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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.
Clark KA, Bushin LB, Seyedsayamdost MR. Aliphatic Ether Bond Formation Expands the Scope of Radical SAM Enzymes in Natural Product Biosynthesis. J Am Chem Soc. 2019 ;141(27):10610-10615.
van Kessel JC, Ulrich LE, Zhulin IB, Bassler BL. Analysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi. mBio. 2013 ;4(4).
Zhou J, Troyanskaya OG. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021 ;18(11):1317-1321.
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.
Moon K, Xu F, Zhang C, Seyedsayamdost MR. Bioactivity-HiTES Unveils Cryptic Antibiotics Encoded in Actinomycete Bacteria. ACS Chem Biol. 2019 ;14(4):767-774.
Sigoillot FD, Lyman S, Huckins JF, Adamson B, Chung E, Quattrochi B, et al. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat Methods. 2012 ;9(4):363-6.
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.
Bushin LB, Clark KA, Pelczer I, Seyedsayamdost MR. Charting an Unexplored Streptococcal Biosynthetic Landscape Reveals a Unique Peptide Cyclization Motif. J Am Chem Soc. 2018 ;140(50):17674-17684.
King SB, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol. 2021 ;17(11):e1009560.
Misra M, Audoly B, Shvartsman SY. Complex structures from patterned cell sheets. Philos Trans R Soc Lond B Biol Sci. 2017 ;372(1720).
D
Donnelly AE, Murphy GS, Digianantonio KM, Hecht MH. A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Nat Chem Biol. 2018 ;14(3):253-255.
Wühr M, Freeman RM, Presler M, Horb ME, Peshkin L, Gygi S, et al.. Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Curr Biol. 2014 ;24(13):1467-1475.
Wang R, Zheng J, Shao X, Ishii Y, Roy A, Bello A, et al. 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.
Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017 ;33(16):2471-2478.
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.
G
Wong AK, Krishnan A, Troyanskaya OG. GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Res. 2018 ;46(W1):W65-W70.
H
da Silveira RAzeredo, Berry MJ. High-fidelity coding with correlated neurons. PLoS Comput Biol. 2014 ;10(11):e1003970.
Ashford P, Hernandez A, Greco TMichael, Buch A, Sodeik B, Cristea IMihaela, et al. HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. Mol Cell Proteomics. 2016 ;15(9):2939-53.
I
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.
K
Adolfsen KJ, Brynildsen MP. A Kinetic Platform to Determine the Fate of Hydrogen Peroxide in Escherichia coli. PLoS Comput Biol. 2015 ;11(11):e1004562.
L
Toettcher JE, Gong D, Lim WA, Weiner OD. Light-based feedback for controlling intracellular signaling dynamics. Nat Methods. 2011 ;8(10):837-9.
Cabreros I, Storey JD. A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis. Genetics. 2019 ;212(4):1009-1029.
M
Sealfon RSG, Mariani LH, Kretzler M, Troyanskaya OG. Machine learning, the kidney, and genotype-phenotype analysis. Kidney Int. 2020 ;97(6):1141-1149.
Covington BC, Seyedsayamdost MR. MetEx, a Metabolomics Explorer Application for Natural Product Discovery. ACS Chem Biol. 2021 ;16(12):2825-2833.