ArticleBioinformatics (Oxford, England)2014
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.
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Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 318 papers.
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318citing papers in PubMed
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Who cites it
318 citing papers in PubMed.
- Single-cell analysis of skin and blood reveals systemic immune responses to ultraviolet B and their impairment in MS.Journal of neuroinflammation · 2026Trial
- Computational mining of B cell receptor repertoires reveals antigen-specific and convergent responses to Ebola vaccination.Frontiers in immunology · 2024Trial
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- Single-Cell Level Characterization of B Cell Depletion and Repopulation Following Rituximab in Systemic Lupus Erythematosus.Arthritis & rheumatology (Hoboken, N.J.) · 2026Article
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- SPEN Loss Drives Extrafollicular Diffuse Large B-cell Lymphoma with Female-Specific Lethality and Therapeutic Vulnerabilities.Cancer discovery · 2026Article
- mRNA-based influenza vaccine expands the B cell response breadth in humans.Nature immunology · 2026Observational
- Variant-specific spike conformational dynamics shape memory B cell selection during recall.bioRxiv : the preprint server for biology · 2026Article
- Central nervous system B cell multiomics reveals a legacy of immune dysregulation in long-term treated HIV infection.Science advances · 2026Article
- Maternal vaccination timing shapes the composition and maturation of antibody clonotypes transferred to the newborn.bioRxiv : the preprint server for biology · 2026Article
- Multiomic analysis identifies glutaminolysis-dependent metabolic enhancement of immune memory utilised for vaccine development.Nature communications · 2026Article
- Affinity-matured B cell responses neutralizing type-I interferons underlie severe viral infections.Cell · 2026Article
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- Reprogramming Dedifferentiation Regulatory Networks Preserves Human Chondrocyte Phenotypes.bioRxiv : the preprint server for biology · 2026Article
- Extensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugs.Journal of neuroinflammation · 2026Article
- Comprehensive Mapping of Immune Nanobody Repertoires with NanoMAP.bioRxiv : the preprint server for biology · 2026Article
- Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease.JCI insight · 2026Article
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- Somatic deficiency of the human E3 ubiquitin ligase CBL in leukocytes impairs B cell but not T cell development and function.Nature immunology · 2026Article
- Allergen-specific human IgE isolated through an allergen-agnostic pipeline-understanding immune response and allergen recognition.Communications biology · 2026Article
258 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Jason A Vander HeidenInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.
Gur YaariInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USAInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.
Mohamed UdumanInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USAInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.
Joel N H SternInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USAInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USAInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.
Kevin C O'ConnorInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USAInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.
David A HaflerInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USAInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.
Francois VigneaultInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.
Steven H KleinsteinInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USAInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.
Funding
Systems investigation of vaccine responses in B cell depleted autoimmune patientsU19AI089992 · NIAID · YALE UNIVERSITY · PI David A. Hafler, RUTH R MONTGOMERY · 2010 to 2026
$50.4MVirginia Mason/UCHSC Autoimmune Prevention CenterU19AI050864 · NIAID · UNIVERSITY OF COLORADO DENVER · PI EISENBARTH, GEORGE S · 2001 to 2011
$29.2MMEDICAL INFORMATICS RESEARCH TRAINING AT YALET15LM007056 · NLM · YALE UNIVERSITY · PI Mark Bender Gerstein, LUCILA OHNO-MACHADO · 1987 to 2026
$22.2MThe role of the innate immune system on Treg reprogramming in human autoimmune diU01AI102011 · NIAID · YALE UNIVERSITY · PI HAFLER, DAVID A., HEROLD, KEVAN C · 2012 to 2016
$3.8MYALE BIOMEDICAL SUPERCOMPUTER: NEUROSCIENCES10RR019895 · NCRR · YALE UNIVERSITY · PI WILLIAMS, KENNETH ROBERT · 2004 to 2004
$1.6MHuman and Translational ImmunologyT32AI089704 · NIAID · YALE UNIVERSITY · PI HEROLD, KEVAN C · 2010 to 2014
$994kNCRR NIH HHS RR19895NCRR NIH HHS S10 RR019895NIAID NIH HHS T32 AI089704NIAID NIH HHS U01 AI102011NIAID NIH HHS U19 AI050864NIAID NIH HHS U19AI050864NIAID NIH HHS U19 AI089992NIAID NIH HHS U19AI089992NLM NIH HHS T15 LM007056NLM NIH HHS T15 LM07056
Abstract
unlabelledDriven by dramatic technological improvements, large-scale characterization of lymphocyte receptor repertoires via high-throughput sequencing is now feasible. Although promising, the high germline and somatic diversity, especially of B-cell immunoglobulin repertoires, presents challenges for analysis requiring the development of specialized computational pipelines. We developed the REpertoire Sequencing TOolkit (pRESTO) for processing reads from high-throughput lymphocyte receptor studies. pRESTO processes raw sequences to produce error-corrected, sorted and annotated sequence sets, along with a wealth of metrics at each step. The toolkit supports multiplexed primer pools, single- or paired-end reads and emerging technologies that use single-molecule identifiers. pRESTO has been tested on data generated from Roche and Illumina platforms. It has a built-in capacity to parallelize the work between available processors and is able to efficiently process millions of sequences generated by typical high-throughput projects. AVAILABILITY AND IMPLEMENTATION: pRESTO is freely available for academic use. The software package and detailed tutorials may be downloaded from http://clip.med.yale.edu/presto.
Indexed as
High-Throughput Nucleotide SequencingLymphocytesReceptors, ImmunologicSequence Analysis, DNASequence Analysis, RNASoftwareReceptors, Immunologic
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