Publications

1198 Publications

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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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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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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Bassler BL, Wingreen NS. Working together at the interface of physics and biology. Phys Biol. 2014;11(5):053010.
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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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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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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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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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Ghersi D, Singh M. Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Res. 2014;42(3):e18.
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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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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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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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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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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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Petkova MD, Little SC, Liu F, Gregor T. Maternal origins of developmental reproducibility. Curr Biol. 2014;24(11):1283–8.
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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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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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Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine R, Troyanskaya OG. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol. 2013;9(3):e1002957.
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Osterfield M, Du X, Schüpbach T, Wieschaus E, Shvartsman SY. Three-dimensional epithelial morphogenesis in the developing Drosophila egg. Dev Cell. 2013;24(4):400–10.
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Little SC, Gregor T. Sorting sloppy Sonic. Cell. 2013;153(3):509–10.
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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.
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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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Koyuncu E, Purdy JG, Rabinowitz JD, Shenk T. Saturated very long chain fatty acids are required for the production of infectious human cytomegalovirus progeny. PLoS Pathog. 2013;9(5):e1003333.
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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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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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Garcia HG, Tikhonov M, Lin A, Gregor T. Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning. Curr Biol. 2013;23(21):2140–5.
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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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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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Borenstein DB, Meir Y, Shaevitz JW, Wingreen NS. Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model. PLoS One. 2013;8(5):e63304.
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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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Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal GG. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution. 2013;67(8):2166–79.
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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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Dwyer RS, Ricci DP, Colwell LJ, Silhavy TJ, Wingreen NS. Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis. Genetics. 2013;195(2):443–55.
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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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Dubuis J, Tkačik G, Wieschaus EF, Gregor T, Bialek W. Positional information, in bits. Proc Natl Acad Sci U S A. 2013;110(41):16301–8.