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Items: 1 to 50 of 62

1.

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response.

MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP.

PLoS Comput Biol. 2018 May 8;13(5):e1006088. doi: 10.1371/journal.pcbi.1006088. eCollection 2018 May.

2.

Genetic background effects in quantitative genetics: gene-by-system interactions.

Sardi M, Gasch AP.

Curr Genet. 2018 Apr 11. doi: 10.1007/s00294-018-0835-7. [Epub ahead of print] Review.

PMID:
29644456
3.

Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance.

Sardi M, Paithane V, Place M, Robinson E, Hose J, Wohlbach DJ, Gasch AP.

PLoS Genet. 2018 Feb 23;14(2):e1007217. doi: 10.1371/journal.pgen.1007217. eCollection 2018 Feb.

4.

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress.

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.

PLoS Biol. 2017 Dec 14;15(12):e2004050. doi: 10.1371/journal.pbio.2004050. eCollection 2017 Dec.

5.

Reply to Hogan: Direct evidence of RNA-protein interactions and rewiring.

Wilinski D, Buter N, Klocko AD, Lapointe CP, Selker EU, Gasch AP, Wickens M.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E10854-E10855. doi: 10.1073/pnas.1717585114. Epub 2017 Dec 5. No abstract available.

6.

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM.

J Proteome Res. 2018 Jan 5;17(1):568-578. doi: 10.1021/acs.jproteome.7b00685. Epub 2017 Dec 15.

PMID:
29195273
7.

The Substrates of Nonsense-Mediated mRNA Decay in Caenorhabditis elegans.

Muir VS, Gasch AP, Anderson P.

G3 (Bethesda). 2018 Jan 4;8(1):195-205. doi: 10.1534/g3.117.300254.

8.

Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins.

Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM.

Anal Chem. 2017 Aug 1;89(15):7841-7846. doi: 10.1021/acs.analchem.7b01784. Epub 2017 Jul 11.

PMID:
28654248
9.

Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering.

Sardi M, Gasch AP.

FEMS Yeast Res. 2017 Aug 1;17(5). doi: 10.1093/femsyr/fox042. Review.

PMID:
28637316
10.

Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner.

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.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):E3944-E3953. doi: 10.1073/pnas.1700128114. Epub 2017 May 2.

11.

SCnorm: robust normalization of single-cell RNA-seq data.

Bacher R, Chu LF, Leng N, Gasch AP, Thomson JA, Stewart RM, Newton M, Kendziorski C.

Nat Methods. 2017 Jun;14(6):584-586. doi: 10.1038/nmeth.4263. Epub 2017 Apr 17.

12.

Recurrent rewiring and emergence of RNA regulatory networks.

Wilinski D, Buter N, Klocko AD, Lapointe CP, Selker EU, Gasch AP, Wickens M.

Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):E2816-E2825. doi: 10.1073/pnas.1617777114. Epub 2017 Mar 20.

13.

Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Narasimhan RA, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Piotrowski JS, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R.

PLoS Genet. 2016 Nov 9;12(11):e1006447. doi: 10.1371/journal.pgen.1006447. eCollection 2016 Nov.

14.

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

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, Tian M, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R.

PLoS Genet. 2016 Oct 14;12(10):e1006372. doi: 10.1371/journal.pgen.1006372. eCollection 2016 Oct. Erratum in: PLoS Genet. 2016 Nov 9;12 (11):e1006447.

15.

Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance.

Sardi M, Rovinskiy N, Zhang Y, Gasch AP.

Appl Environ Microbiol. 2016 Sep 16;82(19):5838-49. doi: 10.1128/AEM.01603-16. Print 2016 Oct 1.

16.

HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.

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, Greene AM, Oduro AK, Lazarova K, Cesnik AJ, Barfknecht J, Cirillo LA, Gasch AP, Shortreed MR, Smith LM, Olivier M.

Genomics. 2016 Jun;107(6):267-73. doi: 10.1016/j.ygeno.2016.05.002. Epub 2016 May 13.

17.

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research.

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.

G3 (Bethesda). 2016 Jun 1;6(6):1757-66. doi: 10.1534/g3.116.029389.

18.

Correction: Dosage compensation can buffer copy-number variation in wild yeast.

Hose J, Yong CM, Sardi M, Wang Z, Newton MA, Gasch AP.

Elife. 2016 Mar 23;5. pii: e15743. doi: 10.7554/eLife.15743. No abstract available.

19.

Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution.

Gasch AP, Hose J, Newton MA, Sardi M, Yong M, Wang Z.

Elife. 2016 Mar 7;5:e14409. doi: 10.7554/eLife.14409.

20.

The Power of Natural Variation for Model Organism Biology.

Gasch AP, Payseur BA, Pool JE.

Trends Genet. 2016 Mar;32(3):147-154. doi: 10.1016/j.tig.2015.12.003. Epub 2016 Jan 7. Review.

21.

A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae.

Clowers KJ, Will JL, Gasch AP.

Mol Ecol. 2015 Dec;24(23):5886-98. doi: 10.1111/mec.13439. Epub 2015 Nov 20.

22.

Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling.

Ho YH, Gasch AP.

Curr Genet. 2015 Nov;61(4):503-11. doi: 10.1007/s00294-015-0491-0. Epub 2015 May 10. Review.

23.

Dosage compensation can buffer copy-number variation in wild yeast.

Hose J, Yong CM, Sardi M, Wang Z, Newton MA, Gasch AP.

Elife. 2015 May 8;4. doi: 10.7554/eLife.05462. Erratum in: Elife. 2016;5. pii: e15743. doi: 10.7554/eLife.15743.

24.

Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

Clowers KJ, Heilberger J, Piotrowski JS, Will JL, Gasch AP.

Mol Biol Evol. 2015 Sep;32(9):2317-27. doi: 10.1093/molbev/msv112. Epub 2015 May 6.

25.

Meeting Report on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems.

Gasch AP, Yvert G.

G3 (Bethesda). 2015 Jun;5(6):1021-3. Epub 2015 Apr 22. No abstract available.

26.

Pathway connectivity and signaling coordination in the yeast stress-activated signaling network.

Chasman D, Ho YH, Berry DB, Nemec CM, MacGilvray ME, Hose J, Merrill AE, Lee MV, Will JL, Coon JJ, Ansari AZ, Craven M, Gasch AP.

Mol Syst Biol. 2014 Nov 19;10:759. doi: 10.15252/msb.20145120.

27.

Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production.

Wohlbach DJ, Rovinskiy N, Lewis JA, Sardi M, Schackwitz WS, Martin JA, Deshpande S, Daum CG, Lipzen A, Sato TK, Gasch AP.

Genome Biol Evol. 2014 Sep;6(9):2557-66.

28.

Engineering and two-stage evolution of a lignocellulosic hydrolysate-tolerant Saccharomyces cerevisiae strain for anaerobic fermentation of xylose from AFEX pretreated corn stover.

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, Tanjore D, Ong IM, Li H, Pohlmann EL, Serate J, Withers ST, Simmons BA, Hodge DB, Westphall MS, Coon JJ, Dale BE, Balan V, Keating DH, Zhang Y, Landick R, Gasch AP, Sato TK.

PLoS One. 2014 Sep 15;9(9):e107499. doi: 10.1371/journal.pone.0107499. eCollection 2014.

29.

Competence for chemical reprogramming of sexual fate correlates with an intersexual molecular signature in Caenorhabditis elegans.

Sorokin EP, Gasch AP, Kimble J.

Genetics. 2014 Oct;198(2):561-75. doi: 10.1534/genetics.114.169409. Epub 2014 Aug 21.

30.

Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae.

Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, Olivier M, Gasch AP, Smith LM.

J Proteome Res. 2014 Aug 1;13(8):3810-25. doi: 10.1021/pr5004938. Epub 2014 Jul 17.

31.

Genetic architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains.

Lewis JA, Broman AT, Will J, Gasch AP.

Genetics. 2014 Sep;198(1):369-82. doi: 10.1534/genetics.114.167429. Epub 2014 Jun 26.

32.

NeuCode labels for relative protein quantification.

Merrill AE, Hebert AS, MacGilvray ME, Rose CM, Bailey DJ, Bradley JC, Wood WW, El Masri M, Westphall MS, Gasch AP, Coon JJ.

Mol Cell Proteomics. 2014 Sep;13(9):2503-12. doi: 10.1074/mcp.M114.040287. Epub 2014 Jun 17.

33.

Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass.

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.

Appl Environ Microbiol. 2014 Jan;80(2):540-54. doi: 10.1128/AEM.01885-13. Epub 2013 Nov 8.

34.

Integrated module and gene-specific regulatory inference implicates upstream signaling networks.

Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP.

PLoS Comput Biol. 2013;9(10):e1003252. doi: 10.1371/journal.pcbi.1003252. Epub 2013 Oct 17.

35.

Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor.

Lewis JA, Gasch AP.

G3 (Bethesda). 2012 Dec;2(12):1607-12. doi: 10.1534/g3.112.004127. Epub 2012 Dec 1.

36.

Cellular memory of acquired stress resistance in Saccharomyces cerevisiae.

Guan Q, Haroon S, Bravo DG, Will JL, Gasch AP.

Genetics. 2012 Oct;192(2):495-505. doi: 10.1534/genetics.112.143016. Epub 2012 Jul 30.

37.

Defining flexible vs. inherent promoter architectures: the importance of dynamics and environmental considerations.

Huebert DJ, Gasch AP.

Nucleus. 2012 Sep-Oct;3(5):399-403. doi: 10.4161/nucl.21172. Epub 2012 Jul 3.

38.

Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators.

Huebert DJ, Kuan PF, Keleş S, Gasch AP.

Mol Cell Biol. 2012 May;32(9):1645-53. doi: 10.1128/MCB.06170-11. Epub 2012 Feb 21.

39.

An Aspergillus nidulans bZIP response pathway hardwired for defensive secondary metabolism operates through aflR.

Yin WB, Amaike S, Wohlbach DJ, Gasch AP, Chiang YM, Wang CC, Bok JW, Rohlfs M, Keller NP.

Mol Microbiol. 2012 Mar;83(5):1024-34. doi: 10.1111/j.1365-2958.2012.07986.x. Epub 2012 Feb 10.

40.

Multiple means to the same end: the genetic basis of acquired stress resistance in yeast.

Berry DB, Guan Q, Hose J, Haroon S, Gebbia M, Heisler LE, Nislow C, Giaever G, Gasch AP.

PLoS Genet. 2011 Nov;7(11):e1002353. doi: 10.1371/journal.pgen.1002353. Epub 2011 Nov 10.

41.

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.

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.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13212-7. doi: 10.1073/pnas.1103039108. Epub 2011 Jul 25.

42.

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast.

Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP.

Mol Syst Biol. 2011 Jul 19;7:514. doi: 10.1038/msb.2011.48.

43.

Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resistance.

Lewis JA, Elkon IM, McGee MA, Higbee AJ, Gasch AP.

Genetics. 2010 Dec;186(4):1197-205. doi: 10.1534/genetics.110.121871. Epub 2010 Sep 20.

44.

Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisiae populations.

Will JL, Kim HS, Clarke J, Painter JC, Fay JC, Gasch AP.

PLoS Genet. 2010 Apr 1;6(4):e1000893. doi: 10.1371/journal.pgen.1000893.

45.

Transient genotype-by-environment interactions following environmental shock provide a source of expression variation for essential genes.

Eng KH, Kvitek DJ, Keles S, Gasch AP.

Genetics. 2010 Feb;184(2):587-93. doi: 10.1534/genetics.109.107268. Epub 2009 Dec 4.

46.

From elements to modules: regulatory evolution in Ascomycota fungi.

Wohlbach DJ, Thompson DA, Gasch AP, Regev A.

Curr Opin Genet Dev. 2009 Dec;19(6):571-8. doi: 10.1016/j.gde.2009.09.007. Epub 2009 Oct 29. Review.

47.

The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress.

Alejandro-Osorio AL, Huebert DJ, Porcaro DT, Sonntag ME, Nillasithanukroh S, Will JL, Gasch AP.

Genome Biol. 2009;10(5):R57. doi: 10.1186/gb-2009-10-5-r57. Epub 2009 May 26.

48.

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates.

Kvitek DJ, Will JL, Gasch AP.

PLoS Genet. 2008 Oct;4(10):e1000223. doi: 10.1371/journal.pgen.1000223. Epub 2008 Oct 17.

49.

Stress-activated genomic expression changes serve a preparative role for impending stress in yeast.

Berry DB, Gasch AP.

Mol Biol Cell. 2008 Nov;19(11):4580-7. doi: 10.1091/mbc.E07-07-0680. Epub 2008 Aug 27.

50.

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