Audrey P. Gasch, Ph.D. - Publications

2000 Stanford University, Palo Alto, CA 
gene expression

70 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
2023 Robinson D, Vanacloig-Pedros E, Cai R, Place M, Hose J, Gasch AP. Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast. Biorxiv : the Preprint Server For Biology. PMID 37503218 DOI: 10.1101/2023.05.11.540375  0.427
2023 Robinson D, Vanacloig-Pedros E, Cai R, Place M, Hose J, Gasch AP. Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast. G3 (Bethesda, Md.). PMID 37481264 DOI: 10.1093/g3journal/jkad159  0.428
2022 Vanacloig-Pedros E, Fisher KJ, Liu L, Debrauske DJ, Young MKM, Place M, Hittinger CT, Sato TK, Gasch AP. Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions. Fems Yeast Research. PMID 35883225 DOI: 10.1093/femsyr/foac036  0.308
2021 Robinson D, Place M, Hose J, Jochem A, Gasch AP. Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories. Elife. 10. PMID 34338637 DOI: 10.7554/eLife.70564  0.424
2020 MacGilvray ME, Shishkova E, Place M, Wagner ER, Coon JJ, Gasch AP. The phosphoproteome response to dithiothreitol reveals unique versus shared features of Saccharomyces cerevisiae stress responses. Journal of Proteome Research. PMID 32597660 DOI: 10.1021/Acs.Jproteome.0C00253  0.361
2020 Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP. The genetic basis of aneuploidy tolerance in wild yeast. Elife. 9. PMID 31909711 DOI: 10.7554/Elife.52063  0.359
2019 Wagner ER, Myers KS, Riley NM, Coon JJ, Gasch AP. PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production. Plos One. 14: e0212389. PMID 31112537 DOI: 10.1371/Journal.Pone.0212389  0.33
2019 Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP. Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. Plos Genetics. 15: e1008037. PMID 30856163 DOI: 10.1371/Journal.Pgen.1008037  0.332
2018 Nemec CM, Singh AK, Ali A, Tseng SC, Syal K, Ringelberg KJ, Ho YH, Hintermair C, Ahmad MF, Kar RK, Gasch AP, Akhtar MS, Eick D, Ansari AZ. Noncanonical CTD kinases regulate RNA polymerase II in a gene-class-specific manner. Nature Chemical Biology. PMID 30598543 DOI: 10.1038/S41589-018-0194-1  0.395
2018 Ho YH, Shishkova E, Hose J, Coon JJ, Gasch AP. Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress. Current Biology : Cb. PMID 30078561 DOI: 10.1016/J.Cub.2018.06.044  0.362
2018 Higgins DA, Young MK, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, et al. Natural Variation in the Multidrug Efflux Pump Underlies Ionic Liquid Tolerance in Yeast. Genetics. PMID 30045857 DOI: 10.1534/Genetics.118.301161  0.369
2018 MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. Plos Computational Biology. 13: e1006088. PMID 29738528 DOI: 10.1371/Journal.Pcbi.1006088  0.347
2018 Sardi M, Gasch AP. Genetic background effects in quantitative genetics: gene-by-system interactions. Current Genetics. PMID 29644456 DOI: 10.1007/S00294-018-0835-7  0.38
2018 Sardi M, Paithane V, Place M, Robinson E, Hose J, Wohlbach DJ, Gasch AP. Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance. Plos Genetics. 14: e1007217. PMID 29474395 DOI: 10.1371/Journal.Pgen.1007217  0.422
2017 Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. Plos Biology. 15: e2004050. PMID 29240790 DOI: 10.1371/Journal.Pbio.2004050  0.408
2017 Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM. Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. Journal of Proteome Research. PMID 29195273 DOI: 10.1021/Acs.Jproteome.7B00685  0.351
2017 Muir VS, Gasch AP, Anderson P. The Substrates of Nonsense-Mediated mRNA Decay in Caenorhabditis elegans. G3 (Bethesda, Md.). PMID 29122854 DOI: 10.1534/G3.117.300254  0.405
2017 Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM. Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Analytical Chemistry. PMID 28654248 DOI: 10.1021/Acs.Analchem.7B01784  0.399
2017 Sardi M, Gasch AP. Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering. Fems Yeast Research. PMID 28637316 DOI: 10.1093/Femsyr/Fox042  0.303
2017 Nemec CM, Yang F, Gilmore JM, Hintermair C, Ho YH, Tseng SC, Heidemann M, Zhang Y, Florens L, Gasch AP, Eick D, Washburn MP, Varani G, Ansari AZ. Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner. Proceedings of the National Academy of Sciences of the United States of America. PMID 28465432 DOI: 10.1073/Pnas.1700128114  0.396
2016 Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Avanasi Narasimhan R, McGee MA, Dickinson Q, La Reau A, Xie D, ... ... Gasch AP, et al. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. Plos Genetics. 12: e1006372. PMID 27741250 DOI: 10.1371/Journal.Pgen.1006372  0.35
2016 Sardi M, Rovinskiy N, Zhang Y, Gasch AP. Leveraging genetic background effects in Saccharomyces cerevisiae to improve lignocellulosic hydrolysate tolerance. Applied and Environmental Microbiology. PMID 27451446 DOI: 10.1128/Aem.01603-16  0.439
2016 Guillen-Ahlers H, Rao PK, Levenstein ME, Kennedy-Darling J, Perumalla DS, Jadhav AY, Glenn JP, Ludwig-Kubinski A, Drigalenko E, Montoya MJ, Göring HH, Anderson CD, Scalf M, Gildersleeve HI, Cole R, ... ... Gasch AP, et al. HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. PMID 27184763 DOI: 10.1016/J.Ygeno.2016.05.002  0.332
2016 McIlwain SJ, Peris D, Sardi M, Moskvin OV, Zhan F, Myers KS, Riley NM, Buzzell A, Parreiras LS, Ong IM, Landick R, Coon JJ, Gasch AP, Sato TK, Hittinger CT. Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research. G3 (Bethesda, Md.). 6: 1757-66. PMID 27172212 DOI: 10.1534/G3.116.029389  0.404
2016 Gasch AP, Hose J, Newton MA, Sardi M, Yong M, Wang Z. Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution. Elife. 5. PMID 26949252 DOI: 10.7554/Elife.14409  0.438
2016 Gasch AP, Hose J, Newton MA, Sardi M, Yong M, Wang Z. Author response: Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution Elife. DOI: 10.7554/Elife.14409.010  0.459
2016 Sverchkov Y, Gasch A, Craven M. Learning context-specific nested effects models from gene knockdown data F1000research. 5. DOI: 10.7490/F1000Research.1112661.1  0.352
2015 Clowers KJ, Will JL, Gasch AP. A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae. Molecular Ecology. PMID 26518477 DOI: 10.1111/Mec.13439  0.431
2015 Ho YH, Gasch AP. Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. Current Genetics. 61: 503-11. PMID 25957506 DOI: 10.1007/S00294-015-0491-0  0.316
2015 Hose J, Yong CM, Sardi M, Wang Z, Newton MA, Gasch AP. Dosage compensation can buffer copy-number variation in wild yeast. Elife. 4. PMID 25955966 DOI: 10.7554/Elife.05462  0.514
2015 Clowers KJ, Heilberger J, Piotrowski JS, Will JL, Gasch AP. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae. Molecular Biology and Evolution. 32: 2317-27. PMID 25953281 DOI: 10.1093/Molbev/Msv112  0.401
2014 Wohlbach DJ, Rovinskiy N, Lewis JA, Sardi M, Schackwitz WS, Martin JA, Deshpande S, Daum CG, Lipzen A, Sato TK, Gasch AP. Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. Genome Biology and Evolution. 6: 2557-66. PMID 25364804 DOI: 10.1093/Gbe/Evu199  0.401
2014 Parreiras LS, Breuer RJ, Avanasi Narasimhan R, Higbee AJ, La Reau A, Tremaine M, Qin L, Willis LB, Bice BD, Bonfert BL, Pinhancos RC, Balloon AJ, Uppugundla N, Liu T, Li C, ... ... Gasch AP, et al. Engineering and two-stage evolution of a lignocellulosic hydrolysate-tolerant Saccharomyces cerevisiae strain for anaerobic fermentation of xylose from AFEX pretreated corn stover. Plos One. 9: e107499. PMID 25222864 DOI: 10.1371/Journal.Pone.0107499  0.306
2014 Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, Olivier M, Gasch AP, Smith LM. Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. Journal of Proteome Research. PMID 24999558 DOI: 10.1021/Pr5004938  0.334
2014 Lewis JA, Broman AT, Will J, Gasch AP. Genetic architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains. Genetics. 198: 369-82. PMID 24970865 DOI: 10.1534/Genetics.114.167429  0.394
2014 Merrill AE, Hebert AS, MacGilvray ME, Rose CM, Bailey DJ, Bradley JC, Wood WW, El Masri M, Westphall MS, Gasch AP, Coon JJ. NeuCode labels for relative protein quantification. Molecular & Cellular Proteomics : McP. 13: 2503-12. PMID 24938287 DOI: 10.1074/Mcp.M114.040287  0.315
2014 Sato TK, Liu T, Parreiras LS, Williams DL, Wohlbach DJ, Bice BD, Ong IM, Breuer RJ, Qin L, Busalacchi D, Deshpande S, Daum C, Gasch AP, Hodge DB. Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass. Applied and Environmental Microbiology. 80: 540-54. PMID 24212571 DOI: 10.1128/Aem.01885-13  0.32
2013 Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP. Integrated module and gene-specific regulatory inference implicates upstream signaling networks. Plos Computational Biology. 9: e1003252. PMID 24146602 DOI: 10.1371/Journal.Pcbi.1003252  0.473
2012 Lewis JA, Gasch AP. Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor. G3 (Bethesda, Md.). 2: 1607-12. PMID 23275883 DOI: 10.1534/G3.112.004127  0.387
2012 Guan Q, Haroon S, Bravo DG, Will JL, Gasch AP. Cellular memory of acquired stress resistance in Saccharomyces cerevisiae. Genetics. 192: 495-505. PMID 22851651 DOI: 10.1534/Genetics.112.143016  0.327
2012 Huebert DJ, Gasch AP. Defining flexible vs. inherent promoter architectures: the importance of dynamics and environmental considerations. Nucleus (Austin, Tex.). 3: 399-403. PMID 22751015 DOI: 10.4161/Nucl.21172  0.436
2012 Huebert DJ, Kuan PF, Keleş S, Gasch AP. Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Molecular and Cellular Biology. 32: 1645-53. PMID 22354995 DOI: 10.1128/Mcb.06170-11  0.486
2012 Yin WB, Amaike S, Wohlbach DJ, Gasch AP, Chiang YM, Wang CC, Bok JW, Rohlfs M, Keller NP. An Aspergillus nidulans bZIP response pathway hardwired for defensive secondary metabolism operates through aflR. Molecular Microbiology. 83: 1024-34. PMID 22283524 DOI: 10.1111/J.1365-2958.2012.07986.X  0.359
2011 Berry DB, Guan Q, Hose J, Haroon S, Gebbia M, Heisler LE, Nislow C, Giaever G, Gasch AP. Multiple means to the same end: the genetic basis of acquired stress resistance in yeast. Plos Genetics. 7: e1002353. PMID 22102822 DOI: 10.1371/Journal.Pgen.1002353  0.371
2011 Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, ... ... Gasch AP, et al. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proceedings of the National Academy of Sciences of the United States of America. 108: 13212-7. PMID 21788494 DOI: 10.1073/Pnas.1103039108  0.427
2011 Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP. A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Molecular Systems Biology. 7: 514. PMID 21772262 DOI: 10.1038/Msb.2011.48  0.328
2010 Lewis JA, Elkon IM, McGee MA, Higbee AJ, Gasch AP. Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resistance. Genetics. 186: 1197-205. PMID 20855568 DOI: 10.1534/Genetics.110.121871  0.391
2010 Will JL, Kim HS, Clarke J, Painter JC, Fay JC, Gasch AP. Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisiae populations. Plos Genetics. 6: e1000893. PMID 20369021 DOI: 10.1371/Journal.Pgen.1000893  0.613
2010 Eng KH, Kvitek DJ, Keles S, Gasch AP. Transient genotype-by-environment interactions following environmental shock provide a source of expression variation for essential genes. Genetics. 184: 587-93. PMID 19966067 DOI: 10.1534/Genetics.109.107268  0.526
2009 Wohlbach DJ, Thompson DA, Gasch AP, Regev A. From elements to modules: regulatory evolution in Ascomycota fungi. Current Opinion in Genetics & Development. 19: 571-8. PMID 19879128 DOI: 10.1016/J.Gde.2009.09.007  0.505
2009 Kuan PF, Huebert D, Gasch A, Keles S. A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions. Statistical Applications in Genetics and Molecular Biology. 8: Article29. PMID 19572828 DOI: 10.2202/1544-6115.1454  0.326
2009 Alejandro-Osorio AL, Huebert DJ, Porcaro DT, Sonntag ME, Nillasithanukroh S, Will JL, Gasch AP. The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biology. 10: R57. PMID 19470158 DOI: 10.1186/Gb-2009-10-5-R57  0.477
2008 Kvitek DJ, Will JL, Gasch AP. Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. Plos Genetics. 4: e1000223. PMID 18927628 DOI: 10.1371/Journal.Pgen.1000223  0.466
2008 Berry DB, Gasch AP. Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. Molecular Biology of the Cell. 19: 4580-7. PMID 18753408 DOI: 10.1091/Mbc.E07-07-0680  0.422
2007 Gasch AP. Comparative genomics of the environmental stress response in ascomycete fungi. Yeast (Chichester, England). 24: 961-76. PMID 17605132 DOI: 10.1002/Yea.1512  0.365
2006 Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB. Flexible promoter architecture requirements for coactivator recruitment. Bmc Molecular Biology. 7: 16. PMID 16646957 DOI: 10.1186/1471-2199-7-16  0.737
2004 Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB. Conservation and evolution of cis-regulatory systems in ascomycete fungi. Plos Biology. 2: e398. PMID 15534694 DOI: 10.1371/Journal.Pbio.0020398  0.78
2004 Koc A, Gasch AP, Rutherford JC, Kim HY, Gladyshev VN. Methionine sulfoxide reductase regulation of yeast lifespan reveals reactive oxygen species-dependent and -independent components of aging. Proceedings of the National Academy of Sciences of the United States of America. 101: 7999-8004. PMID 15141092 DOI: 10.1073/Pnas.0307929101  0.346
2002 Gasch AP, Eisen MB. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology. 3: RESEARCH0059. PMID 12429058 DOI: 10.1186/Gb-2002-3-11-Research0059  0.782
2002 Gasch AP, Werner-Washburne M. The genomics of yeast responses to environmental stress and starvation. Functional & Integrative Genomics. 2: 181-92. PMID 12192591 DOI: 10.1007/S10142-002-0058-2  0.489
2002 Gasch AP. Yeast genomic expression studies using DNA microarrays. Methods in Enzymology. 350: 393-414. PMID 12073326 DOI: 10.1016/S0076-6879(02)50976-9  0.415
2002 Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. The Journal of Biological Chemistry. 277: 31079-88. PMID 12058033 DOI: 10.1074/Jbc.M202718200  0.726
2001 Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Molecular Biology of the Cell. 12: 2987-3003. PMID 11598186 DOI: 10.1091/Mbc.12.10.2987  0.699
2001 Segal E, Taskar B, Gasch A, Friedman N, Koller D. Rich probabilistic models for gene expression. Bioinformatics (Oxford, England). 17: S243-52. PMID 11473015 DOI: 10.1093/Bioinformatics/17.Suppl_1.S243  0.464
2001 Carmel-Harel O, Stearman R, Gasch AP, Botstein D, Brown PO, Storz G. Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae. Molecular Microbiology. 39: 595-605. PMID 11169101 DOI: 10.1046/J.1365-2958.2001.02255.X  0.74
2000 Lee SE, Pellicioli A, Demeter J, Vaze MP, Gasch AP, Malkova A, Brown PO, Botstein D, Stearns T, Foiani M, Haber JE. Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae. Cold Spring Harbor Symposia On Quantitative Biology. 65: 303-14. PMID 12760044 DOI: 10.1101/Sqb.2000.65.303  0.62
2000 Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell. 11: 4241-57. PMID 11102521 DOI: 10.1091/Mbc.11.12.4241  0.758
2000 Lyons TJ, Gasch AP, Gaither LA, Botstein D, Brown PO, Eide DJ. Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proceedings of the National Academy of Sciences of the United States of America. 97: 7957-62. PMID 10884426 DOI: 10.1073/Pnas.97.14.7957  0.76
1999 Spellman P, Gasch A, Eisen M, Kao C, Brown P, Botstein D. Functional clustering of genes using microarray gene expression data Nature Genetics. 23: 75-75. DOI: 10.1038/14406  0.75
1995 Takahashi T, Gasch A, Nishizawa N, Chua NH. The DIMINUTO gene of Arabidopsis is involved in regulating cell elongation Genes and Development. 9: 97-107. PMID 7828854 DOI: 10.1101/gad.9.1.97  0.303
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