Research Interests  
Lab Members and Collaborators  


Maitreya's Google Scholar page

Maitreya's Bibliography at NCBI

ORCID: 0000-0001-9944-2666

Published strains database. To request a strain, please email me at maitreya@uw.edu

Functional interpretation, cataloging, and analysis of 1,341 glucose-6-phosphate dehydrogenase variants. Geck RC, Powell NR, Dunham MJ. AJHG. 2023 Feb 2;110:1–12. [AJHG][GitHub][PDF][bioRxiv]

Caffeine-tolerant mutations selected through an at-home yeast experimental evolution teaching lab. Moresi NG, Geck RC, Skophammer R, Godin D, yEvo Students, Taylor MB, Dunham MJ. bioRxiv. January 20, 2023. [bioRxiv]

yEvo: Experimental evolution in high school classrooms selects for novel mutations and epistatic interactions that impact clotrimazole resistance in S. cerevisiae. Taylor MB, Skophammer R, Warwick AR, Geck RC, Boyer JM, yEvo Students, Walson M, Large CRL, Hickey AS, Rowley PA#, Dunham MJ# (#co-corresponding authors). G3. 2022 Nov 4;12(11):jkac246. doi: 10.1093/g3journal/jkac246.[Pubmed][G3][PDF][SRA][bioRxiv]

Hotspot of de novo telomere addition stabilizes linear amplicons in yeast grown in sulfate-limiting conditions. Hoerr RE, Eng A, Payen C, Di Rienzi SC, Raghuraman MK, Dunham MJ, Brewer BJ, Friedman KL. Jan 16, 2023.[bioRxiv]

High-throughput approaches to functional characterization of genetic variation in yeast. Yeh CC, Jiang P, Dunham MJ. Curr Opin Genet Dev. 2022 Oct;76:101979. doi: 10.1016/j.gde.2022.101979.[Pubmed][Current Opinion in Genetics & Development][PDF]

The genomic landscape of Saccharomyces paradoxus introgression in geographically diverse Saccharomyces cerevisiae strains. Clark A, Dunham MJ, Akey JM. bioRxiv. Aug 3, 2022. [bioRxiv]

yEvo: a modular eukaryotic genetics and evolution research experience for high school students. Taylor MB*, Warwick AR*, Skophammer R, Boyer JM, Geck RC, Gunkelman K, Walson M, Rowley PA#, Dunham MJ# (*co-first authors, #co-corresponding authors). bioRxiv. May 28, 2022. [bioRxiv]

A Modified Fluctuation Assay with a CAN1 Reporter in Yeast. JIang P, Ollodart AR, Dunham MJ.bio-protocol. 2022 June 5;12(11). doi: 10.21769/BioProtoc.4435[bio-protocol]

Directed evolution as an approach to increase fructose utilization in synthetic grape juice by wine yeast AWRI 796. Walker ME, Watson TL, Large CRL, Berkovich Y, Lang TA, Dunham MJ, Formby S, Jiranek V. FEMS Yeast Res. 2022 May 23;22(1):foac022. doi: 10.1093/femsyr/foac022.[Pubmed][FEMS Yeast Research][PDF]

PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment. Yeh CC*, Amorosi CJ*, Showman S, Dunham MJ. (*co-first authors). Bioinformatics. 2022 May 13;38(10):2927-2929. doi: 10.1093/bioinformatics/btac165.[Pubmed] [Bioinformatics][GitHub][bioRxiv]

Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts. Saada OA, Tsouris A, Large C, Friedrich A, Dunham MJ, Schacherer J. Curr Biol. 2022 Mar 28;32(6):1350-1361.e3. doi: 10.1016/j.cub.2022.01.068.[Pubmed][Current Biology][PDF]

A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae. Jiang P, Ollodart AR, Sudhesh V, Herr AJ, Dunham MJ, Harris K. Elife. 2021 Sep 15;10:e68285. doi: 10.7554/eLife.68285.[Pubmed][eLife][bioRxiv][Science in Seattle]

Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays. Geck RC, Boyle G, Amorosi CJ, Fowler DM#, Dunham MJ#. (#co-corresponding authors). Annu Rev Pharmacol Toxicol. 2022 Jan 6;62:531-550. doi: 10.1146/annurev-pharmtox-032221-085807.[Pubmed][Annual Review of Pharmacology and Toxicology][PDF]

Massively parallel characterization of CYP2C9 variant enzyme activity and abundance. Amorosi CJ, Chiasson MA, McDonald MG, Wong LH, Sitko KA, Boyle G, Kowalski JP, Rettie AE, Fowler DM#, Dunham MJ# (co-corresponding authors). Am J Hum Genet. 2021 Sep 2;108(9):1735-1751. doi: 10.1016/j.ajhg.2021.07.001.[Pubmed][AJHG][PDF][bioRxiv][Science in Seattle]

University of Washington Nathan Shock Center: innovation to advance aging research. Kaeberlein M, Bitto A, Dunham MJ, Ladiges W, Lee SI, MacCoss MJ, Mendenhall A, Promislow DEL, Rabinovitch PS, Villén J, Wang L, Wang Y, Young JE. Geroscience. 2021 Oct;43(5):2161-2165. doi: 10.1007/s11357-021-00413-2.[Pubmed][GeroScience][PMC][PDF]

Multiplexing Mutation Rate Assessment: Determining Pathogenicity of Msh2 Variants in S. cerevisiae. Ollodart AR, Yeh CC, Miller AW, Shirts BH, Gordon AS, Dunham MJ. Genetics. 2021 Apr 12;iyab058. doi: 10.1093/genetics/iyab058.[Pubmed][Genetics][PDF][bioRxiv][BioProject]

Transposable element mobilization in interspecific yeast hybrids. Heil CS, Patterson K, Hickey AS, Alcantara E, Dunham MJ. Genome Biol Evol. 2021 Mar 1;13(3):evab033. doi: 10.1093/gbe/evab033.[Pubmed][GBE][PMC][PDF][bioRxiv][BioProject]

High-throughput functional analysis of natural variants in yeast. Yeh CC, Tsouris A, Schacherer J, Dunham MJ. bioRxiv. February 26, 2021. [bioRxiv]

Dietary Change Enables Robust Growth-Coupling of Heterologous Methyltransferase Activity in Yeast. Hansen ASL, Dunham MJ, Arsovska D, Zhang J, Keasling JD, Herrgard MJ, Jensen MK. ACS Synth Biol. 2020 Nov 12. doi: 10.1021/acssynbio.0c00348.[Pubmed][ACS Synth Biol][PDF]

Effect of the Ala234Asp replacement in mitochondrial branched-chain amino acid aminotransferase on the production of BCAAs and fusel alcohols in yeast. Koonthongkaew J, Toyokawa Y, Ohashi M, Large CRL, Dunham MJ, Takagi H. Appl Microbiol Biotechnol. 2020 Sep;104(18):7915-7925. doi: 10.1007/s00253-020-10800-y. [Pubmed][Appl Microbiol Biotechnol.][PDF]

Genomic stability and adaptation of beer brewing yeasts during serial repitching in the brewery. Large CRL, Hanson NA, Tsouris A, Saada OA, Koonthongkaew J, Toyokawa Y, Schmidlin T, Moreno-Habel DA, McConnellogue H, Preiss R, Takagi H, Schacherer J, Dunham MJ. bioRxiv. June 29, 2020. [bioRxiv]

The environmental stress response causes ribosome loss in aneuploid yeast cells. Terhorst A, Sandikci A, Keller A, Whittaker CA, Dunham MJ, Amon A. Proc Natl Acad Sci U S A. 2020 Jul 6:202005648. doi: 10.1073/pnas.2005648117.[Pubmed][PNAS][PDF][bioRxiv]

Interrogation of CYP2D6 Structural Variant Alleles Improves the Correlation Between CYP2D6 Genotype and CYP2D6-Mediated Metabolic Activity. Dalton R, Lee SB, Claw KG, Prasad B, Phillips BR, Shen DD, Wong LH, Fade M, McDonald MG, Dunham MJ, Fowler DM, Rettie AE, Schuetz E, Thornton TA, Nickerson DA, Gaedigk A, Thummel KE, Woodahl EL. Clin Transl Sci. 2020 Jan;13(1):147-156. doi: 10.1111/cts.12695.[Pubmed][Clin Transl Sci][PDF]

Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of Saccharomyces cerevisiae. Sanchez JC, Ollodart A, Large CRL, Clough C, Alvino GM, Tsuchiya M, Crane M, Kwan EX, Kaeberlein M, Dunham MJ, Raghuraman MK, Brewer BJ. Genetics. 2019 Jul 10. pii: genetics.302351.2019. doi: 10.1534/genetics.119.302351.[Pubmed][Genetics][PDF][bioRxiv][BioProject]

Applying Multiplex Assays to Understand Variation in Pharmacogenes. Chiasson M, Dunham MJ, Rettie AE, Fowler DM. Clin Pharmacol Ther. 2019 Aug;106(2):290-294. doi: 10.1002/cpt.1468.[Pubmed][Clinical Pharmacology & Therapeutics][PDF]

A combination of transcription factors mediates inducible interchromosomal pairing. Kim S, Dunham MJ, Shendure J. Elife. 2019 May 13;8. pii: e42499. doi: 10.7554/eLife.42499.[Pubmed][eLife][PDF][GEO][bioRxiv]

A polyploid admixed origin of beer yeasts derived from European and Asian wine populations. Fay JC, Liu P, Ong GT, Dunham MJ, Cromie GA, Jeffrey EW, Ludlow CL, Dudley AM. PLoS Biol. 2019 Mar 5;17(3):e3000147. doi: 10.1371/journal.pbio.3000147. eCollection 2019 Mar.[Pubmed][PLoS Biology][PDF][SRA][bioRxiv][Forbes]

Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species dependent essential genes. Sanchez MR, Payen C, Cheong F, Hovde B, Bissonnette S, Arkin A, Skerker JM, Brem R, Caudy AA, Dunham MJ. Genome Res. 2019 Mar;29(3):396-406. doi: 10.1101/gr.232330.117.[Pubmed][Genome Research][PDF][SRA][bioRxiv]

Fitness benefits of loss of heterozygosity in Saccharomyces hybrids. Lancaster SM, Payen C, Smukowski Heil C, Dunham MJ. Genome Res. 2019 Oct;29(10):1685-1692. doi: 10.1101/gr.245605.118.[Pubmed][Genome Res][PDF][bioRxiv]

Temperature preference can bias parental genome retention during hybrid evolution. Smukowski Heil CS, Large CRL, Patterson K, Hickey AS, Yeh CC, Dunham MJ. PLoS Genet. 2019 Sep;15(9):e1008383. doi: 10.1371/journal.pgen.1008383.[Pubmed][PLoS Genetics][bioRxiv]

Identification of a novel interspecific hybrid yeast from a metagenomic open fermentation sample using Hi-C. Smukowski Heil C*, Burton JN*, Liachko I*, Friedrich A, Hanson NA, Morris CL, Schacherer J, Shendure J, Thomas JH, Dunham MJ (*co-first authors). Yeast. 2018 Jan;35(1):71-84.[Pubmed][Yeast][PDF][BioProject][bioRxiv][ScienceNews][El Espanol][Nightlife radio][N+1][Spektrum][Science]

Expression and functional characterization of breast cancer-associated cytochrome P450 4Z1 in Saccharomyces cerevisiae. McDonald MG, Ray S, Amorosi CJ, Sitko KA, Kowalski JP, Paco L, Nath A, Gallis BM, Totah RA, Dunham MJ, Fowler DM, Rettie AE. Drug Metabolism and Disposition. 2017 Dec;45(12):1364-1371.[Pubmed][DMD][PDF]

Variant Interpretation: Functional Assays to the Rescue. Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Am J Hum Genet. 2017 Sep 7;101(3):315-325.[Pubmed][AJHG][PDF]

Chemostat Culture for Yeast Physiology and Experimental Evolution. Dunham MJ, Kerr EO, Miller AW, Payen C. Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.top077610.[Pubmed][CSH Protocols][PDF]

Chemostat Culture for Yeast Experimental Evolution. Payen C, Dunham MJ. Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot089011.[Pubmed][CSH Protocols][PDF]

Chemostat Culture for Yeast Physiology. Kerr EO, Dunham MJ. Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot089003.[Pubmed][CSH Protocols][PDF]

Assembly of a Mini-Chemostat Array. Miller AW, Kerr EO, Dunham MJ. Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot088997.[Pubmed][CSH Protocols][PDF]

The dynamic three-dimensional organization of the diploid yeast genome. Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, Shendure J, Dunham MJ. Elife. 2017 May 24;6. pii: e23623. doi: 10.7554/eLife.23623.[Pubmed][eLife][PDF][GEO][GitHub][bioRxiv][Cell Systems][F1000]

Experimental evolution reveals favored adaptive routes to cell aggregation in yeast. Hope EA, Amorosi CJ, Miller AW, Dang K, Heil CS, Dunham MJ. Genetics. June 1, 2017 vol. 206 no. 2 1153-1167; https://doi.org/10.1534/genetics.116.198895 [Pubmed][Genetics][PDF][BioProject][bioRxiv][This Week in Evolution podcast][SGD blog]

A multiplex culture system for the long-term growth of fission yeast cells. Callens C, Coelho NC, Miller AW, Domino Sananes MR, Dunham MJ, Denoual M, Coudreuse D. Yeast. 2017 Aug;34(8):343-355. doi: 10.1002/yea.3237.[Pubmed][Yeast][PDF]

Loss of heterozygosity drives adaptation in hybrid yeast. Smukowski Heil CS, DeSevo CG, Pai DA, Tucker CM, Hoang ML, Dunham MJ. Mol Biol Evol. 2017 Jul 1;34(7):1596-1612. doi: 10.1093/molbev/msx098.[Pubmed][MBE][PDF][BioProject][GEO1][GEO2][bioRxiv]

Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes. Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, Zhou Y, Sun J, Crisà A, Ponce de León FA, Schwartz JC, Hammond JA, Waldbieser GC, Schroeder SG, Liu GE, Dunham MJ, Shendure J, Sonstegard TS, Phillippy AM, Van Tassell CP, Smith TP. Nat Genet. 2017 Apr;49(4):643-650. doi: 10.1038/ng.3802. Epub 2017 Mar 6.[Pubmed][Nature Genetics][PDF][BioProject1][BioProject2][SRA][bioRxiv][NHGRI][genomeweb][Nature Genetics News and Views][The Atlantic][Science]

Differential paralog divergence modulates genome evolution across yeast species. Sanchez MR, Miller AW, Liachko I, Sunshine AB, Lynch B, Huang M, Alcantara E, DeSevo CG, Pai DA, Tucker CM, Hoang MJ, Dunham MJ. PLoS Genet. 2017 Feb 14;13(2):e1006585. doi: 10.1371/journal.pgen.1006585. eCollection 2017 Feb.[Pubmed][PLoS Genetics][PDF][BioProject][GEO][bioRxiv]

Evolution of protein phosphorylation across 18 fungal species. Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J. Science. 2016; 354(6309):229-232.[Pubmed][Science][PDF][Science Perspective][EurekAlert][UW HSNewsBeat][post by Pedro Beltrao]

High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations. Payen C, Sunshine AB, Ong GT, Pogachar JL, Zhao W, Dunham MJ. PLoS Genetics. 2016; 12(10):e1006339.[Pubmed][PLoS Genetics][PDF][GEO][SRA][BioProject][bioRxiv]

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome. Burrack LS, Hutton HF, Matter KJ, Clancey SA, Liachko I, Plemmons AE, Saha A, Power EA, Turman B, Thevandavakkam MA, Ay F, Dunham MJ, Berman J. PLoS Genetics. 2016; 12(9):e1006317.[Pubmed][PLoS Genetics][PDF][BioProject]

Characterization of a panARS-based episomal vector in the methylotrophic yeast Pichia pastoris for recombinant protein production and synthetic biology applications. Camattari A, Goh A, Yip LY, Tan AH, Ng SW, Tran A, Liu G, Liachko I, Dunham MJ, Rancati G. Microb Cell Fact. 2016 Aug 11;15(1):139. doi: 10.1186/s12934-016-0540-5.[Pubmed][Microbial Cell Factories][PDF]

Chemostat Culture for Yeast Physiology and Experimental Evolution. Dunham MJ, Kerr EO, Miller AW, Payen C. Budding Yeast: A Laboratory Manual. ed. Boone C, Andrews B, Fields S, Davis T. 2016 Cold Spring Harbor Laboratory Press.[CSHL Press]

The hidden complexity of Mendelian traits across yeast natural populations. Hou J, Sigwalt A, Pflieger D, Peter J, de Montigny J, Dunham MJ, Schacherer J. Cell Rep. 2016 Jul 26;16(4):1106-14. doi: 10.1016/j.celrep.2016.06.048. Epub 2016 Jul 7.[Pubmed][Cell Reports][PDF][bioRxiv]

Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae. Rich MS, Payen C, Rubin AF, Ong GT, Sanchez MR, Yachie N, Dunham MJ, Fields S. Genetics. 2016 May;203(1):191-202. doi: 10.1534/genetics.116.188037. Epub 2016 Mar 2.[Pubmed][Genetics][PDF][GitHub][BioProject][SGD blog]

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation. Hoggard T*, Liachko I* (*co-first authors), Burt C, Meikle T, Jiang K, Craciun G, Dunham M#, Fox CA# (#co-senior authors). G3. 2016 April 1;6(4):993-1012. doi: 10.1534/g3.116.027904.[Pubmed][G3][PDF][BioProject]

Aneuploidy shortens replicative lifespan in Saccharomyces cerevisiae. Sunshine AB, Ong GT, Nickerson DP, Carr D, Murakami CJ, Wasko BM, Shemorry A, Merz AJ, Kaeberlein M, Dunham MJ. Aging Cell. 2016 Jan 13. doi: 10.1111/acel.12443.[Pubmed][Aging Cell][PDF][GEO][BioProject]

Experimental Evolution and Resequencing Analysis of Yeast. Payen C, Dunham MJ. Methods Mol Biol. 2016;1361:361-74. doi: 10.1007/978-1-4939-3079-1_20.[Pubmed][Methods in Molecular Biology:Yeast Functional Genomics][PDF]

Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification. Brewer BJ, Payen C, Di Rienzi SC, Higgins MM, Ong G, Dunham MJ, Raghuraman MK. PLoS Genet. 2015 Dec 23;11(12):e1005699. doi: 10.1371/journal.pgen.1005699. eCollection 2015 Dec.[Pubmed][PLoS Genetics][PDF][GEO1][GEO2][GEO3][GEO4][BioProject]

Methods in Yeast Genetics and Genomics, 2015 Edition: A CSHL Course Manual. Dunham MJ, Gartenberg MR, Brown GW. 2015, Cold Spring Harbor Laboratory Press.[CSHL Press]

Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation. López-Malo M, García-Rios E, Melgar B, Sanchez MR, Dunham MJ, Guillamón JM. BMC Genomics. 2015 Jul 22;16:537. doi: 10.1186/s12864-015-1755-2.[Pubmed][BMC Genomics][PDF][BioProject]

The fitness consequences of aneuploidy are driven by condition-dependent gene effects. Sunshine AB, Payen C, Ong GT, Liachko I, Tan KM, Dunham MJ. PLoS Biology. 2015 May 26;13(5):e1002155. doi: 10.1371/journal.pbio.1002155. eCollection 2015 May.[Pubmed][PLoS Biology][PDF][GEO][PUMA][BioProject: 1 2][F1000]

Accurate identification of centromere locations in yeast genomes using Hi-C. Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. Nucleic Acids Research. 2015 May 4. pii: gkv424. [Epub ahead of print][Pubmed][Nucleic Acids Research][PDF][SRA][Centurion website][BioTechniques]

Control of Plasma Membrane Permeability by ABC Transporters. Khakhina S, Johnson SS, Manoharlal R, Russo SB, Blugeon C, Lemoine S, Sunshine AB, Dunham MJ, Cowart LA, Devaux F, Moye-Rowley WS. Eukaryotic Cell. 2015 May;14(5):442-53. doi: 10.1128/EC.00021-15. Epub 2015 Feb 27.[Pubmed][Eukaryotic Cell][PDF]

The enduring utility of continuous culturing in experimental evolution. Gresham D, Dunham MJ. Genomics. 2014 Oct 2. pii: S0888-7543(14)00192-X. doi: 10.1016/j.ygeno.2014.09.015. [Epub ahead of print][Pubmed][Genomics][PDF]

Ploidy-regulated variation in biofilm-related phenotypes in natural isolates of Saccharomyces cerevisiae. Hope EA, Dunham MJ. G3. 2014 Jul 24;4(9):1773-86. doi: 10.1534/g3.114.013250.[Pubmed][G3][G3 Cover][About the Cover][PDF][Beacon blog]

A Low Cost, Customizable Turbidostat for Use in Synthetic Circuit Characterization. Takahashi CN, Miller AW, Ekness F, Dunham MJ, Klavins E. ACS Synth Biol. 2014 Aug 1. [Epub ahead of print][Pubmed][ACS Synthetic Biology][PDF][Github1][Github2][Turbidostat Construction Wiki]

Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps. Burton JN*, Liachko I* (*co-first authors), Dunham MJ#, Shendure J# (#co-corresponding authors). G3. 2014 May 22;4(7):1339-46. doi: 10.1534/g3.114.011825.[Pubmed][G3][G3 Cover][About the Cover][PDF][SRA (note there's a labeling error, sorry)][G3 press release][GenomeWeb][BioIT World][The Scientist][BitesizeBio][G3 Spotlight]

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# (#co-corresponding authors). G3. 2014 Mar 20;4(3):399-409. doi: 10.1534/g3.113.009365. [Pubmed][G3][PDF][GEO][PUMA][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][PMC][PDF]

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][PMC][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][MNT]

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, Llinás M, Botstein D, Troyanskaya OG#, Dunham MJ# (#co-corresponding authors). Genetics. 2013 Sep;195(1):275-87. Epub 2013 Jul 12.[Pubmed][Genetics][PDF][Function prediction website][GEO1][GEO2][PUMA][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# (#co-corresponding authors). 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# (#co-correspondingauthors). 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# (#co-corresponding authors). BMC Genomics. 2013 Jan 16;14:33.[Pubmed][BMC Genomics][PDF]

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]

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]

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]

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]

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# (#co-corresponding authors). 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]

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]

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][Growth Rate Prediction Tool]

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]

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# (#co-corresponding authors). 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 Dec;15(12):1838-46. doi: 10.1038/cdd.2008.117. Epub 2008 Aug 29.[Pubmed][Cell Death & Differentiation][PDF]

Comparing whole genomes using DNA microarrays. Gresham D#, Dunham MJ#, Botstein D# (#co-corresponding authors). Nat Rev Genet. 2008 Apr;9(4):291-302. [Pubmed][Nature Reviews Genetics][PDF]

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]

Global Mapping of Transposon Location. Gabriel A#, Dapprich J, Kunkel M, Gresham D, Pratt SC, Dunham MJ# (#co-corresponding authors). 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]

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]

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]

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]

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]

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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