Author

S. H. Kleinstein

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Immunology· 11

Signature Assays, Organisms & Methods

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Organism:human· 9 Approach:statistical model· 7 Research Focus:cell type annotation· 6 Research Focus:clustering· 5 Assay:scRNA-seq· 5 Research Focus:differential expression· 4 Assay:bulk RNA-seq· 3 Approach:deep learning· 2

Frequent Co-Authors

K. B. Hoehn· 5 shared O. G. Pybus· 3 shared B. Vander Wyk· 2 shared J. Q. Zhou· 2 shared R. Jiang· 2 shared R. R. Montgomery· 2 shared Y. Zhao· 2 shared A. C. Shaw· 1 shared

Activity by Year

2017-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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5 shared papersImmunology

K. B. Hoehn

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11 papers

Recent·Most cited

Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser

C. G. Jensen, J. A. Sumner, S. H. Kleinstein, K. B. Hoehn

This study evaluates methods for inferring B cell phylogenies using paired heavy and light chain BCR sequences, finding that incorporating light chains improves accuracy and that maximum likelihood methods with separate partitions are most reliable.

bioRxiv · Sep 29, 2023Immunology

Early cellular and molecular signatures correlate with severity of West Nile Virus infection

H.-J. Lee, Y. Zhao, I. Fleming, S. Mehta, X. Wang, B. Vander Wyk, S. E. Ronca, H. Kang, C.-H. Chou, B. Fatou, K. K. Smolen, O. Levy, C. B. Clish, R. J. Xavier, H. Steen, , R. R. Montgomery

The paper identifies cellular and molecular signatures associated with varying severities of West Nile Virus infection using multi-omics analysis of immune responses.

bioRxiv · May 14, 2023Immunology

IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data

A. Peres, W. D. Lees, O. L. Rodriguez, N. Y. Lee, P. Polak, R. Hope, M. Kedmi, A. M. Collins, M. Ohlin, S. H. Kleinstein, C. Watson, G. Yaari

The paper introduces a new V allele naming scheme and genotype inference method for adaptive immune receptor sequencing, validated with genomic long read data and implemented in an R package.

bioRxiv · Dec 26, 2022 · PreprintImmunology

Platelet response to influenza vaccination reflects effects of aging

A. Konstorum, S. Mohanty, Y. Zhao, A. Melillo, B. Vander Wyk, A. Nelson, S. Tsang, T. P. Blevins, R. B. Belshe, D. G. Chawla, M. T. Rondina, R. R. Montgomery, H. G. Allore, S. H. Kleinstein, A. C. Shaw

This study examines how aging and frailty affect platelet function before and after influenza vaccination, revealing age-related changes in activation and translation.

bioRxiv · Apr 6, 2022Immunology

Pipeline for retrieval of COVID-19 immune signatures

A. J. H. Newton, D. Chartash, S. H. Kleinstein, R. A. McDougal

The paper develops a pipeline to retrieve and classify COVID-19 immune signatures from scientific literature using document embeddings and manual validation.

bioRxiv · Dec 29, 2021 · PreprintImmunology

Elevated N-glycosylation of immunoglobulin G variable regions in myasthenia gravis highlights a commonality across autoantibody-associated diseases

C. Mandel-Brehm, M. L. Fichtner, R. Jiang, V. J. Winton, S. E. Vazquez, M. C. Pham, K. B. Hoehn, N. L. Kelleher, R. J. Nowak, S. H. Kleinstein, M. R. Wilson, J. L. DeRisi, K. C. OConnor

This study identifies elevated N-glycosylation in IgG variable regions in myasthenia gravis patients and shows it is not required for autoantigen binding.

bioRxiv · Mar 6, 2021Immunology

Human B cell lineages engaged by germinal centers following influenza vaccination are measurably evolving

K. B. Hoehn, J. S. Turner, F. I. Miller, R. Jiang, O. G. Pybus, A. H. Ellebedy, S. H. Kleinstein

The paper shows that influenza vaccination leads to measurable evolution in B cell lineages engaged by germinal centers, but not in blood lineages.

bioRxiv · Jan 6, 2021Immunology

Phylogenetic analysis of migration, differentiation, and class switching in B cells

K. B. Hoehn, O. G. Pybus, S. H. Kleinstein

The paper develops three summary statistics to infer migration, differentiation, and isotype switching in B cells using BCR sequence data and applies them to HIV and food allergy datasets.

bioRxiv · May 30, 2020Immunology

Immunoglobulin heavy chains are sufficient to determine most B cell clonal relationships

J. Q. Zhou, S. H. Kleinstein

The paper assesses the sufficiency of B cell receptor heavy chains for determining clonal relationships and finds they are sufficient with high confidence.

bioRxiv · Jun 18, 2019Immunology

Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination

K. B. Hoehn, J. A. Vander Heiden, J. Q. Zhou, G. Lunter, O. G. Pybus, S. H. Kleinstein

This study introduces a hierarchical phylogenetic framework to analyze B cell repertoires, revealing age-related changes in SHM motifs and a link between tree length and negative selection.

bioRxiv · Feb 25, 2019Immunology

Performance-optimized partitioning of clonotypes from high-throughput immunoglobulin repertoire sequencing data

N. Nouri, S. H. Kleinstein

The paper introduces a performance-optimized method for partitioning clonotypes from AIRR-seq data, providing user-defined sensitivity and specificity estimates.

bioRxiv · Aug 11, 2017Immunology