Publications

74 Publications
Applied Filters: First Letter Of Last Name: H Reset

H

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Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC. Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies. Genes Dev. 2007;21(2):148–59.
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Hackett SR, Zanotelli VRT, Xu W, Goya J, Park JO, Perlman DH, Gibney PA, Botstein D, Storey JD, Rabinowitz JD. Systems-level analysis of mechanisms regulating yeast metabolic flux. Science. 2016;354(6311). PMID: 27789812
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Haddrill PR, Bachtrog D, Andolfatto P. Positive and negative selection on noncoding DNA in Drosophila simulans. Mol Biol Evol. 2008;25(9):1825–34.
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Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol. 2005;6(8):R67.
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Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P. Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 2005;15(6):790–9.
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Hahm J-H, Kim S, DiLoreto R, Shi C, Lee S-J V, Murphy CT, Nam HG. C. elegans maximum velocity correlates with healthspan and is maintained in worms with an insulin receptor mutation. Nat Commun. 2015;6:8919. PMCID: PMC4656132
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Haley B, Foys B, Levine M. Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila. Proc Natl Acad Sci U S A. 2010;107(25):11435–40.
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Haley B, Hendrix D, Trang V, Levine M. A simplified miRNA-based gene silencing method for Drosophila melanogaster. Dev Biol. 2008;321(2):482–90.
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Halligan DL, Eyre-Walker A, Andolfatto P, Keightley PD. Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Res. 2004;14(2):273–9.
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Hansen CH, Sourjik V, Wingreen NS. A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli. Proc Natl Acad Sci U S A. 2010;107(40):17170–5.
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Hansen CH, Endres RG, Wingreen NS. Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation. PLoS Comput Biol. 2008;4(1):e1.
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Harafuji N, Keys DN, Levine M. Genome-wide identification of tissue-specific enhancers in the Ciona tadpole. Proc Natl Acad Sci U S A. 2002;99(10):6802–5.
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Harbison ST, Carbone MA, Ayroles J, Stone EA, Lyman RF, Mackay TFC. Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep. Nat Genet. 2009;41(3):371–5.
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Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, O’Connor C, Luo J, Nair V, Cebrián C, Spence JR, Bitzer M, Troyanskaya OG, Hodgin JB, Wiggins RC, Freedman BS, Kretzler M, Bank ER cDNA, Network NSS. Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI Insight. 2019;4(1). PMCID: PMC6485369
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Hark AT, Schoenherr CJ, Katz DJ, Ingram RS, Levorse JM, Tilghman SM. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature. 2000;405(6785):486–9.
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Hark AT, Tilghman SM. Chromatin conformation of the H19 epigenetic mark. Hum Mol Genet. 1998;7(12):1979–85.
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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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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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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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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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Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, Angiuoli S V, White O, Botstein D, Dolinski K. The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PLoS One. 2007;2(8):e766.
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Heist T, Fukaya T, Levine M. Large distances separate coregulated genes in living embryos. Proc Natl Acad Sci U S A. 2019;116(30):15062–15067. PMCID: PMC6660726
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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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Hendrix DA, Hong J-W, Zeitlinger J, Rokhsar DS, Levine MS. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci U S A. 2008;105(22):7762–7.
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Hermans D, Gautam S, García-Cañaveras JC, Gromer D, Mitra S, Spolski R, Li P, Christensen S, Nguyen R, Lin J-X, Oh J, Du N, Veenbergen S, Fioravanti J, Ebina-Shibuya R, Bleck C, Neckers LM, Rabinowitz JD, Gattinoni L, Leonard WJ. Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity. Proc Natl Acad Sci U S A. 2020;117(11):6047–6055. PMCID: PMC7084161
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Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, San Luis B, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. 2009;5(3):e1000407.
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Hess DC, Lu W, Rabinowitz JD, Botstein D. Ammonium toxicity and potassium limitation in yeast. PLoS Biol. 2006;4(11):e351.
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Hibbs MA, Dirksen NC, Li K, Troyanskaya OG. Visualization methods for statistical analysis of microarray clusters. BMC Bioinformatics. 2005;6:115.
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Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics. 2007;23(20):2692–9.
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Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG. Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol. 2009;5(3):e1000322.
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Hickman MJ, Petti AA, Ho-Shing O, Silverman SJ, McIsaac S, Lee TA, Botstein D. Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast. Mol Biol Cell. 2011;22(21):4192–204.
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Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B. Neural-specific elongation of 3’ UTRs during Drosophila development. Proc Natl Acad Sci U S A. 2011;108(38):15864–9.
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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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Hirose K, Meir Y, Wingreen NS. Local moment formation in quantum point contacts. Phys Rev Lett. 2003;90(2):026804.
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Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry M. Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 2006;34(Database issue):D442–5.
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Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, L Y Koh J, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews BJ, Botstein D, Graham TR, Yoshida M, Boone C. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat Biotechnol. 2009;27(4):369–77.
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Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry M. Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008;36(Database issue):D577–81.
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Hong S, Zhou W, Fang B, Lu W, Loro E, Damle M, Ding G, Jager J, Zhang S, Zhang Y, Feng D, Chu Q, Dill BD, Molina H, Khurana TS, Rabinowitz JD, Lazar MA, Sun Z. Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion. Nat Med. 2017;23(2):223–234. PMCID: PMC5540654
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Hong J-W, Hendrix DA, Levine MS. Shadow enhancers as a source of evolutionary novelty. Science. 2008;321(5894):1314.
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Hong J-W, Hendrix DA, Papatsenko D, Levine MS. How the Dorsal gradient works: insights from postgenome technologies. Proc Natl Acad Sci U S A. 2008;105(51):20072–6.
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Horlbeck M, Xu A, Wang M, Bennett N, Park C, Bogdanoff D, Adamson B, Chow E, Kampmann M, Peterson T, Nakamura K, Fischbach M, Weissman J, Gilbert L. Mapping the Genetic Landscape of Human Cells. Cell. 2018;174(4):953–967.e22. PMCID: PMC6426455
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Horlbeck M, Gilbert L, Villalta J, Adamson B, Pak R, Chen Y, Fields A, Park C, Corn J, Kampmann M, Weissman J. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. eLife. 2016;5. PMCID: PMC5094855
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Houchmandzadeh B, Wieschaus E, Leibler S. Precise domain specification in the developing Drosophila embryo. Phys Rev E Stat Nonlin Soft Matter Phys. 2005;72(6 Pt 1):061920.
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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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Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017;5(3):221–229.e4. PMID: 28957656
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Hsu A-L, Murphy CT, Kenyon C. Regulation of aging and age-related disease by DAF-16 and heat-shock factor. Science. 2003;300(5622):1142–5.