Publications

Search Publications
Export 38 results:
Author Title [ Year(Asc)]
Filters: Keyword is Computational Biology  [Clear All Filters]
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.
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.
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.
Cabreros I, Storey JD. A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis. Genetics. 2019 ;212(4):1009-1029.
Durán AHernández, Greco TM, Vollmer B, Cristea IM, Grünewald K, Topf M. Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PLoS Biol. 2019 ;17(6):e3000316.
Wang S-W, Bitbol A-F, Wingreen NS. Revealing evolutionary constraints on proteins through sequence analysis. PLoS Comput Biol. 2019 ;15(4):e1007010.
A Arguello E, Leach RW, Kleiner RE. Selection with a Site-Specifically Modified RNA Library Reveals the Binding Preferences of N-Methyladenosine Reader Proteins. Biochemistry. 2019 ;58(31):3386-3395.
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.
Seyedsayamdost MR. Toward a global picture of bacterial secondary metabolism. J Ind Microbiol Biotechnol. 2019 ;46(3-4):301-311.
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
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.
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.
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.
DiMaio D, Dermody TS, Enquist LW. Reductio ad Intellectum. Annu Rev Virol. 2018 ;5(1):ii-iv.
2017
Misra M, Audoly B, Shvartsman SY. Complex structures from patterned cell sheets. Philos Trans R Soc Lond B Biol Sci. 2017 ;372(1720).
Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017 ;33(16):2471-2478.
Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017 ;5(3):221-229.e4.
Beltran PMJean, Federspiel JD, Sheng X, Cristea IM. Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Mol Syst Biol. 2017 ;13(3):922.
Calhoun AJ, Murthy M. Quantifying behavior to solve sensorimotor transformations: advances from worms and flies. Curr Opin Neurobiol. 2017 ;46:90-98.
vonHoldt BM, Shuldiner E, Koch IJanowitz, Kartzinel RY, Hogan A, Brubaker L, et al. Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. Sci Adv. 2017 ;3(7):e1700398.
Ioffe ML, Berry MJ. The structured 'low temperature' phase of the retinal population code. PLoS Comput Biol. 2017 ;13(10):e1005792.
Davis KM, Schramma KR, Hansen WA, Bacik JP, Khare SD, Seyedsayamdost MR, et al. Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. Proc Natl Acad Sci U S A. 2017 ;114(39):10420-10425.
Villoutreix P, Andén J, Lim B, Lu H, Kevrekidis IG, Singer A, et al.. Synthesizing developmental trajectories. PLoS Comput Biol. 2017 ;13(9):e1005742.
Lu Y, Xie S, Zhang W, Zhang C, Gao C, Sun Q, et al. Twa1/Gid8 is a β-catenin nuclear retention factor in Wnt signaling and colorectal tumorigenesis. Cell Res. 2017 ;27(12):1422-1440.
2016
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.