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Papers & Posters


Huang, W. et al. JCI Insight. 2018;3(17):e122525.

Pan, W., et al: All-in-One, Quantitative Immune Repertoire Profiling from Challenging Samples. FOCiS 2018. T.115.

Li, S., et al.: iR-HLA cassette: An automated and integrated solution ffor NGS based HLA-typing. FOCiS 2018. F.3.

Hou, X., et al: Identification of paired heavy and light chains from single B-cells from immunized Malian adults with rapid functional confirmation using iPair-BCR™, NGS, and iScreen™. J Immunol May 1, 2018, 200 (1 Supplement) 174.36

Wu, J, et al. Expanded TCRB CDR3 clonotypes distinguish Crohn’s disease and ulcerative colitis patients. Mucosoal Immunology, July 2018.

Cheng, C., et al. Next generation sequencing reveals changes of the γδ T cell receptor repertoires in patients with pulmonary tuberculosis. Scientific Reports 8, Article number: 3956 (2018).

Hunter, S., et al. Human liver infiltrating γδ T cells are composed of clonally expanded circulating and tissue-resident populations. J. Hepatology 3:69, pp 654-665.

Jiang, Q., et al.  Patient-shared TCRβ-CDR3 clonotypes correlate with favorable prognosis in chronic heptatitis B. European J. Immunol. 2018.

Dickinson, G.S., et al. IL-7 Enables Antibody Responses to Bacterial Polysaccharides by Promoting B Cell Receptor Diversity. J Immunol. 13 July 2018.

Jiang, Q., et al. Analysis of T cell receptor repertoire in monozygotic twins concordant and discordant for chronic hepatitis B infection. Biochem Biophys Research Comm. Vol 497, Iss. 1, 26 Feb 2018, pp 153-159.

Textor, J., et al. Deep Sequencing Reveals Transient Segregation of T cell Repertoires in Splenic T cell Zones During an Immune Response. bioRxiv. 8 December 2017.

Fähnrich, A., et al. CD154 Costimulation Shifts the Local T-Cell Receptor Repertoire Not Only During Thymic Selection but also During Peripheral T-Dependent Humoral Immune Responses. Front. Immunol. 2018; 9:1019.

Tedesco, D., et al. Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic γδ T-Cell Receptor-Positive Cells and Pathogenesis of Cholestatic Liver Disease. Gastroenterology. June 2018, Vol 154: 8, p 2178-2193.

Davey, M.S., et al. The Human Vδ2+ T-cell Compartment Comprises Distinct Innate-like Vγ9+ and Adaptive Vγ9- Subsets. Nature Communications 9, Article Number: 1760 (2018).

Shukla, G.S., et al. Immunization with Tumor Neoantigens Displayed on T7 Phage Nanoparticles Elicits Plasma Antibody and Vaccine-draining Lymph Node B Cell Responses. J. Immunol. Methods. S0022-1759(18)30163-7. doi: 10.1016/j.jim.2018.06.009

Fahl, S.P., et al. Role of a Selecting Ligand in Shaping the Murine γδ-TCR repertoire. PNAS. 115 (8) 1889-1894.

Davey, M.S., et al. Recasting Human Vd1 Lymphocytes in an Adaptive Role. Trends in Imm.: Opinion. 39, 6, P446-459, June 2018.

Zhang, C., et el. Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire. Front. Immunol., 27 April 2018 |

McCaw, T.R., et al. The expression of class II major histocompatibility molecules on breast tumors delays T cell exhaustion, expands the T cell repertoire and slows tumor growth. bioRxiv. 3 April 2018.

Hui, C., et al. Profiling the pattern of the human T-cell receptor γδ complementary determinant region 3 repertoire in patients with lung carcinoma via high-throughput sequencing analysis. 05 February 2018.

Spence, A., et al, Revealing the specificity of regulatory T cells in murine autoimmune diabetes. PNAS.

Mitchell, A.M., et al. CD4+ T Cell Receptor Repertoire in Sarcoidosis Patients. J. Immunol. 198 (1 Supplement) 55.36.

Okano, T., et al. Maternal T and B cell engraftment in two cases of X-linked severe combined immunodeficiency with IgG1 gammopathy. Clinical Immunology. S1521-6616(17)30058-X. doi: 10.1016/j.clim.2017.08.003

Davey, M.S., et al. Clonal selection in the human Vδ1 T cell repertoire indicates γδ TCR-dependent adaptive immune surveillance. Nat. Comm. 8, Article number: 14760(2017).

Barisa, M., et al. E. coli promotes human Vγ9Vδ2 T cell transition from cytokine-producing bactericidal effectors to professional phagocytic killers in a TCR-dependent manner. Scientific Reports 7, Article number: 2805 (2017).

Konishi, H., et al. Capturing the Difference in Humoral Immunity between Normal and Tumor Environments from RNA Sequences of B-Cell Receptors Using Supervised Machine Learning. bioRxiv. 11 Sept 2017.

Mitchell, A.M., et al. Shared ɑβ TCR Usage in Lungs of Sarcoidosis Patients with Löfgren’s Syndrome. J Immunol. 21 August 2017. doi:10.4049/jimmunol.1700570

Probst, P., et al, Sarcoma eradication by doxorubicin and targeted TNF relies upon CD8+ T cell recognition of a retroviral antigen. AACR Journals. May 8, 2017; DOI: 10.1158/0008-5472.CAN-16-2946

Hui, C., et al. Characterization of the diversity of T cell receptor γδ complementary determinant region 3 in human peripheral blood by Immune Repertoire Sequencing. Journal of Immunological Methods. 443 (2017) 9-17.

Katoh, H, et al. Immunogenetic Profiling for Gastric Cancers Identifies Sulfated Glycosaminoglycans as Major and Functional B cell Antigens in Human Malignancies. Cell Reports 20, 1073–1087, August 1, 2017.

Wong, S-C.H., et al. V-J Combinations of T-cell receptor predict responses to erythropoeitin in end-stage renal disease patients. Journal of Biomedical Science, 2017 24:43,

Ritvo, P-G., et al. High-resolution repertoire analysis of Tfr and Tfh cells reveals unexpectedly high diversity indicating a bystander activation of follicular T cells. bioRxiv. 10 December 2017. doi:

Hou, Dongni, et al. Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients. Sci. Rep. 6, 33843; doi: 10.1038/srep33843 (2016).

Muneera Al-Hussaini, et al. Targeting CD123 in acute myeloid leukemia using a T-cell–directed dual-affinity retargeting platform. Blood Jan 2016, 127 (1) 122-131; DOI: 10.1182/blood-2014-05-575704

Byrne-Steele, M., et al.: Using iPair-TCR™ and iPair-TCR+™ to track tumor infiltrating lymphocytes from peripheral blood in a longitudinal breast cancer patient study. SITC 2017.

Pan, W., et al.: Quantitative bulk RNA amplification of all TCR and BCR chains in a single multiplex PCR reaction using dam-PCR™. Immunogenomics 2017

Han, Jian.: Wellness Index: measuring the readiness of our immune system. Immunogenomics. 2016. P562.

Lee, et. al. Characterization of T and B cell repertoire diversity in patients with RAG deficiency, Sci. Immunol. 1, eaah6109 (2016) 16 December 2016

Sims, J. et. al. Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire. PNAS (2016) E3529-E3537.

Al-Hussaini, et. al. Targeting CD123 in acute myeloid leukemia using a T-cell--directed dual-affinity retargeting platform. Blood (2016). 127(1):122-131).

Yang, Yang, et al. Distinct mechanisms define murine B cell lineage immunoglobulin heavychain (IgH) repertoires. eLife 4 (2015): e09083.


Zhao et. al. Humanized Mice Reveal Differential Immunogenicity of Cells Derived from Autologous Induced Pluripotent Stem Cells. Cell Stem Cell 17 (3 Sept 2015), 353-359.


O’Connell, Amy E. et al. Next Generation Sequencing Reveals Skewing of the T and B Cell Receptor Repertoires in Patients with Wiskott–Aldrich Syndrome. Frontiers in Immunology 5 (2014): 340. PMC. Web. 23 June 2015.


Sims, Jennifer, et al. IT-32 Divergence Of Intratumoral And Systemic T Cell Repertoires Reflects Local Monocyte Profiles During Glioma Progression. Neuro-Oncology 16.suppl 5 (2014): v116-v117.


Sims et al.: TCR repertoire divergence reflects micro-environmental immune phenotypes in glioma J ImmunoTherapy of Cancer 2014 2(Suppl 3):O19


Slansky, Jill E. et al. Enhancing the Breadth and Efficacy of Therapeutic Vaccines for Breast Cancer Colorado Univ Health Sciences Center, Public Release. October 2013.


Sims et al.: Tumor-associated T cell receptor repertoires in low- and high-grade gliomas. Journal for ImmunoTherapy of Cancer 2013 1(Suppl 1):P143.


Laetitia Peaudecerf et al.: Thymocytes may persist and differentiate without any input from bone marrow progenitors J Exp Med 2012 209:1401-1408.


Lee, Yu Nee et al. A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency  Journal of Allergy and Clinical Immunology , Volume 133 , Issue 4 , 1099 - 1108.e12


Wang et al.: High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets PNAS 2010 107 (4) 1518-1523


Riser, et al: A Comprehensive Analysis of Relapse in Multiple Sclerosis CMSC Actrims 2015

Byrne-Steele et al.: iRock 2.0 and the iR-Processor: an automated immune repertoire library preparation platform for NGS J Immunol 2014 192:69.19

Byrne-Steele et al.: Automation of immune repertoire amplification on the iC-Processor J Immunol 2014 192:69.19

Alleyne et al.:  Immunosuppression in the Tumor Microenvironment Session: Biomarker: long term study of breast cancer specific CDR3s in peripheral blood (TUM2P.894) J Immunol 2014 192:71.18

Sims, Jennifer, et al. IT-32 Divergence Of Intratumoral And Systemic T Cell Repertoires Reflects Local Monocyte Profiles During Glioma Progression. Neuro-Oncology 16.suppl 5 (2014): v116-v117.

Wang et al.: Immunosupression in the Tumor Microenvironment Session: Breast cancer diagnosis by high throughput sequencing of T cell receptors from peripheral blood samples J Immunol 2014 192:71.29

Han et al.: R10K update: NGS of immune repertoire for biomarker discoveries J Immunol 2013 190: 192.6

Han et al.: Identification and temporal monitoring of breast cancer-associated T cell receptors with high throughput sequencing J Immunol 2012 188: 46.23

Wang et al.: Evaluation of three next generation sequencing platforms for immune repertoire sequencing J Immunol 2012 188: 58.10

Han et al.: R10K: an international collaborative project for biomarker discovery J Immunol 2012 188:58.7

Byrne-Steele, et al.: Development of an alternative method for the identification and production of antigen-specific monoclonal antibodies J Immunol 2011 186: 65.16

Han et al.: Profiling the pattern of human immunoglobulin SHM and CSR in B memory cells via  high-throughput sequencing J Immunol 2011 186:62.11

Han et al.: High throughput sequencing identified specific T cells from breast cancer tissue and peripheral blood J Immunol 2001 186: 48.37

Wang et al.: Immune repertoire high-throughput sequence analysis (IRAS) web service J Immunol 2011 186: 65.20





Han, Jian. Method for Evaluating and Comparing Immunorepertoires. Jian Han, assignee. Patent 9012148. 21 Apr. 2015. Print.

Han, Jian. Amplicon Rescue Multiplex Polymerase Chain Reaction for Amplification of Multiple Targets. HudsonAlpha Institute for Biotechnology, assignee. Patent 7999092. 16 Aug. 2011. Print.