Publications

93 Publications
Applied Filters: First Letter Of Last Name: B Reset

B

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Bachtrog D, Andolfatto P. Selection, recombination and demographic history in Drosophila miranda. Genetics. 2006;174(4):2045–59.
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Bachtrog D, Thornton K, Clark A, Andolfatto P. Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group. Evolution. 2006;60(2):292–302.
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Bae E, Calhoun VC, Levine M, Lewis EB, Drewell RA. Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc Natl Acad Sci U S A. 2002;99(26):16847–52.
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Bailis W, Shyer JA, Zhao J, Canaveras JCG, Khazal FJA, Qu R, Steach HR, Bielecki P, Khan O, Jackson R, Kluger Y, Maher LJ, Rabinowitz J, Craft J, Flavell RA. Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function. Nature. 2019;571(7765):403–407. PMCID: PMC6939459
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Bajad SU, Lu W, Kimball EH, Yuan J, Peterson C, Rabinowitz JD. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J Chromatogr A. 2006;1125(1):76–88.
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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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Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry M. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005;33(Database issue):D374–7.
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Banigan EJ, Gelbart MA, Gitai Z, Wingreen NS, Liu AJ. Filament depolymerization can explain chromosome pulling during bacterial mitosis. PLoS Comput Biol. 2011;7(9):e1002145.
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Banks E, Nabieva E, Chazelle B, Singh M. Organization of physical interactomes as uncovered by network schemas. PLoS Comput Biol. 2008;4(10):e1000203.
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Banks E, Nabieva E, Peterson R, Singh M. NetGrep: fast network schema searches in interactomes. Genome Biol. 2008;9(9):R138.
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Bao Q, Lu W, Rabinowitz JD, Shi Y. Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1. Mol Cell. 2007;25(2):181–92.
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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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Bartlett TM, Bratton BP, Duvshani A, Miguel A, Sheng Y, Martin NR, Nguyen JP, Persat A, Desmarais SM, VanNieuwenhze MS, Huang KC, Zhu J, Shaevitz JW, Gitai Z. A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis. Cell. 2017;168(1-2):172–185.e15. PMCID: PMC5287421
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Bartolomei MS, Zemel S, Tilghman SM. Parental imprinting of the mouse H19 gene. Nature. 1991;351(6322):153–5.
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Bartolomei MS, Webber AL, Brunkow ME, Tilghman SM. Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Genes Dev. 1993;7(9):1663–73.
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Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG. Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. Bioinformatics. 2009;25(10):1307–13.
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Barutcuoglu Z, Schapire RE, Troyanskaya OG. Hierarchical multi-label prediction of gene function. Bioinformatics. 2006;22(7):830–6.
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Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn J-Y, Ou J, San Luis B-J, Bandyopadhyay S, Hibbs M, Hess D, Gingras A-C, Bader GD, Troyanskaya OG, Brown GW, Andrews BJ, Boone C, Myers CL. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods. 2010;7(12):1017–24.
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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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Batsilas L, Berezhkovskii AM, Shvartsman SY. Stochastic model of autocrine and paracrine signals in cell culture assays. Biophys J. 2003;85(6):3659–65.
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Batut P, Bing X, Sisco Z, Raimundo J, Levo M, Levine M. Genome organization controls transcriptional dynamics during development. Science (New York, N.Y.). 2022;375(6580):566–570. PMID: 35113722
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Bejsovec A, Wieschaus E. Segment polarity gene interactions modulate epidermal patterning in Drosophila embryos. Development. 1993;119(2):501–17.
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Bennett BD, Yuan J, Kimball EH, Rabinowitz JD. Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat Protoc. 2008;3(8):1299–311.
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Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009;5(8):593–9.
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Benson KK, Hu W, Weller AH, Bennett AH, Chen ER, Khetarpal SA, Yoshino S, Bone WP, Wang L, Rabinowitz JD, Voight BF, Soccio RE. Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene. Proc Natl Acad Sci U S A. 2019;116(46):23232–23242. PMCID: PMC6859347
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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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Berezhkovskii AM, Sample C, Shvartsman SY. Formation of morphogen gradients: local accumulation time. Phys Rev E Stat Nonlin Soft Matter Phys. 2011;83(5 Pt 1):051906.
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Berezhkovskii AM, Makhnovskii YA, Monine MI, Zitserman VY, Shvartsman SY. Boundary homogenization for trapping by patchy surfaces. J Chem Phys. 2004;121(22):11390–4.
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Berezhkovskii AM, Coppey M, Shvartsman SY. Signaling gradients in cascades of two-state reaction-diffusion systems. Proc Natl Acad Sci U S A. 2009;106(4):1087–92.
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Berezhkovskii AM, Shvartsman SY. Physical interpretation of mean local accumulation time of morphogen gradient formation. J Chem Phys. 2011;135(15):154115.
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Berezhkovskii AM, Batsilas L, Shvartsman SY. Ligand trapping in epithelial layers and cell cultures. Biophys Chem. 2004;107(3):221–7.
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Berezhkovskii AM, Shvartsman SY. Kinetics of receptor occupancy during morphogen gradient formation. J Chem Phys. 2013;138(24):244105.
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Berezhkovskii AM, Sample C, Shvartsman SY. How long does it take to establish a morphogen gradient?. Biophys J. 2010;99(8):L59–61.
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Berezhkovskii AM, Monine MI, Muratov CB, Shvartsman SY. Homogenization of boundary conditions for surfaces with regular arrays of traps. J Chem Phys. 2006;124(3):036103.
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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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Berman GJ, Bialek W, Shaevitz JW. Predictability and hierarchy in Drosophila behavior. Proc Natl Acad Sci U S A. 2016;113(42):11943–11948. PMCID: PMC5081631
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Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A. 2002;99(2):757–62.
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Bialek W, Cavagna A, Giardina I, Mora T, Silvestri E, Viale M, Walczak AM. Statistical mechanics for natural flocks of birds. Proc Natl Acad Sci U S A. 2012;109(13):4786–91.
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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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Bialek W. QnAs with William Bialek. Proc Natl Acad Sci U S A. 2013;110(41):16288.
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Bialek W, Setayeshgar S. Physical limits to biochemical signaling. Proc Natl Acad Sci U S A. 2005;102(29):10040–5.
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Bialek W, Botstein D. Introductory science and mathematics education for 21st-Century biologists. Science. 2004;303(5659):788–90.
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Bialek W, Setayeshgar S. Cooperativity, sensitivity, and noise in biochemical signaling. Phys Rev Lett. 2008;100(25):258101.
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Biemar F, Zinzen R, Ronshaugen M, Sementchenko V, Manak R, Levine MS. Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc Natl Acad Sci U S A. 2005;102(44):15907–11.
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Biemar F, Nix DA, Piel J, Peterson B, Ronshaugen M, Sementchenko V, Bell I, Manak R, Levine MS. Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array. Proc Natl Acad Sci U S A. 2006;103(34):12763–8.
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Biswas S, Kim J, Zhang X, Scholes G. Coherent Two-Dimensional and Broadband Electronic Spectroscopies. Chemical Reviews. 2022;122:4257–4321.
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Blankenship JT, Wieschaus E. Two new roles for the Drosophila AP patterning system in early morphogenesis. Development. 2001;128(24):5129–38.
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Block SM, Asbury CL, Shaevitz JW, Lang MJ. Probing the kinesin reaction cycle with a 2D optical force clamp. Proc Natl Acad Sci U S A. 2003;100(5):2351–6.