Publications

1198 Publications

2014

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Foo SM, Sun Y, Lim B, Ziukaite R, O’Brien K, Nien C-Y, Kirov N, Shvartsman SY, Rushlow CA. Zelda potentiates morphogen activity by increasing chromatin accessibility. Curr Biol. 2014;24(12):1341–6.
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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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Quigley D, Silwal-Pandit L, Dannenfelser R, Langerod A, Vollan HKM, Vaske C, Ursini-Siegel J, Troyanskaya O, Chin S-F, Caldas C, Balmain A, Borresen-Dale A-L, Kristensen V. Lymphocyte invasion in IC10/Basal-like breast tumors is associated with wild-type TP53. Mol Cancer Res. 2014;.
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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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Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics. 2014;30(14):2081–3.
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Rogers RL, Shao L, Sanjak JS, Andolfatto P, Thornton KR. Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group. G3 (Bethesda). 2014;4(12):2345–51.
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Tilghman SM. Twists and turns: a scientific journey. Annu Rev Cell Dev Biol. 2014;30:1–21.
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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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Levine M. Retrospective. Walter Gehring (1939-2014). Science. 2014;345(6194):277.
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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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Khan Z, Wang Y-C, Wieschaus EF, Kaschube M. Quantitative 4D analyses of epithelial folding during Drosophila gastrulation. Development. 2014;141(14):2895–900.
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Wieschaus E, Nüsslein-Volhard C. Walter Gehring (1939–2014). Curr Biol. 2014;24(14):R632–4.
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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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Schumer M, Rosenthal GG, Andolfatto P. How common is homoploid hybrid speciation?. Evolution. 2014;68(6):1553–60.
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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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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.
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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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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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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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Kocher S, Pellissier L, Veller C, Purcell J, Nowak M, Chapuisat M, Pierce N. Transitions in social complexity along elevational gradients reveal a combined impact of season length and development time on social evolution. Proceedings. Biological sciences. 2014;281(1787). PMCID: PMC4071548
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Gilbert L, Horlbeck M, Adamson B, Villalta J, Chen Y, Whitehead E, Guimaraes C, Panning B, Ploegh H, Bassik M, Qi L, Kampmann M, Weissman J. Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell. 2014;159(3):647–61. PMCID: PMC4253859

2013

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Xu Y-F, Létisse F, Absalan F, Lu W, Kuznetsova E, Brown G, Caudy AA, Yakunin AF, Broach JR, Rabinowitz JD. Nucleotide degradation and ribose salvage in yeast. Mol Syst Biol. 2013;9:665.
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Ju W, Greene CS, Eichinger F, Nair V, Hodgin JB, Bitzer M, Lee Y- suk, Zhu Q, Kehata M, Li M, Jiang S, Rastaldi MP, Cohen CD, Troyanskaya OG, Kretzler M. Defining cell-type specificity at the transcriptional level in human disease. Genome Res. 2013;23(11):1862–73.
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Dolinski K, Botstein D. Automating the construction of gene ontologies. Nat Biotechnol. 2013;31(1):34–5.
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Cheung LS, Simakov DSA, Fuchs A, Pyrowolakis G, Shvartsman SY. Dynamic model for the coordination of two enhancers of broad by EGFR signaling. Proc Natl Acad Sci U S A. 2013;110(44):17939–44.
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Stephens GJ, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. Phys Rev Lett. 2013;110(1):018701.
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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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Slotte T, Hazzouri KM, Ågren A, Koenig D, Maumus F, Guo Y-L, Steige K, Platts AE, Escobar JS, Newman K, Wang W, Mandáková T, Vello E, Smith LM, Henz SR, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Chapman J, Prochnik S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet. 2013;45(7):831–5.
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McIsaac S, Silverman SJ, Parsons L, Xu P, Briehof R, McClean MN, Botstein D. Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae. J Vis Exp. 2013;(76):e50382.
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Aure MR, Leivonen S-K, Fleischer T, Zhu Q, Overgaard J, Alsner J, Tramm T, Louhimo R, Alnæs GIG, Perälä M, Busato F, Touleimat N, Tost J, Børresen-Dale A-L, Hautaniemi S, Troyanskaya OG, Lingjærde OC, Sahlberg KK, Kristensen VN. Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biol. 2013;14(11):R126.
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Munivenkatappa A, Devi BI, Gregor TI, Bhat DI, Kumarsamy AD, Shukla DP. Bicycle accident-related head injuries in India. J Neurosci Rural Pract. 2013;4(3):262–6.
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Liu F, Morrison AH, Gregor T. Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network. Proc Natl Acad Sci U S A. 2013;110(17):6724–9.
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Reaves ML, Young BD, Hosios AM, Xu Y-F, Rabinowitz JD. Pyrimidine homeostasis is accomplished by directed overflow metabolism. Nature. 2013;500(7461):237–41.
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Dubuis J, Samanta R, Gregor T. Accurate measurements of dynamics and reproducibility in small genetic networks. Mol Syst Biol. 2013;9:639.
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Deng Y, Coen P, Sun M, Shaevitz JW. Efficient multiple object tracking using mutually repulsive active membranes. PLoS One. 2013;8(6):e65769.
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Tepper RG, Ashraf JM, Kaletsky R, Kleemann G, Murphy CT, Bussemaker HJ. PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity. Cell. 2013;154(3):676–90.
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Fan J, Kamphorst JJ, Mathew R, Chung MK, White E, Shlomi T, Rabinowitz JD. Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia. Mol Syst Biol. 2013;9:712.
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Kim Y, Iagovitina A, Ishihara K, Fitzgerald KM, Deplancke B, Papatsenko D, Shvartsman SY. Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo. Chaos. 2013;23(2):025105.
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Di Talia S, She R, Blythe SA, Lu X, Zhang QF, Wieschaus EF. Posttranslational control of Cdc25 degradation terminates Drosophila’s early cell-cycle program. Curr Biol. 2013;23(2):127–32.