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2022
Li X, Hui S, Mirek ET, Jonsson WO, Anthony TG, Lee WDong, et al. Circulating metabolite homeostasis achieved through mass action. Nat Metab. 2022 ;4(1):141-152.
Pereira TD, Tabris N, Matsliah A, Turner DM, Li J, Ravindranath S, et al. SLEAP: A deep learning system for multi-animal pose tracking. Nat Methods. 2022 ;19(4):486-495.
2021
Zhou J, Troyanskaya OG. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021 ;18(11):1317-1321.
Lovelett RJ, Zhao EM, Lalwani MA, Toettcher JE, Kevrekidis IG, Avalos JL. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol. 2021 ;10(2):219-227.
Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics. 2021 ;37(Suppl_1):i133-i141.
Diegmiller R, Zhang L, Gameiro M, Barr J, Alsous JImran, Schedl P, et al. Mapping parameter spaces of biological switches. PLoS Comput Biol. 2021 ;17(2):e1008711.
Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, et al. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods. 2021 ;18(11):1377-1385.
Covington BC, Seyedsayamdost MR. MetEx, a Metabolomics Explorer Application for Natural Product Discovery. ACS Chem Biol. 2021 ;16(12):2825-2833.
Bass AJ, Storey JD. The optimal discovery procedure for significance analysis of general gene expression studies. Bioinformatics. 2021 ;37(3):367-374.
2020
Tareen A, Wingreen NS, Mukhopadhyay R. Asymmetry between Activators and Deactivators in Functional Protein Networks. Sci Rep. 2020 ;10(1):10131.
Kloosterman AM, Cimermancic P, Elsayed SS, Du C, Hadjithomas M, Donia MS, et al. 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.
Klibaite U, Shaevitz JW. Paired fruit flies synchronize behavior: Uncovering social interactions in Drosophila melanogaster. PLoS Comput Biol. 2020 ;16(10):e1008230.
Stern T, Shvartsman SY, Wieschaus EF. Template-based mapping of dynamic motifs in tissue morphogenesis. PLoS Comput Biol. 2020 ;16(8):e1008049.
M Amin J, Petry S, Yang H, Shaevitz JW. Uniform intensity in multifocal microscopy using a spatial light modulator. PLoS One. 2020 ;15(3):e0230217.
2019
Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, et al. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019 ;15(9):e1008382.
Giovannucci A, Friedrich J, Gunn P, Kalfon J, Brown BL, Koay SAnn, et al. CaImAn an open source tool for scalable calcium imaging data analysis. Elife. 2019 ;8.
Pereira TD, Aldarondo DE, Willmore L, Kislin M, Wang SS-H, Murthy M, et al. Fast animal pose estimation using deep neural networks. Nat Methods. 2019 ;16(1):117-125.
Cabreros I, Storey JD. A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis. Genetics. 2019 ;212(4):1009-1029.
Wang S-W, Bitbol A-F, Wingreen NS. Revealing evolutionary constraints on proteins through sequence analysis. PLoS Comput Biol. 2019 ;15(4):e1007010.
Chen KM, Cofer EM, Zhou J, Troyanskaya OG. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019 ;16(4):315-318.
Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, et al. Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nat Genet. 2019 ;51(6):973-980.
2018
Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018 ;50(8):1171-1179.
Lee Y-S, Wong AK, Tadych A, Hartmann BM, Park CY, DeJesus VA, et al. Interpretation of an individual functional genomics experiment guided by massive public data. Nat Methods. 2018 ;15(12):1049-1052.
2017
Nguyen JP, Linder AN, Plummer GS, Shaevitz JW, Leifer AM. Automatically tracking neurons in a moving and deforming brain. PLoS Comput Biol. 2017 ;13(5):e1005517.
Meshulam L, Gauthier JL, Brody CD, Tank DW, Bialek W. Collective Behavior of Place and Non-place Neurons in the Hippocampal Network. Neuron. 2017 ;96(5):1178-1191.e4.