,
Jain, Shantanu
Bakolitsa, Constantina
Brenner, Steven E.
Radivojac, Predrag
Moult, John
Repo, Susanna
Hoskins, Roger A.
Andreoletti, Gaia
Barsky, Daniel
Chellapan, Ajithavalli
Chu, Hoyin
Dabbiru, Navya
Kollipara, Naveen K.
Ly, Melissa
Neumann, Andrew J.
Pal, Lipika R.
Odell, Eric
Pandey, Gaurav
Peters-Petrulewicz, Robin C.
Srinivasan, Rajgopal
Yee, Stephen F.
Yeleswarapu, Sri Jyothsna
Zuhl, Maya
Adebali, Ogun
Patra, Ayoti
Beer, Michael A.
Hosur, Raghavendra
Peng, Jian
Bernard, Brady M.
Berry, Michael
Dong, Shengcheng
Boyle, Alan P.
Adhikari, Aashish
Chen, Jingqi
Hu, Zhiqiang
Wang, Robert
Wang, Yaqiong
Miller, Maximilian
Wang, Yanran
Bromberg, Yana
Turina, Paola
Capriotti, Emidio
Han, James J.
Ozturk, Kivilcim
Carter, Hannah
Babbi, Giulia
Bovo, Samuele
Di Lena, Pietro
Martelli, Pier Luigi
Savojardo, Castrense
Casadio, Rita
Cline, Melissa S.
De Baets, Greet
Bonache, Sandra
Díez, Orland
Gutiérrez-Enríquez, Sara
Fernández, Alejandro
Montalban, Gemma
Ootes, Lars
Özkan, Selen
Padilla, Natàlia
Riera, Casandra
De la Cruz, Xavier
Diekhans, Mark
Huwe, Peter J.
Wei, Qiong
Xu, Qifang
Dunbrack, Roland L.
Gotea, Valer
Elnitski, Laura
Margolin, Gennady
Fariselli, Piero
Kulakovskiy, Ivan V.
Makeev, Vsevolod J.
Penzar, Dmitry D.
Vorontsov, Ilya E.
Favorov, Alexander V.
Forman, Julia R.
Hasenahuer, Marcia
Fornasari, Maria S.
Parisi, Gustavo
Avsec, Ziga
Çelik, Muhammed H.
Nguyen, Thi Yen Duong
Gagneur, Julien
Shi, Fang-Yuan
Edwards, Matthew D.
Guo, Yuchun
Tian, Kevin
Zeng, Haoyang
Gifford, David K.
Göke, Jonathan
Zaucha, Jan
Gough, Julian
Ritchie, Graham R. S.
Frankish, Adam
Mudge, Jonathan M.
Harrow, Jennifer
Young, Erin L.
Yu, Yao
Huff, Chad D.
Murakami, Katsuhiko
Nagai, Yoko
Imanishi, Tadashi
Mungall, Christopher J.
Jacobsen, Julius O. B.
Kim, Dongsup
Jeong, Chan-Seok
Jones, David T.
Li, Mulin Jun
Guthrie, Violeta Beleva
Bhattacharya, Rohit
Chen, Yun-Ching
Douville, Christopher
Fan, Jean
Kim, Dewey
Masica, David
Niknafs, Noushin
Sengupta, Sohini
Tokheim, Collin
Turner, Tychele N.
Yeo, Hui Ting Grace
Karchin, Rachel
Shin, Sunyoung
Welch, Rene
Keles, Sunduz
Li, Yue
Kellis, Manolis
Corbi-Verge, Carles
Strokach, Alexey V.
Kim, Philip M.
Klein, Teri E.
Mohan, Rahul
Sinnott-Armstrong, Nicholas A.
Wainberg, Michael
Kundaje, Anshul
Gonzaludo, Nina
Mak, Angel C. Y.
Chhibber, Aparna
Lam, Hugo Y. K.
Dahary, Dvir
Fishilevich, Simon
Lancet, Doron
Lee, Insuk
Bachman, Benjamin
Katsonis, Panagiotis
Lua, Rhonald C.
Wilson, Stephen J.
Lichtarge, Olivier
Bhat, Rajendra R.
Sundaram, Laksshman
Viswanath, Vivek
Bellazzi, Riccardo
Nicora, Giovanna
Rizzo, Ettore
Limongelli, Ivan
Mezlini, Aziz M.
Chang, Ray
Kim, Serra
Lai, Carmen
O’Connor, Robert
Topper, Scott
van den Akker, Jeroen
Zhou, Alicia Y.
Zimmer, Anjali D.
Mishne, Gilad
Bergquist, Timothy R.
Breese, Marcus R.
Guerrero, Rafael F.
Jiang, Yuxiang
Kiga, Nikki
Li, Biao
Mort, Matthew
Pagel, Kymberleigh A.
Pejaver, Vikas
Stamboulian, Moses H.
Thusberg, Janita
Mooney, Sean D.
Teerakulkittipong, Nuttinee
Cao, Chen
Kundu, Kunal
Yin, Yizhou
Yu, Chen-Hsin
Kleyman, Michael
Lin, Chiao-Feng
Stackpole, Mary
Mount, Stephen M.
Eraslan, Gökcen
Mueller, Nikola S.
Naito, Tatsuhiko
Rao, Aliz R.
Azaria, Johnathan R.
Brodie, Aharon
Ofran, Yanay
Garg, Aditi
Pal, Debnath
Hawkins-Hooker, Alex
Kenlay, Henry
Reid, John
Mucaki, Eliseos J.
Rogan, Peter K.
Schwarz, Jana M.
Searls, David B.
Lee, Gyu Rie
Seok, Chaok
Krämer, Andreas
Shah, Sohela
Huang, ChengLai V.
Kirsch, Jack F.
Shatsky, Maxim
Cao, Yue
Chen, Haoran
Karimi, Mostafa
Moronfoye, Oluwaseyi
Sun, Yuanfei
Shen, Yang
Shigeta, Ron
Ford, Colby T.
Nodzak, Conor
Uppal, Aneeta
Shi, Xinghua
Joseph, Thomas
Kotte, Sujatha
Rana, Sadhna
Rao, Aditya
Saipradeep, V. G.
Sivadasan, Naveen
Sunderam, Uma
Stanke, Mario
Su, Andrew
Adzhubey, Ivan
Jordan, Daniel M.
Sunyaev, Shamil
Rousseau, Frederic
Schymkowitz, Joost
Van Durme, Joost
Tavtigian, Sean V.
Carraro, Marco
Giollo, Manuel
Tosatto, Silvio C. E.
Adato, Orit
Carmel, Liran
Cohen, Noa E.
Fenesh, Tzila
Holtzer, Tamar
Juven-Gershon, Tamar
Unger, Ron
Niroula, Abhishek
Olatubosun, Ayodeji
Väliaho, Jouni
Yang, Yang
Vihinen, Mauno
Wahl, Mary E.
Chang, Billy
Chong, Ka Chun
Hu, Inchi
Sun, Rui
Wu, William Ka Kei
Xia, Xiaoxuan
Zee, Benny C.
Wang, Maggie H.
Wang, Meng
Wu, Chunlei
Lu, Yutong
Chen, Ken
Yang, Yuedong
Yates, Christopher M.
Kreimer, Anat
Yan, Zhongxia
Yosef, Nir
Zhao, Huying
Wei, Zhipeng
Yao, Zhaomin
Zhou, Fengfeng
Folkman, Lukas
Zhou, Yaoqi
Daneshjou, Roxana
Altman, Russ B.
Inoue, Fumitaka
Ahituv, Nadav
Arkin, Adam P.
Lovisa, Federica
Bonvini, Paolo
Bowdin, Sarah
Gianni, Stefano
Mantuano, Elide
Minicozzi, Velia
Novak, Leonore
Pasquo, Alessandra
Pastore, Annalisa
Petrosino, Maria
Puglisi, Rita
Toto, Angelo
Veneziano, Liana
Chiaraluce, Roberta
Ball, Mad P.
Bobe, Jason R.
Church, George M.
Consalvi, Valerio
Cooper, David N.
Buckley, Bethany A.
Sheridan, Molly B.
Cutting, Garry R.
Scaini, Maria Chiara
Cygan, Kamil J.
Fredericks, Alger M.
Glidden, David T.
Neil, Christopher
Rhine, Christy L.
Fairbrother, William G.
Alontaga, Aileen Y.
Fenton, Aron W.
Matreyek, Kenneth A.
Starita, Lea M.
Fowler, Douglas M.
Löscher, Britt-Sabina
Franke, Andre
Adamson, Scott I.
Graveley, Brenton R.
Gray, Joe W.
Malloy, Mary J.
Kane, John P.
Kousi, Maria
Katsanis, Nicholas
Schubach, Max
Kircher, Martin
Mak, Angel C. Y.
Tang, Paul L. F.
Kwok, Pui-Yan
Lathrop, Richard H.
Clark, Wyatt T.
Yu, Guoying K.
LeBowitz, Jonathan H.
Benedicenti, Francesco
Bettella, Elisa
Bigoni, Stefania
Cesca, Federica
Mammi, Isabella
Marino-Buslje, Cristina
Milani, Donatella
Peron, Angela
Polli, Roberta
Sartori, Stefano
Stanzial, Franco
Toldo, Irene
Turolla, Licia
Aspromonte, Maria C.
Bellini, Mariagrazia
Leonardi, Emanuela
Liu, Xiaoming
Marshall, Christian
McCombie, W. Richard
Elefanti, Lisa
Menin, Chiara
Meyn, M. Stephen
Murgia, Alessandra
Nadeau, Kari C. Y.
Neuhausen, Susan L.
Nussbaum, Robert L.
Pirooznia, Mehdi
Potash, James B.
Dimster-Denk, Dago F.
Rine, Jasper D.
Sanford, Jeremy R.
Snyder, Michael
Cote, Atina G.
Sun, Song
Verby, Marta W.
Weile, Jochen
Roth, Frederick P.
Tewhey, Ryan
Sabeti, Pardis C.
Campagna, Joan
Refaat, Marwan M.
Wojciak, Julianne
Grubb, Soren
Schmitt, Nicole
Shendure, Jay
Spurdle, Amanda B.
Stavropoulos, Dimitri J.
Walton, Nephi A.
Zandi, Peter P.
Ziv, Elad
Burke, Wylie
Chen, Flavia
Carr, Lawrence R.
Martinez, Selena
Paik, Jodi
Harris-Wai, Julie
Yarborough, Mark
Fullerton, Stephanie M.
Koenig, Barbara A.
McInnes, Gregory
Shigaki, Dustin
Chandonia, John-Marc
Furutsuki, Mabel
Kasak, Laura
Yu, Changhua
Chen, Rui
Friedberg, Iddo
Getz, Gad A.
Cong, Qian
Kinch, Lisa N.
Zhang, Jing
Grishin, Nick V.
Voskanian, Alin
Kann, Maricel G.
Tran, Elizabeth
Ioannidis, Nilah M.
Hunter, Jesse M.
Udani, Rupa
Cai, Binghuang
Morgan, Alexander A.
Sokolov, Artem
Stuart, Joshua M.
Minervini, Giovanni
Monzon, Alexander M.
Batzoglou, Serafim
Butte, Atul J.
Greenblatt, Marc S.
Hart, Reece K.
Hernandez, Ryan
Hubbard, Tim J. P.
Kahn, Scott
O’Donnell-Luria, Anne
Ng, Pauline C.
Shon, John
Veltman, Joris
Zook, Justin M.
Funding for this research was provided by:
NHGRI (U24 HG007346)
Article History
Received: 21 January 2023
Accepted: 17 November 2023
First Online: 22 February 2024
Declarations
:
: This work was not Human Subject research. As described in the main text, the CAGI organizational structure includes an Ethics Forum that provides detailed advice on relevant aspects of study design and responsible data governance.
: Principal authors of this paper participated as predictors in many of the CAGI challenges reported. The unified numerical framework employed for reanalysis of the challenges yields results that are consistent with those obtained by the independent assessors of each challenge and in particular selected methods are the highest ranked in the independent assessments. Nevertheless, while every care was taken to mitigate any potential biases in this work, the authors’ participation in CAGI may have affected the presentation of findings, including the selection of challenges, metrics, assessment criteria, and emphasis given on particular results.VBG is a current employee and shareholder of AstraZeneca; RB is a shareholder of enGenome; AJB is a co-founder and consultant to Personalis and NuMedii as well as a consultant to Samsung, Mango Tree Corporation and in the recent past, 10 × Genomics, Helix and Pathway; Carles Corbi-Verge is a computational scientist at the drug discovery company; Cyclica INC and is compensated with income and equity; KC is one of the Regeneron authors and owns options and/or stock of the company; DD is Chief Scientist at Geneyx Genomex Ltd; CD is a consultant to Exact Sciences and is compensated with income and equity; GAG receives research funds from IBM and Pharmacyclics and is an inventor on patent applications related to MSMuTect, MSMutSig, MSIDetect, POLYSOLVER, and SignatureAnalyzer-GPU, and is a founder, consultant, and holds privately held equity in Scorpion Therapeutics; NG is an employee and stockholder at Pacific Biosciences; RH is a paid consultant for Invitae and Scientific Advisory Board member for Variant Bio; AK is a consultant at Illumina Inc., Scientific Advisory Board member of OpenTargets; KK is one of the Regeneron authors and owns options and/or stock of the company; IL is an employer and stockholder of enGenome; MSM owns stock in PhenoTips; GN is an employee of enGenome; AOD-L is a member of the Scientific Advisory Board of Congenica; ER is a shareholder of enGenome; PKR is the founder of CytoGnomix; FPR is a shareholder in Ranomics and SeqWell, an advisor for SeqWell, BioSymetrics, and Constantiam BioSciences, and has received research sponsorships from Biogen, Alnylam, Deep Genomics, and Beam Therapeutics; PCS is the co-founder and shareholder of Sherlock Biosciences, a board member and shareholder of Danaher Corporation, and has filed patents related to this work; PLFT is an employer and stockholder in AccuraGen; RT has filed patents related to this work; MHW is a shareholder of Beth Bioinformatics Co., Ltd.; CMY is an employee and shareholder of Vertex Pharmaceuticals; JZ is an employee of AstraZeneca; SEB receives support at the University of California, Berkeley from a research agreement from TCS.