Publications

1198 Publications

2015

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Abitua PB, Gainous B, Kaczmarczyk AN, Winchell CJ, Hudson C, Kamata K, Nakagawa M, Tsuda M, Kusakabe TG, Levine M. The pre-vertebrate origins of neurogenic placodes. Nature. 2015;524(7566):462–5.
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Lim B, Dsilva C, Levario T, Lu H, Schüpbach T, Kevrekidis I, Shvartsman S. Dynamics of Inductive ERK Signaling in the Drosophila Embryo. Current biology : CB. 2015;25(13):1784–90. PMCID: PMC4675133
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Jindal G, Goyal Y, Burdine R, Rauen K, Shvartsman S. RASopathies: unraveling mechanisms with animal models. Disease models & mechanisms. 2015;8(8):769–82. PMCID: PMC4527292
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Fu F, Kocher S, Nowak M. The risk-return trade-off between solitary and eusocial reproduction. Ecology letters. 2015;18(1):74–84. PMCID: PMC5492949
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Izhar L, Adamson B, Ciccia A, Lewis J, Pontano-Vaites L, Leng Y, Liang A, Westbrook T, Harper W, Elledge S. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors. Cell reports. 2015;11(9):1486–500. PMCID: PMC4464939

2014

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Park CY, Krishnan A, Zhu Q, Wong AK, Lee Y- suk, Troyanskaya OG. Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics. 2014;.
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Wieschaus E, Nüsslein-Volhard C. Walter Gehring (1939–2014). Curr Biol. 2014;24(14):R632–4.
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Du X, Osterfield M, Shvartsman SY. Computational analysis of three-dimensional epithelial morphogenesis using vertex models. Phys Biol. 2014;11(6):066007.
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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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Zhang J, Fan J, Venneti S, Cross JR, Takagi T, Bhinder B, Djaballah H, Kanai M, Cheng EH, Judkins AR, Pawel B, Baggs J, Cherry S, Rabinowitz JD, Thompson CB. Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion. Mol Cell. 2014;56(2):205–18.
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McIsaac S, Gibney PA, Chandran SS, Benjamin KR, Botstein D. Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae. Nucleic Acids Res. 2014;42(6):e48.
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Ye J, Fan J, Venneti S, Wan Y-W, Pawel BR, Zhang J, Finley LWS, Lu C, Lindsten T, Cross JR, Qing G, Liu Z, Simon C, Rabinowitz JD, Thompson CB. Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia. Cancer Discov. 2014;4(12):1406–17.
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Bassler BL, Wingreen NS. Working together at the interface of physics and biology. Phys Biol. 2014;11(5):053010.
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de Abreu DAF, Caballero A, Fardel P, Stroustrup N, Chen Z, Lee K, Keyes WD, Nash ZM, López-Moyado IF, Vaggi F, Cornils A, Regenass M, Neagu A, Ostojic I, Liu C, Cho Y, Sifoglu D, Shen Y, Fontana W, Lu H, Csikasz-Nagy A, Murphy CT, Antebi A, Blanc E, Apfeld J, Zhang Y, Alcedo J, Ch’ng Q. An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology. PLoS Genet. 2014;10(3):e1004225.
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Shi C, Murphy CT. Mating induces shrinking and death in Caenorhabditis mothers. Science. 2014;343(6170):536–40.
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Neumann S, Vladimirov N, Krembel AK, Wingreen NS, Sourjik V. Imprecision of adaptation in Escherichia coli chemotaxis. PLoS One. 2014;9(1):e84904.
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Botstein D. Lasker∼Koshland to genetics pioneer. Cell. 2014;158(6):1230–2.
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Persikov A V, Singh M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res. 2014;42(1):97–108.
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Haselwandter CA, Wingreen NS. The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. PLoS Comput Biol. 2014;10(12):e1003932.
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Zhou J, Troyanskaya OG. Global quantitative modeling of chromatin factor interactions. PLoS Comput Biol. 2014;10(3):e1003525.
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Krotov D, Dubuis J, Gregor T, Bialek W. Morphogenesis at criticality. Proc Natl Acad Sci U S A. 2014;111(10):3683–8.
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Barry RM, Bitbol A-F, Lorestani A, Charles EJ, Habrian CH, Hansen JM, Li H-J, Baldwin EP, Wingreen NS, Kollman JM, Gitai Z. Large-scale filament formation inhibits the activity of CTP synthetase. Elife. 2014;3:e03638.
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Tepper RG, Murphy CT, Bussemaker HJ. DAF-16 and PQM-1: partners in longevity. Aging (Albany NY). 2014;6(1):5–6.
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Deng Y, Sun M, Lin P-H, Ma J, Shaevitz JW. Spatial covariance reconstructive (SCORE) super-resolution fluorescence microscopy. PLoS One. 2014;9(4):e94807.
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Kim J, Ghasemzadeh N, Eapen DJ, Chung NC, Storey JD, Quyyumi AA, Gibson G. Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death. Genome Med. 2014;6(5):40.
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Petkova MD, Little SC, Liu F, Gregor T. Maternal origins of developmental reproducibility. Curr Biol. 2014;24(11):1283–8.
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Rogers RL, Cridland J, Shao L, Hu TT, Andolfatto P, Thornton KR. Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol. 2014;31(7):1750–66.
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Fan J, Teng X, Liu L, Mattaini KR, Looper RE, Heiden MGV, Rabinowitz JD. Human Phosphoglycerate Dehydrogenase Produces the Oncometabolite d-2-Hydroxyglutarate. ACS Chem Biol. 2014;.
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Castellana M, Bialek W. Inverse spin glass and related maximum entropy problems. Phys Rev Lett. 2014;113(11):117204.
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Schumer M, Cui R, Powell DL, Dresner R, Rosenthal GG, Andolfatto P. High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species. Elife. 2014;3.
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Breunig JS, Hackett SR, Rabinowitz JD, Kruglyak L. Genetic basis of metabolome variation in yeast. PLoS Genet. 2014;10(3):e1004142.
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VanderSluis B, Hess DC, Pesyna C, Krumholz EW, Syed T, Szappanos B, Nislow C, Papp B, Troyanskaya OG, Myers CL, Caudy AA. Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection. Genome Biol. 2014;15(4):R64.
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Aristilde L, Lewis IA, Park JO, Rabinowitz JD. Hierarchy in Pentose Sugar Metabolism in Clostridium Acetobutylicum. Appl Environ Microbiol. 2014;.
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Hwang J, Purdy JG, Wu K, Rabinowitz JD, Shenk T. Estrogen-related receptor α is required for efficient human cytomegalovirus replication. Proc Natl Acad Sci U S A. 2014;111(52):E5706–15.
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Berezhkovskii AM, Shvartsman SY. On the GFP-based analysis of dynamic concentration profiles. Biophys J. 2014;106(3):L13–5.
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Berman GJ, Choi DM, Bialek W, Shaevitz JW. Mapping the stereotyped behaviour of freely moving fruit flies. J R Soc Interface. 2014;11(99).
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Fletcher AG, Osterfield M, Baker RE, Shvartsman SY. Vertex models of epithelial morphogenesis. Biophys J. 2014;106(11):2291–304.
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Gregor T, Garcia HG, Little SC. The embryo as a laboratory: quantifying transcription in Drosophila. Trends Genet. 2014;30(8):364–75.
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Broedersz CP, Wang X, Meir Y, Loparo JJ, Rudner DZ, Wingreen NS. Condensation and localization of the partitioning protein ParB on the bacterial chromosome. Proc Natl Acad Sci U S A. 2014;111(24):8809–14.
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Fan J, Ye J, Kamphorst JJ, Shlomi T, Thompson CB, Rabinowitz JD. Quantitative flux analysis reveals folate-dependent NADPH production. Nature. 2014;510(7504):298–302.
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Balagam R, Litwin DB, Czerwinski F, Sun M, Kaplan HB, Shaevitz JW, Igoshin OA. Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility. PLoS Comput Biol. 2014;10(5):e1003619.
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He B, Doubrovinski K, Polyakov O, Wieschaus E. Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation. Nature. 2014;508(7496):392–6.
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Drescher K, Nadell CD, Stone HA, Wingreen NS, Bassler BL. Solutions to the public goods dilemma in bacterial biofilms. Curr Biol. 2014;24(1):50–5.
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Polyakov O, He B, Swan M, Shaevitz JW, Kaschube M, Wieschaus E. Passive mechanical forces control cell-shape change during Drosophila ventral furrow formation. Biophys J. 2014;107(4):998–1010.
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Bialek W, Cavagna A, Giardina I, Mora T, Pohl O, Silvestri E, Viale M, Walczak AM. Social interactions dominate speed control in poising natural flocks near criticality. Proc Natl Acad Sci U S A. 2014;111(20):7212–7.
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Ursell TS, Nguyen J, Monds RD, Colavin A, Billings G, Ouzounov N, Gitai Z, Shaevitz JW, Huang KC. Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization. Proc Natl Acad Sci U S A. 2014;111(11):E1025–34.