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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. [Epub ahead of print]


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. Epub 2019 May 30. No abstract available.


A combination of transcription factors mediates inducible interchromosomal contacts.

Kim S, Dunham MJ, Shendure J.

Elife. 2019 May 13;8. pii: e42499. doi: 10.7554/eLife.42499.


A polyploid admixed origin of beer yeasts derived from European and Asian wine populations.

Fay JC, Liu P, Ong GT, Dunham MJ, Cromie GA, Jeffery EW, Ludlow CL, Dudley AM.

PLoS Biol. 2019 Mar 5;17(3):e3000147. doi: 10.1371/journal.pbio.3000147. eCollection 2019 Mar.


Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes.

Sanchez MR, Payen C, Cheong F, Hovde BT, Bissonnette S, Arkin AP, Skerker JM, Brem RB, Caudy AA, Dunham MJ.

Genome Res. 2019 Mar;29(3):396-406. doi: 10.1101/gr.232330.117. Epub 2019 Jan 11.


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 B, Totah RA, Dunham MJ, Fowler DM, Rettie AE.

Drug Metab Dispos. 2017 Dec;45(12):1364-1371. doi: 10.1124/dmd.117.078188. Epub 2017 Oct 10.


Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer 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.

Yeast. 2018 Jan;35(1):71-84. doi: 10.1002/yea.3280. Epub 2017 Oct 19.


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. doi: 10.1016/j.ajhg.2017.07.014.


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. doi: 10.1101/pdb.top077610.


Chemostat Culture for Yeast Experimental Evolution.

Payen C, Dunham MJ.

Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot089011. doi: 10.1101/pdb.prot089011.


Chemostat Culture for Yeast Physiology.

Kerr EO, Dunham MJ.

Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot089003. doi: 10.1101/pdb.prot089003.


Assembly of a Mini-Chemostat Array.

Miller AW, Kerr EO, Dunham MJ.

Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot088997. doi: 10.1101/pdb.prot088997.


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.


Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast.

Hope EA, Amorosi CJ, Miller AW, Dang K, Heil CS, Dunham MJ.

Genetics. 2017 Jun;206(2):1153-1167. doi: 10.1534/genetics.116.198895. Epub 2017 Apr 26.


A multiplex culture system for the long-term growth of fission yeast cells.

Callens C, Coelho NC, Miller AW, Sananes MRD, Dunham MJ, Denoual M, Coudreuse D.

Yeast. 2017 Aug;34(8):343-355. doi: 10.1002/yea.3237. Epub 2017 Jun 6.


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.


Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.

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.


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 ML, Dunham MJ.

PLoS Genet. 2017 Feb 14;13(2):e1006585. doi: 10.1371/journal.pgen.1006585. eCollection 2017 Feb.


Spatially resolved surface valence gradient and structural transformation of lithium transition metal oxides in lithium-ion batteries.

Liu H, Bugnet M, Tessaro MZ, Harris KJ, Dunham MJ, Jiang M, Goward GR, Botton GA.

Phys Chem Chem Phys. 2016 Oct 26;18(42):29064-29075.


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 Oct 14;354(6309):229-232.


High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations.

Payen C, Sunshine AB, Ong GT, Pogachar JL, Zhao W, Dunham MJ.

PLoS Genet. 2016 Oct 11;12(10):e1006339. doi: 10.1371/journal.pgen.1006339. eCollection 2016 Oct.


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 Genet. 2016 Sep 23;12(9):e1006317. doi: 10.1371/journal.pgen.1006317. eCollection 2016 Sep.


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.


The Hidden Complexity of Mendelian Traits across Natural Yeast Populations.

Hou J, Sigwalt A, Fournier T, Pflieger D, Peter J, de Montigny J, Dunham MJ, Schacherer J.

Cell Rep. 2016 Jul 26;16(4):1106-1114. doi: 10.1016/j.celrep.2016.06.048. Epub 2016 Jul 7.


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.


High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation.

Hoggard T, Liachko I, Burt C, Meikle T, Jiang K, Craciun G, Dunham MJ, Fox CA.

G3 (Bethesda). 2016 Apr 7;6(4):993-1012. doi: 10.1534/g3.116.027904.


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 Apr;15(2):317-24. doi: 10.1111/acel.12443. Epub 2016 Jan 13.


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.


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.


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.


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 Biol. 2015 May 26;13(5):e1002155. doi: 10.1371/journal.pbio.1002155. eCollection 2015 May.


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 Res. 2015 Jun 23;43(11):5331-9. doi: 10.1093/nar/gkv424. Epub 2015 May 4.


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.

Eukaryot Cell. 2015 May;14(5):442-53. doi: 10.1128/EC.00021-15. Epub 2015 Feb 27.


The enduring utility of continuous culturing in experimental evolution.

Gresham D, Dunham MJ.

Genomics. 2014 Dec;104(6 Pt A):399-405. doi: 10.1016/j.ygeno.2014.09.015. Epub 2014 Oct 2. Review.


Ploidy-regulated variation in biofilm-related phenotypes in natural isolates of Saccharomyces cerevisiae.

Hope EA, Dunham MJ.

G3 (Bethesda). 2014 Jul 24;4(9):1773-86. doi: 10.1534/g3.114.013250.


A low cost, customizable turbidostat for use in synthetic circuit characterization.

Takahashi CN, Miller AW, Ekness F, Dunham MJ, Klavins E.

ACS Synth Biol. 2015 Jan 16;4(1):32-8. doi: 10.1021/sb500165g. Epub 2014 Aug 1.


Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps.

Burton JN, Liachko I, Dunham MJ, Shendure J.

G3 (Bethesda). 2014 May 22;4(7):1339-46. doi: 10.1534/g3.114.011825.


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.


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 (Bethesda). 2014 Mar 20;4(3):399-409. doi: 10.1534/g3.113.009365.


Contemporary, yeast-based approaches to understanding human genetic variation.

Dunham MJ, Fowler DM.

Curr Opin Genet Dev. 2013 Dec;23(6):658-64. doi: 10.1016/j.gde.2013.10.001. Epub 2013 Nov 16. Review.


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 21;52(4):485-94. doi: 10.1016/j.molcel.2013.09.026. Epub 2013 Nov 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.


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 E, Cappel D, 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 S, Singer C, Sinha S, Staller M, Stern P, Tang H, Weeks S, Weidmann M, Wolf A, Young C, Yuan J, Crutchfield C, McClean M, Murphy CT, Llinás M, Botstein D, Troyanskaya OG, Dunham MJ.

Genetics. 2013 Sep;195(1):275-87. doi: 10.1534/genetics.113.152918. Epub 2013 Jul 12.


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. doi: 10.1534/genetics.113.152728. Epub 2013 Jul 5.


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. doi: 10.1016/j.devcel.2013.04.007. Epub 2013 May 30.


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. doi: 10.1101/gr.155762.113. Epub 2013 May 29.


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. doi: 10.1093/molbev/mst073. Epub 2013 Apr 25.


Design and use of multiplexed chemostat arrays.

Miller AW, Befort C, Kerr EO, Dunham MJ.

J Vis Exp. 2013 Feb 23;(72):e50262. doi: 10.3791/50262.


Comparative gene expression between two yeast species.

Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA.

BMC Genomics. 2013 Jan 16;14:33. doi: 10.1186/1471-2164-14-33.


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. doi: 10.1101/gr.144659.112. Epub 2012 Dec 12.

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