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SaveA 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, Ozgun; Demir, Emek Share Save Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesiclesKim, 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. Share Save Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid LeukemiaYashar, William M.; Curtiss, Brittany M.; Coleman, Daniel J.; VanCampen, Jake; Kong, Garth; Macaraeg, Jommel; Estabrook, Joseph; Demir, Emek; Long, Nicola; Bottomly, Daniel; McWeeney, Shannon K.; Tyner, Jeffrey W.; Druker, Brian J.; Maxson, Julia E.; Braun, Theodore P. Share Save Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitorsBraun, Theodore P.; Estabrook, Joseph; Schonrock, Zachary; Curtiss, Brittany M.; Darmusey, Lucie; Macaraeg, Jommel; Enright, Trevor; Coblentz, Cody; Callahan, Rowan; Yashar, William; Taherinasab, Akram; Mohammed, Hisham; Coleman, Daniel J.; Druker, Brian J.; Demir, Emek; Lusardi, Theresa A.; Maxson, Julia E. Share Save Share Save An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancerJohnson, Brett E.; Creason, Allison L.; Stommel, Jayne M.; Keck, Jamie M.; Parmar, Swapnil; Betts, Courtney B.; Blucher, Aurora; Boniface, Christopher; Bucher, Elmar; Burlingame, Erik; Camp, Todd; Chin, Koei; Eng, Jennifer; Estabrook, Joseph; Feiler, Heidi S.; Heskett, Michael B.; Hu, Zhi; Kolodzie, Annette; Kong, Ben L.; Labrie, Marilyne; Lee, Jinho; Leyshock, Patrick; Mitri, Souraya; Patterson, Janice; Riesterer, Jessica L.; Sivagnanam, Shamilene; Somers, Julia; Sudar, Damir; Thibault, Guillaume; Weeder, Benjamin R.; Zheng, Christina; Nan, Xiaolin; Thompson, Reid F.; Heiser, Laura M.; Spellman, Paul T.; Thomas, George; Demir, Emek; Chang, Young Hwan; Coussens, Lisa M.; Guimaraes, Alexander R.; Corless, Christopher; Goecks, Jeremy; Bergan, Raymond; Mitri, Zahi; Mills, Gordon B.; Gray, Joe W. Share Save COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms (vol 17, e10387, 2021)Ostaszewski, Marek; Niarakis, Anna; Mazein, Alexander; Kuperstein, Inna; Phair, Robert; Orta-Resendiz, Aurelio; Singh, Vidisha; Aghamiri, Sara Sadat; Acencio, Marcio Luis; Glaab, Enrico; Ruepp, Andreas; Fobo, Gisela; Montrone, Corinna; Brauner, Barbara; Frishman, Goar; Monraz Gomez, Luis Cristobal; Somers, Julia; Hoch, Matti; Kumar Gupta, Shailendra; Scheel, Julia; Borlinghaus, Hanna; Czauderna, Tobias; Schreiber, Falk; Montagud, Arnau; Ponce de Leon, Miguel; Funahashi, Akira; Hiki, Yusuke; Hiroi, Noriko; Yamada, Takahiro G.; Drager, Andreas; Renz, Alina; Naveez, Muhammad; Bocskei, Zsolt; Messina, Francesco; Bornigen, Daniela; Fergusson, Liam; Conti, Marta; Rameil, Marius; Nakonecnij, Vanessa; Vanhoefer, Jakob; Schmiester, Leonard; Wang, Muying; Ackerman, Emily E.; Shoemaker, Jason E.; Zucker, Jeremy; Oxford, Kristie; Teuton, Jeremy; Kocakaya, Ebru; Summak, Gokce Yagmur; Hanspers, Kristina; Kutmon, Martina; Coort, Susan; Eijssen, Lars; Ehrhart, Friederike; Rex, D. A. B.; Slenter, Denise; Martens, Marvin; Pham, Nhung; Haw, Robin; Jassal, Bijay; Matthews, Lisa; Orlic-Milacic, Marija; Senff-Ribeiro, Andrea; Rothfels, Karen; Shamovsky, Veronica; Stephan, Ralf; Sevilla, Cristoffer; Varusai, Thawfeek; Ravel, Jean-Marie; Fraser, Rupsha; Ortseifen, Vera; Marchesi, Silvia; Gawron, Piotr; Smula, Ewa; Heirendt, Laurent; Satagopam, Venkata; Wu, Guanming; Riutta, Anders; Golebiewski, Martin; Owen, Stuart; Goble, Carole; Hu, Xiaoming; Overall, Rupert W.; Maier, Dieter; Bauch, Angela; Gyori, Benjamin M.; Bachman, John A.; Vega, Carlos; Groues, Valentin; Vazquez, Miguel; Porras, Pablo; Licata, Luana; Iannuccelli, Marta; Sacco, Francesca; Nesterova, Anastasia; Yuryev, Anton; de Waard, Anita; Turei, Denes; Luna, Augustin; Babur, Ozgun; Soliman, Sylvain; Valdeolivas, Alberto; Esteban-Medina, Marina; Pena-Chilet, Maria; Rian, Kinza; Helikar, Tomas; Puniya, Bhanwar Lal; Modos, Dezso; Treveil, Agatha; Olbei, Marton; De Meulder, Bertrand; Ballereau, Stephane; Dugourd, Aurelien; Naldi, Aurelien; Noel, Vincent; Calzone, Laurence; Sander, Chris; Demir, Emek; Korcsmaros, Tamas; Freeman, Tom C.; Auge, Franck; Beckmann, Jacques S.; Hasenauer, Jan; Wolkenhauer, Olaf; Willighagen, Egon L.; Pico, Alexander R.; Evelo, Chris T.; Gillespie, Marc E.; Stein, Lincoln D.; Hermjakob, Henning; D'Eustachio, Peter; Saez-Rodriguez, Julio; Dopazo, Joaquin; Valencia, Alfonso; Kitano, Hiroaki; Barillot, Emmanuel; Auffray, Charles; Balling, Rudi; Schneider, Reinhard Share Save Science Forum: Author-sourced capture of pathway knowledge in computable form using BiofactoidWong, Jeffrey, V; Franz, Max; Siper, Metin Can; Fong, Dylan; Durupinar, Funda; Dallago, Christian; Luna, Augustin; Giorgi, John; Rodchenkov, Igor; Babur, Ozgun; Bachman, John A.; Gyori, Benjamin M.; Demir, Emek; Bader, Gary D.; Sander, Chris Share Save The reactome pathway knowledgebase 2022Gillespie, Marc; Jassal, Bijay; Stephan, Ralf; Milacic, Marija; Rothfels, Karen; Senff-Ribeiro, Andrea; Griss, Johannes; Sevilla, Cristoffer; Matthews, Lisa; Gong, Chuqiao; Deng, Chuan; Varusai, Thawfeek; Ragueneau, Eliot; Haider, Yusra; May, Bruce; Shamovsky, Veronica; Weiser, Joel; Brunson, Timothy; Sanati, Nasim; Beckman, Liam; Shao, Xiang; Fabregat, Antonio; Sidiropoulos, Konstantinos; Murillo, Julieth; Viteri, Guilherme; Cook, Justin; Shorser, Solomon; Bader, Gary; Demir, Emek; Sander, Chris; Haw, Robin; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'Eustachio, Peter Share Save COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanismsOstaszewski, Marek; Niarakis, Anna; Mazein, Alexander; Kuperstein, Inna; Phair, Robert; Orta-Resendiz, Aurelio; Singh, Vidisha; Aghamiri, Sara Sadat; Acencio, Marcio Luis; Glaab, Enrico; Ruepp, Andreas; Fobo, Gisela; Montrone, Corinna; Brauner, Barbara; Frishman, Goar; Gomez, Luis Cristobal Monraz; Somers, Julia; Hoch, Matti; Gupta, Shailendra Kumar; Scheel, Julia; Borlinghaus, Hanna; Czauderna, Tobias; Schreiber, Falk; Montagud, Arnau; de Leon, Miguel Ponce; Funahashi, Akira; Hiki, Yusuke; Hiroi, Noriko; Yamada, Takahiro G.; Draeger, Andreas; Renz, Alina; Naveez, Muhammad; Bocskei, Zsolt; Messina, Francesco; Boernigen, Daniela; Fergusson, Liam; Conti, Marta; Rameil, Marius; Nakonecnij, Vanessa; Vanhoefer, Jakob; Schmiester, Leonard; Wang, Muying; Ackerman, Emily E.; Shoemaker, Jason E.; Zucker, Jeremy; Oxford, Kristie; Teuton, Jeremy; Kocakaya, Ebru; Summak, Gokce Yagmur; Hanspers, Kristina; Kutmon, Martina; Coort, Susan; Eijssen, Lars; Ehrhart, Friederike; Rex, Devasahayam Arokia Balaya; Slenter, Denise; Martens, Marvin; Nhung Pham; Haw, Robin; Jassal, Bijay; Matthews, Lisa; Orlic-Milacic, Marija; Ribeiro, Andrea Senff; Rothfels, Karen; Shamovsky, Veronica; Stephan, Ralf; Sevilla, Cristoffer; Varusai, Thawfeek; Ravel, Jean-Marie; Fraser, Rupsha; Ortseifen, Vera; Marchesi, Silvia; Gawron, Piotr; Smula, Ewa; Heirendt, Laurent; Satagopam, Venkata; Wu, Guanming; Riutta, Anders; Golebiewski, Martin; Owen, Stuart; Goble, Carole; Hu, Xiaoming; Overall, Rupert W.; Maier, Dieter; Bauch, Angela; Gyori, Benjamin M.; Bachman, John A.; Vega, Carlos; Groues, Valentin; Vazquez, Miguel; Porras, Pablo; Licata, Luana; Iannuccelli, Marta; Sacco, Francesca; Nesterova, Anastasia; Yuryev, Anton; de Waard, Anita; Turei, Denes; Luna, Augustin; Babur, Ozgun; Soliman, Sylvain; Valdeolivas, Alberto; Esteban-Medina, Marina; Pena-Chilet, Maria; Rian, Kinza; Helikar, Tomas; Puniya, Bhanwar Lal; Modos, Dezso; Treveil, Agatha; Olbei, Marton; De Meulder, Bertrand; Ballereau, Stephane; Dugourd, Aurelien; Naldi, Aurelien; Noel, Vincent; Calzone, Laurence; Sander, Chris; Demir, Emek; Korcsmaros, Tamas; Freeman, Tom C.; Auge, Franck; Beckmann, Jacques S.; Hasenauer, Jan; Wolkenhauer, Olaf; Wilighagen, Egon L.; Pico, Alexander R.; Evelo, Chris T.; Gillespie, Marc E.; Stein, Lincoln D.; Hermjakob, Henning; D'Eustachio, Peter; Saez-Rodriguez, Julio; Dopazo, Joaquin; Valencia, Alfonso; Kitano, Hiroaki; Barillot, Emmanuel; Auffray, Charles; Balling, Rudi; Schneider, Reinhard Share Save Quantitative Phosphoproteomics And Causal Analysis Reveal Distinct And Combinatorial Signaling Mechanisms In Protease-Activated Receptor PAR1 And PAR4 Platelet Activation ProgramsReitsma, Stephanie; Klimek, John; Parra-Izquierdo, Ivan; Babur, Ozgun; Melrose, Alexander; Zheng, Tony; Pang, Jiaqing; McCarty, Owen J.; Minnier, Jessica; Wilmarth, Phillip; Demir, Emek; Reddy, Ashok; David, Larry; Aslan, Joseph Share Save Causal interactions from proteomic profiles: Molecular data meet pathway knowledgeBabur, Ozgun; Luna, Augustin; Korkut, Anil; Durupinar, Funda; Siper, Metin Can; Dogrusoz, Ugur; Jacome, Alvaro Sebastian Vaca; Peckner, Ryan; Christianson, Karen E.; Jaffe, Jacob D.; Spellman, Paul T.; Aslan, Joseph E.; Sander, Chris; Demir, Emek Share Save 2D MXenes with antiviral and immunomodulatory properties: A pilot study against SARS-CoV-2Unal, Mehmet Altay; Bayrakdar, Fatma; Fusco, Laura; Besbinar, Omur; Shuck, Christopher E.; Yalcin, Suleyman; Erken, Mine Turktas; Ozkul, Aykut; Gurcan, Cansu; Panatli, Oguzhan; Summak, Gokce Yagmur; Gokce, Cemile; Orecchioni, Marco; Gazzi, Arianna; Vitale, Flavia; Somers, Julia; Demir, Emek; Yildiz, Serap Suzuk; Nazir, Hasan; Grivel, Jean-Charles; Bedognetti, Davide; Crisanti, Andrea; Akcali, Kamil Can; Gogotsi, Yury; Delogu, Lucia Gemma; Yilmazer, Acelya Share Save Pathway Commons 2019 Update: integration, analysis and exploration of pathway dataRodchenkov, 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 Share Save Share Save Share Save Large-scale automated machine reading discovers new cancer-driving mechanismsValenzuela-Escarcega, Marco A.; Babur, Ozgun; Hahn-Powell, Gus; Bell, Dane; Hicks, Thomas; Noriega-Atala, Enrique; Wang, Xia; Surdeanu, Mihai; Demir, Emek; Morrison, Clayton T. 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