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

Jackson CA, Castro DM, Saldi GA, Bonneau R, Gresham D.

Elife. 2020 Jan 27;9. pii: e51254. doi: 10.7554/eLife.51254.


An evolving view of copy number variants.

Lauer S, Gresham D.

Curr Genet. 2019 Dec;65(6):1287-1295. doi: 10.1007/s00294-019-00980-0. Epub 2019 May 10. Review.


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.

PLoS Comput Biol. 2019 Mar 11;15(3):e1006794. doi: 10.1371/journal.pcbi.1006794. eCollection 2019 Mar.


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

Lauer S, Avecilla G, Spealman P, Sethia G, Brandt N, Levy SF, Gresham D.

PLoS Biol. 2018 Dec 18;16(12):e3000069. doi: 10.1371/journal.pbio.3000069. eCollection 2018 Dec.


Evaluating the Feasibility and Effectiveness of an Australian Safety Planning Smartphone Application: A Pilot Study Within a Tertiary Mental Health Service.

Melvin GA, Gresham D, Beaton S, Coles J, Tonge BJ, Gordon MS, Stanley B.

Suicide Life Threat Behav. 2019 Jun;49(3):846-858. doi: 10.1111/sltb.12490. Epub 2018 Jul 12.


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

Miller D, Brandt N, Gresham D.

PLoS Genet. 2018 May 21;14(5):e1007406. doi: 10.1371/journal.pgen.1007406. eCollection 2018 May.


An incoherent feedforward loop facilitates adaptive tuning of gene expression.

Hong J, Brandt N, Abdul-Rahman F, Yang A, Hughes T, Gresham D.

Elife. 2018 Apr 5;7. pii: e32323. doi: 10.7554/eLife.32323.


Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq).

Abdul-Rahman F, Gresham D.

Methods Mol Biol. 2018;1720:15-24. doi: 10.1007/978-1-4939-7540-2_2.


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

Hong J, Gresham D.

Biotechniques. 2017 Nov 1;63(5):221-226. doi: 10.2144/000114608.


Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth.

Ziv N, Shuster BM, Siegal ML, Gresham D.

Genetics. 2017 Jul;206(3):1645-1657. doi: 10.1534/genetics.116.195180. Epub 2017 May 11.


Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae.

Neymotin B, Ettorre V, Gresham D.

G3 (Bethesda). 2016 Nov 8;6(11):3475-3483. doi: 10.1534/g3.116.032276.


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

Airoldi EM, Miller D, Athanasiadou R, Brandt N, Abdul-Rahman F, Neymotin B, Hashimoto T, Bahmani T, Gresham D.

Mol Biol Cell. 2016 Apr 15;27(8):1383-96. doi: 10.1091/mbc.E14-05-1013. Epub 2016 Mar 3.


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

Doidy J, Li Y, Neymotin B, Edwards MB, Varala K, Gresham D, Coruzzi GM.

BMC Genomics. 2016 Feb 3;17:92. doi: 10.1186/s12864-016-2410-2.


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

Irene C, Theis JF, Gresham D, Soteropoulos P, Newlon CS.

Mol Genet Genomics. 2016 Feb;291(1):271-83. doi: 10.1007/s00438-015-1105-8. Epub 2015 Aug 29.


Evolution: Fitness tracking for adapting populations.

Gresham D.

Nature. 2015 Mar 12;519(7542):164-5. doi: 10.1038/nature14207. Epub 2015 Feb 25. No abstract available.


The enduring utility of continuous culturing in experimental evolution.

Gresham D, Dunham MJ.

Genomics. 2014 Dec;104(6 Pt A):399-405. doi: 10.1016/j.ygeno.2014.09.015. Epub 2014 Oct 2. Review.


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

Ma S, Kemmeren P, Gresham D, Statnikov A.

PLoS One. 2014 Sep 12;9(9):e106479. doi: 10.1371/journal.pone.0106479. eCollection 2014.


Determination of in vivo RNA kinetics using RATE-seq.

Neymotin B, Athanasiadou R, Gresham D.

RNA. 2014 Oct;20(10):1645-52. doi: 10.1261/rna.045104.114. Epub 2014 Aug 26.


The functional basis of adaptive evolution in chemostats.

Gresham D, Hong J.

FEMS Microbiol Rev. 2015 Jan;39(1):2-16. doi: 10.1111/1574-6976.12082. Epub 2014 Dec 4. Review.


Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments.

Hong J, Gresham D.

PLoS Genet. 2014 Jan;10(1):e1004041. doi: 10.1371/journal.pgen.1004041. Epub 2014 Jan 9.


Design and analysis of Bar-seq experiments.

Robinson DG, Chen W, Storey JD, Gresham D.

G3 (Bethesda). 2014 Jan 10;4(1):11-8. doi: 10.1534/g3.113.008565.


The use of chemostats in microbial systems biology.

Ziv N, Brandt NJ, Gresham D.

J Vis Exp. 2013 Oct 14;(80). doi: 10.3791/50168.


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

Ziv N, Siegal ML, Gresham D.

Mol Biol Evol. 2013 Dec;30(12):2568-78. doi: 10.1093/molbev/mst138. Epub 2013 Aug 11.


A sticky solution.

Gresham D.

Elife. 2013 Apr 2;2:e00655. doi: 10.7554/eLife.00655.


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

Geiler-Samerotte KA, Bauer CR, Li S, Ziv N, Gresham D, Siegal ML.

Curr Opin Biotechnol. 2013 Aug;24(4):752-9. doi: 10.1016/j.copbio.2013.03.010. Epub 2013 Apr 6.


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

Torbensen R, Møller HD, Gresham D, Alizadeh S, Ochmann D, Boles E, Regenberg B.

PLoS One. 2012;7(7):e41272. doi: 10.1371/journal.pone.0041272. Epub 2012 Jul 26.


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.

G3 (Bethesda). 2011 Dec;1(7):523-30. doi: 10.1534/g3.111.000885. Epub 2011 Dec 1. Erratum in: G3 (Bethesda). 2012 Nov;2(11):1473.


DNA microarray-based mutation discovery and genotyping.

Gresham D.

Methods Mol Biol. 2011;772:179-91. doi: 10.1007/978-1-61779-228-1_10.


Rational design of temperature-sensitive alleles using computational structure prediction.

Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R.

PLoS One. 2011;6(9):e23947. doi: 10.1371/journal.pone.0023947. Epub 2011 Sep 2.


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

Gresham D, Boer VM, Caudy A, Ziv N, Brandt NJ, Storey JD, Botstein D.

Genetics. 2011 Jan;187(1):299-317. doi: 10.1534/genetics.110.120766. Epub 2010 Oct 13.


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

Gresham D, Usaite R, Germann SM, Lisby M, Botstein D, Regenberg B.

Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18551-6. doi: 10.1073/pnas.1014023107. Epub 2010 Oct 11.


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

Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, Kruglyak L.

Nature. 2010 Apr 15;464(7291):1039-42. doi: 10.1038/nature08923.


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

Gresham D, Curry B, Ward A, Gordon DB, Brizuela L, Kruglyak L, Botstein D.

Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1482-7. doi: 10.1073/pnas.0913883107. Epub 2010 Jan 8.


Caring for the pregnant woman with neurofibromatosis.

Gresham DD, Braunlin JL, Vuckovich SK.

MCN Am J Matern Child Nurs. 2010 Jan-Feb;35(1):18-23; quiz 24-5. doi: 10.1097/01.NMC.0000366805.73293.2c.


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

Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JLY, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C.

Nat Biotechnol. 2009 Apr;27(4):369-77. doi: 10.1038/nbt.1534. Epub 2009 Apr 6.


Predicting cellular growth from gene expression signatures.

Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG.

PLoS Comput Biol. 2009 Jan;5(1):e1000257. doi: 10.1371/journal.pcbi.1000257. Epub 2009 Jan 2.


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

Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, Dunham MJ.

PLoS Genet. 2008 Dec;4(12):e1000303. doi: 10.1371/journal.pgen.1000303. Epub 2008 Dec 12.


Rise of the machines.

Gresham D, Kruglyak L.

PLoS Genet. 2008 Aug 1;4(8):e1000134. doi: 10.1371/journal.pgen.1000134. No abstract available.


Comparing whole genomes using DNA microarrays.

Gresham D, Dunham MJ, Botstein D.

Nat Rev Genet. 2008 Apr;9(4):291-302. doi: 10.1038/nrg2335. Review.


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

Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D.

Mol Biol Cell. 2008 Jan;19(1):352-67. Epub 2007 Oct 24.


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

Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L.

PLoS One. 2007 Mar 28;2(3):e322.


Global mapping of transposon location.

Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, Dunham MJ.

PLoS Genet. 2006 Dec 15;2(12):e212. Epub 2006 Nov 1.


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

Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, Kruglyak L.

Science. 2006 Mar 31;311(5769):1932-6. Epub 2006 Mar 9.


70/30 insulin algorithm versus sliding scale insulin.

Schoeffler JM, Rice DA, Gresham DG.

Ann Pharmacother. 2005 Oct;39(10):1606-10. Epub 2005 Aug 9.


Mutation history of the roma/gypsies.

Morar B, Gresham D, Angelicheva D, Tournev I, Gooding R, Guergueltcheva V, Schmidt C, Abicht A, Lochmuller H, Tordai A, Kalmar L, Nagy M, Karcagi V, Jeanpierre M, Herczegfalvi A, Beeson D, Venkataraman V, Warwick Carter K, Reeve J, de Pablo R, Kucinskas V, Kalaydjieva L.

Am J Hum Genet. 2004 Oct;75(4):596-609. Epub 2004 Aug 20.


The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time.

Zhivotovsky LA, Underhill PA, Cinnioğlu C, Kayser M, Morar B, Kivisild T, Scozzari R, Cruciani F, Destro-Bisol G, Spedini G, Chambers GK, Herrera RJ, Yong KK, Gresham D, Tournev I, Feldman MW, Kalaydjieva L.

Am J Hum Genet. 2004 Jan;74(1):50-61. Epub 2003 Dec 19.


Reversing Babel with GO.

Gresham D.

Nat Genet. 2002 Jul;31(3):230. No abstract available.


Origins and divergence of the Roma (gypsies).

Gresham D, Morar B, Underhill PA, Passarino G, Lin AA, Wise C, Angelicheva D, Calafell F, Oefner PJ, Shen P, Tournev I, de Pablo R, Kuĉinskas V, Perez-Lezaun A, Marushiakova E, Popov V, Kalaydjieva L.

Am J Hum Genet. 2001 Dec;69(6):1314-31. Epub 2001 Nov 9.

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