Found: 32

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  • A framework for considering prior information in network‐based approaches to omics data analysis.

    Published in:
    Proteomics, 2023, v. 23, n. 21/22, p. 1, doi. 10.1002/pmic.202200402
    By:
    • Somers, Julia;
    • Fenner, Madeleine;
    • Kong, Garth;
    • Thirumalaisamy, Dharani;
    • Yashar, William M.;
    • Thapa, Kisan;
    • Kinali, Meric;
    • Nikolova, Olga;
    • Babur, Özgün;
    • Demir, Emek
    Publication type:
    Article

  • Integrating biological pathways and genomic profiles with ChiBE 2.

    Published in:
    BMC Genomics, 2014, v. 15, n. 1, p. 642, doi. 10.1186/1471-2164-15-642
    By:
    • Babur, Özgün;
    • Dogrusoz, Ugur;
    • Çakır, Merve;
    • Aksoy, Bülent Arman;
    • Schultz, Nikolaus;
    • Sander, Chris;
    • Demir, Emek
    Publication type:
    Article

  • Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes.

    Published in:
    BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04147-y
    By:
    • Grzadkowski, Michal R.;
    • Holly, Hannah D.;
    • Somers, Julia;
    • Demir, Emek
    Publication type:
    Article

  • PATIKA mad: Putting microarray data into pathway context.

    Published in:
    Proteomics, 2008, v. 8, n. 11, p. 2196, doi. 10.1002/pmic.200700769
    By:
    • Babur, Ozgun;
    • Colak, Recep;
    • Demir, Emek;
    • Dogrusoz, Ugur
    Publication type:
    Article

  • Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.

    Published in:
    2020
    By:
    • Ostaszewski, Marek;
    • Mazein, Alexander;
    • Gillespie, Marc E.;
    • Kuperstein, Inna;
    • Niarakis, Anna;
    • Hermjakob, Henning;
    • Pico, Alexander R.;
    • Willighagen, Egon L.;
    • Evelo, Chris T.;
    • Hasenauer, Jan;
    • Schreiber, Falk;
    • Dräger, Andreas;
    • Demir, Emek;
    • Wolkenhauer, Olaf;
    • Furlong, Laura I.;
    • Barillot, Emmanuel;
    • Dopazo, Joaquin;
    • Orta-Resendiz, Aurelio;
    • Messina, Francesco;
    • Valencia, Alfonso
    Publication type:
    Correction Notice

  • COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.

    Published in:
    Scientific Data, 2020, v. 7, n. 1, p. 1, doi. 10.1038/s41597-020-0477-8
    By:
    • Ostaszewski, Marek;
    • Mazein, Alexander;
    • Gillespie, Marc E.;
    • Kuperstein, Inna;
    • Niarakis, Anna;
    • Hermjakob, Henning;
    • Pico, Alexander R.;
    • Willighagen, Egon L.;
    • Evelo, Chris T.;
    • Hasenauer, Jan;
    • Schreiber, Falk;
    • Dräger, Andreas;
    • Demir, Emek;
    • Wolkenhauer, Olaf;
    • Furlong, Laura I.;
    • Barillot, Emmanuel;
    • Dopazo, Joaquin;
    • Orta-Resendiz, Aurelio;
    • Messina, Francesco;
    • Valencia, Alfonso
    Publication type:
    Article

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

    Published in:
    eLife, 2015, p. 1, doi. 10.7554/eLife.04640
    By:
    • Korkut, Anil;
    • Wang, Weiqing;
    • Demir, Emek;
    • Arman Aksoy, Bülent;
    • Xiaohong Jing;
    • Molinelli, Evan J.;
    • Babur, Özgiün;
    • Bemis, Debra L.;
    • Onur Sumer, Selcuk;
    • Solit, David B.;
    • Pratilas, Christine A.;
    • Sander, Chris
    Publication type:
    Article

  • Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

    Published in:
    Journal of Integrative Bioinformatics, 2019, v. 16, n. 2, p. 1, doi. 10.1515/jib-2019-0022
    By:
    • Rougny1, Adrien;
    • Touré, Vasundra;
    • Moodie, Stuart;
    • Balaur, Irina;
    • Czauderna, Tobias;
    • Borlinghaus, Hanna;
    • Dogrusoz, Ugur;
    • Mazein, Alexander;
    • Dräger, Andreas;
    • Blinov, Michael L.;
    • Villéger, Alice;
    • Haw, Robin;
    • Demir, Emek;
    • Huaiyu Mi;
    • Sorokin, Anatoly;
    • Schreiber, Falk;
    • Luna, Augustin
    Publication type:
    Article

  • Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.

    Published in:
    Genome Biology, 2015, v. 16, n. 1, p. 45, doi. 10.1186/s13059-015-0612-6
    By:
    • Babur, Özgün;
    • Gönen, Mithat;
    • Aksoy, Bülent Arman;
    • Schultz, Nikolaus;
    • Ciriello, Giovanni;
    • Sander, Chris;
    • Demir, Emek
    Publication type:
    Article

  • Using Biological Pathway Data with Paxtools.

    Published in:
    PLoS Computational Biology, 2013, v. 9, n. 9, p. 1, doi. 10.1371/journal.pcbi.1003194
    By:
    • Demir, Emek;
    • Babur, Özgün;
    • Rodchenkov, Igor;
    • Aksoy, Bülent Arman;
    • Fukuda, Ken I.;
    • Gross, Benjamin;
    • Sümer, Onur Selçuk;
    • Bader, Gary D.;
    • Sander, Chris
    Publication type:
    Article

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

    Published in:
    Bioinformatics, 2021, v. 37, n. 10, p. 1475, doi. 10.1093/bioinformatics/btaa850
    By:
    • 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
    Publication type:
    Article

  • PaxtoolsR: pathway analysis in R using Pathway Commons.

    Published in:
    Bioinformatics, 2016, v. 32, n. 8, p. 1262, doi. 10.1093/bioinformatics/btv733
    By:
    • Luna, Augustin;
    • Babur, Özgün;
    • Aksoy, Bülent Arman;
    • Demir, Emek;
    • Sander, Chris
    Publication type:
    Article

  • Large-scale automated machine reading discovers new cancer-driving mechanisms.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay098
    By:
    • 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
    Publication type:
    Article

  • Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles.

    Published in:
    Bioinformatics, 2014, v. 30, n. 14, p. 2051, doi. 10.1093/bioinformatics/btu164
    By:
    • Aksoy, Bülent Arman;
    • Demir, Emek;
    • Babur, Özgün;
    • Wang, Weiqing;
    • Jing, Xiaohong;
    • Schultz, Nikolaus;
    • Sander, Chris
    Publication type:
    Article

  • Pattern search in BioPAX models.

    Published in:
    Bioinformatics, 2014, v. 30, n. 1, p. 139, doi. 10.1093/bioinformatics/btt539
    By:
    • Babur, Özgün;
    • Aksoy, Bülent Arman;
    • Rodchenkov, Igor;
    • Sümer, Selçuk Onur;
    • Sander, Chris;
    • Demir, Emek
    Publication type:
    Article

  • The BioPAX Validator.

    Published in:
    Bioinformatics, 2013, v. 29, n. 20, p. 2659, doi. 10.1093/bioinformatics/btt452
    By:
    • Rodchenkov, Igor;
    • Demir, Emek;
    • Sander, Chris;
    • Bader, Gary D.
    Publication type:
    Article

  • Software support for SBGN maps: SBGN-ML and LibSBGN.

    Published in:
    Bioinformatics, 2012, v. 28, n. 15, p. 2016, doi. 10.1093/bioinformatics/bts270
    By:
    • van Iersel, Martijn P.;
    • Villéger, Alice C.;
    • Czauderna, Tobias;
    • Boyd, Sarah E.;
    • Bergmann, Frank T.;
    • Luna, Augustin;
    • Demir, Emek;
    • Sorokin, Anatoly;
    • Dogrusoz, Ugur;
    • Matsuoka, Yukiko;
    • Funahashi, Akira;
    • Aladjem, Mirit I.;
    • Mi, Huaiyu;
    • Moodie, Stuart L.;
    • Kitano, Hiroaki;
    • Le Novère, Nicolas;
    • Schreiber, Falk
    Publication type:
    Article

  • BioPAX support in CellDesigner.

    Published in:
    Bioinformatics, 2011, v. 27, n. 24, p. 3437, doi. 10.1093/bioinformatics/btr586
    By:
    • Mi, Huaiyu;
    • Muruganujan, Anushya;
    • Demir, Emek;
    • Matsuoka, Yukiko;
    • Funahashi, Akira;
    • Kitano, Hiroaki;
    • Thomas, Paul D.
    Publication type:
    Article

  • ChiBE: interactive visualization and manipulation of BioPAX pathway models.

    Published in:
    Bioinformatics, 2010, v. 26, n. 3, p. 429, doi. 10.1093/bioinformatics/btp665
    By:
    • Babur, Ozgun;
    • Dogrusoz, Ugur;
    • Demir, Emek;
    • Sander, Chris
    Publication type:
    Article

  • Author- sourced capture of pathway knowledge in computable form using Biofactoid.

    Published in:
    eLife, 2021, p. 1, doi. 10.7554/eLife.68292
    By:
    • 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
    Publication type:
    Article

  • SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

    Published in:
    PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0128985
    By:
    • Sari, Mecit;
    • Bahceci, Istemi;
    • Dogrusoz, Ugur;
    • Sumer, Selcuk Onur;
    • Aksoy, Bülent Arman;
    • Babur, Özgün;
    • Demir, Emek
    Publication type:
    Article

  • Automated Network Analysis Identifies Core Pathways in Glioblastoma.

    Published in:
    PLoS ONE, 2010, v. 5, n. 2, p. 1, doi. 10.1371/journal.pone.0008918
    By:
    • Cerami, Ethan;
    • Demir, Emek;
    • Schultz, Nikolaus;
    • Taylor, Barry S.;
    • Sander, Chris
    Publication type:
    Article

  • Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles.

    Published in:
    Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-05232-z
    By:
    • Kim, Hyun Ji;
    • Rames, Matthew J.;
    • Goncalves, Florian;
    • Kirschbaum, C. Ward;
    • Roskams-Hieter, Breeshey;
    • Spiliotopoulos, Elias;
    • Briand, Josephine;
    • Doe, Aaron;
    • Estabrook, Joseph;
    • Wagner, Josiah T.;
    • Demir, Emek;
    • Mills, Gordon;
    • Ngo, Thuy T. M.
    Publication type:
    Article

  • Pathway Commons, a web resource for biological pathway data.

    Published in:
    Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D685, doi. 10.1093/nar/gkq1039
    By:
    • Cerami, Ethan G.;
    • Gross, Benjamin E.;
    • Demir, Emek;
    • Rodchenkov, Igor;
    • Babur, Özgün;
    • Anwar, Nadia;
    • Schultz, Nikolaus;
    • Bader, Gary D.;
    • Sander, Chris
    Publication type:
    Article

  • Discovering modulators of gene expression.

    Published in:
    Nucleic Acids Research, 2010, v. 38, n. 17, p. 5648, doi. 10.1093/nar/gkq287
    By:
    • Babur, Özgün;
    • Demir, Emek;
    • Gönen, Mithat;
    • Sander, Chris;
    • Dogrusoz, Ugur
    Publication type:
    Article

  • Corrigendum: The BioPAX community standard for pathway data sharing.

    Published in:
    2012
    By:
    • 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
    Publication type:
    Erratum

  • The BioPAX community standard for pathway data sharing.

    Published in:
    2010
    By:
    • 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
    Publication type:
    Correction notice

  • The BioPAX community standard for pathway data sharing.

    Published in:
    Nature Biotechnology, 2010, v. 28, n. 9, p. 935, doi. 10.1038/nbt.1666
    By:
    • 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
    Publication type:
    Article

  • Erratum: The Systems Biology Graphical Notation.

    Published in:
    2009
    By:
    • Le Novère, Nicolas;
    • Hucka, Michael;
    • Mi, Huaiyu;
    • Moodie, Stuart;
    • Schreiber, Falk;
    • Sorokin, Anatoly;
    • Demir, Emek;
    • Wegner, Katja;
    • Aladjem, Mirit I;
    • Wimalaratne, Sarala M;
    • Bergman, Frank T;
    • Gauges, Ralph;
    • Ghazal, Peter;
    • Kawaji, Hideya;
    • Li, Lu;
    • Matsuoka, Yukiko;
    • Villéger, Alice;
    • Boyd, Sarah E;
    • Calzone, Laurence;
    • Courtot, Melanie
    Publication type:
    Correction notice

  • The Systems Biology Graphical Notation.

    Published in:
    Nature Biotechnology, 2009, v. 27, n. 8, p. 735, doi. 10.1038/nbt.1558
    By:
    • Le Novére, Nicolas;
    • Hucka, Michael;
    • Mi, Huaiyu;
    • Moodie, Stuart;
    • Schreiber, Falk;
    • Sorokin, Anatoly;
    • Demir, Emek;
    • Wegner, Katja;
    • Aladjem, Mirit I.;
    • Wimalaratne, Sarala M.;
    • Bergman, Frank T.;
    • Gauges, Ralph;
    • Ghazal, Peter;
    • Kawaji, Hideya;
    • Li, Lu;
    • Matsuoka, Yukiko;
    • Villéger, Alice;
    • Boyd, Sarah E.;
    • Calzone, Laurence;
    • Courtot, Melanie
    Publication type:
    Article

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

    Published in:
    Canadian Journal of Physiology & Pharmacology, 2021, v. 99, n. 5, p. 449, doi. 10.1139/cjpp-2020-0734
    By:
    • Unal, Mehmet Altay;
    • Bitirim, Ceylan Verda;
    • Summak, Gokce Yagmur;
    • Bereketoglu, Sidar;
    • Cevher Zeytin, Inci;
    • Besbinar, Omur;
    • Gurcan, Cansu;
    • Aydos, Dunya;
    • Goksoy, Ezgi;
    • Kocakaya, Ebru;
    • Eran, Zeynep;
    • Murat, Merve;
    • Demir, Nil;
    • Aksoy Ozer, Zeynep Busra;
    • Somers, Julia;
    • Demir, Emek;
    • Nazir, Hasan;
    • Ozkan, Sibel Aysil;
    • Ozkul, Aykut;
    • Azap, Alpay
    Publication type:
    Article

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

    Published in:
    Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-11610-1
    By:
    • Vedanayagam, Jeffrey;
    • Chatila, Walid K.;
    • Aksoy, Bülent Arman;
    • Majumdar, Sonali;
    • Skanderup, Anders Jacobsen;
    • Demir, Emek;
    • Schultz, Nikolaus;
    • Sander, Chris;
    • Lai, Eric C.
    Publication type:
    Article