A. Gasch

Most-cited papers

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

   Rhonda L. Bacher, Li-Fang Chu, Ning Leng, A. Gasch +4 more

   2017Nature Methods265 citations Open access

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

   A. Gasch, F. Yu, James Hose, Leah E. Escalante +9 more

   2017PLoS Biology148 citations Open access

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3. Cellular Memory of Acquired Stress Resistance in Saccharomyces cerevisiae

   Qiao-Ning Guan, S. Haroon, Diego González Bravo, J. Will +1 more

   2012Genetics140 citations Open access

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

   James Hose, Chris Mun Yong, Maria Sardi, Zhi-Shi Wang +2 more

   2015eLife131 citations Open access

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

   Yi-Hsuan Ho, A. Gasch

   2015Current Genetics117 citations Open access

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

   Trey K. Sato, M. Tremaine, Lucas S. Parreiras, Alexander S. Hebert +18 more

   2016PLoS Genetics101 citations Open access

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

   Deborah A Chasman, Yi-Hsuan Ho, David B. Berry, Corey M. Nemec +9 more

   2014Molecular Systems Biology100 citations Open access

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8. Deciphering the impact of genomic variation on function

   Jesse M. Heather A. Harinder Lea M. Gary C. Hannah Nidhi Engreitz Lawson Singh Starita Hon Carter Sahni Red, Jesse M. Heather A. Harinder Lea M. Gary C. Hannah Nidhi Engreitz Lawson Singh Starita Hon Carter Sahni Red, Jesse M. Engreitz, Heather A. Lawson +496 more

   2024Nature94 citations Open access

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

   Wen-Bing Yin, S. Amaike, Dana J. Wohlbach, A. Gasch +5 more

   2012Molecular Microbiology94 citations Open access

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10. Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover

    Lucas S. Parreiras, Rebecca J Breuer, Ragothaman Avanasi Narasimhan, Alan J. Higbee +28 more

    2014PLoS ONE93 citations Open access

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11. Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

    Sushmita Roy, S. Lagree, Z. Hou, J. Thomson +2 more

    2013PLoS Comput. Biol.89 citations Open access

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12. NeuCode Labels for Relative Protein Quantification *

    Anna E. Merrill, Alexander S. Hebert, Matthew E. MacGilvray, Christopher M. Rose +7 more

    2014Molecular & Cellular Proteomics86 citations Open access

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13. The power of natural variation for model organism biology

    A. Gasch, B. Payseur, J. Pool

    2016Trends in Genetics82 citations Open access

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14. The genetic basis of aneuploidy tolerance in wild yeast

    James Hose, Leah E. Escalante, Katie J. Clowers, H. A. Dutcher +5 more

    2020eLife74 citations Open access

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15. Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators

    Dana J. Huebert, Pei-Fen Kuan, S. Keleş, A. Gasch

    2012Molecular and Cellular Biology67 citations Open access

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16. Decoupling yeast cell division and stress defense implicates mRNA repression in translational reallocation during stress

    Yi-Hsuan Ho, Evgenia Shishkova, James Hose, J. Coon +1 more

    2018Current Biology57 citations Open access

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17. Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

    Jeffrey A. Lewis, A. Broman, J. Will, A. Gasch

    2014Genetics55 citations Open access

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

    Maria Sardi, Vaishnavi Paithane, Michael Place, DeElegant Robinson +3 more

    2017bioRxiv54 citations Open access

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

    S. McIlwain, D. Peris, Maria Sardi, O. Moskvin +11 more

    2016G3: Genes, Genomes, Genetics53 citations Open access

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20. Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae.

    Sae-Byuk Lee, M. Tremaine, Michael Place, Lisa Liu +8 more

    2021Metabolic Engineering51 citations Open access

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21. Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

    Noah M. Lancaster, Pavel Sinitcyn, Patrick Forny, Trenton M. Peters-Clarke +20 more

    2024Nature Communications50 citations Open access

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

    A. Gasch, James Hose, M. Newton, Maria Sardi +2 more

    2016eLife49 citations Open access

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23. Harnessing Genetic Diversity in Saccharomyces cerevisiae for Fermentation of Xylose in Hydrolysates of Alkaline Hydrogen Peroxide-Pretreated Biomass

    Trey K. Sato, Tongjun Liu, Lucas S. Parreiras, Daniel L. Williams +10 more

    2013Applied and Environmental Microbiology48 citations Open access

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24. The phosphoproteome response to dithiothreitol reveals unique versus shared features of Saccharomyces cerevisiae stress responses

    Matthew E. MacGilvray, Evgenia Shishkova, Michael Place, E. Wagner +2 more

    2020Journal of Proteome Research46 citations Open access

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25. Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production

    Dana J. Wohlbach, Nikolay Rovinskiy, Jeffrey A. Lewis, Maria Sardi +7 more

    2014Genome Biology and Evolution45 citations Open access

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26. Genetic variation in aneuploidy prevalence and tolerance across Saccharomyces cerevisiae lineages.

    E. Scopel, James Hose, D. Bensasson, A. Gasch

    2021Genetics43 citations Open access

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27. Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast

    Kevin S. Myers, N. Riley, Matthew E. MacGilvray, Trey K. Sato +4 more

    2019PLoS Genetics37 citations Open access

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28. Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer

    Noah M. Lancaster, Pavel Sinitcyn, Patrick Forny, Trenton M. Peters-Clarke +20 more

    2023bioRxiv36 citations Open access

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29. Recurrent rewiring and emergence of RNA regulatory networks

    D. Wilinski, Natascha Buter, Andrew D. Klocko, Christopher P. Lapointe +3 more

    2017Proceedings of the National Academy of Sciences of the United States of America35 citations Open access

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30. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae

    Katie J. Clowers, Justin Heilberger, J. Piotrowski, J. Will +1 more

    2015Molecular biology and evolution35 citations Open access

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

    Anthony J. Cesnik, Michael R. Shortreed, Leah V. Schaffer, R. Knoener +6 more

    2017Journal of Proteome Research34 citations Open access

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32. Non-canonical CTD-kinases regulate RNA polymerase II in a gene-class specific manner

    Corey M. Nemec, A. Singh, Asfa Ali, S. Tseng +10 more

    2018Nature Chemical Biology33 citations Open access

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

    Corey M. Nemec, Fan Yang, J. Gilmore, Corinna Hintermair +10 more

    2017Proceedings of the National Academy of Sciences of the United States of America32 citations Open access

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34. Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast

    Douglas A. Higgins, Megan K M Young, M. Tremaine, Maria Sardi +13 more

    2018Genetics29 citations Open access

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

    Maria Sardi, Nikolay Rovinskiy, Yao-Ping Zhang, A. Gasch

    2016Applied and Environmental Microbiology29 citations Open access

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36. Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories

    DeElegant Robinson, Michael Place, James Hose, Adam Jochem +1 more

    2021bioRxiv28 citations Open access

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37. The role of stress-activated RNA–protein granules in surviving adversity

    Leah E. Escalante, A. Gasch

    2021RNA: A publication of the RNA Society26 citations Open access

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38. Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor

    Jeffrey A. Lewis, A. Gasch

    2012G3: Genes, Genomes, Genetics25 citations Open access

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

    J. Kennedy-Darling, Hector Guillen-Ahlers, Michael R. Shortreed, M. Scalf +5 more

    2014Journal of Proteome Research24 citations Open access

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

    Matthew E. MacGilvray, Evgenia Shishkova, Deborah A Chasman, Michael Place +3 more

    2017bioRxiv21 citations Open access

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

    V. Muir, A. Gasch, P. Anderson

    2017G3: Genes, Genomes, Genetics21 citations Open access

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42. Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast

    DeElegant Robinson, Elena Vanacloig-Pedros, R. Cai, Michael Place +2 more

    2023bioRxiv19 citations Open access

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43. Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

    Julie Rojas, James Hose, H. A. Dutcher, Michael Place +3 more

    2024bioRxiv18 citations Open access

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

    Maria Sardi, A. Gasch

    2018Current Genetics15 citations Open access

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45. CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations

    H. R. Stoneman, R. Wrobel, Michael Place, Michael Graham +8 more

    2020bioRxiv14 citations Open access

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

    Hector Guillen-Ahlers, Prahlad K. Rao, M. Levenstein, J. Kennedy-Darling +21 more

    2016Genomics14 citations Open access

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47. Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense

    E. Wagner, A. Gasch

    2023Journal of Fungi12 citations Open access

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48. Independent Mechanisms for Acquired Salt Tolerance versus Growth Resumption Induced by Mild Ethanol Pretreatment in Saccharomyces cerevisiae

    E. McDaniel, Tara N. Stuecker, Manasa Veluvolu, A. Gasch +1 more

    2018Msphere12 citations Open access

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49. PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production

    E. Wagner, Kevin S. Myers, N. Riley, J. Coon +1 more

    2019bioRxiv11 citations Open access

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

    Katie J. Clowers, J. Will, A. Gasch

    2015Molecular Ecology11 citations Open access

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