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OmniPath: integrated knowledgebase for multi-omics analysis Turei, Denes; Schaul, Jonathan; Palacio-Escat, Nicolas; Bohar, Balazs; Bai, Yunfan; Ceccarelli, Francesco; Cevrim, Elif; Daley, Macabe; Darcan, Melih; Dimitrov, Daniel; Dogan, Tunca; Domingo-Fernandez, Daniel; Dugourd, Aurelien; Gabor, Attila; Gul, Lejla; Hall, Benjamin A.; Hoyt, Charles Tapley; Ivanova, Olga; Klein, Michal; Lawrence, Toby; Mananes, Diego; Modos, Dezso; Muller-Dott, Sophia; Olbei, Marton; Schmidt, Christina; Sen, Bunyamin; Theis, Fabian J.; Unlu, Atabey; Ulusoy, Erva; Valdeolivas, Alberto; Korcsmaros, Tamas; Saez-Rodriguez, Julio Share Save
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Democratizing knowledge representation with BioCypher Lobentanzer, Sebastian; Aloy, Patrick; Baumbach, Jan; Bohar, Balazs; Carey, Vincent J.; Charoentong, Pornpimol; Danhauser, Katharina; Dogan, Tunca; Dreo, Johann; Dunham, Ian; Farr, Elias; Fernandez-Torras, Adria; Gyori, Benjamin M.; Hartung, Michael; Hoyt, Charles Tapley; Klein, Christoph; Korcsmaros, Tamas; Maier, Andreas; Mann, Matthias; Ochoa, David; Pareja-Lorente, Elena; Popp, Ferdinand; Preusse, Martin; Probul, Niklas; Schwikowski, Benno; Sen, Buenyamin; Strauss, Maximilian T.; Turei, Denes; Ulusoy, Erva; Waltemath, Dagmar; Wodke, Judith A. H.; Saez-Rodriguez, Julio Share Save
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UniProt: the Universal Protein Knowledgebase in 2023 Bateman, Alex; Martin, Maria-Jesus; Orchard, Sandra; Magrane, Michele; Ahmad, Shadab; Alpi, Emanuele; Bowler-Barnett, Emily H.; Britto, Ramona; Cukura, Austra; Denny, Paul; Dogan, Tunca; Ebenezer, ThankGod; Fan, Jun; Garmiri, Penelope; Gonzales, Leonardo Jose da Costa; Hatton-Ellis, Emma; Hussein, Abdulrahman; Ignatchenko, Alexandr; Insana, Giuseppe; Ishtiaq, Rizwan; Joshi, Vishal; Jyothi, Dushyanth; Kandasaamy, Swaathi; Lock, Antonia; Luciani, Aurelien; Lugaric, Marija; Luo, Jie; Lussi, Yvonne; MacDougall, Alistair; Madeira, Fabio; Mahmoudy, Mahdi; Mishra, Alok; Moulang, Katie; Nightingale, Andrew; Pundir, Sangya; Qi, Guoying; Raj, Shriya; Raposo, Pedro; Rice, Daniel L.; Saidi, Rabie; Santos, Rafael; Speretta, Elena; Stephenson, James; Totoo, Prabhat; Turner, Edward; Tyagi, Nidhi; Vasudev, Preethi; Warner, Kate; Watkins, Xavier; Zellner, Hermann; Bridge, Alan J.; Aimo, Lucila; Argoud-Puy, Ghis-laine; Auchincloss, Andrea H.; Axelsen, Kristian B.; Bansal, Parit; Baratin, Delphine; Neto, Teresa M. Batista; Blatter, Marie-Claude; Bolleman, Jerven T.; Boutet, Emmanuel; Breuza, Lionel; Gil, Blanca Cabrera; Casals-Casas, Cristina; Echioukh, Kamal Chikh; Coudert, Elisabeth; Cuche, Beatrice; de Castro, Edouard; Estreicher, Anne; Famiglietti, Maria L.; Feuermann, Marc; Gasteiger, Elisabeth; Gaudet, Pascale; Gehant, Sebastien; Gerritsen, Vivienne; Gos, Arnaud; Gruaz, Nadine; Hulo, Chantal; Hyka-Nouspikel, Nevila; Jungo, Florence; Kerhornou, Arnaud; Le Mercier, Philippe; Lieberherr, Damien; Masson, Patrick; Morgat, Anne; Muthukrishnan, Venkatesh; Paesano, Salvo; Pedruzzi, Ivo; Pilbout, Sandrine; Pourcel, Lucille; Poux, Sylvain; Pozzato, Monica; Pruess, Manuela; Redaschi, Nicole; Rivoire, Catherine; Sigrist, Christian J. A.; Sonesson, Karin; Arighi, Cecilia N.; Armin-ski, Leslie; Chen, Chuming; Chen, Yongxing; Huang, Hongzhan; Laiho, Kati; McGarvey, Peter; Natale, Darren A.; Ross, Karen; Vinayaka, C. R.; Wang, Qinghua; Wang, Yuqi; Zhang, Jian; Bye-A-Jee, Hema; Zaru, Rossana; Sundaram, Shyamala; Wu, Cathy H. Share Save
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CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations Dogan, Tunca; Atas, Heval; Joshi, Vishal; Atakan, Ahmet; Rifaioglu, Ahmet Sureyya; Nalbat, Esra; Nightingale, Andrew; Saidi, Rabie; Volynkin, Vladimir; Zellner, Hermann; Cetin-Atalay, Rengul; Martin, Maria; Atalay, Volkan Share Save
Crowdsourced mapping of unexplored target space of kinase inhibitors Cichonska, Anna; Ravikumar, Balaguru; Allaway, Robert J.; Wan, Fangping; Park, Sungjoon; Isayev, Olexandr; Li, Shuya; Mason, Michael; Lamb, Andrew; Tanoli, Ziaurrehman; Jeon, Minji; Kim, Sunkyu; Popova, Mariya; Capuzzi, Stephen; Zeng, Jianyang; Dang, Kristen; Koytiger, Gregory; Kang, Jaewoo; Wells, Carrow I.; Willson, Timothy M.; Oprea, Tudor I.; Schlessinger, Avner; Drewry, David H.; Stolovitzky, Gustavo; Wennerberg, Krister; Guinney, Justin; Aittokallio, Tero; Tan, Mehmet; Huang, Chih-Han; Shih, Edward S. C.; Chen, Tsai-Min; Wu, Chih-Hsun; Fang, Wei-Quan; Chen, Jhih-Yu; Hwang, Ming-Jing; Wang, Xiaokang; Ben Guebila, Marouen; Shamsaei, Behrouz; Singh, Sourav; Nguyen, Thin; Karimi, Mostafa; Wu, Di; Wang, Zhangyang; Shen, Yang; Ozturk, Hakime; Ozkirimli, Elif; Ozgur, Arzucan; Lim, Hansaim; Xie, Lei; Kanev, Georgi K.; Kooistra, Albert J.; Westerman, Bart A.; Terzopoulos, Panagiotis; Ntagiantas, Konstantinos; Fotis, Christos; Alexopoulos, Leonidas; Boeckaerts, Dimitri; Stock, Michiel; De Baets, Bernard; Briers, Yves; Luo, Yunan; Hu, Hailin; Peng, Jian; Dogan, Tunca; Rifaioglu, Ahmet S.; Atas, Heval; Atalay, Rengul Cetin; Atalay, Volkan; Martin, Maria J.; Lee, Junhyun; Yun, Seongjun; Kim, Bumsoo; Chang, Buru; Turu, Gabor; Misak, Adam; Szalai, Bence; Hunyady, Laszlo; Lienhard, Matthias; Prasse, Paul; Bachmann, Ivo; Ganzlin, Julia; Barel, Gal; Herwig, Ralf; Orsolic, Davor; Lucic, Bono; Stepanic, Visnja; Smuc, Tomislav Share Save
UniProt: the universal protein knowledgebase in 2021 Bateman, Alex; Martin, Maria-Jesus; Orchard, Sandra; Magrane, Michele; Agivetova, Rahat; Ahmad, Shadab; Alpi, Emanuele; Bowler-Barnett, Emily H.; Britto, Ramona; Bursteinas, Borisas; Bye-A-Jee, Hema; Coetzee, Ray; Cukura, Austra; Da Silva, Alan; Denny, Paul; Dogan, Tunca; Ebenezer, ThankGod; Fan, Jun; Castro, Leyla Garcia; Garmiri, Penelope; Georghiou, George; Gonzales, Leonardo; Hatton-Ellis, Emma; Hussein, Abdulrahman; Ignatchenko, Alexandr; Insana, Giuseppe; Ishtiaq, Rizwan; Jokinen, Petteri; Joshi, Vishal; Jyothi, Dushyanth; Lock, Antonia; Lopez, Rodrigo; Luciani, Aurelien; Luo, Jie; Lussi, Yvonne; Mac-Dougall, Alistair; Madeira, Fabio; Mahmoudy, Mahdi; Menchi, Manuela; Mishra, Alok; Moulang, Katie; Nightingale, Andrew; Oliveira, Carla Susana; Pundir, Sangya; Qi, Guoying; Raj, Shriya; Rice, Daniel; Lopez, Milagros Rodriguez; Saidi, Rabie; Sampson, Joseph; Sawford, Tony; Speretta, Elena; Turner, Edward; Tyagi, Nidhi; Vasudev, Preethi; Volynkin, Vladimir; Warner, Kate; Watkins, Xavier; Zaru, Rossana; Zellner, Hermann; Bridge, Alan; Poux, Sylvain; Redaschi, Nicole; Aimo, Lucila; Argoud-Puy, Ghislaine; Auchincloss, Andrea; Axelsen, Kristian; Bansal, Parit; Baratin, Delphine; Blatter, Marie-Claude; Bolleman, Jerven; Boutet, Emmanuel; Breuza, Lionel; Casals-Casas, Cristina; de Castro, Edouard; Echioukh, Kamal Chikh; Coudert, Elisabeth; Cuche, Beatrice; Doche, Mikael; Dornevil, Dolnide; Estreicher, Anne; Famiglietti, Maria Livia; Feuermann, Marc; Gasteiger, Elisabeth; Gehant, Sebastien; Gerritsen, Vivienne; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; Hyka-Nouspikel, Nevila; Jungo, Florence; Keller, Guillaume; Kerhornou, Arnaud; Lara, Vicente; Le Mercier, Philippe; Lieberherr, Damien; Lombardot, Thierry; Martin, Xavier; Masson, Patrick; Morgat, Anne; Neto, Teresa Batista; Paesano, Salvo; Pedruzzi, Ivo; Pilbout, Sandrine; Pourcel, Lucille; Pozzato, Monica; Pruess, Manuela; Rivoire, Catherine; Sigrist, Christian; Sonesson, Karin; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Verbregue, Laure; Wu, Cathy H.; Arighi, Cecilia N.; Arminski, Leslie; Chen, Chuming; Chen, Yongxing; Garavelli, John S.; Huang, Hongzhan; Laiho, Kati; McGarvey, Peter; Natale, Darren A.; Ross, Karen; Vinayaka, C. R.; Wang, Qinghua; Wang, Yuqi; Yeh, Lai-Su; Zhang, Jian Share Save
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens Zhou, Naihui; Jiang, Yuxiang; Bergquist, Timothy R.; Lee, Alexandra J.; Kacsoh, Balint Z.; Crocker, Alex W.; Lewis, Kimberley A.; Georghiou, George; Nguyen, Huy N.; Hamid, Md Nafiz; Davis, Larry; Dogan, Tunca; Atalay, Volkan; Rifaioglu, Ahmet S.; Dalkiran, Alperen; Atalay, Rengul Cetin; Zhang, Chengxin; Hurto, Rebecca L.; Freddolino, Peter L.; Zhang, Yang; Bhat, Prajwal; Supek, Fran; Fernandez, Jose M.; Gemovic, Branislava; Perovic, Vladimir R.; Davidovic, Radoslav S.; Sumonja, Neven; Veljkovic, Nevena; Asgari, Ehsaneddin; Mofrad, Mohammad R. K.; Profiti, Giuseppe; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita; Boecker, Florian; Schoof, Heiko; Kahanda, Indika; Thurlby, Natalie; McHardy, Alice C.; Renaux, Alexandre; Saidi, Rabie; Gough, Julian; Freitas, Alex A.; Antczak, Magdalena; Fabris, Fabio; Wass, Mark N.; Hou, Jie; Cheng, Jianlin; Wang, Zheng; Romero, Alfonso E.; Paccanaro, Alberto; Yang, Haixuan; Goldberg, Tatyana; Zhao, Chenguang; Holm, Liisa; Toronen, Petri; Medlar, Alan J.; Zosa, Elaine; Borukhov, Itamar; Novikov, Ilya; Wilkins, Angela; Lichtarge, Olivier; Chi, Po-Han; Tseng, Wei-Cheng; Linial, Michal; Rose, Peter W.; Dessimoz, Christophe; Vidulin, Vedrana; Dzeroski, Saso; Sillitoe, Ian; Das, Sayoni; Lees, Jonathan Gill; Jones, David T.; Wan, Cen; Cozzetto, Domenico; Fa, Rui; Torres, Mateo; Vesztrocy, Alex Warwick; Rodriguez, Jose Manuel; Tress, Michael L.; Frasca, Marco; Notaro, Marco; Grossi, Giuliano; Petrini, Alessandro; Re, Matteo; Valentini, Giorgio; Mesiti, Marco; Roche, Daniel B.; Reeb, Jonas; Ritchie, David W.; Aridhi, Sabeur; Alborzi, Seyed Ziaeddin; Devignes, Marie-Dominique; Koo, Da Chen Emily; Bonneau, Richard; Gligorijevic, Vladimir; Barot, Meet; Fang, Hai; Toppo, Stefano; Lavezzo, Enrico; Falda, Marco; Berselli, Michele; Tosatto, Silvio C. E.; Carraro, Marco; Piovesan, Damiano; Rehman, Hafeez Ur; Mao, Qizhong; Zhang, Shanshan; Vucetic, Slobodan; Black, Gage S.; Jo, Dane; Suh, Erica; Dayton, Jonathan B.; Larsen, Dallas J.; Omdahl, Ashton R.; McGuffin, Liam J.; Brackenridge, Danielle A.; Babbitt, Patricia C.; Yunes, Jeffrey M.; Fontana, Paolo; Zhang, Feng; Zhu, Shanfeng; You, Ronghui; Zhang, Zihan; Dai, Suyang; Yao, Shuwei; Tian, Weidong; Cao, Renzhi; Chandler, Caleb; Amezola, Miguel; Johnson, Devon; Chang, Jia-Ming; Liao, Wen-Hung; Liu, Yi-Wei; Pascarelli, Stefano; Frank, Yotam; Hoehndorf, Robert; Kulmanov, Maxat; Boudellioua, Imane; Politano, Gianfranco; Di Carlo, Stefano; Benso, Alfredo; Hakala, Kai; Ginter, Filip; Mehryary, Farrokh; Kaewphan, Suwisa; Bjorne, Jari; Moen, Hans; Tolvanen, Martti E. E.; Salakoski, Tapio; Kihara, Daisuke; Jain, Aashish; Smuc, Tomislav; Altenhoff, Adrian; Ben-Hur, Asa; Rost, Burkhard; Brenner, Steven E.; Orengo, Christine A.; Jeffery, Constance J.; Bosco, Giovanni; Hogan, Deborah A.; Martin, Maria J.; O'Donovan, Claire; Mooney, Sean D.; Greene, Casey S.; Radivojac, Predrag; Friedberg, Iddo Share Save
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