Gresham:Publications

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==Publications==
==Publications==
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<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publicationsYou can add or remove lines as needed -->
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<biblio>
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1. Gresham D. DNA microarray-based mutation discovery and genotyping. Methods Mol Biol. 2011;772:179-91.
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#Paper1 pmid=19349972
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#Paper2 pmid=19119411
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2. Abbey D, Hickman, M, Gresham D and Berman J.  High-resolution SNP/CGH microarrays reveal the accumulation of loss of heterozygosity in commonly used Candida albicans strains.  G3: Genes, Genomes, Genetics Dec 2011 1:523-530.
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#Paper3 pmid=19079573
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#Paper4 pmid=18670625
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3.    Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R. Rational design of temperature-sensitive alleles using computational structure prediction. PLoS One. 2011;6(9):e23947. Epub 2011 Sep 2.
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#Paper5 pmid=18347592
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#Paper6 pmid=17959824
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4. Gresham D, Boer D, Caudy A, Ziv N, Brandt NJ, Storey JD, Botstein DSystem-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics. 2011 vol. 187 (1) pp. 299-317. (published online Oct 13, 2010).
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#Paper7 pmid=17389913
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#Paper8 pmid=17173485
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5. Gresham D, Usaite R, Germann SM, Lisby M, Botstein D and Regenberg B Adaptation to diverse nitrogen limited environments by deletion or extrachromosomal element formation of the GAP1 locus. PNAS (2010): 107(43): 18551-6.
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#Paper9 pmid=16816424
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#Paper10 pmid=16527929
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6. Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, and Kruglyak L. Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature, 2010. 464 (7291): p. 1039-1042.
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#Paper11 pmid=15322984
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#Paper12 pmid=14691732
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7. Gresham D, Curry B, Ward A, Gordon DB, Brizuela L, Kruglyak L, Botstein D.  Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.  PNAS Jan;26;107(4):1482-7. Epub 2010 Jan 8.
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#Paper13 pmid=12089515
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#Paper14 pmid=11704928
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8. Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nature Biotechnology. 2009 Apr;27(4):369-77
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#Paper15 pmid=11299048
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#Paper16 pmid=11053686
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9. Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, and Troyanskaya OG. Predicting cellular growth from gene expression signatures PLoS Computational Biology. 2009 Jan;5(1):e1000257.
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#Paper17 pmid=10831399
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</biblio>
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10. Gresham D., Desai, M.M., Tucker, C.M., Jenq, H.T., Pai, D.A., Ward, A., DeSevo, C.G., Botstein, D., and Dunham, M.J. The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast. PLoS Genetics. 2008 Dec;4(12):e1000303.
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11. Gresham D, Kruglyak L, "Rise of the machines" PLoS Genetics. 2008 Aug 1;4(8):e100013
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12. Gresham D, Dunham M, Botstein D, “Comparing Whole Genomes with DNA Microarrays” Nature Reviews Genetics (2008) Apr;9(4):291-302.
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13. Brauer MJ, Huttenhower, C, Airoldi, EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D, “Coordination of Growth Rate, Cell Cycle, Stress Response and Metabolic Activity in Yeast” Molecular Biology of the Cell. (2008) Jan;19(1):352-67. Epub 2007 Oct 24.
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14. Schacherer J, Ruderfer D, Gresham D, Dolinski K, Botstein D, Kruglyak L, “Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains” PLoS ONE. (2007) Mar 28;2(3):e322.
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15. Gresham D, Ruderfer D, Pratt, S, Schacherer J, Dunham M, Botstein D, Kruglyak L,  “Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray” Science. 31;311:1932-6 (2006)
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16. Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt S, Dunham M.,  "Global Mapping of Transposon Location." PLoS Genetics (2006) Dec 15;2(12):e212.
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17. Heck JA, Gresham D, Botstein D, Alani E, “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements” Genetics 174, 519-23 (2006).
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18. Morar B, Gresham D, Angelicheva D, Tournev I, Gooding R, Guergueltcheva V, Schmidt C, Abicht A, Lochmuller H, Tordai A, Kalmar L, Nagy M, Karcagi V, Jeanpierre M, Herczegfalvi A, Beeson D, Venkataraman V, Warwick Carter K, ReeveJ, de Pablo R, Kucinskas V, Kalaydjieva L, “Mutation history of the Roma/Gypsies” Am J Hum Genet. 75(4):596-609 (2004).
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19. Zhivotovsky LA, Underhill PA, Cinnioglu C, Kayser M, Morar B, Kivisild T,Scozzari R, Cruciani F, Destro-Bisol G, Spedini G, Chambers GK, Herrera RJ, Yong KK, Gresham D, Tournev I, Feldman MW, Kalaydjieva L, “The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time.” Am J Hum Genet. 74(1):50-61 (2004).
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20. Gresham D, Morar B, Underhill PA, Passarino G, Lin AA, Wise C, Angelicheva D, Calafell F, Oefner PJ, Shen P, Tournev I, de Pablo R, Kucinskas V, Perez-Lezaun A, Marushiakova E, Popov V, Kalaydjieva L,  “Origins and divergence of the Roma (Gypsies)” Am J Hum Genet. 69(6):1314-31 (2001).
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21. Kalaydjieva L, Gresham D, Calafell F,  “Genetic studies of the Roma (Gypsies): a review.” BMC Med Genet. 2(1):5 (2001).
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22. Kalaydjieva L, Gresham D, Gooding R, Heather L, Baas F, de Jonge R, Blechschmidt K, Angelicheva D, Chandler D, Worsley P, Rosenthal A, King RH, Thomas PK., “N-myc downstream-regulated gene 1 is mutated in hereditary motor and sensory neuropathy-Lom” Am J Hum Genet. 67(1):47-58 (2000).
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23. Chandler D, Angelicheva D, Heather L, Gooding R, Gresham D, Yanakiev P, de Jonge R, Baas F, Dye D, Karagyozov L, Savov A, Blechschmidt K, Keats B, Thomas PK, King RH, Starr A, Nikolova A, Colomer J, Ishpekova B, Tournev I, Urtizberea JA, Merlini L, Butinar D, Chabrol B, Voit T, Baethmann M, Nedkova V, Corches A, Kalaydjieva L, “Hereditary motor and sensory neuropathy--Lom (HMSNL): refined genetic mapping in Romani (Gypsy) families from several European countries” Neuromuscul Disord. 2000 Dec;10(8):584-91.

Current revision

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Publications

1. Gresham D. DNA microarray-based mutation discovery and genotyping. Methods Mol Biol. 2011;772:179-91.

2. Abbey D, Hickman, M, Gresham D and Berman J. High-resolution SNP/CGH microarrays reveal the accumulation of loss of heterozygosity in commonly used Candida albicans strains. G3: Genes, Genomes, Genetics Dec 2011 1:523-530.

3. Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R. Rational design of temperature-sensitive alleles using computational structure prediction. PLoS One. 2011;6(9):e23947. Epub 2011 Sep 2.

4. Gresham D, Boer D, Caudy A, Ziv N, Brandt NJ, Storey JD, Botstein D. System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics. 2011 vol. 187 (1) pp. 299-317. (published online Oct 13, 2010).

5. Gresham D, Usaite R, Germann SM, Lisby M, Botstein D and Regenberg B Adaptation to diverse nitrogen limited environments by deletion or extrachromosomal element formation of the GAP1 locus. PNAS (2010): 107(43): 18551-6.

6. Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, and Kruglyak L. Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature, 2010. 464 (7291): p. 1039-1042.

7. Gresham D, Curry B, Ward A, Gordon DB, Brizuela L, Kruglyak L, Botstein D. Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. PNAS Jan;26;107(4):1482-7. Epub 2010 Jan 8.

8. Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nature Biotechnology. 2009 Apr;27(4):369-77

9. Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, and Troyanskaya OG. Predicting cellular growth from gene expression signatures PLoS Computational Biology. 2009 Jan;5(1):e1000257.

10. Gresham D., Desai, M.M., Tucker, C.M., Jenq, H.T., Pai, D.A., Ward, A., DeSevo, C.G., Botstein, D., and Dunham, M.J. The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast. PLoS Genetics. 2008 Dec;4(12):e1000303.

11. Gresham D, Kruglyak L, "Rise of the machines" PLoS Genetics. 2008 Aug 1;4(8):e100013

12. Gresham D, Dunham M, Botstein D, “Comparing Whole Genomes with DNA Microarrays” Nature Reviews Genetics (2008) Apr;9(4):291-302.

13. Brauer MJ, Huttenhower, C, Airoldi, EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D, “Coordination of Growth Rate, Cell Cycle, Stress Response and Metabolic Activity in Yeast” Molecular Biology of the Cell. (2008) Jan;19(1):352-67. Epub 2007 Oct 24.

14. Schacherer J, Ruderfer D, Gresham D, Dolinski K, Botstein D, Kruglyak L, “Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains” PLoS ONE. (2007) Mar 28;2(3):e322.

15. Gresham D, Ruderfer D, Pratt, S, Schacherer J, Dunham M, Botstein D, Kruglyak L, “Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray” Science. 31;311:1932-6 (2006)

16. Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt S, Dunham M., "Global Mapping of Transposon Location." PLoS Genetics (2006) Dec 15;2(12):e212.

17. Heck JA, Gresham D, Botstein D, Alani E, “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements” Genetics 174, 519-23 (2006).

18. Morar B, Gresham D, Angelicheva D, Tournev I, Gooding R, Guergueltcheva V, Schmidt C, Abicht A, Lochmuller H, Tordai A, Kalmar L, Nagy M, Karcagi V, Jeanpierre M, Herczegfalvi A, Beeson D, Venkataraman V, Warwick Carter K, ReeveJ, de Pablo R, Kucinskas V, Kalaydjieva L, “Mutation history of the Roma/Gypsies” Am J Hum Genet. 75(4):596-609 (2004).

19. Zhivotovsky LA, Underhill PA, Cinnioglu C, Kayser M, Morar B, Kivisild T,Scozzari R, Cruciani F, Destro-Bisol G, Spedini G, Chambers GK, Herrera RJ, Yong KK, Gresham D, Tournev I, Feldman MW, Kalaydjieva L, “The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time.” Am J Hum Genet. 74(1):50-61 (2004).

20. Gresham D, Morar B, Underhill PA, Passarino G, Lin AA, Wise C, Angelicheva D, Calafell F, Oefner PJ, Shen P, Tournev I, de Pablo R, Kucinskas V, Perez-Lezaun A, Marushiakova E, Popov V, Kalaydjieva L, “Origins and divergence of the Roma (Gypsies)” Am J Hum Genet. 69(6):1314-31 (2001).

21. Kalaydjieva L, Gresham D, Calafell F, “Genetic studies of the Roma (Gypsies): a review.” BMC Med Genet. 2(1):5 (2001).

22. Kalaydjieva L, Gresham D, Gooding R, Heather L, Baas F, de Jonge R, Blechschmidt K, Angelicheva D, Chandler D, Worsley P, Rosenthal A, King RH, Thomas PK., “N-myc downstream-regulated gene 1 is mutated in hereditary motor and sensory neuropathy-Lom” Am J Hum Genet. 67(1):47-58 (2000).

23. Chandler D, Angelicheva D, Heather L, Gooding R, Gresham D, Yanakiev P, de Jonge R, Baas F, Dye D, Karagyozov L, Savov A, Blechschmidt K, Keats B, Thomas PK, King RH, Starr A, Nikolova A, Colomer J, Ishpekova B, Tournev I, Urtizberea JA, Merlini L, Butinar D, Chabrol B, Voit T, Baethmann M, Nedkova V, Corches A, Kalaydjieva L, “Hereditary motor and sensory neuropathy--Lom (HMSNL): refined genetic mapping in Romani (Gypsy) families from several European countries” Neuromuscul Disord. 2000 Dec;10(8):584-91.

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