1.Qin Y, Kernan K, Fan Z, Park H-J, Kim S, Canna S, Kellum J, Berg R, Wessel D, Pollack M, Meert K, Hall M, Newth C, Lin J, Doctor A, Shanley T, Cornell T, Harrison R, Zuppa A, Banks R, Reeder R, Holubkov R, Notterman D, Dean M, Carcillo J. Machine learning derivation of four computable 24-h pediatric sepsis phenotypes to facilitate enrollment in early personalized anti-inflammatory clinical trials. Crit Care. 2022;26(1):128. PMCID: PMC9077858 Reference Link
1.Metsky H, Welch N, Pillai P, Haradhvala N, Rumker L, Mantena S, Zhang Y, Yang D, Ackerman C, Weller J, Blainey P, Myhrvold C, Mitzenmacher M, Sabeti P. Designing sensitive viral diagnostics with machine learning. Nat Biotechnol. 2022;40(7):1123–1131. PMCID: PMC9287178 Reference Link
1.Pereira T, Tabris N, Matsliah A, Turner D, Li J, Ravindranath S, Papadoyannis E, Normand E, Deutsch D, Wang Y, McKenzie-Smith G, Mitelut C, Castro M, D’Uva J, Kislin M, Sanes D, Kocher S, Wang S, Falkner A, Shaevitz J, Murthy M. SLEAP: A deep learning system for multi-animal pose tracking. Nat Methods. 2022;19(4):486–495. PMCID: PMC9007740 Reference Link
1.Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948 Reference Link
1.Sohrabi S, Mor D, Kaletsky R, Keyes W, Murphy C. High-throughput behavioral screen in C. elegans reveals Parkinson’s disease drug candidates. Commun Biol. 2021;4(1):203. PMCID: PMC7884385 Reference Link
1.Wong A, Sealfon R, Theesfeld C, Troyanskaya O. Decoding disease: from genomes to networks to phenotypes. Nat Rev Genet. 2021;22(12):774–790. PMCID: 6786975 Reference Link
1.Koblan L, Arbab M, Shen M, Hussmann J, Anzalone A, Doman J, Newby G, Yang D, Mok B, Replogle J, Xu A, Sisley T, Weissman J, Adamson B, Liu D. Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning. Nat Biotechnol. 2021;39(11):1414–1425. PMCID: PMC8985520 Reference Link
1.Kloosterman A, Cimermancic P, Elsayed S, Du C, Hadjithomas M, Donia M, Fischbach M, van Wezel G, Medema M. Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides. PLoS Biol. 2020;18(12):e3001026. PMCID: PMC7794033 Reference Link
1.Hoshino A, Kim H, Bojmar L, Gyan K, Cioffi M, Hernandez J, Zambirinis C, Rodrigues G, Molina H, Heissel S, Mark M, Steiner L, Benito-Martin A, Lucotti S, Di Giannatale A, Offer K, Nakajima M, Williams C, Nogués L, Vatter F, Hashimoto A, Davies A, Freitas D, Kenific C, Ararso Y, Buehring W, Lauritzen P, Ogitani Y, Sugiura K, Takahashi N, Alečković M, Bailey K, Jolissant J, Wang H, Harris A, Schaeffer M, García-Santos G, Posner Z, Balachandran V, Khakoo Y, Raju P, Scherz A, Sagi I, Scherz-Shouval R, Yarden Y, Oren M, Malladi M, Petriccione M, De Braganca K, Donzelli M, Fischer C, Vitolano S, Wright G, Ganshaw L, Marrano M, Ahmed A, DeStefano J, Danzer E, Roehrl M, Lacayo N, Vincent T, Weiser M, Brady M, Meyers P, Wexler L, Ambati S, Chou A, Slotkin E, Modak S, Roberts S, Basu E, Diolaiti D, Krantz B, Cardoso F, Simpson A, Berger M, Rudin C, Simeone D, Jain M, Ghajar C, Batra S, Stanger B, Bui J, Brown K, Rajasekhar V, Healey J, de Sousa M, Kramer K, Sheth S, Baisch J, Pascual V, Heaton T, La Quaglia M, Pisapia D, Schwartz R, Zhang H, Liu Y, Shukla A, Blavier L, DeClerck Y, LaBarge M, Bissell M, Caffrey T, Grandgenett P, Hollingsworth M, Bromberg J, Costa-Silva B, Peinado H, Kang Y, Garcia B, O’Reilly E, Kelsen D, Trippett T, Jones D, Matei I, Jarnagin W, Lyden D. Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers. Cell. 2020;182(4):1044–1061.e18. PMCID: PMC7522766 Reference Link
1.Roussarie J-P, Yao V, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, Kasturia S, Albornoz C, Wang W, Schmidt E, Dannenfelser R, Tadych A, Brichta L, Barnea-Cramer A, Heintz N, Hof P, Heiman M, Dolinski K, Flajolet M, Troyanskaya O, Greengard P. Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis. Neuron. 2020;107(5):821–835.e12. PMCID: PMC7580783 Reference Link
1.Sealfon R, Mariani L, Kretzler M, Troyanskaya O. Machine learning, the kidney, and genotype-phenotype analysis. Kidney Int. 2020;97(6):1141–1149. PMCID: PMC8048707 Reference Link
1.Wang R, Zheng J, Shao X, Ishii Y, Roy A, Bello A, Lee R, Zhang J, Wind-Rotolo M, Feng Y. Development of a prognostic composite cytokine signature based on the correlation with nivolumab clearance: translational PK/PD analysis in patients with renal cell carcinoma. J Immunother Cancer. 2019;7(1):348. PMCID: PMC6907258 Reference Link
1.Zhou J, Schor I, Yao V, Theesfeld C, Marco-Ferreres R, Tadych A, Furlong E, Troyanskaya O. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019;15(9):e1008382. PMCID: PMC6779412 Reference Link
1.Lee Y-S, Krishnan A, Oughtred R, Rust J, Chang C, Ryu J, Kristensen V, Dolinski K, Theesfeld C, Troyanskaya O. A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. Cell Syst. 2019;8(2):152–162.e6. PMCID: PMC7374759 Reference Link
1.Bratton B, Shaevitz J, Gitai Z, Morgenstein R. MreB polymers and curvature localization are enhanced by RodZ and predict E. coli’s cylindrical uniformity. Nat Commun. 2018;9(1):2797. PMCID: PMC6052060 Reference Link
1.Klibaite U, Berman G, Cande J, Stern D, Shaevitz J. An unsupervised method for quantifying the behavior of paired animals. Phys Biol. 2017;14(1):015006. PMCID: PMC5414632 Reference Link