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Zhou J, Troyanskaya OG. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods. 2015 ;12(10):931-4.
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.
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Wilson MZ, Ravindran PT, Lim WA, Toettcher JE. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017 ;67(5):757-769.e5.
Whinnett A, Zimmermann M, Willmott KR, Herrera N, Mallarino R, Simpson F, et al. Strikingly variable divergence times inferred across an Amazonian butterfly 'suture zone'. Proc Biol Sci. 2005 ;272(1580):2525-33.
Webb CJ, Zakian VA. Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding. Proc Natl Acad Sci U S A. 2015 ;112(36):11312-7.
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Tkačik G, Dubuis JO, Petkova MD, Gregor T. Positional information, positional error, and readout precision in morphogenesis: a mathematical framework. Genetics. 2015 ;199(1):39-59.
Tanaka H, Stone HA, Nelson DR. Spatial gene drives and pushed genetic waves. Proc Natl Acad Sci U S A. 2017 ;114(32):8452-8457.
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Song M, Hao W, Storey JD. Testing for genetic associations in arbitrarily structured populations. Nat Genet. 2015 ;47(5):550-4.
Snir S, vonHoldt BM, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016 ;12(11):e1005183.
Schumer M, Cui R, Rosenthal GG, Andolfatto P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genet. 2015 ;11(3):e1005041.
Schneidman E, Still S, Berry MJ, Bialek W. Network information and connected correlations. Phys Rev Lett. 2003 ;91(23):238701.
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Postika N, Metzler M, Affolter M, Müller M, Schedl P, Georgiev P, et al.. Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex. PLoS Genet. 2018 ;14(12):e1007702.
Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal Decoding of Cellular Identities in a Genetic Network. Cell. 2019 ;176(4):844-855.e15.
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Mallarino R, Campàs O, Fritz JA, Burns KJ, Weeks OG, Brenner MP, et al.. Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. Proc Natl Acad Sci U S A. 2012 ;109(40):16222-7.
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Kyrchanova O, Mogila V, Wolle D, Deshpande G, Parshikov A, Cleard F, et al. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex. PLoS Genet. 2016 ;12(7):e1006188.
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Even-Tov E, Bendori SOmer, Valastyan J, Ke X, Pollak S, Bareia T, et al. Social Evolution Selects for Redundancy in Bacterial Quorum Sensing. PLoS Biol. 2016 ;14(2):e1002386.
Elyashiv E, Sattath S, Hu TT, Strutsovsky A, McVicker G, Andolfatto P, et al. A Genomic Map of the Effects of Linked Selection in Drosophila. PLoS Genet. 2016 ;12(8):e1006130.
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Bassler BL, Wright M, Silverman MR. Sequence and function of LuxO, a negative regulator of luminescence in Vibrio harveyi. Mol Microbiol. 1994 ;12(3):403-12.
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Adamson B, Smogorzewska A, Sigoillot FD, King RW, Elledge SJ. A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol. 2012 ;14(3):318-28.