Publications

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Preprints

Christopher A Jackson, Maggie Beheler-Amass, Andreas Tjärnberg, Ina Suresh, Angela Shang-mei Hickey, Richard Bonneau, David JJ Gresham Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression bioRxiv 2023.09.21.558277; doi: https://doi.org/10.1101/2023.09.21.55827 [bioRxiv] [SRA]

Xie Y, Liu T, Gresham D, Holt LJ. mRNA condensation fluidizes the cytoplasm. bioRxiv [Preprint]. 2023 Jul 15:2023.05.30.542963. doi: 10.1101/2023.05.30.542963. PMID: 37398029; PMCID: PMC10312499. [bioRxiv] [Pubmed]

Knoll M, Honce R, Meliopoulos V, Schultz-Cherry S, Ghedin E, Gresham D. Host obesity impacts genetic variation in influenza A viral populations. bioRxiv [Preprint]. 2023 Jul 12:2023.07.12.548715. doi: 10.1101/2023.07.12.548715. PMID: 37503024; PMCID: PMC10369978. [bioRxiv] [Pubmed] [github] [SRA] 

Sun S, Tranchina D, Gresham D. Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence. bioRxiv [Preprint]. 2023 Aug 4:2023.08.03.551843. doi: 10.1101/2023.08.03.551843. PMID: 37577636; PMCID: PMC10418281. [bioRxiv] [Pubmed] [ProteomeXchange] 

Tjarnberg A, Beheler-Amass M, Jackson CA, Christiaen LA, Gresham D, Bonneau R. Structure Primed Embedding on the Transcription Factor Manifold Enables Transparent Model Architectures for Gene Regulatory Network and Latent Activity Inference. bioRxiv [Preprint]. 2023 Feb 3:2023.02.02.526909. doi: 10.1101/2023.02.02.526909. PMID: 36778259; PMCID: PMC9915715. [bioRxiv] [Pubmed] [github]

Published articles

70. Avecilla G, Spealman P, Matthews J, Caudal E, Schacherer J, Gresham D. Copy number variation alters local and global mutational tolerance. Genome Res. 2023 Aug 31. doi: 10.1101/gr.277625.122. Epub ahead of print. PMID: 37652668. [Genome Research] [pdf] [bioRxiv] [Pubmed] [github] [SRA]  

69. Spealman P, De T, Chuong JN, Gresham D. Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution. J Mol Evol. 2023 Jun;91(3):356-368. doi: 10.1007/s00239-023-10102-7. Epub 2023 Apr 3. PMID: 37012421; PMCID: PMC10275804. [Journal of Molecular Evolution] [pdf] [Pubmed] 

68. Roder AE, Johnson K, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lassig M, Åuksza M, Das S, Gresham D, Ghedin E. Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data. bioRxiv [Preprint]. 2022 Aug 16:2021.05.05.442873. doi: 10.1101/2021.05.05.442873. Update in: mBio. 2023 Jun 30;:e0104623. PMID: 36656775; PMCID: PMC9836620. [mBio] [pdf] [bioRxiv] [Pubmed] [github] [SRA] 

67. Taylor KY, Agu I, José I, Mäntynen S, Campbell AJ, Mattson C, Chou TW, Zhou B, Gresham D, Ghedin E, Díaz Muñoz SL. Influenza A virus reassortment is strain dependent. PLoS Pathog. 2023 Mar 1;19(3):e1011155. doi: 10.1371/journal.ppat.1011155. PMID: 36857394; PMCID: PMC10010518. [PLoS Pathogens] [pdf] [bioRxiv] [Pubmed] [github] [SRA] 

66. de Santana CO, Spealman P, Gresham D, Perron GG. Metagenomes from Soils along an Agricultural Transect in Ulster County, New York. Microbiol Resour Announc. 2023 Mar 16;12(3):e0101522. doi: 10.1128/mra.01015-22. Epub 2023 Feb 13. PMID: 36779724; PMCID: PMC10019288. [MRA] [pdf] [bioRxiv] [Pubmed] [github] [SRA] 

65. Xie Y, Gresham D, Holt L. Increased mesoscale diffusivity in response to acute glucose starvation. bioRxiv [Preprint]. 2023 Jan 12:2023.01.10.523352. doi: 10.1101/2023.01.10.523352. Update in: MicroPubl Biol. 2023 Feb 21;2023: PMID: 36711511; PMCID: PMC9882054. [microPublication Biology] [pdf] [bioRxiv] [Pubmed] [github] [SRA] 

64. Spealman P, Avecilla G, Matthews J, Suresh I, Gresham D. Complex Genomic Rearrangements following Selection in a Glutamine-Limited Medium over Hundreds of Generations. Microbiol Resour Announc. 2022 Nov 17;11(11):e0072922. doi: 10.1128/mra.00729-22. Epub 2022 Oct 27. PMID: 36301109; PMCID: PMC9670979. [MRA] [pdf] [bioRxiv] [Pubmed] [github] [SRA] 

63. Forst CV, Chung M, Hockman M, Lashua L, Adney E, Hickey A, Carlock M, Ross T, Ghedin E, Gresham D. Vaccination History, Body Mass Index, Age, and Baseline Gene Expression Predict Influenza Vaccination Outcomes. Viruses. 2022 Nov 4;14(11):2446. doi: 10.3390/v14112446. PMID: 36366544; PMCID: PMC9697051. [medRxiv] [github]

62. Skok Gibbs C, Jackson CA, Saldi GA, Tjärnberg A, Shah A, Watters A, De Veaux N, Tchourine K, Yi R, Hamamsy T, Castro DM, Carriero N, Gorissen BL, Gresham D, Miraldi ER, Bonneau R. High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. Bioinformatics. 2022 Apr 28;38(9):2519-2528. doi: 10.1093/bioinformatics/btac117. PMID: 35188184; PMCID: PMC9048651. [Pubmed] [pdf] [Oxford Academics] [github]

61. Avecilla G, Chuong JN, Li F, Sherlock G, Gresham D, Ram Y. Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics. PLoS Biol. 2022 May 27;20(5):e3001633. doi: 10.1371/journal.pbio.3001633. PMID: 35622868; PMCID: PMC9140244. [ArticlPLoS ] [pdf]  [Pubmed] [github] [data on OSF] [bioRxiv]

60. Functional genomics and metabolomics advance the ethnobotany of the Samoan traditional medicine “matalafi”. Seeseei Molimau-Samasoni, Victoria Helen Woolner, Su’emalo Talie Foliga, Katharina Robichon, Vimal Patel, Sarah K. Andreassend, Jeffrey P. Sheridan, Tama Te Kawa, David Gresham, Darach Miller, Daniel J. Sinclair, Anne C. La Flamme, Alexey V. Melnik, Allegra Aron, Pieter C. Dorrestein, Paul H. Atkinson, Robert A. Keyzers, and Andrew B. Munkacsi.  2021 Proc Natl Acad Sci U S A. Nov 9;118(45):e2100880118. doi: 10.1073/pnas.2100880118. [Article] [pdf] [Pubmed]

59. Large-scale differences in diversity and functional adaptations of prokaryotic communities from conserved and anthropogenically impacted mangrove sediments in a tropical estuary. Carolina O. De Santana , Pieter Spealman , Vania Melo , David Gresham, Taise de Jesus, Eddy Oliveira and Fabio Alexandre Chinalia. 2021 PeerJ. Sep 23;9:e12229. doi: 10.7717/peerj.12229. eCollection 2021.[article] [pdf] [code on github] [dataset1 dataset2].

58. Modifying reference sequence and annotation files quickly and reproducibly with reform.  Mohammed Khalfan, Eric Borenstein, Pieter Spealman, Farah Abdul-Rahman, and David Gresham. 2021 published as an NFT [non fungible token/NFT] [pdf] [code on github] [reform web app] [blog post on using NFTs in scientific publishing ]

57. Fluctuating environments maintain genetic diversity through neutral fitness effects and balancing selection. Farah Abdul-Rahman, Daniel Tranchina, and David Gresham. Mol Biol Evol. 2021 Sep 27;38(10):4362-4375. doi: 10.1093/molbev/msab173. [Article] [pdf] [Pubmed] [code on github] [data on SRA] [preprint on bioRxiv] [filtered unnormalized barseq data] [filtered normalized barseq data]

56. Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove. Santana, C.O. ; Spealman, P. ; Melo, V.M.M ; Gresham, D. ; Jesus, T.B. , Chinalia, F.A. Biogeosciences. 2021 April 06. https://doi.org/10.5194/bg-18-2259-2021 [Article][pdf][OSF][code on github][preprint on bioRxiv]

55. Cellular Quiescence in Budding Yeast. Siyu Sun and David Gresham. Yeast. 2020 Dec 22. https://doi.org/10.1002/yea.3545 [Article][pdf][Pubmed]

54. A Bright IDEA. Jackson C, Gresham D. Mol Syst Biol. 2020 Apr;16(4):e9502. doi: 10.15252/msb.20209502. [Article][pdf][Pubmed]

53. 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]

52. Genetic interaction profiles of regulatory kinases 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][Pubmed]

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

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] [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 Biology][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]https://www.ncbi.nlm.nih.gov/bioproject/PRJNA704647/