Publications

81 Publications
Applied Filters: First Letter Of Title: G Reset

G

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Sweeton D, Parks S, Costa M, Wieschaus E. Gastrulation in Drosophila: the formation of the ventral furrow and posterior midgut invaginations. Development. 1991;112(3):775–89.
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Sandell LL, Guan X-J, Ingram R, Tilghman SM. Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta. Proc Natl Acad Sci U S A. 2003;100(8):4622–7.
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Nofal M, Wang T, Yang L, Jankowski C, Li S, Han S, Parsons L, Frese A, Gitai Z, Anthony T, Wühr M, Sabatini D, Rabinowitz J. GCN2 adapts protein synthesis to scavenging-dependent growth. Cell systems. 2022;13(2):158–172.e9. PMCID: PMC8961722
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Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks B, van de Rijn M. Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. Am J Pathol. 2003;163(6):2383–95.
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Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai K-M, Ji J, Dudoit S, Ng IOL, van de Rijn M, Botstein D, Brown PO. Gene expression patterns in human liver cancers. Mol Biol Cell. 2002;13(6):1929–39.
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Schaner ME, Ross DT, Ciaravino G, Sorlie T, Troyanskaya O, Diehn M, Wang YC, Duran GE, Sikic TL, Caldeira S, Skomedal H, Tu I-P, Hernandez-Boussard T, Johnson SW, O’Dwyer PJ, Fero MJ, Kristensen GB, Borresen-Dale A-L, Hastie T, Tibshirani R, van de Rijn M, Teng NN, Longacre TA, Botstein D, Brown PO, Sikic BI. Gene expression patterns in ovarian carcinomas. Mol Biol Cell. 2003;14(11):4376–86.
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Kim J, Ghasemzadeh N, Eapen DJ, Chung NC, Storey JD, Quyyumi AA, Gibson G. Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death. Genome Med. 2014;6(5):40.
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Sørlie T, Perou CM, Fan C, Geisler S, Aas T, Nobel A, Anker G, Akslen LA, Botstein D, Børresen-Dale A-L, Lønning PE. Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer. Mol Cancer Ther. 2006;5(11):2914–8.
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Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A. 2004;101(3):811–6.
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Liang Y, Diehn M, Watson N, Bollen AW, Aldape KD, Nicholas K, Lamborn KR, Berger MS, Botstein D, Brown PO, Israel MA. Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci U S A. 2005;102(16):5814–9.
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Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi J-T, van de Rijn M, Botstein D, Brown PO. Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol. 2004;2(2):E7.
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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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Consortium GO. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010;38(Database issue):D331–5.
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Kim Y, Andreu MJ, Lim B, Chung K, Terayama M, Jiménez G, Berg CA, Lu H, Shvartsman SY. Gene regulation by MAPK substrate competition. Dev Cell. 2011;20(6):880–7.
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Levine M, Davidson EH. Gene regulatory networks for development. Proc Natl Acad Sci U S A. 2005;102(14):4936–42.
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Jaffe A, Storey J, Ji H, Leek J. Gene set bagging for estimating the probability a statistically significant result will replicate. BMC bioinformatics. 2013;14:360. PMCID: PMC3890500
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Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, Ahringer J, Li H, Kenyon C. Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature. 2003;424(6946):277–83.
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Vrana PB, Fossella JA, Matteson P, del Rio T, O’Neill MJ, Tilghman SM. Genetic and epigenetic incompatibilities underlie hybrid dysgenesis in Peromyscus. Nat Genet. 2000;25(1):120–4.
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Slotte T, Hazzouri KM, Stern D, Andolfatto P, Wright SI. Genetic architecture and adaptive significance of the selfing syndrome in Capsella. Evolution. 2012;66(5):1360–74.
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Reisser C, Dick C, Kruglyak L, Botstein D, Schacherer J, Hess D. Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case. G3 (Bethesda). 2013;.
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Breunig JS, Hackett SR, Rabinowitz JD, Kruglyak L. Genetic basis of metabolome variation in yeast. PLoS Genet. 2014;10(3):e1004142.
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Zwarts L, Broeck LV, Cappuyns E, Ayroles J, Magwire MM, Vulsteke V, Clements J, Mackay TFC, Callaerts P. The genetic basis of natural variation in mushroom body size in Drosophila melanogaster. Nat Commun. 2015;6:10115. PMCID: PMC4682101
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Corbett-Detig RB, Zhou J, Clark A, Hartl DL, Ayroles J. Genetic incompatibilities are widespread within species. Nature. 2013;504(7478):135–7.
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Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, L Y Koh J, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin Z-Y, Liang W, Marback M, Paw J, San Luis B-J, Shuteriqi E, Tong AHY, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras A-C, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C. The genetic landscape of a cell. Science. 2010;327(5964):425–31.
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Rossi JM, Chen H, Tilghman SM. Genetic map of the fused locus on mouse chromosome 17. Genomics. 1994;23(1):178–84.
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Lang GI, Botstein D, Desai MM. Genetic variation and the fate of beneficial mutations in asexual populations. Genetics. 2011;188(3):647–61.
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Mackay TFC, Stone EA, Ayroles J. The genetics of quantitative traits: challenges and prospects. Nat Rev Genet. 2009;10(8):565–77.
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Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G. GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics. 2004;5:141.
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Batut P, Bing X, Sisco Z, Raimundo J, Levo M, Levine M. Genome organization controls transcriptional dynamics during development. Science (New York, N.Y.). 2022;375(6580):566–570. PMID: 35113722
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Ranade K, Hinds D, Hsiung CA, Chuang L-M, Chang M-S, Chen Y-T, Pesich R, Hebert J, Chen Y-DI, Dzau V, Olshen R, Curb D, Botstein D, Cox DR, Risch N. A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins. Am J Hypertens. 2003;16(2):158–62.
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Lakhina V, Murphy CT. Genome Sequencing Fishes out Longevity Genes. Cell. 2015;163(6):1312–3. PMID: 26638067
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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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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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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
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Diehn M, Bhattacharya R, Botstein D, Brown PO. Genome-scale identification of membrane-associated human mRNAs. PLoS Genet. 2006;2(1):e11.
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Markstein M, Markstein P, Markstein V, Levine MS. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci U S A. 2002;99(2):763–8.
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Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem. 2002;277(34):31079–88.
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Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L. Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS One. 2007;2(3):e322.
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O’Connell B, Adamson B, Lydeard J, Sowa M, Ciccia A, Bredemeyer A, Schlabach M, Gygi S, Elledge S, Harper W. A genome-wide camptothecin sensitivity screen identifies a mammalian MMS22L-NFKBIL2 complex required for genomic stability. Molecular cell. 2010;40(4):645–57. PMCID: PMC3006237
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Pritykin Y, Ghersi D, Singh M. Genome-Wide Detection and Analysis of Multifunctional Genes. PLoS Comput Biol. 2015;11(10):e1004467.
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Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham M, Botstein D, Kruglyak L. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science. 2006;311(5769):1932–6.
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Lakhina V, Arey R, Kaletsky R, Kauffman A, Stein G, Keyes W, Xu D, Murphy CT. Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs. Neuron. 2015;85(2):330–45.
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Adamson B, Smogorzewska A, Sigoillot F, King R, Elledge S. A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nature cell biology. 2012;14(3):318–28. PMCID: PMC3290715
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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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Krishnan A, Zhang R, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG. Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nat Neurosci. 2016;19(11):1454–1462. PMID: 27479844