Dutcher HA and Gasch AP (2024) Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis. RNA 31(1):100-112 PMID:39471998
Dutcher HA, et al. (2024) The response to single-gene duplication implicates translation as a key vulnerability in aneuploid yeast. PLoS Genet 20(10):e1011454 PMID:39453980
Rojas J, et al. (2024) Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model. Cell Genom 4(10):100656 PMID:39317188
Wagner ER and Gasch AP (2023) Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense. J Fungi (Basel) 9(8) PMID:37623557
Gambacorta FV, et al. (2022) Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. Synth Syst Biotechnol 7(2):738-749 PMID:35387233
Vanacloig-Pedros E, et al. (2022) Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions. FEMS Yeast Res 21(1) PMID:35883225
Robinson D, et al. (2021) Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories. Elife 10 PMID:34338637
Scopel EFC, et al. (2021) Genetic variation in aneuploidy prevalence and tolerance across Saccharomyces cerevisiae lineages. Genetics 217(4) PMID:33734361
MacGilvray ME, et al. (2020) Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. J Proteome Res 19(8):3405-3417 PMID:32597660
Stoneman HR, et al. (2020) CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations. G3 (Bethesda) 10(11):4287-4294 PMID:32963084
Wagner ER, et al. (2019) PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production. PLoS One 14(5):e0212389 PMID:31112537
Cesnik AJ, et al. (2018) Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. J Proteome Res 17(1):568-578 PMID:29195273
Higgins DA, et al. (2018) Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 210(1):219-234 PMID:30045857
Ho YH, et al. (2018) Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress. Curr Biol 28(16):2673-2680.e4 PMID:30078561
MacGilvray ME, et al. (2018) Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput Biol 13(5):e1006088 PMID:29738528
McDaniel EA, et al. (2018) Independent Mechanisms for Acquired Salt Tolerance versus Growth Resumption Induced by Mild Ethanol Pretreatment in Saccharomyces cerevisiae. mSphere 3(6) PMID:30487155
Sardi M, et al. (2018) Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance. PLoS Genet 14(2):e1007217 PMID:29474395
Sardi M, et al. (2018) Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis. G3 (Bethesda) 8(12):3881-3890 PMID:30301737
Dai Y, et al. (2017) Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Anal Chem 89(15):7841-7846 PMID:28654248
Nemec CM, et al. (2017) Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner. Proc Natl Acad Sci U S A 114(20):E3944-E3953 PMID:28465432
Gasch AP, et al. (2016) Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution. Elife 5:e14409 PMID:26949252
Guillen-Ahlers H, et al. (2016) HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics 107(6):267-73 PMID:27184763
McIlwain SJ, et al. (2016) Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research. G3 (Bethesda) 6(6):1757-66 PMID:27172212
Sato TK, et al. (2016) Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLoS Genet 12(11):e1006447 PMID:27828955
Sato TK, et al. (2016) Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLoS Genet 12(10):e1006372 PMID:27741250
Clowers KJ, et al. (2015) A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae. Mol Ecol 24(23):5886-98 PMID:26518477
Gasch AP and Yvert G (2015) Meeting Report on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems. G3 (Bethesda) 5(6):1021-3 PMID:25908568
Ho YH and Gasch AP (2015) Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. Curr Genet 61(4):503-11 PMID:25957506
Kennedy-Darling J, et al. (2014) Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. J Proteome Res 13(8):3810-25 PMID:24999558
Lewis JA, et al. (2014) Genetic architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains. Genetics 198(1):369-82 PMID:24970865
Parreiras LS, et al. (2014) 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(9):e107499 PMID:25222864
Sato TK, et al. (2014) Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass. Appl Environ Microbiol 80(2):540-54 PMID:24212571
Huebert DJ and Gasch AP (2012) Defining flexible vs. inherent promoter architectures: the importance of dynamics and environmental considerations. Nucleus 3(5):399-403 PMID:22751015
Huebert DJ, et al. (2012) Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 32(9):1645-53 PMID:22354995
Lewis JA and Gasch AP (2012) Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor. G3 (Bethesda) 2(12):1607-12 PMID:23275883
Berry DB, et al. (2011) Multiple means to the same end: the genetic basis of acquired stress resistance in yeast. PLoS Genet 7(11):e1002353 PMID:22102822
Wohlbach DJ, et al. (2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc Natl Acad Sci U S A 108(32):13212-7 PMID:21788494
Eng KH, et al. (2010) Transient genotype-by-environment interactions following environmental shock provide a source of expression variation for essential genes. Genetics 184(2):587-93 PMID:19966067
Lewis JA, et al. (2010) Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resistance. Genetics 186(4):1197-205 PMID:20855568
Will JL, et al. (2010) Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisiae populations. PLoS Genet 6(4):e1000893 PMID:20369021
Alejandro-Osorio AL, et al. (2009) The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biol 10(5):R57 PMID:19470158
Berry DB and Gasch AP (2008) Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. Mol Biol Cell 19(11):4580-7 PMID:18753408
Kvitek DJ, et al. (2008) Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet 4(10):e1000223 PMID:18927628
Koc A, et al. (2004) Methionine sulfoxide reductase regulation of yeast lifespan reveals reactive oxygen species-dependent and -independent components of aging. Proc Natl Acad Sci U S A 101(21):7999-8004 PMID:15141092
Gasch AP and Eisen MB (2002) Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 3(11):RESEARCH0059 PMID:12429058
Gasch AP and Werner-Washburne M (2002) The genomics of yeast responses to environmental stress and starvation. Funct Integr Genomics 2(4-5):181-92 PMID:12192591
Yoshimoto H, et al. (2002) Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem 277(34):31079-88 PMID:12058033
Carmel-Harel O, et al. (2001) Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae. Mol Microbiol 39(3):595-605 PMID:11169101
Gasch AP, et al. (2001) Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell 12(10):2987-3003 PMID:11598186
Gasch AP, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11(12):4241-57 PMID:11102521
Lee SE, et al. (2000) Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae. Cold Spring Harb Symp Quant Biol 65:303-14 PMID:12760044
Lyons TJ, et al. (2000) Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc Natl Acad Sci U S A 97(14):7957-62 PMID:10884426