Search PubMed for latest publications
Lee, S.G., Tremaine, M., Place, M., Liu, L., Pier, A., Krause, D.J., Xie, D., Zhang, Y., Landick, R., Gasch, A.P., Hittinger, C.T., Sato, T.K. (2021). Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae. Metab. Eng. 68:119-130.
Robinson, D., Place, M., Hose, J., Jochem, A., Gasch, A.P.* (2021). Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories. eLife, 10:e70564
Escalante E. and Gasch, A.P.* (2021). The role of stress-induced RNA-protein granules in surviving adversity. RNA, rna.078738.121
Scopel, E., Hose, J., Bensasson, D., Gasch, A.P.* (2021). Genetic variation in aneuploidy prevalence and tolerance across Saccharomyces cerevisiae lineages. Genetics, 217(4):iyab015
MacGilvray, M.E., Shishkova, E., Place, M., Wagner, E.R., Coon, J.J., Gasch, A.P.* (2020). The phosphoproteome response to dithiothreitol reveals unique versus shared features of Saccharomyces cerevisiae stress responses. J. Proteome Research, 7;19(8):3405-3417
Stoneman, H., Wrobel, R. L., Place, M., Graham, M., Krause, D.J., deChiara, M.D., Liti, G., Schacherer, J., Landick, R., Gasch, A.P., Sato, T.K., Hittinger, C.T. (2020). CRISpy-pop: a web tool for designing CRISPR/Cas9-driven genetic modifications in diverse populations. G3, g3.401498.2020
Hose, J, Escalante, L.E., Clowers, K.J., Dutcher, H.A., Robinson, D.E., Bouriakov, V., Coon, J.J., Shishkova, E., Gasch, A.P.* (2020). The genetic basis of aneuploidy tolerance in wild yeast. (2020). eLife, 9. pii: e52063. doi: 10.7554/eLife.52063.
Sverchkov, Y., Ho, Y.H., Gasch, A.P., Craven, M. (2019). Context-specific Nested Effects Models. Journal of Computational Biology. J. Comput. Biol. 27(3):403-417.
Wagner ER, Myers, KS, Riley, NM, Coon, JJ, Gasch, AP. (2019) PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production. PLoS ONE, in press.
Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP. (2019). Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. PLoS Genet.15(3):e1008037.
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. (2019). Noncanonical CTD kinases regulate RNA polymerase II in a gene-class-specific manner. Nat Chem Biol.15(2):123-131.
McDaniel EA, Stuecker TN, Veluvolu M, Gasch AP, Lewis JA. (2018). Independent Mechanisms for Acquired Salt Tolerance versus Growth Resumption Induced by Mild Ethanol Pretreatment in Saccharomyces cerevisiae. mSphere.3(6). pii: e00574-18.
Ho YH, Shishkova E, Hose J, Coon JJ, Gasch AP. (2018). Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress. Curr Biol.28(16):2673-2680.e4.
Sardi M, Krause M, Heilberger J, Gasch AP. (2018). Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis. G3: Genes, Genomes, Genetics. 8(12):3881-3890.
Higgins DA, Young MKM, 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, Thelen MP, Sato TK. (2018). Natural Variation in the Multidrug Efflux Pump SGE1Underlies Ionic Liquid Tolerance in Yeast. Genetics.210(1):219-234.
MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. (2018). Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput Biol.13(5):e1006088.
Sardi M, Gasch AP. (2018). Genetic background effects in quantitative genetics: gene-by-system interactions. Curr Genet.64(6):1173-1176.
Sardi M, Paithane V, Place M, Robinson E, Hose J, Wohlbach DJ, Gasch AP. (2018). Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance.PLoS Genet. 14(2):e1007217.
Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM.(2018). Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.J Proteome Res.17(1):568-578.
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.(2017). Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol.2017 15(12):e2004050.
Muir, V.S., Gasch, A.P., Anderson, P. (2017) The substrates of nonsense-mediated mRNA decay in C. elegans. G3. pii: g3.300254.2017. doi: 10.1534/g3.117.300254.
Sardi M., Gasch A.P.*(2017). Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering. FEMS Yeast Research. doi: 10.1093/femsyr/fox042.
Bacher R., Chu L.F., Leng N., Gasch A.P., Thomson JA, Stewart RM, Newton M, Kendziorski C.(2017). SCnorm: robust normalization of single-cell RNA-seq data. Nature Methods.Jun;14(6):584-586. doi: 10.1038/nmeth.4263.
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.(2017). Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner. PNAS.114(20):E3944-E3953.
Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM. (2017). Multiplexed sequence-specific capture of chromatin and mass spectrometric discovery of associated proteins. Anal Chem. 2017 89(15):7841-7846.
Wilinski D, Buter N, Klocko AD, Lapointe CP, Selker EU, Gasch AP, Wickens M.(2017). Recurrent rewiring and emergence of RNA regulatory networks. PNAS. 114(14):E2816-E2825.
Sato, T.K., Tremaine, M., Parreiras,L.S., Hebert, A.S., Myers, K.S., Alan J. Higbee, A.J., Sardi, M., McIlwain, S.J., Ong, I.M., Breuer, R.J., Narasimhan, R.A., McGee, M.A., Dickinson, Q., Reau, A.L., Xie, D., Tian, M., Reed, J.L., Hittinger, C.T., Coon, J.J., Gasch, A.P.*, Landick, R. (2016). Directed evolution reveals unexpected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae. PLoS Genetics. DOI:10.1371/journal/pgen.1006372
Sardi, M., Rovinskiy, N., Zhang, Y., Gasch, A.P. (2016). Leveraging genetic background effects in Saccharomyces cerevisiaeto improve lignocellulosic hydrolysate tolerance. Applied Environmental Microbiology. 16;82(19):5838-49
Gasch, A.P.*, Payseur, B.A.*, Pool, J.(2016). The power of natural variation for model organism biology. Trends in Genetics. 32(3):147-54
Gasch, A.P.*, Hose, J, Newton, MA, Sardi, M, Yong, M, Wang, Z.(2016). Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution. Elife. 10.7554/eLife.14409.
McIlwain, S.J., Peris, D., Sardi, M., Moskvin, O.V., Zhan, F., Myers, K., Riley, N.R., Buzzell, A., Parreiras, L.S., Ong, I.M., Landick, R., Coon, J.J., Gasch, A.P., Sato, T.K., Hittinger, C.T. (2016). Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research. G3: Genes, Genomes, Genetics. 6(6):1757-66
Guillen-Ahlers, H., Rao, P.K., Levenstein, M.E., Kennedy-Darling, J., Perumalla, D.S., Jadhav, A.Y., Glenn, J.P., Ludwig-Kubinski, A., Drigalenko, E., Montoya, M.J., Göring, H.H., Anderson, C.D., Scalf, M., Gildersleeve, H.I., Cole, R., Greene, A.M., Oduro, A.K., Lazarova, K., Cesnik, A.J., Barfknecht, J., Cirillo, L.A., Gasch, A.P., Shortreed, M.R., Smith, L.M., Olivier, M. (2016). HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics.107(6):267-73.
Clowers, K., Will, J.L., Gasch, A.P.(2015). A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae. Molecular Ecology. 24(23):5886-98
Hose, J., Yong, M., Sardi, M., Wang, Z, Newton, M.A., Gasch, A.P.(2015). Dosage compensation can buffer copy-number variation in wild yeast. eLife. 10.7554/eLife.05462
Ho, Y.H. and Gasch, A.P.(2015). Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. Current Genetics. 61(4):503-11
Clowers, K., Heilberger, J., Will, J.L., Piotrowski, J., Gasch, A.P.*(2015). Ecological and genetic barriers differentiate natural populations of Saccharomyces cerevisiae. Molecular Biology and Evolution. 32(9):2317-27
Chasman, D.#, Ho, Y.H.#, Berry, D.B., Nemec, C.M., MacGilvray, M.E., Hose, J., Merrill, A. E., Lee, M. V., Will, J.L., Coon, J.J., Ansari, A.Z., Craven, M., Gasch, A.P.*(2014). Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Molecular Systems Biology. 10(11):759. 1-23
Wohlbach, D.W., Rovinskiy, N., Lewis, J.A., Sardi, M., Schackwitz, W.S., Martin, J.A., Deshpande, S., Daum, C., Lipzen, A., Sato, T.K., Gasch, A.P.(2014). Comparative genomics of Saccharomyces cerevisiaenatural isolates for bioenergy production. Genome Biology and Evolution. Sep 5;6(9):2557-66 PUBMED
Sorokin, E. Gasch, A.P., Kimble, J.E.(2014) Genomic analysis of in vivo cell fate reprogramming.Genetics. 198(2):561-75
Parreirras L.S., Bruer, R.J., Narasimhan, R.A., Higbee, A.J., La Reau, A., Tremaine, M., Qin, L., Willis, L.B., Bice, B.D., Bonfert, B.L., Pinhancos, R.C., Balloon, A.J., Uppugundla, N., Liu, T., Li, C., Tanjore, D., Ong, I.M., Li, H., Pohlmann, E.L., Serate, J., Withers, S.T., Simmons, B.A., Hodge, D.B., Westphall, M.S., Coon, J.J., Dale, B.E., Balan, V., Keating, D.H., Zhang, Y., Landick, R., Gasch, A.P., Sato, T.K.(2014). Engineering and two-stage evolution of a lignocellulosic hydrolysate-tolerant Saccharomyces cerevisiae strain for anaerobic fermentation of xylose from AFEXTM pretreated corn stover. PLoS ONE.Sep 15;9(9):e107499. PUBMED
Kennedy-Darling, J. Guillen-Ahlers, H., Shortreed, M., Scalf, M., Frey, B., Kendziorski, C., Olivier, M., Gasch, A.P., Smith, L. (2014). Discovery of chromatin-associated proteins via sequence-specific capture and mass spectrometric protein identification in Saccharomyces cerevisiae. Journal of Proteome Research. In press. PUBMED
Lewis, J.A., Broman, A.T., Will, J.L., Gasch, A.P.(2014). Genetics architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains. Genetics. Genetics. Sep;198(1):369-82 PUBMED
Merrill, A.E., Hebert, A.S., Potts, G.K., MacGilvray, M.E., Rose, C.M., Voigt, E.A., Bailey, D.J., Bradley, J.C., Wood, W.W., El Masri, M., Westphall, M.S., Yin, J., Gasch, A.P., Coon, J.C.(2014). NeuCode labels for relative protein quantification. Molecular and Cellular Proteomics. 13(9):2503-12. PUBMED
Sato T.K., Liu T., Parreiras L.S., Williams D.L., Wohlbach D.J., Bice B.D., Ong I.M., Breuer R.J., Qin L., Busalacchi D., Deshpande S., Daum C., Gasch A.P., Hodge DB. (2014) Harnessing Genetic Diversity in Saccharomyces cerevisiae for Fermentation of Xylose in Hydrolysates of Alkaline Hydrogen Peroxide-Pretreated Biomass. Applied and Environmental Microbiology 80(2): 540-554. PUBMED
Roy S.*, Lagree, S. Hou Z., Thomson, JA, Stewart R., Gasch A.P. (2013) Integrated module and gene-specific regulatory inference implicates upstream signaling networks. PLoS Computational Biology. 9(10)e1003252. PUBMED
Lewis J.A., Gasch A.P.(2012) Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor. G3: Genes, Genomes, & Genetics. Dec;2(12):1607-12. PUBMED PDF
Guan Q., Haroon S., Bravo D.G., Will J.L., Gasch AP.(2012) Cellular memory of acquired stress resistance in Saccharomyces cerevisiae. Genetics. Oct;192(2):495-505. PUBMED PDF
Huebert D.J., Gasch A.P.(2012) Defining flexible vs. inherent promoter architectures: the importance of dynamics and environmental considerations. Nucleus. Sep-Oct;3(5):399-403 PUBMEDPDF
Huebert D.J., Kuan P.F., Keles S., Gasch A.P. (2012) Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol. May;32(9):1645-53. PUBMEDPDF
Yin W.B., Amaike S., Wohlbach D.J., Gasch A.P., Chiang Y.M., Wang C.C., Bok J.W., Rohlfs M., Keller N.P.(2012) An Aspergillus nidulans bZIP response pathway hardwired for defensive secondary metabolism operates through aflR. Mol Microbiol. 83(5):1024-34 PUBMED PDF
Berry, D.B., Guan, Q., Hose, J., Haroon, S., Gebbia, M., Heisler, L.E., Nislow, C., Giaever, G., Gasch, A.P. (2011). Multiple means to the same end: the genetic basis of acquired stress resistance in yeast PLoS Genetics, 7(11):e1002353 PUBMED PDF
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, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP. (2011). Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. PNASAug 9;108(32):13212-7 PUBMED PDF
Lee, M.V., Topper, S.E., Hubler, S.L., Hose, J., Wenger, C.D., Coon, J.J., Gasch, A.P. (2011). A Dynamic Model of Proteome Changes Reveals New Roles for Transcript Alteration in Yeast. Molecular Systems Biology, Jul 19;7:514. doi: 10.1038/msb.2011.48 PUBMED PDF
Lewis, J.A., Elkon, I.M., McGee, M.A., Higbee, A.J., and Gasch A.P. (2010). Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resisatnce. Genetics PUBMED PDF
Eng, K.H.*, Kvitek, D.J.*, Keles, S., and Gasch A.P. (2010). Transient genotype-by-environment interactions following environmental shock provide a source of expression variation for essential genes.Genetics PUBMED PDF
Will J.L., Kim, H.S., Fay, J.C., and Gasch A.P. (2010). Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genetics PUBMED PDF
Wohlbach, D.J.*, Thompson, D.A.*, Gasch A.P., Regev, A. (2009). From elements to modules: regulatory evolution in Ascomycota fungi. Curr Opin Genet Dev. PUBMED PDF
Alejandro-Osorio*, A.L., Huebert, D.J.*, Porcaro, D.T., Sonntag, M.E., Nillasithanukroh, S., Will, J.L., and Gasch A.P. (2009). The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biology PUBMED PDF
Kvitek D.J, Will J.L., and Gasch A.P. (2008). Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genetics PUBMED PDF
Berry D.B. and Gasch A.P. (2008). Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. Mol Biol. Cell PUBMED PDF
Gasch A.P. (2007). Comparative genomics of the environmental stress response in ascomycete fungi. Yeast PUBMED PDF
Gasch A.P., Moses, A.M., Chiang, D.Y., Fraser, F.B., Berardini, M. and Eisen M.B. (2004). Conservation and evolution of cis-regulatory systems in ascomycete fungi PLoS Biology, 2(12): e398 PUBMED PDF
Gasch A.P. and Eisen M.B. (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology, 3(11):research0059.1-0059.22 PUBMED PDF
Read the paper in Estonian! (Translation by Anna Galovich)
Gasch, A.P. (2002). The Environmental Stress Response: a common yeast response to environmental stresses. In Yeast Stress Responses. S. Hohmann and P. Mager (ed). Volume 1, Topics in Current Genetics (series editor S. Hohmann) Springer-Verlag Heidelberg p. 11-70 PDF
Gasch, A.P., Werner-Washburne, M. (2002). The genomics of yeast responses to environmental stress and starvation. Funct. Integr. Genomics 2(4-5):181-192 PUBMED PDF
Gasch, A.P. (2002). Yeast genomic expression studies using DNA microarrays. In Guide to Yeast Genetics and Molecular and Cellular Biology. C. Guthrie and G.R. Fink (ed). Methods in Enzymology. 350: 393-414Doc
Yoshimoto, H., Saltsman, K., Gasch, A.P., Li H.X., Ogawa, N., Botstein, D., Brown, P.O., Cyert, M.S.(2002). Genome-wide analysis of gene expression regulated by the calcinneurin/Crz1p signaling pathway inSaccharomyces cerevisiae. J Biol Chem. 277(34):31079-31088 PUBMED
Gasch, A.P., Huang, M., Metzner, S., Elledge, S.J., Botstein, D., Brown, P.O. (2001). Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol. Biol. Cell12(10):2987-3003 PUBMED
Segal, E., Taskar, B., Gasch, A.P., Friedman, N., Koller, D. (2001). Rich Probabilistic Models for Gene Expression. ISMB 17(1):243-252 PUBMED
Lee, S.L., Pellichioli, A., Demeter, J., Vaze, M., Gasch, A.P. Malkova, A., Brown, P.O., Stearns, T., Foiani, M. and Haber, J.E. (2001). Arrest, adaptation and recovery following a chromosome double-strand break in Saccharomyces cerevisiae. Cold Spring Harb. Symp. Quant. Biol. 65: 303-314
Carmel-Harel, O., Stearman, R., Gasch, A.P., Botstein, D., Brown, P.O., and Storz, G. (2001). Role of Thioredoxin Reductase in Regulating the Yap1p-Dependent Response to Oxidative Stress in Saccharomyces cerevisiae. Mol. Micro. 39(3):595-605 PUBMED
Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., Botstein, D., Brown, P.O. (2000). Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11(12):4241-4257 PUBMED
Lyons, T.J., Gasch, A.P., Gaither, L.A., Botstein, D., Brown, P.O., Eide, D.J. (2000). Genome- wide characterization of the Zap1p zinc-responsive regulon in yeast. PNAS 97(14):7957-7963 PUBMED
Weinreich, M.D., Gasch, A.P., Reznikoff, W.S. (1994). Evidence that the cis preference of the Tn5 transposase is caused by nonproductive multimerization. Genes & Dev. 8(19):2363-2374 PUBMED