Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
Naihui Zhou, Huy N. Nguyen, Md Nafiz Hamid & Iddo Friedberg
Program in Bioinformatics and Computational Biology, Ames, IA, USA
Naihui Zhou, Md Nafiz Hamid & Larry Davis
Indiana University Bloomington, Bloomington, Indiana, USA
Yuxiang Jiang
Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
Timothy R. Bergquist & Sean D. Mooney
Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
Alexandra J. Lee
Geisel School of Medicine at Dartmouth, Hanover, NH, USA
Balint Z. Kacsoh & Deborah A. Hogan
Department of Molecular and Systems Biology, Hanover, NH, USA
Balint Z. Kacsoh
Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
Alex W. Crocker, Kimberley A. Lewis & Deborah A. Hogan
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
George Georghiou, Maria J. Martin & Claire O’Donovan
Program in Computer Science, Ames, IA, USA
Huy N. Nguyen
Department of Computer Engineering, Hacettepe University, Ankara, Turkey
Tunca Dogan
Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey
Volkan Atalay, Ahmet S. Rifaioglu & Alperen Dalkıran
Department of Computer Engineering, Iskenderun Technical University, Hatay, Turkey
Ahmet S. Rifaioglu
CanSyL, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
Rengul Cetin Atalay
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
Chengxin Zhang, Peter L. Freddolino & Yang Zhang
Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
Rebecca L. Hurto, Peter L. Freddolino & Yang Zhang
Achira Labs, Bangalore, India
Prajwal Bhat
Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
Fran Supek
Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
Fran Supek
INB Coordination Unit, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
José M. Fernández
(former) INB GN2, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Barcelona, Catalonia, Spain
José M. Fernández
Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja & Nevena Veljkovic
Molecular Cell Biomechanics Laboratory, Departments of Bioengineering, University of California Berkeley, Berkeley, CA, USA
Ehsaneddin Asgari
Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Berkeley, CA, USA
Ehsaneddin Asgari
Departments of Bioengineering and Mechanical Engineering, Berkeley, CA, USA
Mohammad R.K. Mofrad
Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli & Rita Casadio
National Research Council, IBIOM, Bologna, Italy
Giuseppe Profiti
University of Bonn: INRES Crop Bioinformatics, Bonn, North Rhine-Westphalia, Germany
Florian Boecker
INRES Crop Bioinformatics, University of Bonn, Bonn, Germany
Heiko Schoof
Gianforte School of Computing, Montana State University, Bozeman, Montana, USA
Indika Kahanda
University of Bristol, Computer Science, Bristol, Bristol, United Kingdom
Natalie Thurlby
Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany
Alice C. McHardy
RESIST, DFG Cluster of Excellence 2155, Brunswick, Germany
Alice C. McHardy
Interuniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
Alexandre Renaux
Machine Learning Group, Université libre de Bruxelles, Brussels, Belgium
Alexandre Renaux
Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
Alexandre Renaux
European Molecular Biolo gy Labora tory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
Tunca Dogan & Rabie Saidi
MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
Julian Gough
University of Kent, School of Computing, Canterbury, United Kingdom
Alex A. Freitas & Fabio Fabris
School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
Magdalena Antczak & Mark N. Wass
University of Missouri, Computer Science, Columbia, Missouri, USA
Jie Hou
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
Jie Hou & Jianlin Cheng
University of Miami, Coral Gables, Florida, USA
Zheng Wang
Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom
Alfonso E. Romero, Alberto Paccanaro & Mateo Torres
School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland
Haixuan Yang
Technical University of Munich, Garching, Germany
Haixuan Yang
Faculty for Informatics, Garching, Germany
Chenguang Zhao
Department for Bioinformatics and Computational Biology, Garching, Germany
Chenguang Zhao
School of Computing Sciences and Computer Engineering, Hattiesburg, Mississippi, USA
Chenguang Zhao
Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland
Liisa Holm, Petri Törönen & Alan J. Medlar
Institute of Biotechnology, University of Helsinki, Helsinki, Finland
Elaine Zosa
Compugen Ltd., Holon, Israel
Itamar Borukhov
Baylor College of Medicine, Department of Biochemistry and Molecular Biology, Houston, TX, USA
Ilya Novikov
Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA
Angela Wilkins & Olivier Lichtarge
National TsingHua University, Hsinchu, Taiwan
Po-Han Chi
Department of Electrical Engineering in National Tsing Hua University, Hsinchu City, Taiwan
Wei-Cheng Tseng
The Hebrew University of Jerusalem, Jerusalem, Israel
Michal Linial
University of California San Diego, San Diego Supercomputer Center, La Jolla, California, USA
Peter W. Rose
Department of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
Christophe Dessimoz
Department of Genetics, Evolution & Environment, and Department of Computer Science, University College London, London, UK
Christophe Dessimoz
Swiss Institute of Bioinformatics, Lausanne, Switzerland
Christophe Dessimoz
Department of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia
Vedrana Vidulin
Jozef Stefan Institute, Ljubljana, Slovenia
Saso Dzeroski
Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
Saso Dzeroski
Research Department of Structural and Molecular Biology, University College London, London, England
Ian Sillitoe
Research Department of Structural and Molecular Biology, University College London, London, United Kingdom
Sayoni Das, Jonathan Gill Lees & Christine A. Orengo
Department of Health and Life Sciences, Oxford Brookes University, London, UK
Jonathan Gill Lees
Department of Computer Science, University College London, London, United Kingdom
Cen Wan, Domenico Cozzetto & Rui Fa
The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom
David T. Jones, Cen Wan, Domenico Cozzetto & Rui Fa
Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom
David T. Jones & Alex Warwick Vesztrocy
SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
Alex Warwick Vesztrocy
Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
Jose Manuel Rodriguez
Spanish National Cancer Research Centre (CNIO), Madrid, Spain
Michael L. Tress
Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy
Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini & Marco Mesiti
Institut de Biologie Computationnelle, LIRMM, CNRS-UMR 5506, Universite de Montpellier, Montpellier, France
Marco Mesiti
Department of Informatics, Bioinformatics and Computational Biology—i12, Technische Universitat Munchen, Munich, Germany
Daniel B. Roche & Jonas Reeb
University of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France
David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi & Marie-Dominique Devignes
University of Lorraine, Nancy, Lorraine, France
Marie-Dominique Devignes
Inria, Nancy, France
Seyed Ziaeddin Alborzi & Marie-Dominique Devignes
Department of Biology, New York University, New York, NY, USA
Da Chen Emily Koo
NYU Center for Data Science, New York, 10010, NY, USA
Richard Bonneau
Flatiron Institute, CCB, New York, 10010, NY, USA
Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation, New York, New York, USA
Vladimir Gligorijević
Center for Data Science, New York University, New York, 10011, NY, USA
Meet Barot
Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
Hai Fang
Department of Molecular Medicine, University of Padova, Padova, Italy
Stefano Toppo, Enrico Lavezzo & Michele Berselli
Department of Biology, University of Padova, Padova, Italy
Marco Falda
CNR Institute of Neuroscience, Padova, Italy
Silvio C.E. Tosatto
Department of Biomedical Sciences, University of Padua, Padova, Italy
Silvio C.E. Tosatto, Marco Carraro & Damiano Piovesan
Department of Computer Science, National University of Computer and Emerging Sciences, Peshawar, Khyber Pakhtoonkhwa, Pakistan
Hafeez Ur Rehman
Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
Qizhong Mao, Shanshan Zhang & Slobodan Vucetic
University of California, Riverside, Philadelphia, PA, USA
Qizhong Mao
Department of Biology, Brigham Young University, Provo, UT, USA
Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen & Ashton R. Omdahl
Bioinformatics Research Group, Provo, UT, USA
Gage S. Black, Dane Jo, Jonathan B. Dayton, Dallas J. Larsen & Ashton R. Omdahl
School of Biological Sciences, University of Reading, Reading, England, United Kingdom
Liam J. McGuffin & Danielle A. Brackenridge
Department of Pharmaceutical Chemistry, San Francisco, CA, USA
Patricia C. Babbitt
UC Berkeley - UCSF Graduate Program in Bioengineering, University of California, San Francisco, 94158, CA, USA
Jeffrey M. Yunes
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 94158, CA, USA
Patricia C. Babbitt & Jeffrey M. Yunes
Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy
Paolo Fontana
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, Shanghai, China
Feng Zhang
Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, Shanghai, China
Feng Zhang
School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China
Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai & Shuwei Yao
Institute of Science and Technology for Brain-Inspired Intelligence and Shanghai Institute of Artificial Intelligence Algorithms, Fudan University, Shanghai, China
Shanfeng Zhu, Ronghui You & Shuwei Yao
Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
Shanfeng Zhu, Ronghui You, Zihan Zhang & Suyang Dai
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
Weidong Tian
Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
Weidong Tian
Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
Renzhi Cao, Caleb Chandler, Miguel Amezola & Devon Johnson
Department of Computer Science, National Chengchi University, Taipei, Taiwan
Jia-Ming Chang, Wen-Hung Liao & Yi-Wei Liu
Okinawa Institute of Science and Technology, Tancha, Okinawa, Japan
Stefano Pascarelli
Tel Aviv University, Tel Aviv, Israel
Yotam Frank
Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Jeddah, Saudi Arabia
Robert Hoehndorf & Maxat Kulmanov
Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Imane Boudellioua
Computer, Electrical and Mathematical Sciences Engineering Division (CEMSE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Imane Boudellioua
Control and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy
Gianfranco Politano, Stefano Di Carlo & Alfredo Benso
Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland
Kai Hakala, Filip Ginter, Farrokh Mehryary & Suwisa Kaewphan
University of Turku Graduate School (UTUGS), Turku, Finland
Kai Hakala, Farrokh Mehryary & Suwisa Kaewphan
University of Turku, Turku, Finland
Filip Ginter & Hans Moen
Turku Centre for Computer Science (TUCS), Turku, Finland
Suwisa Kaewphan
Department of Future Technologies, Faculty of Science and Engineering, University of Turku, Turku, FI-20014, Finland
Jari Björne & Tapio Salakoski
Turku Centre for Computer Science (TUCS), Agora, Vesilinnantie 3, Turku, FI-20500, Finland
Jari Björne & Tapio Salakoski
Department of Future Technologies, University of Turku, Turku, Finland
Martti E.E. Tolvanen
Department of Biological Sciences, Department of Computer Science, Purdue University, 47907, IN, USA
Daisuke Kihara
Department of Pediatrics, University of Cincinnati, Cincinnati, 45229, OH, USA
Daisuke Kihara
Department of Computer Science, Purdue University, West Lafayette, IN, USA
Aashish Jain
Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia
Tomislav Šmuc
Department of Computer Science, ETH Zurich, Zurich, Switzerland
Adrian Altenhoff
SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
Adrian Altenhoff
Department of Computer Science, Colorado State University, Fort Collins, CO, USA
Asa Ben-Hur
Department of Informatics, Bioinformatics & Computational Biology—i12, Technische Universitat Munchen, Munich, Germany
Tatyana Goldberg & Burkhard Rost
Institute for Food and Plant Sciences WZW, Technische Universität München, Freising, Germany
Burkhard Rost
University of California, Berkeley, CA, USA
Steven E. Brenner
Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
Constance J. Jeffery
Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
Giovanni Bosco
Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
Casey S. Greene
Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
Casey S. Greene
Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
Predrag Radivojac
The experiment was designed by IF, PR, CSG, SDM, COD, MJM, and NZ. NZ, YJ, MNH, HNN, AJL, and LD performed the computational analyses. NZ, SDM, and TM were responsible for managing the participants’ submissions to the CAFA challenge. KAL, AWC, and DAH performed the experimental work in C. albicans and P. aeruginosa. BZK and GB performed the experimental work in D. melanogaster. CJJ, MJM, COD, and GG provided the novel biocurated data for the benchmarks and incorporated data into UniprotKB. All other co-authors developed the computational function prediction methods participating in the challenge, performed the computational protein function predictions, and submitted the results for analysis in CAFA3. NZ, IF, CSG, DAH, and PR wrote the manuscript. All authors have read and approved the final manuscript.