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Maitreya's Google Scholar page

2014

Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps. Burton JN, Liachko I, Dunham MJ, Shendure J. G3. 2014 May 22. pii: g3.114.011825. doi: 10.1534/g3.114.011825. [Epub ahead of print][Pubmed][G3][SRA][G3 press release][GenomeWeb][BioIT World]

GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris. Liachko I, Youngblood RA, Tsui K, Bubb KL, Queitsch C, Raghuraman MK, Nislow C, Brewer BJ, Dunham MJ. PLoS Genet. 2014 Mar 6;10(3):e1004169. doi: 10.1371/journal.pgen.1004169. eCollection 2014 Mar. [Pubmed][PLoS Genetics][PDF][SRA: 1 2 3 4 5]

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection. Payen C, Di Rienzi SC, Ong GT, Pogachar JL, Sanchez JC, Sunshine AB, Raghuraman MK, Brewer BJ, Dunham MJ. G3. 2014 Mar 20;4(3):399-409. doi: 10.1534/g3.113.009365. [Pubmed][G3][PDF][GEO][NCBI Biosamples:1 2 3 4 5 6 7]

An Autonomously Replicating Sequence for use in a wide range of budding yeasts. Liachko I, Dunham MJ. FEMS Yeast Res. 2014 Mar;14(2):364-7. doi: 10.1111/1567-1364.12123. Epub 2013 Dec 2. [Pubmed][FEMS Yeast Research][PDF]

2013

Contemporary, yeast-based approaches to understanding human genetic variation. Dunham MJ, Fowler DM. Curr Opin Genet Dev. 2013 Nov 16. doi:pii: S0959-437X(13)00136-6. 10.1016/j.gde.2013.10.001. [Epub ahead of print][Pubmed][Current Opinion in Genetics & Development][PDF]

Genome-wide Consequences of Deleting Any Single Gene. Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM. Mol Cell. 2013 Nov 6. doi:pii: S1097-2765(13)00748-X. 10.1016/j.molcel.2013.09.026. [Epub ahead of print][Pubmed][Molecular Cell][PDF][SRA][BioProject][Johns Hopkins Press Release][SGD][The Scientist][Futurity][Science Blog][Science Daily][Red Orbit][Bioscience Technology][Health News Digest][E! Science News]

A New System for Comparative Functional Genomics of Saccharomyces Yeasts. Caudy AA, Guan Y, Jia Y, Hansen C, Desevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D, Bauerle C, Bisaria N, Bradley PH, Breunig JS, Bush EC, Cappel DA, Capra E, Chen W, Clore J, Combs PA, Doucette C, Demuren O, Fellowes P, Freeman S, Frenkel E, Gadala-Maria D, Gawande R, Glass D, Grossberg S, Gupta A, Hammonds-Odie L, Hoisos A, Hsi J, Hsu YH, Inukai S, Karczewski KJ, Ke X, Kojima M, Leachman S, Lieber D, Liebowitz A, Liu J, Liu Y, Martin T, Mena J, Mendoza R, Myhrvold C, Millian C, Pfau S, Raj S, Rich M, Rokicki J, Rounds W, Salazar M, Salesi M, Sharma R, Silverman SJ, Singer C, Sinha S, Staller M, Stern P, Tang H, Weeks S, Weidmann M, Wolf A, Young C, Yuan J, Crutchfield C, McClean MN, Murphy CT, LlinĂ¡s M, Botstein D, Troyanskaya OG, Dunham MJ. Genetics. 2013 Sep;195(1):275-87. Epub 2013 Jul 12.[Pubmed][Genetics][PDF][Function prediction website][GEO1][GEO2][Lewis-Sigler Institute article]

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EG, Davis TN, Dunham MJ, Maccoss MJ, Akey JM. Genome Res. 2013 Sep;23(9):1496-504. Epub 2013 May 29.[Pubmed][Genome Research][PDF][web site]

Coupling Unbiased Mutagenesis to High-throughput DNA Sequencing Uncovers Functional Domains in the Ndc80 Kinetochore Protein of Saccharomyces cerevisiae. Tien JF, Fong KK, Umbreit NT, Payen C, Zelter A, Asbury CL, Dunham MJ, Davis TN. Genetics. 2013 Sep;195(1):159-70. Epub 2013 Jul 5.[Pubmed][Genetics][PDF]

The yeast alix homolog bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes. Pashkova N, Gakhar L, Winistorfer SC, Sunshine AB, Rich M, Dunham MJ, Yu L, Piper RC. Dev Cell. 2013 Jun 10;25(5):520-33. [Pubmed][Developmental Cell][PDF][annotation script]

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 Jul;30(7):1605-13. [Pubmed][MBE][PDF]

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 Saccharomyces cerevisiae. 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.[Pubmed][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][PUMA][Experiment Recommender][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. [Pubmed][Methods in Enzymology][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]

Functional analysis of gene duplications in Saccharomyces cerevisiae. Guan Y, Dunham MJ, Troyanskaya OG. Genetics. 2006 Dec 6. [Pubmed][Genetics][PDF]

Mapping Novel Traits by Array-assisted Bulk Segregant Analysis in Saccharomyces cerevisiae. Brauer MJ, Christianson CM, Pai DA, Dunham MJ. Genetics. 2006 Jul;173(3):1813-6. Epub 2006 Apr 19. [Pubmed][Genetics][PDF][Web Supplement]

Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, Kruglyak L. Science. 2006 Mar 31;311(5769):1932-6. Epub 2006 Mar 9. [Pubmed][Science][PDF][Web Supplement]

2004

Accurate detection of aneuploidies in array CGH and gene expression microarray data. Myers CL, Dunham MJ, Kung SY, Troyanskaya OG. Bioinformatics. 2004 Dec 12;20(18):3533-43. Epub 2004 Jul 29. [Pubmed][Bioinformatics][PDF][Press Release]

2002

Characteristic Genome Rearrangements in Experimental Evolution of S. cerevisiae. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig RF, Botstein D. Proc Natl Acad Sci USA. 2002 Dec 10;99(25):16144-9. [Pubmed][PNAS][PDF][Web supplement][GEO][PUMA][Science Editor's Choice]

2001

Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Haab BB, Dunham MJ, Brown PO. Genome Biology. 2001;2(2):RESEARCH0004. [Pubmed][Genome Biology][PDF][Web supplement][GEO][PUMA][Genome Biology Minireview]

2000

Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Byrne ME, Barley R, Curtis M, Arroyo JM, Dunham M, Hudson A, Martienssen RA. Nature. 2000 Dec 21-28;408(6815):967-71. [Pubmed][Nature][PDF]

1999

ika1 and rag1 as Markers for the Development of the Zebrafish Immune System. Dunham MJ and Steiner L. Biology Undergraduate Journal. Volume 2, Spring 1999. [MIT BUG Journal(only viewable at MIT)][PDF]


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