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2022
Nollmann M, Bennabi I, Götz M, Gregor T. The Impact of Space and Time on the Functional Output of the Genome. Cold Spring Harb Perspect Biol. 2022 ;14(4).
Do T, Thokkadam A, Leach R, A Link J. Phenotype-Guided Comparative Genomics Identifies the Complete Transport Pathway of the Antimicrobial Lasso Peptide Ubonodin in . ACS Chem Biol. 2022 ;17(8):2332-2343.
2021
King SB, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol. 2021 ;17(11):e1009560.
Chen X, Robinson DG, Storey JD. The functional false discovery rate with applications to genomics. Biostatistics. 2021 ;22(1):68-81.
Hussmann JA, Ling J, Ravisankar P, Yan J, Cirincione A, Xu A, et al. Mapping the genetic landscape of DNA double-strand break repair. Cell. 2021 ;184(22):5653-5669.e25.
2020
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.
Richter F, Morton SU, Kim SWon, Kitaygorodsky A, Wasson LK, Chen KM, et al. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nat Genet. 2020 ;52(8):769-777.
Kobren SNadimpalli, Chazelle B, Singh M. PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. Cell Syst. 2020 ;11(1):63-74.e7.
2019
Lee Y-S, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, et al. A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. Cell Syst. 2019 ;8(2):152-162.e6.
Li X, Patena W, Fauser F, Jinkerson RE, Saroussi S, Meyer MT, et al. A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. Nat Genet. 2019 ;51(4):627-635.
Arey RN, Kaletsky R, Murphy CT. Nervous system-wide profiling of presynaptic mRNAs reveals regulators of associative memory. Sci Rep. 2019 ;9(1):20314.
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
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.
Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature. 2018 ;563(7732):501-507.
Gong Y, Cao R, Ding G, Hong S, Zhou W, Lu W, et al. Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle. Mol Cell Endocrinol. 2018 ;471:22-32.
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
Przytycki PF, Singh M. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes. Genome Med. 2017 ;9(1):79.
Liszczak GP, Brown ZZ, Kim SH, Oslund RC, David Y, Muir TW. Genomic targeting of epigenetic probes using a chemically tailored Cas9 system. Proc Natl Acad Sci U S A. 2017 ;114(4):681-686.
Celià-Terrassa T, Kang Y. Mouse genomic screen reveals novel host regulator of metastasis. Genome Biol. 2017 ;18(1):31.
Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017 ;5(3):221-229.e4.
2016
vonHoldt BM, Kays R, Pollinger JP, Wayne RK. Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol. 2016 ;25(11):2443-53.
Schumer M, Cui R, Powell DL, Rosenthal GG, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol. 2016 ;25(11):2661-79.
Mallarino R, Hoekstra HE, Manceau M. Developmental genetics in emerging rodent models: case studies and perspectives. Curr Opin Genet Dev. 2016 ;39:182-186.
Robinson JA, Del Vecchyo DOrtega-, Fan Z, Kim BY, vonHoldt BM, Marsden CD, et al. Genomic Flatlining in the Endangered Island Fox. Curr Biol. 2016 ;26(9):1183-9.