Publications

Papers

View publications on Google Scholar and PubMed.

54. Inverted duplicate DNA sequences increase
translocation rates through sequencing nanopores
resulting in reduced base calling accuracy. Pieter Spealman , Jaden Burrell , and David Gresham. Nucleic Acid Research. 2020 April 07. https://doi.org/10.1093/nar/gkaa206 [Article][pdf][preprint on bioRxiv][OSF][code on GitHub][data]

53. Microbial community structure and ecology in sediments of a pristine mangrove forest. Santana, C.O. ; Spealman, P. ; Melo, V.M.M ; Gresham, D. ; Jesus, T.B. , Chinalia, F.A. https://doi.org/10.1101/833814 [pdf][preprint on bioRxiv][OSF]

52. Regulatory kinase genetic interaction profiles differ between environmental conditions and cellular states. Siyu Sun, Anastasia Baryshnikova, Nathan Brandt, David Gresham. Mol Syst Biol (2020)16:e9167. https://doi.org/10.1101/735720 [Article][pdf][preprint on bioRxiv][OSF]

51. Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. Christopher A JacksonDayanne M CastroGiuseppe-Antonio SaldiRichard Bonneau, David Gresham. eLife. 2020 January 27. doi: 10.7554/eLife.51254 [eLife][pdf][preprint on bioRxiv]

50. An evolving view of copy number variants. Lauer S, Gresham D. Curr Genet. 2019 May 10. doi: 10.1007/s00294-019-00980-0. [Article][pdf] [Pubmed]

49. 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. [PLoS][preprint on bioRxiv] [pdf] [Pubmed]

48. Meeting Report: Experimental and Evolutionary Approaches to Yeast and Other Organisms 2018, G3: GENES, GENOMES, GENETICS March 1, 2019 vol. 9 no. 3 635-638; https://doi.org/10.1534/g3.118.201003 [G3 website] [pdf]

47. Single-cell copy number variant detection reveals the dynamics and diversity of adaptation. Stephanie Lauer, Grace Avecilla, Pieter Spealman, Gunjan Sethia, Nathan Brandt, Sasha Levy, David Gresham. PLoS Biol. 2018 December 18;16(12): e3000069. doi: https://doi.org/10.1101/381590 [PLoS][pdf ][Pubmed][SRA][dataset and code on OSF][preprint on bioRxiv]

46. 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. [PLoS][pdf] [Pubmed] [SRA] [dataset and code on OSF] [preprint on bioRxiv]

45. 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. [eLife][pdf] [Pubmed] [preprint on bioRxiv]

44. Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq). Abdul-Rahman F, Gresham D. mRNA Decay. Methods in Molecular Biol. 2018;1720:15-24. doi: 10.1007/978-1-4939-7540-2_2. [Article][pdf] [Pubmed]

43. Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing. Jungeui Hong and David Gresham. Biotechniques. 2017 Nov 1;63(5):221-226. doi: 10.2144/000114608 [Biotechniques][pdf] [Pubmed] [preprint on bioRxiv]

42. Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth. Naomi Ziv, Bentley M. Shuster, Mark L. Siegal and David Gresham. Genetics. 2017 July vol. 206 no. 3 pp. 1645-1657; https://doi.org/10.1534/genetics.116.195180 [Genetics][pdf] [Pubmed] [dataset and code on OSF]

41. Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae. Neymotin B, Ettore V, Gresham D. G3 (Bethesda). 2016 Sep 15. pii: g3.116.032276. doi: 10.1534/g3.116.032276.  [G3][pdf] [dataset and R code on OSF]  [preprint on bioRxiv]

40. 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. [Mol Biol Cell][pdf] [Pubmed] [data on OSF]

39. 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. Sci Rep. 2016 Feb 23;6:21874. doi: 10.1038/srep21874. [Science reports][pdf] [Pubmed]

38. “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. [BMC Genomics][pdf] [Pubmed]

37. 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. [Article][pdf] [Pubmed]

36. Evolution: Fitness tracking for adapting populations. Gresham D. Nature News and Views. 2015 Feb 25. doi:10.1038/nature14207. [Nature][pdf] [Pubmed]

35. The enduring utility of continuous culturing in experimental evolution. Gresham D, Dunham MJ.Genomics. 2014 Oct 2. pii: S0888-7543(14)00192-X. doi: 10.1016/j.ygeno.2014.09.015. [Article][pdf] [Pubmed]

34. 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. [PLoS][pdf] [Pubmed]

33. Determination of in vivo RNA kinetics using RATE-seq.  Benjy Neymotin, Rodoniki Athanasiadou, David Gresham. RNA. 2014 Oct;20(10):1645-52. doi: 10.1261/rna.045104.114. Epub 2014 Aug 26. [RNA article][pdf][Pubmed] [SRA] [Data and Supplemental Info][rateSeqFit]

32. The functional basis of adaptive evolution in chemostats.  Gresham D, Hong J.  FEMS Microbiology. 2014 Aug 6. doi: 10.1111/1574-6976.12082. [FEMS Microbiology][pdf] [Pubmed]

31. 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. [PLoS][pdf] [Pubmed] [SRA] [Supplement]

30. Design and Analysis of Bar-seq Experiments. Robinson DG, Chen W, Storey JD, Gresham D.  G3. 2013 Nov 5. doi:pii: g3.113.008565v1 [G3][pdf] [Pubmed]

29. 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. [Jove][pdf] [Pubmed]

28. 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. [Mol Biol Evol][pdf] [Pubmed]

27. 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. [Biotechnology][pdf] [Pubmed]

26. A sticky solution. Gresham D. Elife. 2013;2:e00655. doi: 10.7554/eLife.00655. Epub 2013 Apr 2. [eLife][pdf] [PubMed]

25. 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. [PLoS][pdf] [Pubmed]

24. DNA microarray-based mutation discovery and genotyping. Gresham D.  Methods Mol Biol. 2011;772:179-91 [Article][pdf] [PubMed]

23. High-resolution SNP/CGH microarrays reveal the accumulation of loss of heterozygosity in commonly used Candida albicans strains. Abbey D, Hickman, M, Gresham D and Berman J. G3: Genes, Genomes, Genetics Dec 2011 1:523-530. [pdf] [PubMed]

22. Rational design of temperature-sensitive alleles using computational structure prediction. Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE and Bonneau R. PLoS One. 2011;6(9):e23947. Epub 2011 Sep 2. [PLoS][pdf] [PubMed]

21. System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Gresham D, Boer D, Caudy A, Ziv N, Brandt NJ, Storey JD and Botstein D. Genetics. 2011 vol. 187 (1) pp. 299-317. (published online Oct 13, 2010). [Genetics][pdf] [PubMed]

20. 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 and Regenberg B.  PNAS (2010): 107(43): 18551-6. [PNAS][pdf] [PubMed]

19. 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, and Kruglyak L.  Nature, 2010. 464 (7291): p. 1039-1042. [Nature][pdf] [PubMed]

18. 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.  PNAS Jan;26;107(4):1482-7. Epub 2010 Jan 8. [PNAS][pdf] [PubMed]

17. Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nature Biotechnology. 2009 Apr;27(4):369-77 [Nature][pdf] [PubMed]

16. Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, and Troyanskaya OG. Predicting cellular growth from gene expression signatures PLoS Computational Biology. 2009 Jan;5(1):e1000257. [PLoS][pdf] [PubMed]

15. Gresham D., Desai, M.M., Tucker, C.M., Jenq, H.T., Pai, D.A., Ward, A., DeSevo, C.G., Botstein, D., and Dunham, M.J. The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast. PLoS Genetics. 2008 Dec;4(12):e1000303. [PLoS][pdf] [PubMed]

14. Gresham D, Kruglyak L, “Rise of the machines” PLoS Genetics. 2008 Aug 1;4(8):e100013 [PLoS][pdf] [PubMed]

13. Gresham D, Dunham M, Botstein D, “Comparing Whole Genomes with DNA Microarrays” Nature Reviews Genetics (2008) Apr;9(4):291-302. [Nature][pdf] [PubMed]

12. Brauer MJ, Huttenhower, C, Airoldi, EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D, “Coordination of Growth Rate, Cell Cycle, Stress Response and Metabolic Activity in Yeast” Molecular Biology of the Cell. (2008) Jan;19(1):352-67. Epub 2007 Oct 24. [MBoC][pdf] [PubMed]

11. Schacherer J, Ruderfer D, Gresham D, Dolinski K, Botstein D, Kruglyak L, “Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains” PLoS ONE. (2007) Mar 28;2(3):e322. [PLoS][pdf] [PubMed]

10. Gresham D, Ruderfer D, Pratt, S, Schacherer J, Dunham M, Botstein D, Kruglyak L, “Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray” Science. 31;311:1932-6 (2006) [Science][pdf] [PubMed]

9. Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt S, Dunham M., “Global Mapping of Transposon Location.” PLoS Genetics (2006) Dec 15;2(12):e212. [PLoS][pdf] [PubMed]

8. Heck JA, Gresham D, Botstein D, Alani E, “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements” Genetics 174, 519-23 (2006). [Genetics][pdf] [PubMed]

7. 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, ReeveJ, de Pablo R, Kucinskas V, Kalaydjieva L, “Mutation history of the Roma/Gypsies” Am J Hum Genet. 75(4):596-609 (2004). [AJHG][pdf] [PubMed]

6. Zhivotovsky LA, Underhill PA, Cinnioglu 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, “The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time.” Am J Hum Genet. 74(1):50-61 (2004). [AJHG][pdf] [PubMed]

5. Gresham D. Reversing Babel with GO. Nat Genet. 2002 Jul;31(3):230. [Nature][pdf] [PubMed]

4. 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, Kucinskas V, Perez-Lezaun A, Marushiakova E, Popov V, Kalaydjieva L, “Origins and divergence of the Roma (Gypsies)” Am J Hum Genet. 69(6):1314-31 (2001). [AJHG][pdf] [PubMed]

3. Kalaydjieva L, Gresham D, Calafell F, “Genetic studies of the Roma (Gypsies): a review.” BMC Med Genet. 2(1):5 (2001). [BMC][pdf] [PubMed]

2. Kalaydjieva L, Gresham D, Gooding R, Heather L, Baas F, de Jonge R, Blechschmidt K, Angelicheva D, Chandler D, Worsley P, Rosenthal A, King RH, Thomas PK., “N-myc downstream-regulated gene 1 is mutated in hereditary motor and sensory neuropathy-Lom” Am J Hum Genet. 67(1):47-58 (2000). [AJHG][pdf] [PubMed]

1. Chandler D, Angelicheva D, Heather L, Gooding R, Gresham D, Yanakiev P, de Jonge R, Baas F, Dye D, Karagyozov L, Savov A, Blechschmidt K, Keats B, Thomas PK, King RH, Starr A, Nikolova A, Colomer J, Ishpekova B, Tournev I, Urtizberea JA, Merlini L, Butinar D, Chabrol B, Voit T, Baethmann M, Nedkova V, Corches A, Kalaydjieva L, “Hereditary motor and sensory neuropathy–Lom (HMSNL): refined genetic mapping in Romani (Gypsy) families from several European countries” Neuromuscul Disord. 2000 Dec;10(8):584-91. [Neuromuscular Disorders][pdf] [PubMed]Inverted duplicate DNA sequences increase
translocation rates through sequencing nanopores
resulting in reduced base calling accuracy

Alumni Theses