Publications

1198 Publications

2015

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Lakhina V, Murphy CT. For longevity, perception is everything. Cell. 2015;160(5):807–9.
1.
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;.
1.
Wieschaus E, Nüsslein-Volhard C. Walter Gehring (1939–2014). Curr Biol. 2014;24(14):R632–4.
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Ghersi D, Singh M. Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Res. 2014;42(3):e18.
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Robinson DG, Chen W, Storey JD, Gresham D. Design and analysis of Bar-seq experiments. G3 (Bethesda). 2014;4(1):11–8.
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Karsli-Uzunbas G, Guo JY, Price S, Teng X, Laddha S V, Khor S, Kalaany NY, Jacks T, Chan CS, Rabinowitz JD, White E. Autophagy is required for glucose homeostasis and lung tumor maintenance. Cancer Discov. 2014;4(8):914–27.
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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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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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Abouchar L, Petkova MD, Steinhardt CR, Gregor T. Fly wing vein patterns have spatial reproducibility of a single cell. J R Soc Interface. 2014;11(97):20140443.
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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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Schumer M, Rosenthal GG, Andolfatto P. How common is homoploid hybrid speciation?. Evolution. 2014;68(6):1553–60.
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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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Mathew R, Khor S, Hackett SR, Rabinowitz JD, Perlman DH, White E. Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity. Mol Cell. 2014;55(6):916–30.
1.
Haupaix N, Abitua PB, Sirour C, Yasuo H, Levine M, Hudson C. Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS. Dev Biol. 2014;394(1):170–80.
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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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Shi C, Murphy CT. Mating induces shrinking and death in Caenorhabditis mothers. Science. 2014;343(6170):536–40.
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Castellana M, Wilson MZ, Xu Y, Joshi P, Cristea IM, Rabinowitz JD, Gitai Z, Wingreen NS. Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol. 2014;32(10):1011–8.
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Levine M, Cattoglio C, Tjian R. Looping back to leap forward: transcription enters a new era. Cell. 2014;157(1):13–25.
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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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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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Marstrand TT, Storey JD. Identifying and mapping cell-type-specific chromatin programming of gene expression. Proc Natl Acad Sci U S A. 2014;111(6):E645–54.
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Bothma JP, Garcia HG, Esposito E, Schlissel G, Gregor T, Levine M. Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. Proc Natl Acad Sci U S A. 2014;111(29):10598–603.
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Jiang P, Singh M. CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Res. 2014;42(5):2833–47.
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Persikov A V, Rowland EF, Oakes BL, Singh M, Noyes MB. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res. 2014;42(3):1497–508.
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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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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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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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Fletcher AG, Osterfield M, Baker RE, Shvartsman SY. Vertex models of epithelial morphogenesis. Biophys J. 2014;106(11):2291–304.
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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.
1.
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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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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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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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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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.
1.
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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Zhou J, Troyanskaya OG. Global quantitative modeling of chromatin factor interactions. PLoS Comput Biol. 2014;10(3):e1003525.
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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.
1.
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.
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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.