Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires
出版年份 2018 全文链接
标题
Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires
作者
关键词
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出版物
Frontiers in Immunology
Volume 9, Issue -, Pages -
出版商
Frontiers Media SA
发表日期
2018-02-21
DOI
10.3389/fimmu.2018.00224
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- A Phylogenetic Codon Substitution Model for Antibody Lineages
- (2017) Kenneth B. Hoehn et al. GENETICS
- On being the right size: antibody repertoire formation in the mouse and human
- (2017) Andrew M. Collins et al. IMMUNOGENETICS
- Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering
- (2017) Cristina Parola et al. IMMUNOLOGY
- B-cell receptor repertoire sequencing in patients with primary immunodeficiency: a review
- (2017) Marie Ghraichy et al. IMMUNOLOGY
- Antibody-secreting plasma cells persist for decades in human intestine
- (2017) Ole J.B. Landsverk et al. JOURNAL OF EXPERIMENTAL MEDICINE
- Comment on “A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data”
- (2017) Corey T. Watson et al. JOURNAL OF IMMUNOLOGY
- A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data
- (2017) Yaxuan Yu et al. JOURNAL OF IMMUNOLOGY
- Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads
- (2017) Alexander Shlemov et al. JOURNAL OF IMMUNOLOGY
- Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data
- (2017) Namita T. Gupta et al. JOURNAL OF IMMUNOLOGY
- Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires
- (2017) Victor Greiff et al. JOURNAL OF IMMUNOLOGY
- Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery
- (2017) Ufuk Kirik et al. MOLECULAR IMMUNOLOGY
- Quantifiable predictive features define epitope-specific T cell receptor repertoires
- (2017) Pradyot Dash et al. NATURE
- Identifying specificity groups in the T cell receptor repertoire
- (2017) Jacob Glanville et al. NATURE
- An atlas of B-cell clonal distribution in the human body
- (2017) Wenzhao Meng et al. NATURE BIOTECHNOLOGY
- Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire
- (2017) Ryan O Emerson et al. NATURE GENETICS
- VDJdb: a curated database of T-cell receptor sequences with known antigen specificity
- (2017) Mikhail Shugay et al. NUCLEIC ACIDS RESEARCH
- Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging
- (2017) Charles F. A. de Bourcy et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Single-cell transcriptomics to explore the immune system in health and disease
- (2017) Michael J. T. Stubbington et al. SCIENCE
- Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires
- (2017) Simon Friedensohn et al. TRENDS IN BIOTECHNOLOGY
- The Individual and Population Genetics of Antibody Immunity
- (2017) Corey T. Watson et al. TRENDS IN IMMUNOLOGY
- Novel Approaches to Analyze Immunoglobulin Repertoires
- (2017) Hedda Wardemann et al. TRENDS IN IMMUNOLOGY
- Strong Clonal Relatedness between Serum and Gut IgA despite Different Plasma Cell Origins
- (2017) Rasmus Iversen et al. Cell Reports
- Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics
- (2017) Jing Chen et al. Cell Reports
- Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development
- (2017) Victor Greiff et al. Cell Reports
- T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences
- (2017) Asaf Madi et al. eLife
- A Phylogenetic Codon Substitution Model for Antibody Lineages
- (2017) Kenneth B. Hoehn et al. GENETICS
- Functionally Convergent B Cell Receptor Sequences in Transgenic Rats Expressing a Human B Cell Repertoire in Response to Tetanus Toxoid and Measles Antigens
- (2017) Jean-Philippe Bürckert et al. Frontiers in Immunology
- Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile
- (2017) Theres Oakes et al. Frontiers in Immunology
- Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses
- (2017) Ilja V. Khavrutskii et al. Frontiers in Immunology
- Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics
- (2017) Martijn M. VanDuijn et al. Frontiers in Immunology
- Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization
- (2017) Yuxin Sun et al. Frontiers in Immunology
- Quantification of Inter-Sample Differences in T-Cell Receptor Repertoires Using Sequence-Based Information
- (2017) Ryo Yokota et al. Frontiers in Immunology
- Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation
- (2017) Zizhang Sheng et al. Frontiers in Immunology
- Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data
- (2017) Felix Breden et al. Frontiers in Immunology
- The chronically inflamed central nervous system provides niches for long-lived plasma cells
- (2017) Karolin Pollok et al. Acta Neuropathologica Communications
- A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data
- (2017) Leonard Apeltsin et al. Scientific Reports
- repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
- (2016) Yuval Elhanati et al. BIOINFORMATICS
- Deep sequencing and human antibody repertoire analysis
- (2016) Scott D Boyd et al. CURRENT OPINION IN IMMUNOLOGY
- A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data
- (2016) Ang Cui et al. JOURNAL OF IMMUNOLOGY
- Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution
- (2016) Michelle Kendall et al. MOLECULAR BIOLOGY AND EVOLUTION
- The Diversity and Molecular Evolution of B-Cell Receptors during Infection
- (2016) Kenneth B. Hoehn et al. MOLECULAR BIOLOGY AND EVOLUTION
- MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
- (2016) Sudhir Kumar et al. MOLECULAR BIOLOGY AND EVOLUTION
- Applications of Deep Learning in Biomedicine
- (2016) Polina Mamoshina et al. MOLECULAR PHARMACEUTICS
- Deep learning for computational biology
- (2016) Christof Angermueller et al. Molecular Systems Biology
- Landscape of tumor-infiltrating T cell repertoire of human cancers
- (2016) Bo Li et al. NATURE GENETICS
- Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination
- (2016) Ali H Ellebedy et al. NATURE IMMUNOLOGY
- Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination
- (2016) Jiwon Lee et al. NATURE MEDICINE
- T cell fate and clonality inference from single-cell transcriptomes
- (2016) Michael J T Stubbington et al. NATURE METHODS
- Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells
- (2016) Florian Rubelt et al. Nature Communications
- Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity
- (2016) Martin M. Corcoran et al. Nature Communications
- Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples
- (2016) Joseph Kaplinsky et al. Nature Communications
- Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses
- (2016) Ya-Hui Chang et al. Scientific Reports
- System-wide Analysis of the T Cell Response
- (2016) Ruxandra Covacu et al. Cell Reports
- B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation
- (2016) Jacob D. Galson et al. Genome Medicine
- Statistical inference of a convergent antibody repertoire response to influenza vaccine
- (2016) Nicolas B. Strauli et al. Genome Medicine
- Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection
- (2016) Zizhang Sheng et al. PLoS Computational Biology
- Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
- (2016) Duncan K. Ralph et al. PLoS Computational Biology
- SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts
- (2016) Chaim A. Schramm et al. Frontiers in Immunology
- A Public Database of Memory and Naive B-Cell Receptor Sequences
- (2016) William S. DeWitt et al. PLoS One
- IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity
- (2016) Yuval Avnir et al. Scientific Reports
- IgSimulator: a versatile immunosequencing simulator: Fig. 1.
- (2015) Yana Safonova et al. BIOINFORMATICS
- Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1.
- (2015) Namita T. Gupta et al. BIOINFORMATICS
- tcR: an R package for T cell receptor repertoire advanced data analysis
- (2015) Vadim I. Nazarov et al. BMC BIOINFORMATICS
- Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes
- (2015) Leng-Siew Yeap et al. CELL
- Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection
- (2015) Xueling Wu et al. CELL
- Primary immunoglobulin repertoire development: time and space matter
- (2015) Alessandra Granato et al. CURRENT OPINION IN IMMUNOLOGY
- Serology in the 21st century: the molecular-level analysis of the serum antibody repertoire
- (2015) Yariv Wine et al. CURRENT OPINION IN IMMUNOLOGY
- Long-Lived Plasma Cells Are Contained within the CD19−CD38hiCD138+ Subset in Human Bone Marrow
- (2015) Jessica L. Halliley et al. IMMUNITY
- Analysis of Celiac Disease Autoreactive Gut Plasma Cells and Their Corresponding Memory Compartment in Peripheral Blood Using High-Throughput Sequencing
- (2015) Omri Snir et al. JOURNAL OF IMMUNOLOGY
- High Preexisting Serological Antibody Levels Correlate with Diversification of the Influenza Vaccine Response
- (2015) Sarah F. Andrews et al. JOURNAL OF VIROLOGY
- Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota
- (2015) Cornelia Lindner et al. NATURE IMMUNOLOGY
- MiXCR: software for comprehensive adaptive immunity profiling
- (2015) Dmitriy A Bolotin et al. NATURE METHODS
- The evolution within us
- (2015) Sarah Cobey et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals
- (2015) Kenneth B. Hoehn et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- The analysis of clonal expansions in normal and autoimmune B cell repertoires
- (2015) Uri Hershberg et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Inferring processes underlying B-cell repertoire diversity
- (2015) Yuval Elhanati et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach
- (2015) Daniel J. Laydon et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles
- (2015) Daniel Gadala-Maria et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- High-throughput pairing of T cell receptor α and β sequences
- (2015) Bryan Howie et al. Science Translational Medicine
- Characterizing and Comparing Phylogenies from their Laplacian Spectrum
- (2015) Eric Lewitus et al. SYSTEMATIC BIOLOGY
- Synthetic immunology: modulating the human immune system
- (2015) Barbara Geering et al. TRENDS IN BIOTECHNOLOGY
- Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires
- (2015) Victor Greiff et al. TRENDS IN IMMUNOLOGY
- A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status
- (2015) Victor Greiff et al. Genome Medicine
- Profiling tissue-resident T cell repertoires by RNA sequencing
- (2015) Scott D. Brown et al. Genome Medicine
- Practical guidelines for B-cell receptor repertoire sequencing analysis
- (2015) Gur Yaari et al. Genome Medicine
- Influenza vaccine response profiles are affected by vaccine preparation and preexisting immunity, but not HIV infection
- (2015) Christoph T Berger et al. Human Vaccines & Immunotherapeutics
- VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
- (2015) Mikhail Shugay et al. PLoS Computational Biology
- Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences
- (2015) Jacob D. Galson et al. EBioMedicine
- Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence
- (2014) Niclas Thomas et al. BIOINFORMATICS
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements
- (2014) Katherine J.L. Jackson et al. Cell Host & Microbe
- T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity
- (2014) Asaf Madi et al. GENOME RESEARCH
- The promise and challenge of high-throughput sequencing of the antibody repertoire
- (2014) George Georgiou et al. NATURE BIOTECHNOLOGY
- Unifying immunology with informatics and multiscale biology
- (2014) Brian A Kidd et al. NATURE IMMUNOLOGY
- Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery
- (2014) William H. Robinson Nature Reviews Rheumatology
- The immune epitope database (IEDB) 3.0
- (2014) Randi Vita et al. NUCLEIC ACIDS RESEARCH
- Zipf’s Law and Criticality in Multivariate Data without Fine-Tuning
- (2014) David J. Schwab et al. PHYSICAL REVIEW LETTERS
- Assessing T Cell Clonal Size Distribution: A Non-Parametric Approach
- (2014) Olesya V. Bolkhovskaya et al. PLoS One
- Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells
- (2014) J. Kaplinsky et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Quantifying selection in immune receptor repertoires
- (2014) Yuval Elhanati et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- B-cell repertoire responses to varicella-zoster vaccination in human identical twins
- (2014) Chen Wang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Identification and characterization of the constituent human serum antibodies elicited by vaccination
- (2014) Jason J. Lavinder et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines
- (2014) S. Becattini et al. SCIENCE
- B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes
- (2014) J. N. H. Stern et al. Science Translational Medicine
- Characterizing immune repertoires by high throughput sequencing: strategies and applications
- (2014) Jorg J.A. Calis et al. TRENDS IN IMMUNOLOGY
- Rphylip: an R interface for PHYLIP
- (2014) Liam J. Revell et al. Methods in Ecology and Evolution
- Quantification of HTLV-1 Clonality and TCR Diversity
- (2014) Daniel J. Laydon et al. PLoS Computational Biology
- BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
- (2014) Remco Bouckaert et al. PLoS Computational Biology
- Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation
- (2013) Corey T. Watson et al. AMERICAN JOURNAL OF HUMAN GENETICS
- TCR Repertoire Analysis by Next Generation Sequencing Allows Complex Differential Diagnosis of T Cell-Related Pathology
- (2013) M. Dziubianau et al. AMERICAN JOURNAL OF TRANSPLANTATION
- Convergent Antibody Signatures in Human Dengue
- (2013) Poornima Parameswaran et al. Cell Host & Microbe
- Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations
- (2013) Rachael J.M. Bashford-Rogers et al. GENOME RESEARCH
- Sequencing of modern Lepus VDJ genes shows that the usage of VHn genes has been retained in both Oryctolagus and Lepus that diverged 12 million years ago
- (2013) Ana Pinheiro et al. IMMUNOGENETICS
- High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire
- (2013) Brandon J DeKosky et al. NATURE BIOTECHNOLOGY
- Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response
- (2013) Y. Wine et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains
- (2013) J. Zhu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Huge Overlap of Individual TCR Beta Repertoires
- (2013) Mikhail Shugay et al. Frontiers in Immunology
- Models of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data
- (2013) Gur Yaari et al. Frontiers in Immunology
- A minimal model of peptide binding predicts ensemble properties of serum antibodies
- (2012) Victor Greiff et al. BMC GENOMICS
- Wrestling with the repertoire: The promise and perils of next generation sequencing for antigen receptors
- (2012) Paul D. Baum et al. EUROPEAN JOURNAL OF IMMUNOLOGY
- Methods for diversity and overlap analysis in T-cell receptor populations
- (2012) Grzegorz A. Rempala et al. JOURNAL OF MATHEMATICAL BIOLOGY
- Molecular phylogenetics: principles and practice
- (2012) Ziheng Yang et al. NATURE REVIEWS GENETICS
- T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks
- (2012) A. Boc et al. NUCLEIC ACIDS RESEARCH
- Statistical inference of the generation probability of T-cell receptors from sequence repertoires
- (2012) A. Murugan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features
- (2011) Rotem Ben-Hamo et al. BMC Systems Biology
- Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes
- (2011) R. L. Warren et al. GENOME RESEARCH
- The Inference of Phased Haplotypes for the Immunoglobulin H Chain V Region Gene Loci by Analysis of VDJ Gene Rearrangements
- (2011) M. J. Kidd et al. JOURNAL OF IMMUNOLOGY
- Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation
- (2011) J. Glanville et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- phangorn: phylogenetic analysis in R
- (2010) Klaus Peter Schliep BIOINFORMATICS
- Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements
- (2010) S. D. Boyd et al. JOURNAL OF IMMUNOLOGY
- Model for comparative analysis of antigen receptor repertoires
- (2010) Grzegorz A. Rempala et al. JOURNAL OF THEORETICAL BIOLOGY
- Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells
- (2010) Sai T Reddy et al. NATURE BIOTECHNOLOGY
- By-passing in vitro screening—next generation sequencing technologies applied to antibody display and in silico candidate selection
- (2010) U. Ravn et al. NUCLEIC ACIDS RESEARCH
- Maximum entropy models for antibody diversity
- (2010) T. Mora et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire
- (2009) J. Glanville et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- High-Throughput Sequencing of the Zebrafish Antibody Repertoire
- (2009) J. A. Weinstein et al. SCIENCE
- IgTree©: Creating Immunoglobulin variable region gene lineage trees
- (2008) Michal Barak et al. JOURNAL OF IMMUNOLOGICAL METHODS
- Method for assessing the similarity between subsets of the T cell receptor repertoire
- (2007) Vanessa Venturi et al. JOURNAL OF IMMUNOLOGICAL METHODS
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