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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.
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.
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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.
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.
Wang S-W, Bitbol A-F, Wingreen NS. Revealing evolutionary constraints on proteins through sequence analysis. PLoS Comput Biol. 2019 ;15(4):e1007010.
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.
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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.
Villoutreix P, Andén J, Lim B, Lu H, Kevrekidis IG, Singer A, et al.. Synthesizing developmental trajectories. PLoS Comput Biol. 2017 ;13(9):e1005742.
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).
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Toettcher JE, Gong D, Lim WA, Weiner OD. Light-based feedback for controlling intracellular signaling dynamics. Nat Methods. 2011 ;8(10):837-9.
Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ. Searching for collective behavior in a large network of sensory neurons. PLoS Comput Biol. 2014 ;10(1):e1003408.
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Stern T, Shvartsman SY, Wieschaus EF. Template-based mapping of dynamic motifs in tissue morphogenesis. PLoS Comput Biol. 2020 ;16(8):e1008049.
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.
Seyedsayamdost MR. Toward a global picture of bacterial secondary metabolism. J Ind Microbiol Biotechnol. 2019 ;46(3-4):301-311.
Seyedsayamdost MR, Cleto S, Carr G, Vlamakis H, Vieira MJoão, Kolter R, et al.. Mixing and matching siderophore clusters: structure and biosynthesis of serratiochelins from Serratia sp. V4. J Am Chem Soc. 2012 ;134(33):13550-3.
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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.
Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017 ;33(16):2471-2478.
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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.
Misra M, Audoly B, Shvartsman SY. Complex structures from patterned cell sheets. Philos Trans R Soc Lond B Biol Sci. 2017 ;372(1720).
Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, et al. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 2015 ;11(9):625-31.
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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.
Liszczak G, Muir TW. Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter. Angew Chem Int Ed Engl. 2019 ;58(13):4144-4162.
Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell. 2004 ;118(1):69-82.
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Ioffe ML, Berry MJ. The structured 'low temperature' phase of the retinal population code. PLoS Comput Biol. 2017 ;13(10):e1005792.
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Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017 ;5(3):221-229.e4.