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

Genome Biology

Volumn 17, Issue 1, 2016, Pages

  Jiang, Yuxiang ^a   Oron, Tal Ronnen ^b   Clark, Wyatt T ^c   Bankapur, Asma R ^d   D'Andrea, Daniel ^e   Lepore, Rosalba ^e   Funk, Christopher S ^f   Kahanda, Indika ^g   Verspoor, Karin M ^h,i   Ben Hur, Asa ^g   Koo, Da Chen Emily ^j   Penfold Brown, Duncan ^j,k   Shasha, Dennis ^l   Youngs, Noah ^k,l,m   Bonneau, Richard ^j,l,m   Lin, Alexandra ⁿ   Sahraeian, Sayed M E ⁿ   Martelli, Pier Luigi ^o   Profiti, Giuseppe ^o   Casadio, Rita ^o   Cao, Renzhi ^p   Zhong, Zhaolong ^p   Cheng, Jianlin ^p   Altenhoff, Adrian ^q,r   Skunca, Nives ^q,r   Dessimoz, Christophe ^r,s,bt   Dogan, Tunca ^t   Hakala, Kai ^u   Kaewphan, Suwisa ^u,v   Mehryary, Farrokh ^u   Salakoski, Tapio ^u,v   Ginter, Filip ^u   Fang, Hai ^w   Smithers, Ben ^w   Oates, Matt ^w   Gough, Julian ^w   Törönen, Petri ^x   Koskinen, Patrik ^x   Holm, Liisa ^x,bs   Chen, Ching Tai ^y   Hsu, Wen Lian ^y   Bryson, Kevin ^s   Cozzetto, Domenico ^s   Minneci, Federico ^s   Jones, David T ^s   Chapman, Samuel ^z   Bkc, Dukka ^z   Khan, Ishita K ^aa   Kihara, Daisuke ^aa,br   Ofer, Dan ^ab   Rappoport, Nadav ^ab   Stern, Amos ^ab   Cibrian Uhalte, Elena ^t   Denny, Paul ^s   Foulger, Rebecca E ^s   Hieta, Reija ^t   Legge, Duncan ^t   Lovering, Ruth C ^s   Magrane, Michele ^t   Melidoni, Anna N ^s   Mutowo Meullenet, Prudence ^t   Pichler, Klemens ^t   Shypitsyna, Aleksandra ^t   Li, Biao ^b   Zakeri, Pooya ^ad,ae   ElShal, Sarah ^ad,ae   Tranchevent, Léon Charles ^af,ag,ah   Das, Sayoni ^s   Dawson, Natalie L ^s   Lee, David ^s   Lees, Jonathan G ^s   Sillitoe, Ian ^s   Bhat, Prajwal ^ai   Nepusz, Tamás ^aj   Romero, Alfonso E ^ak   Sasidharan, Rajkumar ^al   Yang, Haixuan ^am   Paccanaro, Alberto ^ak   Gillis, Jesse ^an   Sedeño Cortés, Adriana E ^ao   Pavlidis, Paul ^ap   Feng, Shou ^a   Cejuela, Juan M ^aq   Goldberg, Tatyana ^aq   Hamp, Tobias ^aq   Richter, Lothar ^aq   Salamov, Asaf ^ar   Gabaldon, Toni ^as,at,au   Marcet Houben, Marina ^as,at   Supek, Fran ^as,at,av   Gong, Qingtian ^aw,ax   Ning, Wei ^aw,ax   Zhou, Yuanpeng ^aw,ax   Tian, Weidong ^aw,ax   Falda, Marco ^ay   Fontana, Paolo ^az   Lavezzo, Enrico ^ay   Toppo, Stefano ^ay   Ferrari, Carlo ^ay   Giollo, Manuel ^ay   Piovesan, Damiano ^ay   Tosatto, Silvio C E ^ay   del Pozo, Angela ^ba   Fernández, José M ^bb   Maietta, Paolo ^bb   Valencia, Alfonso ^bb   Tress, Michael L ^bb   Benso, Alfredo ^bc   Di Carlo, Stefano ^bc   Politano, Gianfranco ^bc   Savino, Alessandro ^bc   Rehman, Hafeez Ur ^bd   Re, Matteo ^be   Mesiti, Marco ^be   Valentini, Giorgio ^be   Bargsten, Joachim W ^bf   van Dijk, Aalt D J ^bf   Gemovic, Branislava ^bg   Glisic, Sanja ^bg   Perovic, Vladmir ^bg   Veljkovic, Veljko ^bg   Veljkovic, Nevena ^bg   Almeida e Silva, Danillo C ^bh   Vencio, Ricardo Z N ^bh   Sharan, Malvika ^bi   Vogel, Jörg ^bi   Kansakar, Lakesh ^bj   Zhang, Shanshan ^bj   Vucetic, Slobodan ^bj   Wang, Zheng ^bk   Sternberg, Michael J E ^ac   Wass, Mark N ^bl   Huntley, Rachael P ^t   Martin, Maria J ^t   O'Donovan, Claire ^t   Robinson, Peter N ^bm   Moreau, Yves ^ad   Tramontano, Anna ^e   Babbitt, Patricia C ^bn   Brenner, Steven E ⁿ   Linial, Michal ^ab   Orengo, Christine A ^s   Rost, Burkhard ^aq   Greene, Casey S ^bo   Mooney, Sean D ^bp   Friedberg, Iddo ^d,bq   Radivojac, Predrag ^a   more..

^a INDIANA UNIVERSITY   (United States)

^b BUCK INSTITUTE FOR RESEARCH ON AGING   (United States)

^c YALE UNIVERSITY   (United States)

^d MIAMI UNIVERSITY   (United States)

^e SAPIENZA UNIVERSITY OF ROME   (Italy)

^f UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^g Colorado State University   (United States)

^h UNIVERSITY OF MELBOURNE   (Australia)

ⁱ UNIVERSITY OF MELBOURNE   (Australia)

^j NEW YORK UNIVERSITY   (United States)

^k Media6degrees (M6D)   (United States)

^l POLYTECHNIC UNIVERSITY   (United States)

^m Simons Center for Data Analysis   (United States)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

^o UNIVERSITY OF BOLOGNA   (Italy)

^p University of Missouri   (United States)

^q ETH ZURICH   (Switzerland)

^r SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^s UNIVERSITY COLLEGE LONDON   (United Kingdom)

^t EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^u UNIVERSITY OF TURKU   (Finland)

^v TURKU CENTRE FOR COMPUTER SCIENCE   (Finland)

^w UNIVERSITY OF BRISTOL   (United Kingdom)

^x UNIVERSITY OF HELSINKI   (Finland)

^y INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^z North Carolina Agricultural and Technical State University   (United States)

^aa Purdue University   (United States)

^ab HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^ac IMPERIAL COLLEGE LONDON   (United Kingdom)

^ad UNIVERSITY OF LEUVEN   (Belgium)

^ae IMinds Medical Information Technology Department   (Belgium)

^af CENTRE DE RECHERCHE EN CANCÉROLOGIE DE LYON   (France)

^ag UNIVERSITÉ LYON 1   (France)

^ah CENTRE LÉON BÉRARD   (France)

^ai Cerenode Inc   (United States)

^aj MOLDE UNIVERSITY COLLEGE   (Norway)

^ak UNIVERSITY OF LONDON   (United Kingdom)

^al UNIVERSITY OF CALIFORNIA   (United States)

^am NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^an Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^ao UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^ap UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^aq TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^ar DOE JOINT GENOME INSTITUTE   (United States)

^as CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^at UNIVERSITAT POMPEU FABRA   (Spain)

^au INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^av RUDER BO KOVI INSTITUTE   (Croatia)

^aw FUDAN UNIVERSITY   (China)

^ax CHILDREN S HOSPITAL OF FUDAN UNIVERSITY   (China)

^ay UNIVERSITY OF PADOVA   (Italy)

^az RESEARCH AND INNOVATION CENTRE   (Italy)

^ba HOSPITAL UNIVERSITARIO LA PAZ   (Spain)

^bb Centro Nacional de Investigaciones Oncológicas   (Spain)

^bc POLITECNICO DI TORINO   (Italy)

^bd NATIONAL UNIVERSITY OF COMPUTER AND EMERGING SCIENCES   (Pakistan)

^be UNIVERSITY OF MILAN   (Italy)

^bf WAGENINGEN UNIVERSITY   (Netherlands)

^bg UNIVERSITY OF BELGRADE   (Serbia)

^bh UNIVERSITY OF SÃO PAULO   (Brazil)

^bi UNIVERSITY OF WÜRZBURG   (Germany)

^bj Temple University   (United States)

^bk UNIVERSITY OF SOUTHERN MISSISSIPPI   (United States)

^bl UNIVERSITY OF KENT   (United Kingdom)

^bm CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^bn UNIVERSITY OF CALIFORNIA   (United States)

^bo UNIVERSITY OF PENNSYLVANIA   (United States)

^bp UNIVERSITY OF WASHINGTON   (United States)

^bq IOWA STATE UNIVERSITY   (United States)

^br PURDUE UNIVERSITY   (United States)

^bs UNIVERSITY OF HELSINKI   (Finland)

^bt UNIVERSITY OF LAUSANNE   (Switzerland)

more..

Author keywords

Disease gene prioritization; Protein function prediction

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; AREA UNDER THE CURVE; ARTICLE; CALCULATION; MATHEMATICAL ANALYSIS; ONTOLOGY; PHENOTYPE; PREDICTION; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN TARGETING; RECEIVER OPERATING CHARACTERISTIC; RELIABILITY; SCORING SYSTEM; ALGORITHM; BIOLOGY; CHEMISTRY; GENE ONTOLOGY; GENETICS; HUMAN; MOLECULAR GENETICS; SOFTWARE; STRUCTURE ACTIVITY RELATION;

PROTEIN;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENE ONTOLOGY; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84986207718     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-1037-6     Document Type: Article

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