An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Autor: Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, C., Dukka B K., Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio, del Pozo, Angela, Fernández, José M, Maietta, Paolo, Valencia, Alfonso, Tress, Michael L, Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W, van Dijk, Aalt DJ, Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C, Vencio, Ricardo ZN, Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael JE, Wass, Mark N, Huntley, Rachael P, Martin, Maria J, O'Donovan, Claire, Robinson, Peter N, Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C, Brenner, Steven E, Linial, Michal, Orengo, Christine A, Rost, Burkhard, Greene, Casey S, Mooney, Sean D, Friedberg, Iddo, Radivojac, Predrag

Background: The increasing volume and variety of genotypic and phenotypic data is a major defining characteristic of modern biomedical sciences. At the same time, the limitations in technology for generating data and the inherently stochastic nature

Externí odkaz: http://arxiv.org/abs/1601.00891

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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Autor: 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, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, 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, Törönen, 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, Warwick Vesztrocy, Alex, 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, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico

Publikováno v: Genome biology, vol 20, iss 1

BACKGROUND:The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. RESULTS:Here, we report on the results of the third CAFA chall

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::be043e675e6dbbc59e8700a00783d11e
https://escholarship.org/uc/item/0zt8n2q8

A large-scale evaluation of computational protein function prediction

Autor: Radivojac, Predrag, Clark, Wyatt T, Oron, Tal Ronnen, Schnoes, Alexandra M, Wittkop, Tobias, Sokolov, Artem, Graim, Kiley, Funk, Christopher, Verspoor, Karin, Ben-Hur, Asa, Pandey, Gaurav, Yunes, Jeffrey M, Talwalkar, Ameet S, Repo, Susanna, Souza, Michael L, Piovesan, Damiano, Casadio, Rita, Wang, Zheng, Cheng, Jianlin, Fang, Hai, Gough, Julian, Koskinen, Patrik, Törönen, Petri, Nokso-Koivisto, Jussi, Holm, Liisa, Cozzetto, Domenico, Buchan, Daniel WA, Bryson, Kevin, Jones, David T, Limaye, Bhakti, Inamdar, Harshal, Datta, Avik, Manjari, Sunitha K, Joshi, Rajendra, Chitale, Meghana, Kihara, Daisuke, Lisewski, Andreas M, Erdin, Serkan, Venner, Eric, Lichtarge, Olivier, Rentzsch, Robert, Yang, Haixuan, Romero, Alfonso E, Bhat, Prajwal, Paccanaro, Alberto, Hamp, Tobias, Kaßner, Rebecca, Seemayer, Stefan, Vicedo, Esmeralda, Schaefer, Christian, Achten, Dominik, Auer, Florian, Boehm, Ariane, Braun, Tatjana, Hecht, Maximilian, Heron, Mark, Hönigschmid, Peter, Hopf, Thomas A, Kaufmann, Stefanie, Kiening, Michael, Krompass, Denis, Landerer, Cedric, Mahlich, Yannick, Roos, Manfred, Björne, Jari, Salakoski, Tapio, Wong, Andrew, Shatkay, Hagit, Gatzmann, Fanny, Sommer, Ingolf, Wass, Mark N, Sternberg, Michael JE, Škunca, Nives, Supek, Fran, Bošnjak, Matko, Panov, Panče, Džeroski, Sašo, Šmuc, Tomislav, Kourmpetis, Yiannis AI, van Dijk, Aalt DJ, ter Braak, Cajo JF, Zhou, Yuanpeng, Gong, Qingtian, Dong, Xinran, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Di Camillo, Barbara, Toppo, Stefano, Lan, Liang, Djuric, Nemanja, Guo, Yuhong, Vucetic, Slobodan, Bairoch, Amos, Linial, Michal, Babbitt, Patricia C, Brenner, Steven E, Orengo, Christine, Rost, Burkhard

Publikováno v: Nature methods, vol 10, iss 3

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::4f97cbc72b61030caff5fd3b0d90cf6d
https://escholarship.org/uc/item/67q6v0dj

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Autor: Zhou N; Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.; Program in Bioinformatics and Computational Biology, Ames, IA, USA., Jiang Y; Indiana University Bloomington, Bloomington, Indiana, USA., Bergquist TR; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA., Lee AJ; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA., Kacsoh BZ; Geisel School of Medicine at Dartmouth, Hanover, NH, USA.; Department of Molecular and Systems Biology, Hanover, NH, USA., Crocker AW; Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA., Lewis KA; Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA., Georghiou G; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom., Nguyen HN; Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.; Program in Computer Science, Ames, IA, USA., Hamid MN; Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.; Program in Bioinformatics and Computational Biology, Ames, IA, USA., Davis L; Program in Bioinformatics and Computational Biology, Ames, IA, USA., Dogan T; Department of Computer Engineering, Hacettepe University, Ankara, Turkey.; European Molecular Biolo gy Labora tory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Atalay V; Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey., Rifaioglu AS; Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey.; Department of Computer Engineering, Iskenderun Technical University, Hatay, Turkey., Dalkıran A; Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey., Cetin Atalay R; CanSyL, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey., Zhang C; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA., Hurto RL; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA., Freddolino PL; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA., Zhang Y; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA., Bhat P; Achira Labs, Bangalore, India., Supek F; Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain., Fernández JM; INB Coordination Unit, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain.; (former) INB GN2, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Barcelona, Catalonia, Spain., Gemovic B; Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia., Perovic VR; Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia., Davidović RS; Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia., Sumonja N; Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia., Veljkovic N; Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia., Asgari E; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering, University of California Berkeley, Berkeley, CA, USA.; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Berkeley, CA, USA., Mofrad MRK; Departments of Bioengineering and Mechanical Engineering, Berkeley, CA, USA., Profiti G; Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.; National Research Council, IBIOM, Bologna, Italy., Savojardo C; Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Martelli PL; Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Casadio R; Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Boecker F; University of Bonn: INRES Crop Bioinformatics, Bonn, North Rhine-Westphalia, Germany., Schoof H; INRES Crop Bioinformatics, University of Bonn, Bonn, Germany., Kahanda I; Gianforte School of Computing, Montana State University, Bozeman, Montana, USA., Thurlby N; University of Bristol, Computer Science, Bristol, Bristol, United Kingdom., McHardy AC; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany.; RESIST, DFG Cluster of Excellence 2155, Brunswick, Germany., Renaux A; Interuniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium.; Machine Learning Group, Université libre de Bruxelles, Brussels, Belgium.; Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium., Saidi R; European Molecular Biolo gy Labora tory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Gough J; MRC Laboratory of Molecular Biology, Cambridge, United Kingdom., Freitas AA; University of Kent, School of Computing, Canterbury, United Kingdom., Antczak M; School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom., Fabris F; University of Kent, School of Computing, Canterbury, United Kingdom., Wass MN; School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom., Hou J; University of Missouri, Computer Science, Columbia, Missouri, USA.; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Cheng J; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Wang Z; University of Miami, Coral Gables, Florida, USA., Romero AE; Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom., Paccanaro A; Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom., Yang H; School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland.; Technical University of Munich, Garching, Germany., Goldberg T; Department of Informatics, Bioinformatics & Computational Biology-i12, Technische Universitat Munchen, Munich, Germany., Zhao C; Faculty for Informatics, Garching, Germany.; Department for Bioinformatics and Computational Biology, Garching, Germany.; School of Computing Sciences and Computer Engineering, Hattiesburg, Mississippi, USA., Holm L; Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland., Törönen P; Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland., Medlar AJ; Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland., Zosa E; Institute of Biotechnology, University of Helsinki, Helsinki, Finland., Borukhov I; Compugen Ltd., Holon, Israel., Novikov I; Baylor College of Medicine, Department of Biochemistry and Molecular Biology, Houston, TX, USA., Wilkins A; Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA., Lichtarge O; Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA., Chi PH; National TsingHua University, Hsinchu, Taiwan., Tseng WC; Department of Electrical Engineering in National Tsing Hua University, Hsinchu City, Taiwan., Linial M; The Hebrew University of Jerusalem, Jerusalem, Israel., Rose PW; University of California San Diego, San Diego Supercomputer Center, La Jolla, California, USA., Dessimoz C; Department of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.; Department of Genetics, Evolution & Environment, and Department of Computer Science, University College London, London, UK.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Vidulin V; Department of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia., Dzeroski S; Jozef Stefan Institute, Ljubljana, Slovenia.; Jozef Stefan International Postgraduate School, Ljubljana, Slovenia., Sillitoe I; Research Department of Structural and Molecular Biology, University College London, London, England., Das S; Research Department of Structural and Molecular Biology, University College London, London, United Kingdom., Lees JG; Research Department of Structural and Molecular Biology, University College London, London, United Kingdom.; Department of Health and Life Sciences, Oxford Brookes University, London, UK., Jones DT; The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom.; Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom., Wan C; Department of Computer Science, University College London, London, United Kingdom.; The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom., Cozzetto D; Department of Computer Science, University College London, London, United Kingdom.; The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom., Fa R; Department of Computer Science, University College London, London, United Kingdom.; The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom., Torres M; Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom., Warwick Vesztrocy A; Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom.; SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland., Rodriguez JM; Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain., Tress ML; Spanish National Cancer Research Centre (CNIO), Madrid, Spain., Frasca M; Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy., Notaro M; Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy., Grossi G; Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy., Petrini A; Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy., Re M; Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy., Valentini G; Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy., Mesiti M; Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy.; Institut de Biologie Computationnelle, LIRMM, CNRS-UMR 5506, Universite de Montpellier, Montpellier, France., Roche DB; Department of Informatics, Bioinformatics and Computational Biology-i12, Technische Universitat Munchen, Munich, Germany., Reeb J; Department of Informatics, Bioinformatics and Computational Biology-i12, Technische Universitat Munchen, Munich, Germany., Ritchie DW; University of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France., Aridhi S; University of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France., Alborzi SZ; University of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France.; Inria, Nancy, France., Devignes MD; University of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France.; University of Lorraine, Nancy, Lorraine, France.; Inria, Nancy, France., Koo DCE; Department of Biology, New York University, New York, NY, USA., Bonneau R; NYU Center for Data Science, New York, 10010, NY, USA.; Flatiron Institute, CCB, New York, 10010, NY, USA., Gligorijević V; Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation, New York, New York, USA., Barot M; Center for Data Science, New York University, New York, 10011, NY, USA., Fang H; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Toppo S; Department of Molecular Medicine, University of Padova, Padova, Italy., Lavezzo E; Department of Molecular Medicine, University of Padova, Padova, Italy., Falda M; Department of Biology, University of Padova, Padova, Italy., Berselli M; Department of Molecular Medicine, University of Padova, Padova, Italy., Tosatto SCE; CNR Institute of Neuroscience, Padova, Italy.; Department of Biomedical Sciences, University of Padua, Padova, Italy., Carraro M; Department of Biomedical Sciences, University of Padua, Padova, Italy., Piovesan D; Department of Biomedical Sciences, University of Padua, Padova, Italy., Ur Rehman H; Department of Computer Science, National University of Computer and Emerging Sciences, Peshawar, Khyber Pakhtoonkhwa, Pakistan., Mao Q; Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA.; University of California, Riverside, Philadelphia, PA, USA., Zhang S; Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA., Vucetic S; Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA., Black GS; Department of Biology, Brigham Young University, Provo, UT, USA.; Bioinformatics Research Group, Provo, UT, USA., Jo D; Department of Biology, Brigham Young University, Provo, UT, USA.; Bioinformatics Research Group, Provo, UT, USA., Suh E; Department of Biology, Brigham Young University, Provo, UT, USA., Dayton JB; Department of Biology, Brigham Young University, Provo, UT, USA.; Bioinformatics Research Group, Provo, UT, USA., Larsen DJ; Department of Biology, Brigham Young University, Provo, UT, USA.; Bioinformatics Research Group, Provo, UT, USA., Omdahl AR; Department of Biology, Brigham Young University, Provo, UT, USA.; Bioinformatics Research Group, Provo, UT, USA., McGuffin LJ; School of Biological Sciences, University of Reading, Reading, England, United Kingdom., Brackenridge DA; School of Biological Sciences, University of Reading, Reading, England, United Kingdom., Babbitt PC; Department of Pharmaceutical Chemistry, San Francisco, CA, USA.; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 94158, CA, USA., Yunes JM; UC Berkeley - UCSF Graduate Program in Bioengineering, University of California, San Francisco, 94158, CA, USA.; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 94158, CA, USA., Fontana P; Research and Innovation Center, Edmund Mach Foundation, San Michele all'Adige, Italy., Zhang F; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, Shanghai, China.; Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, Shanghai, China., Zhu S; School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.; Institute of Science and Technology for Brain-Inspired Intelligence and Shanghai Institute of Artificial Intelligence Algorithms, Fudan University, Shanghai, China.; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China., You R; School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.; Institute of Science and Technology for Brain-Inspired Intelligence and Shanghai Institute of Artificial Intelligence Algorithms, Fudan University, Shanghai, China.; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China., Zhang Z; School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China., Dai S; School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China., Yao S; School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.; Institute of Science and Technology for Brain-Inspired Intelligence and Shanghai Institute of Artificial Intelligence Algorithms, Fudan University, Shanghai, China., Tian W; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, Shanghai, China.; Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Cao R; Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA., Chandler C; Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA., Amezola M; Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA., Johnson D; Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA., Chang JM; Department of Computer Science, National Chengchi University, Taipei, Taiwan., Liao WH; Department of Computer Science, National Chengchi University, Taipei, Taiwan., Liu YW; Department of Computer Science, National Chengchi University, Taipei, Taiwan., Pascarelli S; Okinawa Institute of Science and Technology, Tancha, Okinawa, Japan., Frank Y; Tel Aviv University, Tel Aviv, Israel., Hoehndorf R; Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Jeddah, Saudi Arabia., Kulmanov M; Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Jeddah, Saudi Arabia., Boudellioua I; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.; Computer, Electrical and Mathematical Sciences Engineering Division (CEMSE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia., Politano G; Control and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy., Di Carlo S; Control and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy., Benso A; Control and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy., Hakala K; Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.; University of Turku Graduate School (UTUGS), Turku, Finland., Ginter F; Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.; University of Turku, Turku, Finland., Mehryary F; Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.; University of Turku Graduate School (UTUGS), Turku, Finland., Kaewphan S; Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.; University of Turku Graduate School (UTUGS), Turku, Finland.; Turku Centre for Computer Science (TUCS), Turku, Finland., Björne J; Department of Future Technologies, Faculty of Science and Engineering, University of Turku, Turku, FI-20014, Finland.; Turku Centre for Computer Science (TUCS), Agora, Vesilinnantie 3, Turku, FI-20500, Finland., Moen H; University of Turku, Turku, Finland., Tolvanen MEE; Department of Future Technologies, University of Turku, Turku, Finland., Salakoski T; Department of Future Technologies, Faculty of Science and Engineering, University of Turku, Turku, FI-20014, Finland.; Turku Centre for Computer Science (TUCS), Agora, Vesilinnantie 3, Turku, FI-20500, Finland., Kihara D; Department of Biological Sciences, Department of Computer Science, Purdue University, 47907, IN, USA.; Department of Pediatrics, University of Cincinnati, Cincinnati, 45229, OH, USA., Jain A; Department of Computer Science, Purdue University, West Lafayette, IN, USA., Šmuc T; Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia., Altenhoff A; Department of Computer Science, ETH Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Ben-Hur A; Department of Computer Science, Colorado State University, Fort Collins, CO, USA., Rost B; Department of Informatics, Bioinformatics & Computational Biology-i12, Technische Universitat Munchen, Munich, Germany.; Institute for Food and Plant Sciences WZW, Technische Universität München, Freising, Germany., Brenner SE; University of California, Berkeley, CA, USA., Orengo CA; Research Department of Structural and Molecular Biology, University College London, London, United Kingdom., Jeffery CJ; Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA., Bosco G; Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA., Hogan DA; Geisel School of Medicine at Dartmouth, Hanover, NH, USA.; Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA., Martin MJ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom., O'Donovan C; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom., Mooney SD; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA., Greene CS; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA., Radivojac P; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA. predrag@northeastern.edu., Friedberg I; Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA. idoerg@iastate.edu.

Publikováno v: Genome biology [Genome Biol] 2019 Nov 19; Vol. 20 (1), pp. 244. Date of Electronic Publication: 2019 Nov 19.