2013
Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains. Connelly CF, Skelly DA, Dunham MJ, Akey JM. Mol Biol Evol. 2013 Apr 25. [Epub ahead of print][Pubmed][MBE accepted preprint]
High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Liachko I, Youngblood RA, Keich U, Dunham MJ. Genome Res. 2013 Apr;23(4):698-704.[Pubmed][Genome Research][PDF][SRA: 1 2 3]
Design and use of multiplexed chemostat arrays. Miller AW, Befort C, Mitchell E, Dunham MJ.
J Vis Exp. 2013 (72).[Pubmed][JoVE][PDF][GEO][PUMA]
Comparative gene expression between two yeast species. Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA. BMC Genomics. 2013 Jan 16;14:33.[Pubmed][BMC Genomics][PDF]
2012
In-class incentives that encourage students to take concepts assessments seriously. Smith MK, Thomas K, Dunham MJ. In-class incentives that encourage students to take concepts assessments seriously. Journal of College Science Teaching. 2012, 42(2): 57-61. [Journal of College Science Teaching][PDF (email me)]
Multiple pathways regulate minisatellite stability during stationary phase in yeast.
Kelly MK, Brosnan L, Jauert PA, Dunham MJ, Kirkpatrick DT. G3. 2012 Oct;2(10):1185-95. [Pubmed][G3][PDF]
Transcriptional consequences of aneuploidy. Sheltzer JM, Torres EM, Dunham MJ, Amon A. Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12644-9. [Pubmed][PNAS][PDF][GEO][PUMA][Nature Reviews Genetics Highlight]
Two flavors of bulk segregant analysis in yeast. Dunham MJ. Ed. Rifkin SA. Methods in Molecular Biology. Quantitative Trait Loci (QTL). 2012;871:41-54. [Pubmed][Methods in Molecular Biology][PDF (email me)]
Mutability and mutational spectrum of chromosome transmission fidelity genes. Stirling PC, Crisp MJ, Basrai MA, Tucker CM, Dunham MJ, Spencer FA, Hieter P. Chromosoma. 2012 Jun;121(3):263-75.[Pubmed][Chromosoma][PDF]
2011
Genetic Analysis of Desiccation Tolerance in Sachharomyces cerevisiae (sic). Calahan D, Dunham M, Desevo C, Koshland DE. Genetics. 2011 Oct;189(2):507-19. Epub 2011 Aug 11.[Pubmed][Genetics][PDF][Issue Highlight]
Nucleosome-coupled expression differences in closely-related species. Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG. BMC Genomics. 2011 Sep 26;12:466.[Pubmed][BMC Genomics][PDF][supplement][GEO]
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. Zill OA, Scannell DR, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. G3. 2011 June;1(1):11-25.[G3][PDF][GBrowse][website][G3 press release][Science Daily][GenomeWeb]
Origin-dependent inverted-repeat amplification: a replication-based model for generating palindromic amplicons. Brewer BJ, Payen C, Raghuraman MK, Dunham MJ. PLoS Genet. 2011 Mar;7(3):e1002016.[Pubmed][PLoS Genetics][PDF]
2010
Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination. Hoang ML, Tan FJ, Lai DC, Celniker SE, Hoskins RA, Dunham MJ, Zheng Y, Koshland D. PLoS Genet. 2010 Dec 2;6(12):e1001228.[Pubmed][PLoS Genetics][PDF]
Yeast evolution and ecology meet genomics. Dunham MJ, Louis EJ. EMBO Rep. 2011 Jan;12(1):8-10.[Pubmed][EMBO Reports][PDF]
Identification of Aneuploidy-tolerating Mutations. Torres EM, Dephoure N, Panneerselvam A, Tucker CM, Whittaker C, Gygi SP, Dunham MJ, Amon A. Cell. 2010 Oct 1;143(1):71-83.[Pubmed][Cell][PDF][GEO][PUMA][Cell Highlight][Nature highlight][Nature Reviews Cancer highlight][HHMI Research News]
Systematic planning of genome-scale experiments in poorly-studied species. Guan Y, Dunham MJ, Caudy AC, Troyanskaya OG. PLoS Comput Biol. 2010 Mar 5;6(3):e1000698.[Pubmed][PLoS Computational Biology][PDF][GEO][Nature Reviews Genetics Highlight]
Experimental Evolution in Yeast: A Practical Guide. Dunham MJ. Methods in Enzymology. Volume 470. Guide to Yeast Genetics: Functional Genomics, Proteomics and Other Systems Analysis. Ed. Weissman J, Guthrie C, Fink G. [Elsevier][PDF (email me)]
Whole-genome sequencing of a laboratory-evolved yeast strain. Araya CL, Payen C, Dunham MJ, Fields S. BMC Genomics. 2010 Feb 3;11:88. [Pubmed][BMC Genomics][PDF][SRA: 1 2 3 4]
2009
Telomere behavior in a hybrid yeast. Martin OC, DeSevo CG, Guo BZ, Koshland DE, Dunham MJ, Zheng Y. Cell Res. 2009 Jul;19(7):910-2. [Pubmed][Cell Research][PDF][GEO][PUMA]
Translocation and Assembly of Mitochondrially Coded Saccharomyces cerevisiae Cytochrome c Oxidase Subunit Cox2 by Oxa1 and Yme1 in the Absence of Cox18. Fiumera HL, Dunham MJ, Saracco SA, Butler CA, Kelly JA, Fox TD. Genetics. 2009 Jun;182(2):519-28. Epub 2009 Mar 23. [Pubmed][Genetics][PDF]
Predicting cellular growth from gene expression signatures. Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. PLoS Comput Biol. 2009 Jan;5(1):e1000257. Epub 2009 Jan 2. [Pubmed][PLoS Computational Biology][PDF]
The Ras/cAMP pathway and the CDK-like kinase Ime2 regulate the MAPK Smk1 and spore morphogenesis in Saccharomyces cerevisiae. McDonald CM, Wagner M, Dunham MJ, Shin ME, Ahmed NT, Winter E. Genetics. 2009 Feb;181(2):511-23. Epub 2008 Dec 15. [Pubmed][Genetics][PDF]
2008
The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast. Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, and Dunham MJ. PLoS Genet. 2008 Dec;4(12):e1000303. Epub 2008 Dec 12. [Pubmed][PLoS Genetics][PDF][supplement][GEO][PUMA]
Fis1 deficiency selects for compensatory mutations responsible for cell death and growth control defects. Cheng WC, Teng X, Park HK, Tucker CM, Dunham MJ, and Hardwick JM. Cell Death Differ. 2008 Aug 29. (Epub ahead of print) [Pubmed][Cell Death & Differentiation][PDF]
Comparing whole genomes using DNA microarrays. Gresham D, Dunham MJ, Botstein D. Nat Rev Genet. 2008 Apr;9(4):291-302. [Pubmed][Nature Reviews Genetics][PDF]
2007
Effects
of aneuploidy on cellular physiology and cell division in haploid
yeast. Torres EM, Sokolsky T, Tucker CM, Chan LY, Boselli M, Dunham MJ
and Amon A. Science. 2007 Aug 17;317(5840):916-24. [Pubmed][Science][PDF][GEO][PUMA][Science Perspective][The Scientist News][Nature Reviews Molecular Cell Biology Research Highlight][JCB Research Highlight]
Viewing the Larger
Context of Genomic Horizontal Integration. Matthew Hibbs, Grant
Wallace, Maitreya Dunham, Kai Li, and Olga Troyanskaya. Proceedings of
the 11th Int. Conf. on Information Visualization (IV07), 2007.[IEEE][PDF]
Synthetic ecology: a
model system for cooperation. Dunham MJ. Proc Natl Acad Sci U S A. 2007
Feb 6;104(6):1741-2. Epub 2007 Jan 31. [Pubmed][PNAS][PDF]
2006
Global Mapping of
Transposon Location. Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt
SC, Dunham MJ. PLoS Genet. 2006 Dec 15;2(12):e212. [Pubmed][PLoS Genetics][PDF][supplement][GEO][PUMA]
