Harvard Catalyst Profiles

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James Malcolm Heather, Ph.D.


Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Peacock T, Heather JM, Ronel T, Chain B. Decombinator V4: an improved AIRR compliant-software package for T-cell receptor sequence annotation? Bioinformatics. 2021 May 05; 37(6):876-878. PMID: 32853330.
    Citations:    Fields:    
  2. Turner CT, Brown J, Shaw E, Uddin I, Tsaliki E, Roe JK, Pollara G, Sun Y, Heather JM, Lipman M, Chain B, Noursadeghi M. Persistent T Cell Repertoire Perturbation and T Cell Activation in HIV After Long Term Treatment. Front Immunol. 2021; 12:634489. PMID: 33732256.
    Citations:    Fields:    
  3. de Greef PC, Oakes T, Gerritsen B, Ismail M, Heather JM, Hermsen R, Chain B, de Boer RJ. The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes. Elife. 2020 03 18; 9. PMID: 32187010.
    Citations: 9     Fields:    Translation:HumansCells
  4. Spindler MJ, Nelson AL, Wagner EK, Oppermans N, Bridgeman JS, Heather JM, Adler AS, Asensio MA, Edgar RC, Lim YW, Meyer EH, Hawkins RE, Cobbold M, Johnson DS. Massively parallel interrogation and mining of natively paired human TCRaß repertoires. Nat Biotechnol. 2020 05; 38(5):609-619. PMID: 32393905.
    Citations: 5     Fields:    Translation:HumansCells
  5. Millar DG, Ramjiawan RR, Kawaguchi K, Gupta N, Chen J, Zhang S, Nojiri T, Ho WW, Aoki S, Jung K, Chen I, Shi F, Heather JM, Shigeta K, Morton LT, Sepulveda S, Wan L, Joseph R, Minogue E, Khatri A, Bardia A, Ellisen LW, Corcoran RB, Hata AN, Pai SI, Jain RK, Fukumura D, Duda DG, Cobbold M. Antibody-mediated delivery of viral epitopes to tumors harnesses CMV-specific T cells for cancer therapy. Nat Biotechnol. 2020 04; 38(4):420-425. PMID: 32042168.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  6. Heather JM, Myers PT, Shi F, Aziz-Zanjani MO, Mahoney KE, Perez M, Morin B, Brittsan C, Shabanowitz J, Hunt DF, Cobbold M. Murine xenograft bioreactors for human immunopeptidome discovery. Sci Rep. 2019 12 06; 9(1):18558. PMID: 31811195.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  7. Wong GK, Barmettler S, Heather JM, Millar D, Penny SA, Huissoon A, Richter A, Cobbold M. Aberrant X chromosome skewing and acquired clonal hematopoiesis in adult-onset common variable immunodeficiency. JCI Insight. 2019 07 25; 4(14). PMID: 31341110.
    Citations: 1     Fields:    Translation:HumansCells
  8. Lan YY, Heather JM, Eisenhaure T, Garris CS, Lieb D, Raychowdhury R, Hacohen N. Extranuclear DNA accumulates in aged cells and contributes to senescence and inflammation. Aging Cell. 2019 04; 18(2):e12901. PMID: 30706626.
    Citations: 21     Fields:    Translation:HumansAnimalsCells
  9. Uddin I, Joshi K, Oakes T, Heather JM, Swanton C, Chain B. An Economical, Quantitative, and Robust Protocol for High-Throughput T Cell Receptor Sequencing from Tumor or Blood. Methods Mol Biol. 2019; 1884:15-42. PMID: 30465193.
    Citations: 5     Fields:    Translation:HumansCells
  10. Gkazi AS, Margetts BK, Attenborough T, Mhaldien L, Standing JF, Oakes T, Heather JM, Booth J, Pasquet M, Chiesa R, Veys P, Klein N, Chain B, Callard R, Adams SP. Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation. Front Immunol. 2018; 9:2547. PMID: 30455696.
    Citations: 7     Fields:    Translation:HumansCells
  11. Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform. 2018 07 20; 19(4):554-565. PMID: 28077404.
    Citations: 28     Fields:    Translation:HumansCells
  12. Oakes T, Heather JM, Best K, Byng-Maddick R, Husovsky C, Ismail M, Joshi K, Maxwell G, Noursadeghi M, Riddell N, Ruehl T, Turner CT, Uddin I, Chain B. Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile. Front Immunol. 2017; 8:1267. PMID: 29075258.
    Citations: 22     Fields:    
  13. Sun Y, Best K, Cinelli M, Heather JM, Reich-Zeliger S, Shifrut E, Friedman N, Shawe-Taylor J, Chain B. Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization. Front Immunol. 2017; 8:430. PMID: 28450864.
    Citations: 13     Fields:    
  14. Wong GK, Heather JM, Barmettler S, Cobbold M. Immune dysregulation in immunodeficiency disorders: The role of T-cell receptor sequencing. J Autoimmun. 2017 Jun; 80:1-9. PMID: 28400082.
    Citations: 7     Fields:    Translation:HumansCells
  15. Cinelli M, Sun Y, Best K, Heather JM, Reich-Zeliger S, Shifrut E, Friedman N, Shawe-Taylor J, Chain B. Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires. Bioinformatics. 2017 04 01; 33(7):951-955. PMID: 28073756.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  16. Oakes T, Popple AL, Williams J, Best K, Heather JM, Ismail M, Maxwell G, Gellatly N, Dearman RJ, Kimber I, Chain B. The T Cell Response to the Contact Sensitizer Paraphenylenediamine Is Characterized by a Polyclonal Diverse Repertoire of Antigen-Specific Receptors. Front Immunol. 2017; 8:162. PMID: 28261218.
    Citations: 4     Fields:    
  17. Pollara G, Murray MJ, Heather JM, Byng-Maddick R, Guppy N, Ellis M, Turner CT, Chain BM, Noursadeghi M. Validation of Immune Cell Modules in Multicellular Transcriptomic Data. PLoS One. 2017; 12(1):e0169271. PMID: 28045996.
    Citations: 11     Fields:    Translation:HumansCells
  18. Wong GK, Millar D, Penny S, Heather JM, Mistry P, Buettner N, Bryon J, Huissoon AP, Cobbold M. Accelerated Loss of TCR Repertoire Diversity in Common Variable Immunodeficiency. J Immunol. 2016 09 01; 197(5):1642-9. PMID: 27481850.
    Citations: 5     Fields:    Translation:HumansCells
  19. Heather JM, Best K, Oakes T, Gray ER, Roe JK, Thomas N, Friedman N, Noursadeghi M, Chain B. Dynamic Perturbations of the T-Cell Receptor Repertoire in Chronic HIV Infection and following Antiretroviral Therapy. Front Immunol. 2015; 6:644. PMID: 26793190.
    Citations: 31     Fields:    
  20. Heather JM, Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics. 2016 Jan; 107(1):1-8. PMID: 26554401.
    Citations: 111     Fields:    
  21. Best K, Oakes T, Heather JM, Shawe-Taylor J, Chain B. Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding. Sci Rep. 2015 Oct 13; 5:14629. PMID: 26459131.
    Citations: 23     Fields:    Translation:HumansCells
  22. Thomas N, Heather J, Pollara G, Simpson N, Matjeka T, Shawe-Taylor J, Noursadeghi M, Chain B. The immune system as a biomonitor: explorations in innate and adaptive immunity. Interface Focus. 2013 Apr 06; 3(2):20120099. PMID: 24427535.
    Citations: 2     
  23. Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B. Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics. 2013 Mar 01; 29(5):542-50. PMID: 23303508.
    Citations: 47     Fields:    Translation:Humans
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.