Publications

1198 Publications

2012

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McIsaac S, Petti AA, Bussemaker HJ, Botstein D. Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol Biol Cell. 2012;23(15):2993–3007.
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Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ, Hibbs MA, Troyanskaya OG. Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol. 2012;8(9):e1002694.
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Helman A, Lim B, Andreu MJ, Kim Y, Shestkin T, Lu H, Jiménez G, Shvartsman SY, Paroush Z. RTK signaling modulates the Dorsal gradient. Development. 2012;139(16):3032–9.
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Rushlow CA, Shvartsman SY. Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient. Curr Opin Genet Dev. 2012;22(6):542–6.
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Perry MW, Bothma JP, Luu RD, Levine M. Precision of hunchback expression in the Drosophila embryo. Curr Biol. 2012;22(23):2247–52.
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Zhen Y, Andolfatto P. Methods to detect selection on noncoding DNA. Methods Mol Biol. 2012;856:141–59.
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Wang S, Furchtgott L, Huang KC, Shaevitz JW. Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall. Proc Natl Acad Sci U S A. 2012;109(10):E595–604.
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Huang W, Richards S, Carbone MA, Zhu D, Anholt R, Ayroles J, Duncan L, Jordan KW, Lawrence F, Magwire MM, Warner CB, Blankenburg K, Han Y, Javaid M, Jayaseelan J, Jhangiani SN, Muzny D, Ongeri F, Perales L, Wu Y-Q, Zhang Y, Zou X, Stone EA, Gibbs RA, Mackay TFC. Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci U S A. 2012;109(39):15553–9.
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Peterson CN, Levchenko I, Rabinowitz JD, Baker TA, Silhavy TJ. RpoS proteolysis is controlled directly by ATP levels in Escherichia coli. Genes Dev. 2012;26(6):548–53.
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van Teeffelen S, Shaevitz JW, Gitai Z. Image analysis in fluorescence microscopy: bacterial dynamics as a case study. Bioessays. 2012;34(5):427–36.
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Pilizota T, Shaevitz JW. Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli. PLoS One. 2012;7(4):e35205.
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Cooper RM, Wingreen NS, Cox EC. An excitable cortex and memory model successfully predicts new pseudopod dynamics. PLoS One. 2012;7(3):e33528.
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Ober U, Ayroles J, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TFC, Simianer H. Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genet. 2012;8(5):e1002685.
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Gelbart MA, He B, Martin AC, Thiberge SY, Wieschaus EF, Kaschube M. Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis. Proc Natl Acad Sci U S A. 2012;109(47):19298–303.
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Rabinowitz JD, Vastag L. Teaching the design principles of metabolism. Nat Chem Biol. 2012;8(6):497–501.
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Sourjik V, Wingreen NS. Responding to chemical gradients: bacterial chemotaxis. Curr Opin Cell Biol. 2012;24(2):262–8.
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Morrison AH, Scheeler M, Dubuis J, Gregor T. Quantifying the Bicoid morphogen gradient in living fly embryos. Cold Spring Harb Protoc. 2012;2012(4):398–406.
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Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles J, Dermitzakis ET, Stone EA, Jensen JD, Mackay TFC, Deplancke B. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genet. 2012;8(11):e1003055.
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Hilgers V, Lemke SB, Levine M. ELAV mediates 3’ UTR extension in the Drosophila nervous system. Genes Dev. 2012;26(20):2259–64.
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Reaves ML, Sinha S, Rabinowitz JD, Kruglyak L, Redfield RJ. Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells. Science. 2012;337(6093):470–3.
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Garrigan D, Kingan SB, Geneva AJ, Andolfatto P, Clark A, Thornton KR, Presgraves DC. Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Res. 2012;22(8):1499–511.
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Shvartsman SY, Baker RE. Mathematical models of morphogen gradients and their effects on gene expression. Wiley Interdiscip Rev Dev Biol. 2012;1(5):715–30.
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Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R, Sørlie T, Wärnberg F, Haakensen VD, Helland Åslaug, Naume B, Perou CM, Haussler D, Troyanskaya OG, Børresen-Dale A-L. Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A. 2012;109(8):2802–7.
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Chopra VS, Kong N, Levine M. Transcriptional repression via antilooping in the Drosophila embryo. Proc Natl Acad Sci U S A. 2012;109(24):9460–4.
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Simakov DSA, Cheung LS, Pismen LM, Shvartsman SY. EGFR-dependent network interactions that pattern Drosophila eggshell appendages. Development. 2012;139(15):2814–20.
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Wang Y-C, Khan Z, Kaschube M, Wieschaus EF. Differential positioning of adherens junctions is associated with initiation of epithelial folding. Nature. 2012;484(7394):390–3.
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Jiménez G, Shvartsman SY, Paroush Z. The Capicua repressor--a general sensor of RTK signaling in development and disease. J Cell Sci. 2012;125(Pt 6):1383–91.
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Huang KC, Ehrhardt DW, Shaevitz JW. The molecular origins of chiral growth in walled cells. Curr Opin Microbiol. 2012;15(6):707–14.
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Petti AA, McIsaac S, Ho-Shing O, Bussemaker HJ, Botstein D. Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Mol Biol Cell. 2012;23(15):3008–24.
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Farley E, Levine M. HOT DNAs: a novel class of developmental enhancers. Genes Dev. 2012;26(9):873–6.
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Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L. Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Mol Syst Biol. 2012;8:602.
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Kanodia JS, Liang H-L, Kim Y, Lim B, Zhan M, Lu H, Rushlow CA, Shvartsman SY. Pattern formation by graded and uniform signals in the early Drosophila embryo. Biophys J. 2012;102(3):427–33.
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Botstein D. Why we need more basic biology research, not less. Mol Biol Cell. 2012;23(21):4160–1.
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Tkačik G, Walczak AM, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. Phys Rev E Stat Nonlin Soft Matter Phys. 2012;85(4 Pt 1):041903.
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Abitua PB, Wagner E, Navarrete IA, Levine M. Identification of a rudimentary neural crest in a non-vertebrate chordate. Nature. 2012;492(7427):104–7.
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Aardema ML, Zhen Y, Andolfatto P. The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies. Mol Ecol. 2012;21(2):340–9.
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Greene CS, Troyanskaya OG. Chapter 2: Data-driven view of disease biology. PLoS Comput Biol. 2012;8(12):e1002816.
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Fuchs A, Cheung LS, Charbonnier E, Shvartsman SY, Pyrowolakis G. Transcriptional interpretation of the EGF receptor signaling gradient. Proc Natl Acad Sci U S A. 2012;109(5):1572–7.
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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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Chikina MD, Troyanskaya OG. An effective statistical evaluation of ChIPseq dataset similarity. Bioinformatics. 2012;28(5):607–13.
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Clasquin MF, Melamud E, Rabinowitz JD. LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine. Curr Protoc Bioinformatics. 2012;Chapter 14:Unit14.11.
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Mackay TFC, Richards S, Stone EA, Barbadilla A, Ayroles J, Zhu D, Casillas S, Han Y, Magwire MM, Cridland J, Richardson MF, Anholt R, Barrón M, Bess C, Blankenburg K, Carbone MA, Castellano D, Chaboub L, Duncan L, Harris Z, Javaid M, Jayaseelan JC, Jhangiani SN, Jordan KW, Lara F, Lawrence F, Lee SL, Librado P, Linheiro RS, Lyman RF, Mackey AJ, Munidasa M, Muzny DM, Nazareth L, Newsham I, Perales L, Pu L-L, Qu C, Ràmia M, Reid JG, Rollmann SM, Rozas J, Saada N, Turlapati L, Worley KC, Wu Y-Q, Yamamoto A, Zhu Y, Bergman C, Thornton KR, Mittelman D, Gibbs RA. The Drosophila melanogaster Genetic Reference Panel. Nature. 2012;482(7384):173–8.
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Lagha M, Bothma JP, Levine M. Mechanisms of transcriptional precision in animal development. Trends Genet. 2012;28(8):409–16.
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Xu Y-F, Amador-Noguez D, Reaves ML, Feng X-J, Rabinowitz JD. Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase. Nat Chem Biol. 2012;8(6):562–8.
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He B, Caudy AA, Parsons L, Rosebrock A, Pane A, Raj S, Wieschaus E. Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster. Genome Res. 2012;22(12):2507–19.
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Slavov N, Airoldi EM, van Oudenaarden A, Botstein D. A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes. Mol Biol Cell. 2012;23(10):1986–97.