Steven H Kleinstein PhD

Associate Professor of Pathology and of Immunobiology

Research Interests

Computational immunology; Systems biology; Bioinformatics; Disease/tissue/pathway/process modeling and simulation; B cell immunoglobulin repertoire analysis; Influenza

Current Projects

Information on projects is available from our lab website:

Research Summary

Our group combines techniques from dynamic modeling, systems biology and bioinformatics to better understand the immune response.

Extensive Research Description

Selected Publications

  • Stern JNH*, Yaari G*, Vander Heiden JA*, Church G, Donahue WF, Hintzen RQ, Huttner AJ, Laman JD, Nagra RM, Nylander A, Pitt D, Ramanan S, Siddiqui BA, Vigneault F, Kleinstein SH**, Hafler DA** and O’Connor KC**. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Science Translational Medicine. 2014. Aug 6;6(248):248ra107. doi:10.1126/scitranslmed.3008879. PMID: 25100741.
  • Vander Heiden JA*, Yaari G*, Uduman M, Stern JNH, O’Connor KC, Hafler DA, Vigneault F and Kleinstein SH. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014. Jul 1;30(13):1930-2. doi: 10.1093/bioinformatics/btu138. PMCID: PMC4071206.
  • Yaari G, Vander Heiden J, Uduman M, Gadala-Maria D, Gupta N, Stern J.N.H., O’Connor KC, Hafler DA, Laserson U, Vigneault F and Kleinstein SH. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput Immunoglobulin sequencing data. Frontiers in Immunology. 2013. 2013 Nov 15;4:358. doi: 10.3389/fimmu.2013.00358. PMCID: PMC3828525.
  • Bolen CR*, Ding S*, Robek MD**, Kleinstein SH**. Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression. Hepatology. 2013. Aug 8. doi:10.1002/hep.26657. PMID: 23929627.
  • Yaari G*, Bolen CR*, Thakar J and Kleinstein SH. Quantitative Set Analysis for Gene Expression: A method to quantify gene set differential expression including gene-gene correlations. Nucleic Acids Research. 2013. doi: 10.1093/nar/gkt660. PMID: 23921631.
  • Yaari G, Uduman M and Kleinstein SH. Quantifying selection in high-throughput Immunoglobulin sequencing datasets. Nucleic Acids Research. 2012. doi:10.1093/nar/gks457. PMID: 22641856. PMCID: PMC3458526.

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