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David Gresham

Associate Professor Of Biology

    20002020

    Research output per year

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    Research Output

    2020

    Gene regulatory network reconstruction using single-cell rna sequencing of barcoded genotypes in diverse environments

    Jackson, C. A., Castro, D. M., Saldi, G. A., Bonneau, R. & Gresham, D., Jan 2020, In : eLife. 9, e51254.

    Research output: Contribution to journalArticle

    Open Access
    2019

    A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory

    Athanasiadou, R., Neymotin, B., Brandt, N., Wang, W., Christiaen, L., Gresham, D. & Tranchina, D., Mar 2019, In : PLoS computational biology. 15, 3, e1006794.

    Research output: Contribution to journalArticle

    Open Access

    An evolving view of copy number variants

    Lauer, S. & Gresham, D., Dec 1 2019, In : Current Genetics. 65, 6, p. 1287-1295 9 p.

    Research output: Contribution to journalReview article

    Meeting report: Experimental and evolutionary approaches to yeast and other organisms 2018

    Gresham, D. & Rancati, G., Mar 1 2019, In : G3: Genes, Genomes, Genetics. 9, 3, p. 635-638 4 p.

    Research output: Contribution to journalArticle

    2018

    An incoherent feedforward loop facilitates adaptive tuning of gene expression

    Hong, J., Brandt, N., Abdul-Rahman, F., Yang, A., Hughes, T. & Gresham, D., Apr 5 2018, In : eLife. 7, e32323.

    Research output: Contribution to journalArticle

    Determining mRNA decay rates using RNA approach to equilibrium sequencing (RATE-seq)

    Abdul-Rahman, F. & Gresham, D., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 15-24 10 p. (Methods in Molecular Biology; vol. 1720).

    Research output: Chapter in Book/Report/Conference proceedingChapter

    Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

    Lauer, S., Avecilla, G., Spealman, P., Sethia, G., Brandt, N., Levy, S. F. & Gresham, D., Dec 2018, In : PLoS biology. 16, 12, e3000069.

    Research output: Contribution to journalArticle

    Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen

    Miller, D., Brandt, N. & Gresham, D., May 2018, In : PLoS genetics. 14, 5, e1007406.

    Research output: Contribution to journalArticle

    2017

    Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing

    Hong, J. & Gresham, D., Nov 2017, In : BioTechniques. 63, 5, p. 221-226 6 p.

    Research output: Contribution to journalArticle

    Resolving the complex genetic basis of phenotypic variation and variability of cellular growth

    Ziv, N., Shuster, B. M., Siegal, M. L. & Gresham, D., Jul 2017, In : Genetics. 206, 3, p. 1645-1657 13 p.

    Research output: Contribution to journalArticle

    2016

    A common mechanism involving the TORC1 pathway can lead to amphotericin B-persistence in biofilm and planktonic Saccharomyces cerevisiae populations

    Bojsen, R., Regenberg, B., Gresham, D. & Folkesson, A., Feb 23 2016, In : Scientific reports. 6, 21874.

    Research output: Contribution to journalArticle

    "Hit-and-Run" transcription: De novo transcription initiated by a transient bZIP1 "hit" persists after the "run"

    Doidy, J., Li, Y., Neymotin, B., Edwards, M. B., Varala, K., Gresham, D. & Coruzzi, G. M., Feb 3 2016, In : BMC Genomics. 17, 1, 92.

    Research output: Contribution to journalArticle

    Hst3p, a histone deacetylase, promotes maintenance of Saccharomyces cerevisiae chromosome III lacking efficient replication origins

    Irene, C., Theis, J. F., Gresham, D., Soteropoulos, P. & Newlon, C. S., Feb 1 2016, In : Molecular Genetics and Genomics. 291, 1, p. 271-283 13 p.

    Research output: Contribution to journalArticle

    Multiple transcript properties related to translation affect mRNA degradation rates in Saccharomyces cerevisiae

    Neymotin, B., Ettorre, V. & Gresham, D., Jan 1 2016, In : G3: Genes, Genomes, Genetics. 6, 11, p. 3475-3483 9 p.

    Research output: Contribution to journalArticle

    Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

    Airoldi, E. M., Miller, D., Athanasiadou, R., Brandt, N., Abdul-Rahman, F., Neymotin, B., Hashimoto, T., Bahmani, T. & Gresham, D., Apr 15 2016, In : Molecular biology of the cell. 27, 8, p. 1383-1396 14 p.

    Research output: Contribution to journalArticle

    2015

    Evolution: Fitness tracking for adapting populations

    Gresham, D., Mar 12 2015, In : Nature. 519, 7542, p. 164-165 2 p.

    Research output: Contribution to journalShort survey

    The functional basis of adaptive evolution in chemostats

    Gresham, D. & Hong, J., Jan 1 2015, In : FEMS Microbiology Reviews. 39, 1, p. 2-16 15 p.

    Research output: Contribution to journalArticle

    2014

    De-novo learning of genome-scale regulatory networks in S. cerevisiae

    Ma, S., Kemmeren, P., Gresham, D. & Statnikov, A., Sep 2014, In : PloS one. 9, 9, e0106479.

    Research output: Contribution to journalArticle

    Design and analysis of bar-seq experiments

    Robinson, D. G., Chen, W., Storey, J. D. & Gresham, D., Jan 2014, In : G3: Genes, Genomes, Genetics. 4, 1, p. 11-18 8 p.

    Research output: Contribution to journalArticle

    Determination of in vivo RNA kinetics using RATE-seq

    Neymotin, B., Athanasiadou, R. & Gresham, D., Oct 1 2014, In : RNA. 20, 10, p. 1645-1652 8 p.

    Research output: Contribution to journalArticle

    Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

    Hong, J. & Gresham, D., Jan 1 2014, In : PLoS genetics. 10, 1, e1004041.

    Research output: Contribution to journalArticle

    The enduring utility of continuous culturing in experimental evolution

    Gresham, D. & Dunham, M. J., Sep 24 2014, In : Genomics. 104, 6, p. 399-405 7 p.

    Research output: Contribution to journalArticle

    2013

    A sticky solution

    Gresham, D., Apr 2 2013, In : eLife. 2013, 2, e00655.

    Research output: Contribution to journalArticle

    Genetic and nongenetic determinants of cell growth variation assessed by high-throughput microscopy

    Ziv, N., Siegal, M. L. & Gresham, D., Dec 1 2013, In : Molecular Biology and Evolution. 30, 12, p. 2568-2578 11 p.

    Research output: Contribution to journalArticle

    The details in the distributions: Why and how to study phenotypic variability

    Geiler-Samerotte, K. A., Bauer, C. R., Li, S., Ziv, N., Gresham, D. & Siegal, M. L., Aug 1 2013, In : Current Opinion in Biotechnology. 24, 4, p. 752-759 8 p.

    Research output: Contribution to journalReview article

    The use of chemostats in microbial systems biology

    Ziv, N., Brandt, N. J. & Gresham, D., Oct 14 2013, In : Journal of Visualized Experiments. 80, e50168.

    Research output: Contribution to journalArticle

    2012

    Amino acid transporter genes are essential for FLO11-dependent and FLO11-independent biofilm formation and invasive growth in Saccharomyces cerevisiae

    Torbensen, R., Møller, H. D., Gresham, D., Alizadeh, S., Ochmann, D., Boles, E. & Regenberg, B., Jul 26 2012, In : PloS one. 7, 7, e41272.

    Research output: Contribution to journalArticle

    2011

    DNA microarray-based mutation discovery and genotyping.

    Gresham, D., 2011, In : Methods in molecular biology (Clifton, N.J.). 772, p. 179-191 13 p.

    Research output: Contribution to journalArticle

    High-resolution SNP/CGH microarrays reveal the accumulation of loss of heterozygosity in commonly used Candida albicans strains

    Abbey, D., Hickman, M., Gresham, D. & Berman, J., Dec 1 2011, In : G3: Genes, Genomes, Genetics. 1, 7, p. 523-530 8 p.

    Research output: Contribution to journalArticle

    Rational design of temperature-sensitive alleles using computational structure prediction

    Poultney, C. S., Butterfoss, G. L., Gutwein, M. R., Drew, K., Gresham, D., Gunsalus, K. C., Shasha, D. E. & Bonneau, R., Sep 2 2011, In : PloS one. 6, 9, e23947.

    Research output: Contribution to journalArticle

    System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae

    Gresham, D., Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D. & Botstein, D., Jan 1 2011, In : Genetics. 187, 1, p. 299-317 19 p.

    Research output: Contribution to journalArticle

    2010

    Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

    Gresham, D., Usaite, R., Germann, S. M., Lisby, M., Botstein, D. & Regenberg, B., Oct 26 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 43, p. 18551-18556 6 p.

    Research output: Contribution to journalArticle

    Dissection of genetically complex traits with extremely large pools of yeast segregants

    Ehrenreich, I. M., Torabi, N., Jia, Y., Kent, J., Martis, S., Shapiro, J. A., Gresham, D., Caudy, A. A. & Kruglyak, L., Apr 15 2010, In : Nature. 464, 7291, p. 1039-1042 4 p.

    Research output: Contribution to journalArticle

    Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes

    Gresham, D., Curry, B., Ward, A., Gordon, D. B., Brizuela, L., Kruglyak, L. & Botstein, D., Jan 26 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 4, p. 1482-1487 6 p.

    Research output: Contribution to journalArticle

    2009

    A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds

    Ho, C. H., Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., Koh, J. L. Y., Porter, J., Gray, C. A., Andersen, R. J., Giaever, G., Nislow, C., Andrews, B., Botstein, D., Graham, T. R., Yoshida, M. & Boone, C., Apr 1 2009, In : Nature Biotechnology. 27, 4, p. 369-377 9 p.

    Research output: Contribution to journalArticle

    Predicting cellular growth from gene expression signatures

    Airoldi, E. M., Huttenhower, C., Gresham, D., Lu, C., Caudy, A. A., Dunham, M. J., Broach, J. R., Botstein, D. & Troyanskaya, O. G., Jan 1 2009, In : PLoS computational biology. 5, 1, e1000257.

    Research output: Contribution to journalArticle

    2008

    Comparing whole genomes using DNA microarrays

    Gresham, D., Dunham, M. J. & Botstein, D., Apr 1 2008, In : Nature Reviews Genetics. 9, 4, p. 291-302 12 p.

    Research output: Contribution to journalReview article

    Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast

    Brauer, M. J., Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G. & Botstein, D., Jan 1 2008, In : Molecular biology of the cell. 19, 1, p. 352-367 16 p.

    Research output: Contribution to journalArticle

    Rise of the machines

    Gresham, D. & Kruglyak, L., Aug 1 2008, In : PLoS genetics. 4, 8, e1000134.

    Research output: Contribution to journalShort survey

    The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast

    Gresham, D., Desai, M. M., Tucker, C. M., Jenq, H. T., Pai, D. A., Ward, A., DeSevo, C. G., Botstein, D. & Dunham, M. J., Dec 1 2008, In : PLoS genetics. 4, 12, e1000303.

    Research output: Contribution to journalArticle

    2007

    Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains

    Schacherer, J., Ruderfer, D. M., Gresham, D., Dolinski, K., Botstein, D. & Kruglyak, L., Mar 28 2007, In : PloS one. 2, 3, e322.

    Research output: Contribution to journalArticle

    2006

    Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements

    Heck, J. A., Gresham, D., Botstein, D. & Alani, E., Sep 27 2006, In : Genetics. 174, 1, p. 519-523 5 p.

    Research output: Contribution to journalArticle

    Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA Microarray

    Gresham, D., Ruderfer, D. M., Pratt, S. C., Schacherer, J., Dunham, M. J., Botstein, D. & Kruglyak, L., Mar 31 2006, In : Science. 311, 5769, p. 1932-1936 5 p.

    Research output: Contribution to journalArticle

    Global mapping of transposon location

    Gabriel, A., Dapprich, J., Kunkel, M., Gresham, D., Pratt, S. C. & Dunham, M. J., Dec 1 2006, In : PLoS genetics. 2, 12, p. 2026-2038 13 p.

    Research output: Contribution to journalArticle

    2004

    Mutation history of the Roma/Gypsies

    Morar, B., Gresham, D., Angelicheva, D., Tournev, I., Gooding, R., Guergueltcheva, V., Schmidt, C., Abicht, A., Lochmüller, H., Tordai, A., Kalmár, L., Nagy, M., Karcagi, V., Jeanpierre, M., Herczegfalvi, A., Beeson, D., Venkataraman, V., Carter, K. W., Reeve, J., De Pablo, R. & 2 others, Kučinskas, V. & Kalaydjieva, L., Oct 2004, In : American Journal of Human Genetics. 75, 4, p. 596-609 14 p.

    Research output: Contribution to journalArticle

    2003

    A molecular signature of behavior

    Gresham, D., Nov 1 2003, In : Nature Genetics. 35, 3, 1 p.

    Research output: Contribution to journalShort survey

    Apoptosis: Cheating death

    Gresham, D., Feb 2003, In : Nature Reviews Molecular Cell Biology. 4, 2, 1 p.

    Research output: Contribution to journalArticle

    Apoptosis: Cheating death

    Gresham, D., Feb 2003, In : Nature Reviews Cancer. 3, 2, 1 p.

    Research output: Contribution to journalComment/debate

    2002

    Reversing Babel with GO

    Gresham, D., Jul 1 2002, In : Nature Genetics. 31, 3, 1 p.

    Research output: Contribution to journalShort survey

    2001

    Genetic studies of the Roma (Gypsies): A review

    Kalaydjieva, L., Gresham, D. & Calafell, F., Apr 2 2001, In : BMC Medical Genetics. 2, 5.

    Research output: Contribution to journalReview article