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A
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.
Kang YGwi, Lee JTaek, Kang JYeal, Kim GHye, Kim TKyun. Analysis of Longitudinal Outcome Data with Missing Values in Total Knee Arthroplasty. J Arthroplasty. 2016 ;31(1):81-6.
Zhou J, Troyanskaya OG. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021 ;18(11):1317-1321.
Tareen A, Wingreen NS, Mukhopadhyay R. Asymmetry between Activators and Deactivators in Functional Protein Networks. Sci Rep. 2020 ;10(1):10131.
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.
B
Ochoa A, Storey JD, Llinás M, Singh M. Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PLoS Comput Biol. 2015 ;11(11):e1004509.
Nguyen JP, Bratton BP, Shaevitz JW. Biophysical Measurements of Bacterial Cell Shape. Methods Mol Biol. 2016 ;1440:227-45.
C
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.
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.
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.
D
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.
Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017 ;33(16):2471-2478.
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.
E
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.
F
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.
Machens CK, Romo R, Brody CD. Flexible control of mutual inhibition: a neural model of two-interval discrimination. Science. 2005 ;307(5712):1121-4.
Segev R, Puchalla J, Berry MJ. Functional organization of ganglion cells in the salamander retina. J Neurophysiol. 2006 ;95(4):2277-92.
I
Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics. 2021 ;37(Suppl_1):i133-i141.
Bitbol A-F, Dwyer RS, Colwell LJ, Wingreen NS. Inferring interaction partners from protein sequences. Proc Natl Acad Sci U S A. 2016 ;113(43):12180-12185.
Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, et al. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 2015 ;43(3):605-14.
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.
M
Marre O, Amodei D, Deshmukh N, Sadeghi K, Soo F, Holy TE, et al. Mapping a complete neural population in the retina. J Neurosci. 2012 ;32(43):14859-73.
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.
Balasubramanian V, Kimber D, Berry MJ. Metabolically efficient information processing. Neural Comput. 2001 ;13(4):799-815.