Publications

73 Publications
Applied Filters: First Letter Of Title: E Reset

E

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Stolfi A, Gainous B, Young JJ, Mori A, Levine M, Christiaen L. Early chordate origins of the vertebrate second heart field. Science. 2010;329(5991):565–8.
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Brunkow ME, Tilghman SM. Ectopic expression of the H19 gene in mice causes prenatal lethality. Genes Dev. 1991;5(6):1092–101.
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Liu GS, Bratton BP, Gitai Z, Shaevitz JW. The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane. PLoS One. 2017;12(10):e0185810. PMCID: PMC5627921
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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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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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Liu G, Rogers J, Murphy CT, Rongo C. EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan. EMBO J. 2011;30(15):2990–3003.
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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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Chen LS, Storey JD. Eigen-R2 for dissecting variation in high-dimensional studies. Bioinformatics. 2008;24(19):2260–2.
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Oktaba K, Zhang W, Lotz TS, Jun DJ, Lemke SB, Ng SP, Esposito E, Levine M, Hilgers V. ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System. Mol Cell. 2015;57(2):341–8.
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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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Christiaen L, Wagner E, Shi W, Levine M. Electroporation of transgenic DNAs in the sea squirt Ciona. Cold Spring Harb Protoc. 2009;2009(12):pdb.prot5345.
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Gokhale S, Lu W, Zhu S, Liu Y, Hart RP, Rabinowitz JD, Xie P. Elevated Choline Kinase α-Mediated Choline Metabolism Supports the Prolonged Survival of TRAF3-Deficient B Lymphocytes. J Immunol. 2020;204(2):459–471. PMCID: PMC6946882
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Mancini-Dinardo D, Steele SJS, Levorse JM, Ingram RS, Tilghman SM. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 2006;20(10):1268–82.
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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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Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HAF, Marchetto MCN, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang J, Ventura M, Banci L, Antonacci F, Akey J, Amemiya CT, Gage FH, Reymond A, Eichler EE. Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. Nature. 2016;536(7615):205–9. PMCID: PMC4988886
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Miller J, Zeng C, Wingreen NS, Tang C. Emergence of highly designable protein-backbone conformations in an off-lattice model. Proteins. 2002;47(4):506–12.
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Stephens GJ, de Mesquita MB, Ryu WS, Bialek W. Emergence of long timescales and stereotyped behaviors in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2011;108(18):7286–9.
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Yao V, Wong AK, Troyanskaya OG. Enabling Precision Medicine through Integrative Network Models. J Mol Biol. 2018;430(18 Pt A):2913–2923. PMID: 30003887
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Chi J-T, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO. Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci U S A. 2003;100(19):10623–8.
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Song Y, Park JO, Tanner L, Nagano Y, Rabinowitz JD, Shvartsman SY. Energy budget of Drosophila embryogenesis. Curr Biol. 2019;29(12):R566-R567. PMID: 31211973
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Shaevitz JW, Fletcher DA. Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function. J Opt Soc Am A Opt Image Sci Vis. 2007;24(9):2622–7.
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Bothma JP, Garcia HG, Ng S, Perry MW, Gregor T, Levine M. Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo. Elife. 2015;4.
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Schmidt J V, Levorse JM, Tilghman SM. Enhancer competition between H19 and Igf2 does not mediate their imprinting. Proc Natl Acad Sci U S A. 1999;96(17):9733–8.
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Fukaya T, Lim B, Levine M. Enhancer Control of Transcriptional Bursting. Cell. 2016;166(2):358–68. PMCID: PMC4970759
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Leighton PA, Saam JR, Ingram RS, Stewart CL, Tilghman SM. An enhancer deletion affects both H19 and Igf2 expression. Genes Dev. 1995;9(17):2079–89.
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Zartman JJ, Shvartsman SY. Enhancer organization: transistor with a twist or something in a different vein?. Curr Biol. 2007;17(24):R1048–50.
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Zhang Y, Kurupati R, Liu L, Zhou XY, Zhang G, Hudaihed A, Filisio F, Giles-Davis W, Xu X, Karakousis GC, Schuchter LM, Xu W, Amaravadi R, Xiao M, Sadek N, Krepler C, Herlyn M, Freeman GJ, Rabinowitz JD, Ertl HCJ. Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy. Cancer Cell. 2017;32(3):377–391.e9. PMID: 28898698
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Kenyon C, Murphy CT. Enrichment of regulatory motifs upstream of predicted DAF-16 targets. Nat Genet. 2006;38(4):397–8; author reply 398.
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Nemenman I, Bialek W, van Steveninck R de R. Entropy and information in neural spike trains: progress on the sampling problem. Phys Rev E Stat Nonlin Soft Matter Phys. 2004;69(5 Pt 2):056111.
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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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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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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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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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Futran AS, Link J, Seger R, Shvartsman SY. ERK as a model for systems biology of enzyme kinetics in cells. Curr Biol. 2013;23(21):R972–9.
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Weaver C, Patel A, Shvartsman S, Levine M, Treen N. ERK signaling dissolves ERF repression condensates in living embryos. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(9). PMCID: PMC8892517
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Li SH-J, Li Z, Park JO, King CG, Rabinowitz JD, Wingreen NS, Gitai Z. Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions. Nat Microbiol. 2018;3(8):939–947. PMCID: PMC6278830
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Houchmandzadeh B, Wieschaus E, Leibler S. Establishment of developmental precision and proportions in the early Drosophila embryo. Nature. 2002;415(6873):798–802.
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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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Wyart M, Botstein D, Wingreen NS. Evaluating gene expression dynamics using pairwise RNA FISH data. PLoS Comput Biol. 2010;6(11):e1000979.
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Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P. An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution. 2013;67(4):1155–68.
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Mignot T, Shaevitz JW, Hartzell PL, Zusman DR. Evidence that focal adhesion complexes power bacterial gliding motility. Science. 2007;315(5813):853–6.
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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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Jin Y, Gittelman RM, Lu Y, Liu X, Li MD, Ling F, Akey J. Evolution of DNAase I hypersensitive sites in MHC regulatory regions of primates. Genetics. 2018;209(2):579–589.
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Jeong S, Rebeiz M, Andolfatto P, Werner T, True J, Carroll SB. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell. 2008;132(5):783–93.
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