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Preprints on BioRxiiv

Gasch A.P., Yu, BF, Hose, J, Escalante, LE, Place, M, Bacher, R, Kanbar, J, Ciobanu, D, Sandor L, Grigoriev, IV, Kendziorski, K, Quake, SR, McClean, MN.  (2017).  Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress.  doi:

MacGilvray, ME, Shishkova, E, Chasman, D, Place, M, Gitter, A, Coon, JJ, Gasch, AP.  (2017).  Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response.  doi:

Published Manuscripts

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 cerevisiaeGenomics. 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.  eLife10.7554/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 cerevisiae natural 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 cerevisiaeJournal of Proteome Research. In pressPUBMED

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 PUBMED PDF

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. PUBMED PDF

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 

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 isolatesPLoS 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 isolatesPLoS 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  

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Congratulations to Maria Sardi for her position at Cargill

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Congrats to Dee Robinson on his GSTP fellowship

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