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Steven Kleinstein, PhD

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Anthony N Brady Professor of Pathology


Co-Director of Graduate Studies, Computational Biology and Bioinformatics



Anthony N Brady Professor of Pathology

Co-Director of Graduate Studies, Computational Biology and Bioinformatics


Dr. Steven Kleinstein is a computational immunologist with a combination of big data analysis and immunology domain expertise. His research interests include both developing new computational methods and applying these methods to study human immune responses. Dr. Kleinstein received a B.A.S. in Computer Science from the University of Pennsylvania and a Ph.D. in Computer Science from Princeton University. He is currently Professor of Pathology (with a secondary appointment in Immunobiology) at the Yale School of Medicine, and a member of the Interdepartmental Program in Computational Biology and Bioinformatics (CBB), and the Human and Translational Immunology Program.

Specific areas of research focus include:

  • High-throughput single-cell B cell receptor (BCR) repertoire profiling (AIRR-seq, Rep-seq, scRNA-seq+VDJ)
  • Multi-omic immune signatures of human infection and vaccination responses


Education & Training

Princeton University, Computer Science (2002)
The University of Pennsylvania, Computer Science (1994)



High-throughput B cell receptor (BCR) repertoire sequencing

Next-generation sequencing (NGS) technologies have revolutionized our ability to carry out large-scale adaptive immune receptor repertoire sequencing (AIRR-seq) experiments. AIRR-seq is increasingly being applied to gain insights into immune responses in healthy individuals and those with a range of diseases, including autoimmunity, infection, allergy, cancer and aging. As NGS technologies improve, these experiments are producing ever larger datasets, with tens- to hundreds-of-thousands of single cells (or tens- to hundreds-of-millions of BCR sequences when run in bulk), requiring the development of new computational methods to manage and analyze these “Big Data”. For an overview, please check out our review.

We have developed many widely used computational methods for bulk and single-cell AIRR-seq data processing and analysis. These methods are available to the wider scientific community through the Immcantation framework, which provides a start-to-finish analytical ecosystem for high-throughput AIRR-seq datasets, with a focus on B cell receptor (BCR) repertoire profiling. Working in close collaboration with basic experimental and clinical groups, we have been applying our methods to gain biological insights in several systems, including: infection (SARS-CoV-2, HIV, Salmonella, West Nile virus, Lyme), vaccination (influenza), allergy (allergic rhinitis, atopic asthma) and autoimmune disease (Multiple Sclerosis, Myasthenia Gravis). We are also active members of the AIRR Community.

Multi-omic immune signatures of human infection and vaccination responses

Individual variations in immune status and function produce significant heterogeneity in infection and vaccination responses. For example, West Nile virus infection is usually asymptomatic, but can cause severe neurological disease and death, particularly in older patients. Our research leverages recent advances in immune profiling methods to characterize diverse states of human immune system (in health and disease, and following infection and vaccination). We have developed several computational methods for large-scale genetic network modeling, including:

  • QuSAGE, which quantifies pathway activity from high-throughput transcriptional profiling data while accounting for gene-gene correlations
  • LogMiNeR, which leverages prior knowledge networks to improve model interpretability in the analysis of high-throughput transcriptional profiling data.
  • SPEC, which predicts the specific cellular source (e.g., B cells, T cells, etc.) of a gene expression signature using data from total PBMCs
  • TIDAL, which integrates genome-wide expression kinetics and time-dependent promoter analysis to reconstruct transcriptional regulatory networks

For a complete list, check out our software page.

A major biological focus area for this research is the response to influenza infection and vaccination. As part of the multi-institutional Program for Research on Immune Modeling and Experimentation (PRIME), we developed data-driven models for the response of multiple human cell types to infection with different strains of influenza (including the infamous 1918 pandemic strain). We also study influenza vaccination responses as part of the NIH/NIAID Human Immunology Project Consortium (HIPC) and the SARS-CoV-2 infection response as part of IMPACC.

Medical Subject Headings (MeSH)

Autoimmune Diseases; Autoimmune Diseases of the Nervous System; Computational Biology; Computing Methodologies; Immune System Diseases; Immune System Phenomena; Influenza Vaccines; Information Science; Lyme Disease; Mathematical Concepts; Patient-Specific Modeling; Pattern Recognition, Automated; Virus Diseases; West Nile virus

Research at a Glance

Yale Co-Authors

Frequent collaborators of Steven Kleinstein's published research.


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