>200 publications | >90,000 citations | H-index 78 tracked by publons

(top 1% of Web of Science cited researchers for field, Clarivate Analytics, 2018, 2019 and 2020)

  1. Despins CA, Brown SD, Robinson AV, Mungall AJ, Allen-Vercoe E, Holt RA. Modulation of the host cell transcriptome and epigenome by Fusobacterium nucleatum. mBio. 2021 (In press)
  2. Kidman J, Principe N, Watson M, Lassmann T, Holt RA, Nowak AK, Lesterhuis WJ, Lake RA, Chee J. Characteristics of TCR Repertoire Associated With Successful Immune Checkpoint Therapy Responses. Front Immunol.. 2020 Oct 14;11:587014. doi:10.3389/fimmu.2020.587014. PMID: 33163002; PMCID: PMC7591700
  3. Khalife R, Montroy J, Grigor EJM, Fergusson DA, Atkins H, Seftel M, Presseau J, Thavorn K, Holt RA, Hay K, Lalu MM, Kekre N. Building Canadian capacity for CAR-T cells in relapsed/refractory acute lymphoblastic leukaemia: a retrospective cohort study. Br J Haematol. 2020 Jul 20. 191(1). doi: 10.1111/bjh.16940. PMID: 32688454
  4. Rive CM, Yung E, Hughes CS, Brown SD, Sharma G, Dreolini L, Warren C, Karasinska JM, Loree JM, Yapp DT, Morin GB, Renouf DJ, Schaeffer DF, Turcotte S and Holt RA. Recombinant T cell receptors specific for HLA-A*02:01-restricted neoepitopes containing KRAS codon 12 hotspot mutations. BioRxiv. https://doi.org/10.1101/2020.06.15.149021
  5. Rive CM, Yung E, Dreolini L, Woodsworth DJ, Holt RA. Selective B cell depletion upon infusion of replication-incompetent anti-CD19 CAR lentivirus. BioRxiv. https://doi.org/10.1101/2020.05.15.098335
  6. Cochrane K, Robinson AV, Holt RA, Allen-Vercoe E. A survey of Fusobacterium nucleatum genes modulated by host cell infection. Microbial Genomics. 2020 Feb;6(2):e000300. doi: 10.1099/mgen.0.000300. PMID: 31661053
  7. Dreolini L, Cullen M, Yung E, Laird L, Webb JR, Nelson BH, Hay KA, Balasundaram M, Kekre N and Holt RA. A Rapid and Sensitive Nucleic Acid Amplification Technique for Mycoplasma Screening of Cell Therapy Products. Molecular Therapy - Methods & Clinical Development. 2020 Jan 30;17:393-399. doi: 10.1016/j.omtm.2020.01.009. eCollection 2020 Jun 12. PMID: 32128343; PMCID: PMC7044503.
  8. Sharma G, Rive C and Holt RA. Rapid selection and identification of functional CD8+ T-cell epitopes from large peptide coding libraries. Nature Communications. 2019;10:4553. doi: 10.1038/s41467-019-12444-7
  9. Grigor EJM, Fergusson D, Kekre N, Montroy J, Atkins H, Seftel M, Daugaard M, Presseau J, Thavorn K, Hutton B, Holt RA, Lalu MM. Risks and Benefits of Chimeric Antigen Receptor T-Cell (CAR-T) Therapy in Cancer: A Systematic Review and Meta-Analysis. Transfusion Medicine Reviews. 2019 Apr;33(2):98-110. doi: 10.1016/j.tmrv.2019.01.005. PMID: 30948292
  10. Korecki AJ, Hickmott JW, Lam SL, Dreolini L, Mathelier A, Baker O, Kuehne C, Bonaguro RJ, Smith J, Tan CV, Zhou M, Goldowitz D, Deussing JM, Stewart AF, Wasserman WW, Holt RA, Simpson EM. Twenty-seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain; Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele. Genetics. 2019 Apr;211(4):1155-1177. doi: 10.1534/genetics.119.301984. [Epub ahead of print]. PMID: 30765420
  11. Zhang AW, McPherson A, Milne K, Kroeger DR, Hamilton PT, Miranda A, Funnell T, Little N, de Souza CPE, Laan S, LeDoux S, Cochrane DR, Lim JLP, Yang W, Roth A, Smith MA, Ho J, Tse K, Zeng T, Shlafman I, Mayo MR, Moore R, Failmezger H, Heindl A, Wang YK, Bashashati A, Grewal DS, Brown SD, Lai D, Wan ANC, Nielsen CB, Huebner C, Tessier-Cloutier B, Anglesio MS, Bouchard-Côté A, Yuan Y, Wasserman WW, Gilks CB, Karnezis AN, Aparicio S, McAlpine JN, Huntsman DG, Holt RA, Nelson BH, Shah SP. Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer. Cell. 2018 Jun 14;173(7):1755-1769.e22. doi: 10.1016/j.cell.2018.03.073. PMID: 29754820
  12. Brown SD, Holt RA. Neoantigen characteristics in the context of the complete predicted MHC class I self-immunopeptidome. Oncoimmunology 2018 Dec 22;8(3):1556080. doi: 10.1080/2162402X.2018.1556080
  13. Sneddon S, Dick I, Lee G, Musk AWB, Patch A-M, Pearson JV, Waddel N, Allcock RJN, Holt RA, Robinson BWS, Creaney J. Malignant cells from pleural fluids in malignant mesothelioma patients reveal novel mutations. Lung Cancer 2018 May;119:64-70. doi: 10.1016/j.lungcan.2018.03.009
  14. Thorsson V, Gibbs DL, Brown SD, ... Holt, RA, ... Shmulevich I. The Immune Landscape of Cancer. Immunity 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023
  15. Woodsworth DJ, Dreolini L, Abraham L, Holt RA. Targeted cell-to-cell delivery of protein payloads via the granzyme-perforin pathway Molecular Therapy-Methods & Clinical Development 2017 Oct 10;7:132-145. doi: 10.1016/j.omtm.2017.10.003
  16. Martin SD, Wick DA, Nielsen JS, Little N, Holt RA, Nelson BH. A library-based screening method identifies neoantigen-reactive T cells in peripheral blood prior to relapse of ovarian cancer. OncoImmunology 2017 Sep 21;7(1):e1371895. doi: 10.1080/2162402X.2017.1371895
  17. Holt RA. Interpreting the T-cell receptor repertoire. Nature Biotechnology 2017 Sep 11;35(9):829-830. doi: 10.1038/nbt.3957
  18. Sneddon S, Patch AM, Dick IM, Kazakoff S, Pearson JV, Waddell N, Allcock RJN, Holt RA, Robinson BWS, Creaney J. Whole exome sequencing of an abestos-induced wild-type murine model of malignant mesothelioma. BMC Cancer 2017 Jun 2;17(1):396. doi: 10.1186/s12885-017-3382-6
  19. Bouquet J, Gardy JL, Brown SD, Pfeil J, Miller RR, Morshed M, Avina-Zubieta A, Shojania K, McCabe M, Parker S, Uyaguari M, Federman S, Tang P, Steiner T, Otterstater M, Holt RA, Moore R, Chiu CY, Patrick DM. RNA-seq analysis of gene expression, viral pathogen, and B-cell/T-cell receptor signatures in complex chronic disease Clinical Infectious Diseases 2017 Feb 15;64(4):476-481. doi: 10.1093/cid/ciw767
  20. Holt RA, Cochrane K. Tumor potentiating mechanisms of Fusobacterium nucleatum, a multifaceted microbe. Gastroenterology 2017 Mar;152(4):694-696. doi: 10.1053/j.gastro.2017.01.024
  21. Woodsworth DJ, Holt RA. Cell-based therapeutics: making a faustian pact with biology. Trends on Molecular Medicine 2017 Feb;23(2):104-115. doi: 10.1016/j.molmed.2016.12.004
  22. Brown SD, Hapgood G, Steidl C, Weng AP, Savage KJ, Holt RA. Defining the clonality of peripheral T cell lymphomas using RNA-seq. Bioinformatics 2017 Apr 15;33(8):1111-1115. doi: 10.1093/bioinformatics/btw810
  23. Martin SD, Brown SD, Wick DA, Nielsen JS, Kroeger DR, Twumasi-Boateng K, Holt RA, Nelson BH. Low mutation burden in ovarian cancer may limit the utility of neoantigen-targeted vaccines. PloS one. 2016 May 18;11(5):e0155189. doi: 10.1371/journal.pone.0155189
  24. Brown SD, Raeburn LA, Holt RA. Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Medicine. 2015 Nov 30;7:125. doi: 10.1186/s13073-015-0248-x
  25. Holt RA. Immunogenomics: a foundation for intelligent immune design. Genome Medicine. 2015 Nov 19;7(1):116. doi: 10.1186/s13073-015-0247-y
  26. The Cancer Genome Atlas Research Network. Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-96. doi: 10.1016/j.cell.2015.05.044
  27. Gibb EA, Warren RL, Wilson GE, Brown SD, Robertson G, Morin GB and Holt RA. Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma. Genome Medicine. 2015 Mar 5;7(1):22. doi: 10.1186/s13073-015-0142-6
  28. Sharma G and Holt RA. T-cell epitope discovery technologies. Human Immunology. 2014 Jun;75(6):514-519.
  29. Brown SD, Warren RL, Gibb E, Martin SD, Nelson BH, Holt RA. Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Research. 2014 May;24(5):743-50. doi: 10.1101/gr.165985.113
  30. Wick D, Webb JR, Nielsen JS, Martin S, Kroeger DR, Milne K, Castellarin M, Twumasi-Boating K, Watson PH, Holt RA, Nelson BH. Surveillance of the tumor mutanome by T cells during progression from primary to recurrent ovarian cancer. Clinical Cancer Research. 2014 Mar 1;20(5):1125-34. doi: 10.1158/1078-0432.CCR-13-2147
  31. Woodsworth DJ, Castellarin M, Holt RA. Sequence analysis of T-cell repertoires in health and disease. Genome Medicine. 2013 Oct 30;5(10):98. doi: 10.1186/gm502
  32. Watson CT, Steinberg KM, Huddleston J, Sudmant P, Warren RL, Malig M, Schein J, Willsey JA, Joy JB, Scott JK, Graves, Wilson RK, Holt RA, Eichler EE, Breden F. Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. American Journal of Human Genetics. 2013 Apr 4;92(4):530-46. doi: 10.1016/j.ajhg.2013.03.004
  33. Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA. Derivation of HLA types from shotgun sequence datasets. Genome Medicine. 2012 Dec 10;4(12):95. doi: 10.1186/gm396
  34. Castellarin M, Milne K, Zeng T, Tse K, Mayo M, Zhao YJ, Webb JR, Watson PH, Nelson BH, Holt RA. Clonal evolution of high-grade serous ovarian carcinoma from primary to recurrent disease. Journal of Pathology. 2013 Mar;229(4):515-24. doi: 10.1002/path.4105
  35. The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252
  36. Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Research. 2012 Feb;22(2):299-306. doi: 10.1101/gr.126516.111
  37. Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chenard C, Friedman JM, Suttle CA, Zhao Y, Holt RA. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissues. PLoS One. 2011;6(5):e19838. doi: 10.1371/journal.pone.0019838
  38. Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA. Exhaustive T- cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Research. 2011 May;21(5):790-7. doi: 10.1101/gr.115428.110
  39. Gardy JL et al. Whole Genome Sequencing and Social Network Analysis of a Tuberculosis Outbreak. New England Journal of Medicine. 2011 Feb 24;364(8):730-9. doi: 10.1056/NEJMoa1003176
  40. Jones SJM et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology. 2010;11(8):R82. doi: 10.1186/gb-2010-11-8-r82
  41. Mead CL, Kuzyk MA, Moradian A, Wilson GM, Holt RA, Morin GB. Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin. Journal of Neurochemistry. 2010 Jun;113(6):1491-503. doi: 10.1111/j.1471-4159.2010.06690.x
  42. Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Research. 2009 Oct;19(10):1817-24. doi: 10.1101/gr.092924.109
  43. Horspool DR, Coope RJ and Holt RA. Efficient assembly of very short oligonucleotides using T4 DNA Ligase. BMC Research Notes. 2010 Nov 9;3:291. doi: 10.1186/1756-0500-3-291
  44. Holt RA et al. Rebuilding microbial genomes. Bioessays. 2007 Jun;29(6):580-90
  45. Warren RL, Sutton GG, Jones SJM and Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 2007 Feb 15;23(4):500-1
  46. Wilson GE, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG and Holt RA. Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Research. 2006 Feb;16(2):173-81
  47. Marra MA, Jones SJ, Astell CR, Holt RA et al., The Genome Sequence of the SARS-Associated Coronavirus. Science. 2003 May 30;300(5624):1399-404
  48. Holt RA et al., The Genome Sequence of the Malaria Mosquito Anopheles gambiae. Science. 2002 Oct 4;298(5591):129-49
  49. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al., The Sequence of the Human Genome. Science. 2001 Feb 16;291(5507):1304-51
  50. Adams MD, Celniker SE, Holt RA et al. The Genome Sequence of Drosophila melanogaster. Science. 2000 Mar 24;287(5461):2185-95