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Evaluation and optimization of sequence-based gene regulatory deep learning models.
Rafi AM, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Kim D, Shin Y, Kwak IY, Meshcheryakov G, Lando A, Zinkevich A, Kim BC, Lee J, Kang T, Vaishnav ED, Yadollahpour P; Random Promoter DREAM Challenge Consortium; Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer C. Rafi AM, et al. bioRxiv [Preprint]. 2024 Feb 17:2023.04.26.538471. doi: 10.1101/2023.04.26.538471. bioRxiv. 2024. PMID: 38405704 Free PMC article. Preprint.
A Continuously Benchmarked and Crowdsourced Challenge for Rapid Development and Evaluation of Models to Predict COVID-19 Diagnosis and Hospitalization.
Yan Y, Schaffter T, Bergquist T, Yu T, Prosser J, Aydin Z, Jabeer A, Brugere I, Gao J, Chen G, Causey J, Yao Y, Bryson K, Long DR, Jarvik JG, Lee CI, Wilcox A, Guinney J, Mooney S; DREAM Challenge Consortium. Yan Y, et al. JAMA Netw Open. 2021 Oct 1;4(10):e2124946. doi: 10.1001/jamanetworkopen.2021.24946. JAMA Netw Open. 2021. PMID: 34633425 Free PMC article.
Evaluation of crowdsourced mortality prediction models as a framework for assessing artificial intelligence in medicine.
Bergquist T, Schaffter T, Yan Y, Yu T, Prosser J, Gao J, Chen G, Charzewski Ł, Nawalany Z, Brugere I, Retkute R, Prusokas A, Prusokas A, Choi Y, Lee S, Choe J, Lee I, Kim S, Kang J, Mooney SD, Guinney J; Patient Mortality Prediction DREAM Challenge Consortium. Bergquist T, et al. J Am Med Inform Assoc. 2023 Dec 22;31(1):35-44. doi: 10.1093/jamia/ocad159. J Am Med Inform Assoc. 2023. PMID: 37604111
A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection.
Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R; Respiratory Viral DREAM Challenge Consortium; Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK. Fourati S, et al. Nat Commun. 2018 Oct 24;9(1):4418. doi: 10.1038/s41467-018-06735-8. Nat Commun. 2018. PMID: 30356117 Free PMC article.
Developing better digital health measures of Parkinson's disease using free living data and a crowdsourced data analysis challenge.
Sieberts SK, Borzymowski H, Guan Y, Huang Y, Matzner A, Page A, Bar-Gad I, Beaulieu-Jones B, El-Hanani Y, Goschenhofer J, Javidnia M, Keller MS, Li YC, Saqib M, Smith G, Stanescu A, Venuto CS, Zielinski R; BEAT-PD DREAM Challenge Consortium; Jayaraman A, Evers LJW, Foschini L, Mariakakis A, Pandey G, Shawen N, Synder P, Omberg L. Sieberts SK, et al. PLOS Digit Health. 2023 Mar 28;2(3):e0000208. doi: 10.1371/journal.pdig.0000208. eCollection 2023 Mar. PLOS Digit Health. 2023. PMID: 36976789 Free PMC article.