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Cytoscape Web: bringing network biology to the browser Ono, Keiichiro; Fong, Dylan; Gao, Chengzhan; Churas, Christopher; Pillich, Rudolf; Lenkiewicz, Joanna; Pratt, Dexter; Pico, Alexander R.; Hanspers, Kristina; Xin, Yihang; Morris, John; Kucera, Mike; Franz, Max; Lopes, Christian; Bader, Gary; Ideker, Trey Share Save
Machine learning reveals prominent spontaneous behavioral changes and treatment efficacy in humanized and transgenic Alzheimer's disease models Miller, Stephanie R.; Luxem, Kevin; Lauderdale, Kelli; Nambiar, Pranav; Honma, Patrick S.; Ly, Katie K.; Bangera, Shreya; Bullock, Mary; Shin, Jia; Kaliss, Nick; Qiu, Yuechen; Cai, Catherine; Shen, Kevin; Mallen, K. Dakota; Yan, Zhaoqi; Mendiola, Andrew S.; Saito, Takashi; Saido, Takaomi C.; Pico, Alexander R.; Thomas, Reuben; Roberson, Erik D.; Akassoglou, Katerina; Bauer, Pavol; Remy, Stefan; Palop, Jorge J. Share Save
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Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing Maier, Andreas; Hartung, Michael; Abovsky, Mark; Adamowicz, Klaudia; Bader, Gary D.; Baier, Sylvie; Blumenthal, David B.; Chen, Jing; Elkjaer, Maria L.; Garcia-Hernandez, Carlos; Helmy, Mohamed; Hoffmann, Markus; Jurisica, Igor; Kotlyar, Max; Lazareva, Olga; Levi, Hagai; List, Markus; Lobentanzer, Sebastian; Loscalzo, Joseph; Malod-Dognin, Noel; Manz, Quirin; Matschinske, Julian; Mee, Miles; Oubounyt, Mhaned; Pastrello, Chiara; Pico, Alexander R.; Pillich, Rudolf T.; Poschenrieder, Julian M.; Pratt, Dexter; Przulj, Natasa; Sadegh, Sepideh; Saez-Rodriguez, Julio; Sarkar, Suryadipto; Shaked, Gideon; Shamir, Ron; Trummer, Nico; Turhan, Ugur; Wang, Rui-Sheng; Zolotareva, Olga; Baumbach, Jan Share Save
Incident heart failure in chronic kidney disease: proteomics informs biology and risk stratification Dubin, Ruth F.; Deo, Rajat; Ren, Yue; Wang, Jianqiao; Pico, Alexander R.; Mychaleckyj, Josyf C.; Kozlitina, Julia; Arthur, Victoria; Lee, Hongzhe; Shah, Amil; Feldman, Harold; Bansal, Nisha; Zelnick, Leila; Rao, Panduranga; Sukul, Nidhi; Raj, Dominic S.; Mehta, Rupal; Rosas, Sylvia E.; Bhat, Zeenat; Weir, Matthew R.; He, Jiang; Chen, Jing; Kansal, Mayank; Kimmel, Paul L.; Ramachandran, Vasan S.; Waikar, Sushrut S.; Segal, Mark R.; Ganz, Peter Share Save
In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response Chen, Xuewen; Haribowo, Augustinus G.; Baik, Alan H.; Fossati, Andrea; Stevenson, Erica; Chen, Yiwen R.; Reyes, Nabora S.; Peng, Tien; Matthay, Michael A.; Traglia, Michela; Pico, Alexander R.; Jarosz, Daniel F.; Buchwalter, Abigail; Ghaemmaghami, Sina; Swaney, Danielle L.; Jain, Isha H. Share Save
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WikiPathways 2024: next generation pathway database Agrawal, Ayushi; Balci, Hasan; Hanspers, Kristina; Coort, Susan L.; Martens, Marvin; Slenter, Denise N.; Ehrhart, Friederike; Digles, Daniela; Waagmeester, Andra; Wassink, Isabel; Abbassi-Daloii, Tooba; Lopes, Elisson N.; Iyer, Aishwarya; Acosta, Javier Millan; Willighagen, Lars G.; Nishida, Kozo; Riutta, Anders; Basaric, Helena; Evelo, Chris T.; Willighagen, Egon L.; Kutmon, Martina; Pico, Alexander R. Share Save
Defining blood-induced microglia functions in neurodegeneration through multiomic profiling Mendiola, Andrew S.; Yan, Zhaoqi; Dixit, Karuna; Johnson, Jeffrey R.; Bouhaddou, Mehdi; Meyer-Franke, Anke; Shin, Min-Gyoung; Yong, Yu; Agrawal, Ayushi; MacDonald, Eilidh; Muthukumar, Gayathri; Pearce, Clairice; Arun, Nikhita; Cabriga, Belinda; Meza-Acevedo, Rosa; Alzamora, Maria del Pilar S.; Zamvil, Scott S.; Pico, Alexander R.; Ryu, Jae Kyu; Krogan, Nevan J.; Akassoglou, Katerina Share Save
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms 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; 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
The Dynamic Platelet Transcriptome in Obesity and Weight Loss Mirhashemi, Marzieh Ezzaty; Shah, Ravi, V; Kitchen, Robert R.; Rong, Jian; Spahillari, Aferdita; Pico, Alexander R.; Vitseva, Olga; Levy, Daniel; Demarco, Danielle; Shah, Sajani; Iafrati, Mark D.; Larson, Martin G.; Tanriverdi, Kahraman; Freedman, Jane E. Share Save
Mir-30d Regulates Cardiac Remodeling by Intracellular and Paracrine Signaling Li, Jin; Salvador, Ane M.; Li, Guoping; Valkov, Nedyalka; Ziegler, Olivia; Yeri, Ashish; Xiao, Chun Yang; Meechoovet, Bessie; Alsop, Eric; Rodosthenous, Rodosthenis S.; Kundu, Piyusha; Huan, Tianxiao; Levy, Daniel; Tigges, John; Pico, Alexander R.; Ghiran, Ionita; Silverman, Michael G.; Meng, Xiangmin; Kitchen, Robert; Xu, Jiahong; Van Keuren-Jensen, Kendall; Shah, Ravi; Xiao, Junjie; Das, Saumya Share Save
Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103+ and Gut CD4+ T Cells Yukl, Steven A.; Khan, Shahzada; Chen, Tsui-Hua; Trapecar, Martin; Wu, Frank; Xie, Guorui; Telwatte, Sushama; Fulop, Daniel; Pico, Alexander R.; Laird, Gregory M.; Ritter, Kristen D.; Jones, Norman G.; Lu, Chuanyi M.; Siliciano, Robert F.; Roan, Nadia R.; Milush, Jeffrey M.; Somsouk, Ma; Deeks, Steven G.; Hunt, Peter W.; Sanjabi, Shomyseh Share Save
Comprehensive Metabolic Phenotyping Refines Cardiovascular Risk in Young Adults Murthy, Venkatesh L.; Reis, Jared P.; Pico, Alexander R.; Kitchen, Robert; Lima, Joao A. C.; Lloyd-Jones, Donald; Allen, Norrina B.; Carnethon, Mercedes; Lewis, Gregory D.; Nayor, Matthew; Vasan, Ramachandran S.; Freedman, Jane E.; Clish, Clary B.; Shah, Ravi V. Share Save
WikiPathways: connecting communities Martens, Marvin; Ammar, Ammar; Riutta, Anders; Waagmeester, Andra; Slenter, Denise N.; Hanspers, Kristina; Miller, Ryan A.; Digles, Daniela; Lopes, Elisson N.; Ehrhart, Friederike; Dupuis, Lauren J.; Winckers, Laurent A.; Coort, Susan L.; Willighagen, Egon L.; Evelo, Chris T.; Pico, Alexander R.; Kutmon, Martina Share Save
Metabolic Architecture of Acute Exercise Response in Middle-Aged Adults in the Community Nayor, Matthew; Shah, Ravi, V; Miller, Patricia E.; Blodgett, Jasmine B.; Tanguay, Melissa; Pico, Alexander R.; Murthy, Venkatesh L.; Malhotra, Rajeev; Houstis, Nicholas E.; Deik, Amy; Pierce, Kerry A.; Bullock, Kevin; Dailey, Lucas; Velagaleti, Raghava S.; Moore, Stephanie A.; Ho, Jennifer E.; Baggish, Aaron L.; Clish, Clary B.; Larson, Martin G.; Vasan, Ramachandran S.; Lewis, Gregory D. Share Save
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Molecular Signature of Multisystem Cardiometabolic Stress and Its Association With Prognosis Murthy, Venkatesh L.; Yu, Bing; Wang, Wenshuang; Zhang, Xiuyan; Alkis, Taryn; Pico, Alexander R.; Yeri, Ashish; Bhupathiraju, Shilpa N.; Bressler, Jan; Ballantyne, Christie M.; Freedman, Jane E.; Ordovas, Jose; Boerwinkle, Eric; Tucker, Katherine L.; Shah, Ravi Share Save
Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation (Apri, 10.1038/s41590-020-0654-0, 2020) Mendiola, Andrew S.; Ryu, Jae Kyu; Bardehle, Sophia; Meyer-Franke, Anke; Ang, Kenny Kean-Hooi; Wilson, Chris; Baeten, Kim M.; Hanspers, Kristina; Merlini, Mario; Thomas, Sean; Petersen, Mark A.; Williams, Alexander; Thomas, Reuben; Rafalski, Victoria A.; Meza-Acevedo, Rosa; Tognatta, Reshmi; Yan, Zhaoqi; Pfaff, Samuel J.; Machado, Michael R.; Bedard, Catherine; Coronado, Pamela E. Rios; Jiang, Xiqian; Wang, Jin; Pleiss, Michael A.; Green, Ari J.; Zamvil, Scott S.; Pico, Alexander R.; Bruneau, Benoit G.; Arkin, Michelle R.; Akassoglou, Katerina Share Save
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