Maitreya Jnana Dunham - Publications

Affiliations: 
2003 Stanford University, Palo Alto, CA 

66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Dalton R, Lee SB, Claw KG, Prasad B, Phillips BR, Shen DD, Hong Wong L, Fade M, McDonald MG, Dunham MJ, Fowler DM, Rettie AE, Schuetz E, Thornton TA, Nickerson DA, et al. Interrogation of CYP2D6 structural variant alleles improves the correlation between CYP2D6 genotype and CYP2D6-mediated metabolic activity. Clinical and Translational Science. PMID 31536170 DOI: 10.1111/cts.12695  0.36
2019 Chiasson M, Dunham MJ, Rettie AE, Fowler DM. Applying Multiplex Assays to Understand Variation in Pharmacogenes. Clinical Pharmacology and Therapeutics. PMID 31145826 DOI: 10.1002/cpt.1468  0.36
2019 Sanchez MR, Payen C, Cheong F, Hovde BT, Bissonnette S, Arkin AP, Skerker JM, Brem RB, Caudy AA, Dunham MJ. Transposon insertional mutagenesis in reveals trans-acting effects influencing species-dependent essential genes. Genome Research. PMID 30635343 DOI: 10.1101/gr.232330.117  0.48
2017 McDonald MG, Ray S, Amorosi CJ, Sitko KA, Kowalski JP, Paco L, Nath A, Gallis BM, Totah RA, Dunham MJ, Fowler DM, Rettie AE. Expression and functional characterization of breast cancer-associated cytochrome P450 4Z1 in Saccharomyces cerevisiae. Drug Metabolism and Disposition: the Biological Fate of Chemicals. PMID 29018033 DOI: 10.1124/dmd.117.078188  0.44
2017 Heil CS, Burton JN, Liachko I, Friedrich A, Hanson NA, Morris CL, Schacherer J, Shendure J, Thomas JH, Dunham MJ. Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C. Yeast (Chichester, England). PMID 28892574 DOI: 10.1002/yea.3280  0.44
2017 Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Variant Interpretation: Functional Assays to the Rescue. American Journal of Human Genetics. 101: 315-325. PMID 28886340 DOI: 10.1016/j.ajhg.2017.07.014  0.36
2017 Dunham MJ, Kerr EO, Miller AW, Payen C. Chemostat Culture for Yeast Physiology and Experimental Evolution. Cold Spring Harbor Protocols. 2017: pdb.top077610. PMID 28679718 DOI: 10.1101/pdb.top077610  0.44
2017 Miller AW, Kerr EO, Dunham MJ. Assembly of a Mini-Chemostat Array. Cold Spring Harbor Protocols. 2017: pdb.prot088997. PMID 28679698 DOI: 10.1101/pdb.prot088997  0.44
2017 Hope EA, Amorosi CJ, Miller AW, Dang K, Heil CS, Dunham MJ. Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast. Genetics. PMID 28450459 DOI: 10.1534/genetics.116.198895  0.44
2017 Callens C, Coelho NC, Miller AW, Domino Sananes MR, Dunham MJ, Denoual M, Coudreuse D. A multiplex culture system for the long-term growth of fission yeast cells. Yeast (Chichester, England). PMID 28426144 DOI: 10.1002/yea.3237  0.44
2017 Sanchez MR, Miller AW, Liachko I, Sunshine AB, Lynch B, Huang M, Alcantara E, DeSevo CG, Pai DA, Tucker CM, Hoang ML, Dunham MJ. Differential paralog divergence modulates genome evolution across yeast species. Plos Genetics. 13: e1006585. PMID 28196070 DOI: 10.1371/journal.pgen.1006585  0.44
2016 Rich MS, Payen C, Rubin AF, Ong GT, Sanchez MR, Yachie N, Dunham MJ, Fields S. The Effects of Cis-Regulatory Mutations in the SUL1 Gene on Sulfate-Limited Fitness in Yeast. Genetics. PMID 26936925 DOI: 10.1534/genetics.116.188037  0.48
2016 Hoggard T, Liachko I, Burt C, Meikle T, Jiang K, Craciun G, Dunham M, Fox CA. High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation. G3 (Bethesda, Md.). PMID 26865697 DOI: 10.1534/g3.116.027904  0.48
2016 Sunshine AB, Ong GT, Nickerson DP, Carr D, Murakami CJ, Wasko BM, Shemorry A, Merz AJ, Kaeberlein M, Dunham MJ. Aneuploidy shortens replicative lifespan in Saccharomyces cerevisiae. Aging Cell. PMID 26762766 DOI: 10.1111/acel.12443  0.48
2016 Payen C, Dunham MJ. Experimental Evolution and Resequencing Analysis of Yeast. Methods in Molecular Biology (Clifton, N.J.). 1361: 361-74. PMID 26483032 DOI: 10.1007/978-1-4939-3079-1_20  0.48
2015 Brewer BJ, Payen C, Di Rienzi SC, Higgins MM, Ong G, Dunham MJ, Raghuraman MK. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification. Plos Genetics. 11: e1005699. PMID 26700858 DOI: 10.1371/journal.pgen.1005699  0.48
2015 Sunshine AB, Payen C, Ong GT, Liachko I, Tan KM, Dunham MJ. The fitness consequences of aneuploidy are driven by condition-dependent gene effects. Plos Biology. 13: e1002155. PMID 26011532 DOI: 10.1371/journal.pbio.1002155  0.48
2015 Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Research. 43: 5331-9. PMID 25940625 DOI: 10.1093/nar/gkv424  0.48
2015 Khakhina S, Johnson SS, Manoharlal R, Russo SB, Blugeon C, Lemoine S, Sunshine AB, Dunham MJ, Cowart LA, Devaux F, Moye-Rowley WS. Control of Plasma Membrane Permeability by ABC Transporters. Eukaryotic Cell. 14: 442-53. PMID 25724885 DOI: 10.1128/EC.00021-15  0.48
2015 Takahashi CN, Miller AW, Ekness F, Dunham MJ, Klavins E. A low cost, customizable turbidostat for use in synthetic circuit characterization. Acs Synthetic Biology. 4: 32-8. PMID 25036317 DOI: 10.1021/sb500165g  0.48
2015 López-Malo M, García-Rios E, Melgar B, Sanchez MR, Dunham MJ, Guillamón JM. Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation Bmc Genomics. 16. DOI: 10.1186/s12864-015-1755-2  0.48
2014 Gresham D, Dunham MJ. The enduring utility of continuous culturing in experimental evolution. Genomics. 104: 399-405. PMID 25281774 DOI: 10.1016/j.ygeno.2014.09.015  0.48
2014 Hope EA, Dunham MJ. Ploidy-regulated variation in biofilm-related phenotypes in natural isolates of Saccharomyces cerevisiae. G3 (Bethesda, Md.). 4: 1773-86. PMID 25060625 DOI: 10.1534/g3.114.013250  0.48
2014 Liachko I, Youngblood RA, Tsui K, Bubb KL, Queitsch C, Raghuraman MK, Nislow C, Brewer BJ, Dunham MJ. GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris. Plos Genetics. 10: e1004169. PMID 24603708 DOI: 10.1371/journal.pgen.1004169  0.48
2014 Payen C, Di Rienzi SC, Ong GT, Pogachar JL, Sanchez JC, Sunshine AB, Raghuraman MK, Brewer BJ, Dunham MJ. The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection. G3 (Bethesda, Md.). 4: 399-409. PMID 24368781 DOI: 10.1534/g3.113.009365  0.48
2014 Liachko I, Dunham MJ. An autonomously replicating sequence for use in a wide range of budding yeasts. Fems Yeast Research. 14: 364-7. PMID 24205893 DOI: 10.1111/1567-1364.12123  0.48
2013 Dunham MJ, Fowler DM. Contemporary, yeast-based approaches to understanding human genetic variation. Current Opinion in Genetics & Development. 23: 658-64. PMID 24252429 DOI: 10.1016/j.gde.2013.10.001  0.48
2013 Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM. Genome-wide consequences of deleting any single gene. Molecular Cell. 52: 485-94. PMID 24211263 DOI: 10.1016/j.molcel.2013.09.026  0.48
2013 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, ... ... Dunham MJ, et al. A new system for comparative functional genomics of Saccharomyces yeasts. Genetics. 195: 275-87. PMID 23852385 DOI: 10.1534/genetics.113.152918  0.48
2013 Pashkova N, Gakhar L, Winistorfer SC, Sunshine AB, Rich M, Dunham MJ, Yu L, Piper RC. The yeast Alix homolog Bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes. Developmental Cell. 25: 520-33. PMID 23726974 DOI: 10.1016/j.devcel.2013.04.007  0.48
2013 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, et al. Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Research. 23: 1496-504. PMID 23720455 DOI: 10.1101/gr.155762.113  0.48
2013 Connelly CF, Skelly DA, Dunham MJ, Akey JM. Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains. Molecular Biology and Evolution. 30: 1605-13. PMID 23619145 DOI: 10.1093/molbev/mst073  0.48
2013 Miller AW, Befort C, Kerr EO, Dunham MJ. Design and use of multiplexed chemostat arrays. Journal of Visualized Experiments : Jove. e50262. PMID 23462663 DOI: 10.3791/50262  0.48
2013 Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA. Comparative gene expression between two yeast species. Bmc Genomics. 14: 33. PMID 23324262 DOI: 10.1186/1471-2164-14-33  0.48
2013 Liachko I, Youngblood RA, Keich U, Dunham MJ. High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Research. 23: 698-704. PMID 23241746 DOI: 10.1101/gr.144659.112  0.48
2012 Kelly MK, Brosnan L, Jauert PA, Dunham MJ, Kirkpatrick DT. Multiple pathways regulate minisatellite stability during stationary phase in yeast. G3 (Bethesda, Md.). 2: 1185-95. PMID 23050229 DOI: 10.1534/g3.112.003673  0.48
2012 Sheltzer JM, Torres EM, Dunham MJ, Amon A. Transcriptional consequences of aneuploidy. Proceedings of the National Academy of Sciences of the United States of America. 109: 12644-9. PMID 22802626 DOI: 10.1073/pnas.1209227109  0.48
2012 Dunham MJ. Two flavors of bulk segregant analysis in yeast. Methods in Molecular Biology (Clifton, N.J.). 871: 41-54. PMID 22565832 DOI: 10.1007/978-1-61779-785-9_4  0.48
2012 Stirling PC, Crisp MJ, Basrai MA, Tucker CM, Dunham MJ, Spencer FA, Hieter P. Mutability and mutational spectrum of chromosome transmission fidelity genes. Chromosoma. 121: 263-75. PMID 22198145 DOI: 10.1007/s00412-011-0356-3  0.48
2011 Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda, Md.). 1: 11-25. PMID 22384314 DOI: 10.1534/g3.111.000273  0.48
2011 Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG. Nucleosome-coupled expression differences in closely-related species. Bmc Genomics. 12: 466. PMID 21942931 DOI: 10.1186/1471-2164-12-466  0.48
2011 Brewer BJ, Payen C, Raghuraman MK, Dunham MJ. Origin-dependent inverted-repeat amplification: a replication-based model for generating palindromic amplicons. Plos Genetics. 7: e1002016. PMID 21437266 DOI: 10.1371/journal.pgen.1002016  0.48
2011 Dunham MJ, Louis EJ. Yeast evolution and ecology meet genomics. Embo Reports. 12: 8-10. PMID 21151040 DOI: 10.1038/embor.2010.204  0.48
2010 Hoang ML, Tan FJ, Lai DC, Celniker SE, Hoskins RA, Dunham MJ, Zheng Y, Koshland D. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination. Plos Genetics. 6: e1001228. PMID 21151956 DOI: 10.1371/journal.pgen.1001228  0.48
2010 Dunham MJ. Experimental evolution in yeast: a practical guide. Methods in Enzymology. 470: 487-507. PMID 20946822 DOI: 10.1016/S0076-6879(10)70019-7  0.48
2010 Torres EM, Dephoure N, Panneerselvam A, Tucker CM, Whittaker CA, Gygi SP, Dunham MJ, Amon A. Identification of aneuploidy-tolerating mutations. Cell. 143: 71-83. PMID 20850176 DOI: 10.1016/j.cell.2010.08.038  0.48
2010 Guan Y, Dunham M, Caudy A, Troyanskaya O. Systematic planning of genome-scale experiments in poorly studied species Plos Computational Biology. 6. PMID 20221257 DOI: 10.1371/journal.pcbi.1000698  0.48
2010 Araya CL, Payen C, Dunham MJ, Fields S. Whole-genome sequencing of a laboratory-evolved yeast strain. Bmc Genomics. 11: 88. PMID 20128923 DOI: 10.1186/1471-2164-11-88  0.48
2009 Fiumera HL, Dunham MJ, Saracco SA, Butler CA, Kelly JA, Fox TD. Translocation and assembly of mitochondrially coded Saccharomyces cerevisiae cytochrome c oxidase subunit Cox2 by Oxa1 and Yme1 in the absence of Cox18. Genetics. 182: 519-28. PMID 19307606 DOI: 10.1534/genetics.109.101196  0.48
2009 Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. Plos Computational Biology. 5: e1000257. PMID 19119411 DOI: 10.1371/journal.pcbi.1000257  0.48
2009 McDonald CM, Wagner M, Dunham MJ, Shin ME, Ahmed NT, Winter E. The Ras/cAMP pathway and the CDK-like kinase Ime2 regulate the MAPK Smk1 and spore morphogenesis in Saccharomyces cerevisiae. Genetics. 181: 511-23. PMID 19087957 DOI: 10.1534/genetics.108.098434  0.48
2008 Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, Dunham MJ. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. Plos Genetics. 4: e1000303. PMID 19079573 DOI: 10.1371/journal.pgen.1000303  0.48
2008 Cheng WC, Teng X, Park HK, Tucker CM, Dunham MJ, Hardwick JM. Fis1 deficiency selects for compensatory mutations responsible for cell death and growth control defects. Cell Death and Differentiation. 15: 1838-46. PMID 18756280 DOI: 10.1038/cdd.2008.117  0.48
2008 Gresham D, Dunham MJ, Botstein D. Comparing whole genomes using DNA microarrays. Nature Reviews. Genetics. 9: 291-302. PMID 18347592 DOI: 10.1038/nrg2335  0.48
2007 Torres EM, Sokolsky T, Tucker CM, Chan LY, Boselli M, Dunham MJ, Amon A. Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science (New York, N.Y.). 317: 916-24. PMID 17702937 DOI: 10.1126/science.1142210  0.48
2007 Dunham MJ. Synthetic ecology: a model system for cooperation. Proceedings of the National Academy of Sciences of the United States of America. 104: 1741-2. PMID 17267618 DOI: 10.1073/pnas.0611067104  0.48
2007 Guan Y, Dunham MJ, Troyanskaya OG. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics. 175: 933-43. PMID 17151249 DOI: 10.1534/genetics.106.064329  0.48
2007 Hibbs M, Wallace G, Dunham M, Li K, Troyanskaya O. Viewing the larger context of genomic data through horizontal integration Proceedings of the International Conference On Information Visualisation. 326-332. DOI: 10.1109/IV.2007.120  0.48
2007 Wallace G, Hibbs M, Dunham M, Sealfon R, Troyanskaya O, Li K. Scalable, dynamic analysis and visualization for genomic datasets Proceedings - 21st International Parallel and Distributed Processing Symposium, Ipdps 2007; Abstracts and Cd-Rom. DOI: 10.1109/IPDPS.2007.370529  0.48
2006 Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, Dunham MJ. Global mapping of transposon location. Plos Genetics. 2: e212. PMID 17173485 DOI: 10.1371/journal.pgen.0020212  0.48
2006 Brauer MJ, Christianson CM, Pai DA, Dunham MJ. Mapping novel traits by array-assisted bulk segregant analysis in Saccharomyces cerevisiae. Genetics. 173: 1813-6. PMID 16624899 DOI: 10.1534/genetics.106.057927  0.48
2006 Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, Kruglyak L. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science (New York, N.Y.). 311: 1932-6. PMID 16527929 DOI: 10.1126/science.1123726  0.48
2004 Myers CL, Dunham MJ, Kung SY, Troyanskaya OG. Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics (Oxford, England). 20: 3533-43. PMID 15284100 DOI: 10.1093/bioinformatics/bth440  0.48
2002 Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 99: 16144-9. PMID 12446845 DOI: 10.1073/pnas.242624799  0.48
2001 Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biology. 2: RESEARCH0004. PMID 11182887  0.48
2000 Byrne ME, Barley R, Curtis M, Arroyo JM, Dunham M, Hudson A, Martienssen RA. Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature. 408: 967-71. PMID 11140682 DOI: 10.1038/35050091  0.48
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