reactome pathway knowledgebase 2022

    The reactome pathway knowledgebase 2022 by Marc Gillespie, Bijay Jassal, Ralf Stephan, M Orlic-Milacic, Karen Rothfels, Andrea Senff‐Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Deng Chuan, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon I. Shorser, Gary D. Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio

    Published 2021
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  19. 19
    The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance

    The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance by Sunil K. Joshi, Tamilla Nechiporuk, Daniel Bottomly, Paul Piehowski, Julie A. Reisz, Janét Pittsenbarger, Andy Kaempf, Sara J.C. Gosline, Yi-Ting Wang, Joshua Hansen, Marina Gritsenko, Chelsea Hutchinson, Karl Weitz, Jamie Moon, Francesca Cendali, Thomas Fillmore, Chia‐Feng Tsai, Athena Schepmoes, Tujin Shi, Osama A. Arshad, Jason McDermott, Özgün Babur, Kevin Watanabe‐Smith, Emek Demir, Angelo D’Alessandro, Tao Liu, Cristina E. Tognon, Jeffrey W. Tyner, Shannon K. McWeeney, Karin Rodland, Brian J. Druker, Elie Traer

    Published 2021
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  20. 20
    The Systems Biology Graphical Notation

    The Systems Biology Graphical Notation by Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I. Aladjem, Sarala Wimalaratne, Frank T Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji, Lu Li, Yukiko Matsuoka, Alice Villéger, Sarah Boyd, Laurence Calzone, Mélanie Courtot, Uḡur Doḡrusöz, Tom C. Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B. Kell, Chris Sander, Herbert M. Sauro, Jacky L. Snoep, Kurt W. Kohn, Hiroaki Kitano

    Published 2009
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