231 total publications 1996-2018 | 70,458 total citations | H-index 76 | i10-index 138 tracked by Google Scholar as of June 15, 2018

  1. 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
  2. Thorsson V, Gibbs DL, Brown SD, ... Holt, RA, ... Shmulevich I. The Immune Landscape of Cancer Immunity 2018 April
  3. 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 October
  4. 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 September
  5. Holt RA. Interpreting the T-cell receptor repertoire. Nature Biotechnology 2017 September
  6. 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 June
  7. 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 2017 February
  8. Holt RA, Cochrane K. Tumor potentiating mechanisms of Fusobacterium nucleatum, a multifaceted microbe. Gastroenterology 2017 January
  9. Woodsworth DJ, Holt RA. Cell-based therapeutics: making a faustian pact with biology. Trends on Molecular Medicine 2017 January
  10. Brown SD, Hapgood G, Steidl C, Weng AP, Savage KJ, Holt RA. Defining the clonality of peripheral T cell lymphomas using RNA-seq. Bioinformatics 2016 December
  11. 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
  12. Brown SD, Raeburn LA, Holt RA. Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Medicine. 2015 Nov 30;7(1):125
  13. Holt RA. Immunogenomics: a foundation for intelligent immune design. Genome Medicine. 2015 Nov 19;7(1):116
  14. The Cancer Genome Atlas Research Network. Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-96
  15. 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.
  16. Sharma G and Holt RA. T-cell epitope discovery technologies. Human Immunology. 2014 Jun;75(6):514-519.
  17. 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. PMID: 24782321.
  18. 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.
  19. Woodsworth DJ, Castellarin M, Holt RA. Sequence analysis of T-cell repertoires in health and disease. Genome Medicine. 2013 Oct 30;5(10):98.
  20. 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.
  21. 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.
  22. 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 March 229(4):515-524
  23. The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 478(7407):330-7.
  24. 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.
  25. 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.
  26. 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. 21(5):790-7. 2011
  27. Gardy JL et al. Whole Genome Sequencing and Social Network Analysis of a Tuberculosis Outbreak. New England Journal of Medicine. 364(8):730-9. 2010
  28. Jones SJM et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology. 9;11(8):R82. 2010
  29. Mead CL, Kuzyk MA, Moradian A, Wilson GM, Holt RA, Morin GB. Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin. Journal of Neurochemistry. 113(6):1491-1503. 2010
  30. Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Research. 19(10):1817-18124. 2009.
  31. Horspool DR, Coope RJ and Holt RA. Efficient assembly of very short oligonucleotides using T4 DNA Ligase. BMC Research Notes. 3(1):291. 2010
  32. Holt RA et al. Rebuilding microbial genomes. Bioessays. 29: 580-590. 2007.
  33. Warren RL, Sutton GG, Jones SJM and Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23: 500-501. 2007.
  34. 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. 16:173-181. 2006.
  35. Marra MA, Jones SJ, Astell CR, Holt RA et al., The Genome Sequence of the SARS-Associated Coronavirus. Science. 300:1399-1404. 2003.
  36. Holt RA et al., The Genome Sequence of the Malaria Mosquito Anopheles gambiae. Science. 298:129-149. 2002.
  37. 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. 291:1304-1351. 2001.
  38. Adams MD, Celniker SE, Holt RA et al. The Genome Sequence of Drosophila melanogaster. Science. 287(5461):2185-2195. 2000