Epernicus: Gavin Sherlock, Ph.D.

Gavin Sherlock, Ph.D.

Position:
Associate Professor

Genetics

Stanford University (Stanford, CA)
Degrees:

Ph.D., Molecular Biology, The University of Manchester (Manchester, UK)

B.Sc., Genetics, The University of Manchester (Manchester, UK)
Past Advisors:

David Botstein (as Post Doctoral Fellow)

Bruce Futcher (as Post Doctoral Fellow)

John Rosamond (as Graduate Student - Ph.D.)
Research:

Communities:

Gavin Sherlock's Genealogy

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Gavin Sherlock's Publications (83)

Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency.
Wenger JW, Piotrowski J, Nagarajan S, Chiotti K, Sherlock G, Rosenzweig F

PLoS genetics. 2011 Aug;7(8):e1002202
DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer.
Kobayashi Y, Absher DM, Gulzar ZG, Young SR, McKenney JK, Peehl DM, Brooks JD, Myers RM, Sherlock G

Genome research. 2011 Jul;21(7):1017-27
Integrated genomic analyses of ovarian carcinoma.

Nature. 2011 Jun 30;474(7353):609-15
A user's guide to the encyclopedia of DNA elements (ENCODE).
Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE

PLoS biology. 2011 Apr;9(4):e1001046
Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape.
Kvitek DJ, Sherlock G

PLoS genetics. 2011 Apr;7(4):e1002056
Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.
Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ, Ball CA

Bioinformatics (Oxford, England). 2010 Oct 1;26(19):2470-1
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.
Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, Sherlock G, Snyder M

Genome research. 2010 Oct;20(10):1451-8
A genome-wide analysis reveals no nuclear dobzhansky-muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities.
Kao KC, Schwartz K, Sherlock G

PLoS genetics. 2010 Jul;6(7):e1001038
Microarray karyotyping of maltose-fermenting Saccharomyces yeasts with differing maltotriose utilization profiles reveals copy number variation in genes involved in maltose and maltotriose utilization.
Duval EH, Alves Jr SL, Dunn B, Sherlock G, Stambuk BU

Journal of applied microbiology. 2010 Jul;109(1):248-59
TB database 2010: overview and update.
Galagan JE, Sisk P, Stolte C, Weiner B, Koehrsen M, Wymore F, Reddy TB, Zucker JD, Engels R, Gellesch M, Hubble J, Jin H, Larson L, Mao M, Nitzberg M, White J, Zachariah ZK, Sherlock G, Ball CA, Schoolnik GK

Tuberculosis (Edinburgh, Scotland). 2010 Jul;90(4):225-35
Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae.
Wenger JW, Schwartz K, Sherlock G

PLoS genetics. 2010 May;6(5):e1000942
New tools at the Candida Genome Database: biochemical pathways and full-text literature search.
Skrzypek MS, Arnaud MB, Costanzo MC, Inglis DO, Shah P, Binkley G, Miyasato SR, Sherlock G

Nucleic acids research. 2010 Jan;38(Database issue):D428-32
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.
Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G

Nucleic acids research. 2010 Jan;38(Database issue):D420-7
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z

BMC genomics. 2010;11:663
Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis.
Stambuk BU, Dunn B, Alves SL, Duval EH, Sherlock G

Genome research. 2009 Dec;19(12):2271-8
Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans.
Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G

Trends in microbiology. 2009 Jul;17(7):295-303
Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA

Nature. 2009 Jun 4;459(7247):657-62
Implementation of GenePattern within the Stanford Microarray Database.
Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, Reddy TB, Wymore F, Zachariah ZK, Sherlock G, Ball CA

Nucleic acids research. 2009 Jan;37(Database issue):D898-901
TB database: an integrated platform for tuberculosis research.
Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK

Nucleic acids research. 2009 Jan;37(Database issue):D499-508
Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae.
Kao KC, Sherlock G

Nature genetics. 2008 Dec;40(12):1499-504
Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.
Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G

PLoS genetics. 2008 Dec;4(12):e1000299
Changes to NIH grant system may backfire.
Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE

Science (New York, N.Y.). 2008 Nov 21;322(5905):1187-8
Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Nature. 2008 Oct 23;455(7216):1061-8
Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus.
Dunn B, Sherlock G

Genome research. 2008 Oct;18(10):1610-23
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD

Nature biotechnology. 2008 Mar;26(3):305-12

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