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dc.contributor.authorZhou, Naihui
dc.contributor.authorJiang, Yuxiang
dc.contributor.authorBergquist, Timothy R
dc.contributor.authorLee, Alexandra J
dc.contributor.authorKacsoh, Balint Z
dc.contributor.authorCrocker, Alex W
dc.contributor.authorLewis, Kimberley A
dc.contributor.authorGeorghiou, George
dc.contributor.authorNguyen, Huy N
dc.contributor.authorHamid, Md Nafiz
dc.contributor.authorDavis, Larry
dc.contributor.authorDogan, Tunca
dc.contributor.authorAtalay, Volkan
dc.contributor.authorRifaioglu, Ahmet S
dc.contributor.authorDalkıran, Alperen
dc.contributor.authorCetin Atalay, Rengul
dc.contributor.authorZhang, Chengxin
dc.contributor.authorHurto, Rebecca L
dc.contributor.authorFreddolino, Peter L
dc.contributor.authorZhang, Yang
dc.contributor.authorBhat, Prajwal
dc.contributor.authorSupek, Fran
dc.contributor.authorFernández, José M
dc.contributor.authorGemovic, Branislava
dc.contributor.authorPerovic, Vladimir R
dc.contributor.authorDavidović, Radoslav S
dc.contributor.authorSumonja, Neven
dc.contributor.authorVeljkovic, Nevena
dc.contributor.authorAsgari, Ehsaneddin
dc.contributor.authorMofrad, Mohammad R K
dc.contributor.authorProfiti, Giuseppe
dc.contributor.authorSavojardo, Castrense
dc.contributor.authorMartelli, Pier Luigi
dc.contributor.authorCasadio, Rita
dc.contributor.authorBoecker, Florian
dc.contributor.authorSchoof, Heiko
dc.contributor.authorKahanda, Indika
dc.contributor.authorThurlby, Natalie
dc.contributor.authorMcHardy, Alice C
dc.contributor.authorRenaux, Alexandre
dc.contributor.authorSaidi, Rabie
dc.contributor.authorGough, Julian
dc.contributor.authorFreitas, Alex A
dc.contributor.authorAntczak, Magdalena
dc.contributor.authorFabris, Fabio
dc.contributor.authorWass, Mark N
dc.contributor.authorHou, Jie
dc.contributor.authorCheng, Jianlin
dc.contributor.authorWang, Zheng
dc.contributor.authorRomero, Alfonso E
dc.contributor.authorPaccanaro, Alberto
dc.contributor.authorYang, Haixuan
dc.contributor.authorGoldberg, Tatyana
dc.contributor.authorZhao, Chenguang
dc.contributor.authorHolm, Liisa
dc.contributor.authorTörönen, Petri
dc.contributor.authorMedlar, Alan J
dc.contributor.authorZosa, Elaine
dc.contributor.authorBorukhov, Itamar
dc.contributor.authorNovikov, Ilya
dc.contributor.authorWilkins, Angela
dc.contributor.authorLichtarge, Olivier
dc.contributor.authorChi, Po-Han
dc.contributor.authorTseng, Wei-Cheng
dc.contributor.authorLinial, Michal
dc.contributor.authorRose, Peter W
dc.contributor.authorDessimoz, Christophe
dc.contributor.authorVidulin, Vedrana
dc.contributor.authorDzeroski, Saso
dc.contributor.authorSillitoe, Ian
dc.contributor.authorDas, Sayoni
dc.contributor.authorLees, Jonathan Gill
dc.contributor.authorJones, David T
dc.contributor.authorWan, Cen
dc.contributor.authorCozzetto, Domenico
dc.contributor.authorFa, Rui
dc.contributor.authorTorres, Mateo
dc.contributor.authorWarwick Vesztrocy, Alex
dc.contributor.authorRodriguez, Jose Manuel
dc.contributor.authorTress, Michael L
dc.contributor.authorFrasca, Marco
dc.contributor.authorNotaro, Marco
dc.contributor.authorGrossi, Giuliano
dc.contributor.authorPetrini, Alessandro
dc.contributor.authorRe, Matteo
dc.contributor.authorValentini, Giorgio
dc.contributor.authorMesiti, Marco
dc.contributor.authorRoche, Daniel B
dc.contributor.authorReeb, Jonas
dc.contributor.authorRitchie, David W
dc.contributor.authorAridhi, Sabeur
dc.contributor.authorAlborzi, Seyed Ziaeddin
dc.contributor.authorDevignes, Marie-Dominique
dc.contributor.authorKoo, Da Chen Emily
dc.contributor.authorBonneau, Richard
dc.contributor.authorGligorijević, Vladimir
dc.contributor.authorBarot, Meet
dc.contributor.authorFang, Hai
dc.contributor.authorToppo, Stefano
dc.contributor.authorLavezzo, Enrico
dc.contributor.authorFalda, Marco
dc.contributor.authorBerselli, Michele
dc.contributor.authorTosatto, Silvio C E
dc.contributor.authorCarraro, Marco
dc.contributor.authorPiovesan, Damiano
dc.contributor.authorUr Rehman, Hafeez
dc.contributor.authorMao, Qizhong
dc.contributor.authorZhang, Shanshan
dc.contributor.authorVucetic, Slobodan
dc.contributor.authorBlack, Gage S
dc.contributor.authorJo, Dane
dc.contributor.authorSuh, Erica
dc.contributor.authorDayton, Jonathan B
dc.contributor.authorLarsen, Dallas J
dc.contributor.authorOmdahl, Ashton R
dc.contributor.authorMcGuffin, Liam J
dc.contributor.authorBrackenridge, Danielle A
dc.contributor.authorBabbitt, Patricia C
dc.contributor.authorYunes, Jeffrey M
dc.contributor.authorFontana, Paolo
dc.contributor.authorZhang, Feng
dc.contributor.authorZhu, Shanfeng
dc.contributor.authorYou, Ronghui
dc.contributor.authorZhang, Zihan
dc.contributor.authorDai, Suyang
dc.contributor.authorYao, Shuwei
dc.contributor.authorTian, Weidong
dc.contributor.authorCao, Renzhi
dc.contributor.authorChandler, Caleb
dc.contributor.authorAmezola, Miguel
dc.contributor.authorJohnson, Devon
dc.contributor.authorChang, Jia-Ming
dc.contributor.authorLiao, Wen-Hung
dc.contributor.authorLiu, Yi-Wei
dc.contributor.authorPascarelli, Stefano
dc.contributor.authorFrank, Yotam
dc.contributor.authorHoehndorf, Robert
dc.contributor.authorKulmanov, Maxat
dc.contributor.authorBoudellioua, Imene
dc.contributor.authorPolitano, Gianfranco
dc.contributor.authorDi Carlo, Stefano
dc.contributor.authorBenso, Alfredo
dc.contributor.authorHakala, Kai
dc.contributor.authorGinter, Filip
dc.contributor.authorMehryary, Farrokh
dc.contributor.authorKaewphan, Suwisa
dc.contributor.authorBjörne, Jari
dc.contributor.authorMoen, Hans
dc.contributor.authorTolvanen, Martti E E
dc.contributor.authorSalakoski, Tapio
dc.contributor.authorKihara, Daisuke
dc.contributor.authorJain, Aashish
dc.contributor.authorŠmuc, Tomislav
dc.contributor.authorAltenhoff, Adrian
dc.contributor.authorBen-Hur, Asa
dc.contributor.authorRost, Burkhard
dc.contributor.authorBrenner, Steven E
dc.contributor.authorOrengo, Christine A
dc.contributor.authorJeffery, Constance J
dc.contributor.authorBosco, Giovanni
dc.contributor.authorHogan, Deborah A
dc.contributor.authorMartin, Maria J
dc.contributor.authorO'Donovan, Claire
dc.contributor.authorMooney, Sean D
dc.contributor.authorGreene, Casey S
dc.contributor.authorRadivojac, Predrag
dc.contributor.authorFriedberg, Iddo
dc.date.accessioned2019-12-05T11:58:55Z
dc.date.available2019-12-05T11:58:55Z
dc.date.issued2019-11-21
dc.identifier.citationZhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., … Hamid, M. N. (2019). The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 20(1). doi:10.1186/s13059-019-1835-8
dc.identifier.doi10.1186/s13059-019-1835-8
dc.identifier.doi10.1101/653105
dc.identifier.urihttp://hdl.handle.net/10754/660434
dc.description.abstractBACKGROUND: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 challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. CONCLUSION:We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.
dc.description.sponsorshipNZ and IF acknowledge the invaluable input from Michael C Gerten and Shatabdi Sen and all members of the Friedberg Lab for the ongoing support for stimulating discussions.
dc.description.sponsorshipThe work of IF was funded, in part, by the National Science Foundation award DBI-1458359. The work of CSG and AJL was funded, in part, by the National Science Foundation award DBI-1458390 and GBMF 4552 from the Gordon and Betty Moore Foundation. The work of DAH and KAL was funded, in part, by the National Science Foundation award DBI-1458390, National Institutes of Health NIGMS P20 GM113132, and the Cystic Fibrosis Foundation CFRDP STANTO19R0. The work of AP, HY, AR, and MT was funded by BBSRC grants BB/K004131/1, BB/F00964X/1 and BB/M025047/1, Consejo Nacional de Ciencia y Tecnología Paraguay (CONACyT) grants 14-INV-088 and PINV15-315, and NSF Advances in BioInformatics grant 1660648. The work of JC was partially supported by an NIH grant (R01GM093123) and two NSF grants (DBI 1759934 and IIS1763246). ACM acknowledges the support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2155 “RESIST” - Project ID 39087428. DK acknowledges the support from the National Institutes of Health (R01GM123055) and the National Science Foundation (DMS1614777, CMMI1825941). PB acknowledges the support from the National Institutes of Health (R01GM60595). GB and BZK acknowledge the support from the National Science Foundation (NSF 1458390) and NIH DP1MH110234. FS was funded by the ERC StG 757700 “HYPER-INSIGHT” and by the Spanish Ministry of Science, Innovation and Universities grant BFU2017-89833-P. FS further acknowledges the funding from the Severo Ochoa award to the IRB Barcelona. TS was funded by the Centre of Excellence project “BioProspecting of Adriatic Sea”, co-financed by the Croatian Government and the European Regional Development Fund (KK.01.1.1.01.0002). The work of SK was funded by ATT Tieto käyttöön grant and Academy of Finland. JB and HM acknowledge the support of the University of Turku, the Academy of Finland and CSC – IT Center for Science Ltd. TB and SM were funded by the NIH awards UL1 TR002319 and U24 TR002306. The work of CZ and ZW was funded by the National Institutes of Health R15GM120650 to ZW and start-up funding from the University of Miami to ZW. The work of PWR was supported by the National Cancer Institute of the National Institutes of Health under Award Number U01CA198942. PR acknowledges NSF grant DBI-1458477. PT acknowledges the support from Helsinki Institute for Life Sciences. The work of AJM was funded by the Academy of Finland (No. 292589). The work of FZ and WT was funded by the National Natural Science Foundation of China (31671367, 31471245, 91631301) and the National Key Research and Development Program of China (2016YFC1000505, 2017YFC0908402]. CS acknowledges the support by the Italian Ministry of Education, University and Research (MIUR) PRIN 2017 project 2017483NH8. SZ is supported by the National Natural Science Foundation of China (No. 61872094 and No. 61572139) and Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01). PLF and RLH were supported by the National Institutes of Health NIH R35-GM128637 and R00-GM097033. JG, DTJ, CW, DC, and RF were supported by the UK Biotechnology and Biological Sciences Research Council (BB/N019431/1, BB/L020505/1, and BB/L002817/1) and Elsevier. The work of YZ and CZ was funded in part by the National Institutes of Health award GM083107, GM116960, and AI134678; the National Science Foundation award DBI1564756; and the Extreme Science and Engineering Discovery Environment (XSEDE) award MCB160101 and MCB160124. The work of BG, VP, RD, NS, and NV was funded by the Ministry of Education, Science and Technological Development of the Republic of Serbia, Project No. 173001. The work of YWL, WHL, and JMC was funded by the Taiwan Ministry of Science and Technology (106-2221-E-004-011-MY2). YWL, WHL, and JMC further acknowledge the support from “the Human Project from Mind, Brain and Learning” of the NCCU Higher Education Sprout Project by the Taiwan Ministry of Education and the National Center for High-performance Computing for computer time and facilities. The work of IK and AB was funded by Montana State University and NSF Advances in Biological Informatics program through grant number 0965768. BR, TG, and JR are supported by the Bavarian Ministry for Education through funding to the TUM. The work of RB, VG, MB, and DCEK was supported by the Simons Foundation, NIH NINDS grant number 1R21NS103831-01 and NSF award number DMR-1420073. CJJ acknowledges the funding from a University of Illinois at Chicago (UIC) Cancer Center award, a UIC College of Liberal Arts and Sciences Faculty Award, and a UIC International Development Award. The work of ML was funded by Yad Hanadiv (grant number 9660 /2019). The work of OL and IN was funded by the National Institute of General Medical Science of the National Institute of Health through GM066099 and GM079656. Research Supporting Plan (PSR) of University of Milan number PSR2018-DIP-010-MFRAS. AWV acknowledges the funding from the BBSRC (CASE studentship BB/M015009/1). CD acknowledges the support from the Swiss National Science Foundation (150654). CO and MJM are supported by the EMBL-European Bioinformatics Institute core funds and the CAFA BBSRC BB/N004876/1. GG is supported by CAFA BBSRC BB/N004876/1. SCET acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 778247 (IDPfun) and from COST Action BM1405 (NGP-net). SEB was supported by NIH/NIGMS grant R01 GM071749. The work of MLT, JMR, and JMF was supported by the National Human Genome Research Institute of the National of Health, grant numbers U41 HG007234. The work of JMF and JMR was also supported by INB Grant (PT17/0009/0001 - ISCIII-SGEFI / ERDF). VA acknowledges the funding from TUBITAK EEEAG-116E930. RCA acknowledges the funding from KanSil 2016K121540. GV acknowledges the funding from Università degli Studi di Milano - Project “Discovering Patterns in Multi-Dimensional Data” and Project “Machine Learning and Big Data Analysis for Bioinformatics”. SZ is supported by the National Natural Science Foundation of China (No. 61872094 and No. 61572139) and Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01). RY and SY are supported by the 111 Project (NO. B18015), the key project of Shanghai Science & Technology (No. 16JC1420402), Shanghai Municipal Science and Technology Major Project (No. 2018SHZDZX01), and ZJLab. ST was supported by project Ribes Network POR-FESR 3S4H (No. TOPP-ALFREVE18-01) and PRID/SID of University of Padova (No. TOPP-SID19-01). CZ and ZW were supported by the NIGMS grant R15GM120650 to ZW and start-up funding from the University of Miami to ZW. The work of MK and RH was supported by the funding from King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. URF/1/3454-01-01 and URF/1/3790-01-01. The work of SDM is funded, in part, by NSF award DBI-1458443.
dc.publisherSpringer Nature
dc.relation.urlhttps://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1835-8
dc.relation.urlhttps://deepblue.lib.umich.edu/bitstream/2027.42/152164/1/13059_2019_Article_1835.pdf
dc.relation.urlhttps://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-019-1835-8
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dc.titleThe CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
dc.typeArticle
dc.contributor.departmentBio-Ontology Research Group (BORG)
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalGenome biology
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionVeterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.
dc.contributor.institutionIndiana University Bloomington, Bloomington, Indiana, USA.
dc.contributor.institutionDepartment of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
dc.contributor.institutionDepartment of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
dc.contributor.institutionGeisel School of Medicine at Dartmouth, Hanover, NH, USA.
dc.contributor.institutionDepartment of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
dc.contributor.institutionEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.
dc.contributor.institutionProgram in Bioinformatics and Computational Biology, Ames, IA, USA.
dc.contributor.institutionDepartment of Computer Engineering, Hacettepe University, Ankara, Turkey.
dc.contributor.institutionDepartment of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey.
dc.contributor.institutionCanSyL, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.
dc.contributor.institutionDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
dc.contributor.institutionDepartment of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
dc.contributor.institutionAchira Labs, Bangalore, India.
dc.contributor.institutionInstitute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
dc.contributor.institutionINB Coordination Unit, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain.
dc.contributor.institutionLaboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia.
dc.contributor.institutionMolecular Cell Biomechanics Laboratory, Departments of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
dc.contributor.institutionDepartments of Bioengineering and Mechanical Engineering, Berkeley, CA, USA.
dc.contributor.institutionBologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
dc.contributor.institutionUniversity of Bonn: INRES Crop Bioinformatics, Bonn, North Rhine-Westphalia, Germany.
dc.contributor.institutionINRES Crop Bioinformatics, University of Bonn, Bonn, Germany.
dc.contributor.institutionGianforte School of Computing, Montana State University, Bozeman, Montana, USA.
dc.contributor.institutionUniversity of Bristol, Computer Science, Bristol, Bristol, United Kingdom.
dc.contributor.institutionComputational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany.
dc.contributor.institutionInteruniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium.
dc.contributor.institutionEuropean Molecular Biolo gy Labora tory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
dc.contributor.institutionMRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
dc.contributor.institutionUniversity of Kent, School of Computing, Canterbury, United Kingdom.
dc.contributor.institutionSchool of Biosciences, University of Kent, Canterbury, Kent, United Kingdom.
dc.contributor.institutionUniversity of Missouri, Computer Science, Columbia, Missouri, USA.
dc.contributor.institutionDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
dc.contributor.institutionUniversity of Miami, Coral Gables, Florida, USA.
dc.contributor.institutionCentre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom.
dc.contributor.institutionSchool of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland.
dc.contributor.institutionDepartment of Informatics, Bioinformatics & Computational Biology-i12, Technische Universitat Munchen, Munich, Germany.
dc.contributor.institutionFaculty for Informatics, Garching, Germany.
dc.contributor.institutionInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland.
dc.contributor.institutionInstitute of Biotechnology, University of Helsinki, Helsinki, Finland.
dc.contributor.institutionCompugen Ltd., Holon, Israel.
dc.contributor.institutionBaylor College of Medicine, Department of Biochemistry and Molecular Biology, Houston, TX, USA.
dc.contributor.institutionBaylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA.
dc.contributor.institutionNational TsingHua University, Hsinchu, Taiwan.
dc.contributor.institutionDepartment of Electrical Engineering in National Tsing Hua University, Hsinchu City, Taiwan.
dc.contributor.institutionThe Hebrew University of Jerusalem, Jerusalem, Israel.
dc.contributor.institutionUniversity of California San Diego, San Diego Supercomputer Center, La Jolla, California, USA.
dc.contributor.institutionDepartment of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
dc.contributor.institutionDepartment of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia.
dc.contributor.institutionJozef Stefan Institute, Ljubljana, Slovenia.
dc.contributor.institutionResearch Department of Structural and Molecular Biology, University College London, London, England.
dc.contributor.institutionResearch Department of Structural and Molecular Biology, University College London, London, United Kingdom.
dc.contributor.institutionThe Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom.
dc.contributor.institutionDepartment of Computer Science, University College London, London, United Kingdom.
dc.contributor.institutionDepartment of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
dc.contributor.institutionCardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
dc.contributor.institutionSpanish National Cancer Research Centre (CNIO), Madrid, Spain.
dc.contributor.institutionUniversità degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy.
dc.contributor.institutionDepartment of Informatics, Bioinformatics and Computational Biology-i12, Technische Universitat Munchen, Munich, Germany.
dc.contributor.institutionUniversity of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France.
dc.contributor.institutionDepartment of Biology, New York University, New York, NY, USA.
dc.contributor.institutionNYU Center for Data Science, New York, 10010, NY, USA.
dc.contributor.institutionCenter for Computational Biology (CCB), Flatiron Institute, Simons Foundation, New York, New York, USA.
dc.contributor.institutionCenter for Data Science, New York University, New York, 10011, NY, USA.
dc.contributor.institutionWellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
dc.contributor.institutionDepartment of Molecular Medicine, University of Padova, Padova, Italy.
dc.contributor.institutionDepartment of Biology, University of Padova, Padova, Italy.
dc.contributor.institutionCNR Institute of Neuroscience, Padova, Italy.
dc.contributor.institutionDepartment of Biomedical Sciences, University of Padua, Padova, Italy.
dc.contributor.institutionDepartment of Computer Science, National University of Computer and Emerging Sciences, Peshawar, Khyber Pakhtoonkhwa, Pakistan.
dc.contributor.institutionDepartment of Computer and Information Sciences, Temple University, Philadelphia, PA, USA.
dc.contributor.institutionDepartment of Biology, Brigham Young University, Provo, UT, USA.
dc.contributor.institutionSchool of Biological Sciences, University of Reading, Reading, England, United Kingdom.
dc.contributor.institutionDepartment of Pharmaceutical Chemistry, San Francisco, CA, USA.
dc.contributor.institutionUC Berkeley - UCSF Graduate Program in Bioengineering, University of California, San Francisco, 94158, CA, USA.
dc.contributor.institutionResearch and Innovation Center, Edmund Mach Foundation, San Michele all'Adige, Italy.
dc.contributor.institutionState Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, Shanghai, China.
dc.contributor.institutionSchool of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.
dc.contributor.institutionState 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.
dc.contributor.institutionDepartment of Computer Science, Pacific Lutheran University, Tacoma, WA, USA.
dc.contributor.institutionDepartment of Computer Science, National Chengchi University, Taipei, Taiwan.
dc.contributor.institutionOkinawa Institute of Science and Technology, Tancha, Okinawa, Japan.
dc.contributor.institutionTel Aviv University, Tel Aviv, Israel.
dc.contributor.institutionControl and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy.
dc.contributor.institutionDepartment of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.
dc.contributor.institutionDepartment of Future Technologies, Faculty of Science and Engineering, University of Turku, Turku, FI-20014, Finland.
dc.contributor.institutionUniversity of Turku, Turku, Finland.
dc.contributor.institutionDepartment of Future Technologies, University of Turku, Turku, Finland.
dc.contributor.institutionDepartment of Biological Sciences, Department of Computer Science, Purdue University, 47907, IN, USA.
dc.contributor.institutionDepartment of Computer Science, Purdue University, West Lafayette, IN, USA.
dc.contributor.institutionDivision of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia.
dc.contributor.institutionDepartment of Computer Science, ETH Zurich, Zurich, Switzerland.
dc.contributor.institutionDepartment of Computer Science, Colorado State University, Fort Collins, CO, USA.
dc.contributor.institutionUniversity of California, Berkeley, CA, USA.
dc.contributor.institutionBiological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.
dc.contributor.institutionDepartment of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
dc.contributor.institutionDepartment of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
dc.contributor.institutionKhoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
kaust.personHoehndorf, Robert
kaust.personKulmanov, Maxat
kaust.personBoudellioua, Imene
kaust.grant.numberURF/1/3454-01-01
kaust.grant.numberURF/1/3790-01-01
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.c.4745834
refterms.dateFOA2019-12-05T12:01:23Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Dataset]</i> <br/> Naihui Zhou, Yuxiang Jiang, Bergquist, T., Lee, A., Balint Kacsoh, Crocker, A., Lewis, K., Georghiou, G., Nguyen, H., Md Nafiz Hamid, Davis, L., Tunca Dogan, Atalay, V., Rifaioglu, A., Dalkıran, A., Rengul Cetin Atalay, Chengxin Zhang, Hurto, R., Freddolino, P., … Friedberg, I. (2019). <i>The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens</i>. figshare. https://doi.org/10.6084/M9.FIGSHARE.C.4745834. DOI: <a href="https://doi.org/10.6084/m9.figshare.c.4745834" >10.6084/m9.figshare.c.4745834</a> Handle: <a href="http://hdl.handle.net/10754/665161" >10754/665161</a></a></li></ul>
kaust.acknowledged.supportUnitOffice of Sponsored Research (OSR)
dc.date.published-online2019-11-19
dc.date.published-print2019-12


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