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Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data

PLoS computational biology, 2020-06, Vol.16 (6), p.e1007977-e1007977

2020

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Practical guidelines for B-cell receptor repertoire sequencing analysis

Genome medicine, 2015-11, Vol.7 (120), p.121-121, Article 121

2015

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A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data

Bioinformatics, 2018-07, Vol.34 (13), p.i341-i349

2018

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Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data

Bioinformatics, 2015-10, Vol.31 (20), p.3356-3358

2015

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Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

Proceedings of the National Academy of Sciences - PNAS, 2015-02, Vol.112 (8), p.E862-E870

2015

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

PLoS computational biology, 2022-04, Vol.18 (4), p.e1009885-e1009885

2022

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Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses

Cell, 2015-09, Vol.162 (6), p.1217-1228

2015

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Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation

Immunity (Cambridge, Mass.), 2015-07, Vol.43 (1), p.120-131

2015

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Language model-based B cell receptor sequence embeddings can effectively encode receptor specificity

Nucleic acids research, 2024-01, Vol.52 (2), p.548-557

2024

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Quantifying selection in high-throughput Immunoglobulin sequencing data sets

Nucleic acids research, 2012-09, Vol.40 (17), p.e134-e134

2012

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Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders

Science (American Association for the Advancement of Science), 2021-07, Vol.373 (6553)

2021

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Migrant memory B cells secrete luminal antibody in the vagina

Nature (London), 2019-07, Vol.571 (7763), p.122-126

2019

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Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4 + Cell Properties during Viral Infection

Immunity (Cambridge, Mass.), 2011-10, Vol.35 (4), p.633-646

2011

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Polycomb Repressive Complex 2-Mediated Chromatin Repression Guides Effector CD8+ T Cell Terminal Differentiation and Loss of Multipotency

Immunity (Cambridge, Mass.), 2017-04, Vol.46 (4), p.596-608

2017

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Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations

Nucleic acids research, 2013-10, Vol.41 (18), p.e170-e170

2013

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Germinal Center B Cell and T Follicular Helper Cell Development Initiates in the Interfollicular Zone

Immunity (Cambridge, Mass.), 2011-06, Vol.34 (6), p.947-960

2011

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pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

Bioinformatics (Oxford, England), 2014-07, Vol.30 (13), p.1930-1932

2014

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Dynamic expression profiling of type I and type III interferon‐stimulated hepatocytes reveals a stable hierarchy of gene expression

Hepatology (Baltimore, Md.), 2014-04, Vol.59 (4), p.1262-1272

2014

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Cutting Edge: Ig H Chains Are Sufficient to Determine Most B Cell Clonal Relationships

The Journal of immunology (1950), 2019-10, Vol.203 (7), p.1687-1692

2019

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B cell phylogenetics in the single cell era

Trends in immunology, 2024-01, Vol.45 (1), p.62-74

2024

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The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection

The Journal of experimental medicine, 2015-11, Vol.212 (12), p.2041-2056

2015

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Alignment free identification of clones in B cell receptor repertoires

Nucleic acids research, 2021-02, Vol.49 (4), p.e21-e21

2021

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B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes

Science translational medicine, 2014-08, Vol.6 (248), p.248ra107

2014

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

Proceedings of the National Academy of Sciences - PNAS, 2019-11, Vol.116 (45), p.22664-22672

2019

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Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006899-e1006899

2019

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Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data

Practical guidelines for B-cell receptor repertoire sequencing analysis

A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

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

Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses

Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation

Language model-based B cell receptor sequence embeddings can effectively encode receptor specificity

Quantifying selection in high-throughput Immunoglobulin sequencing data sets

Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders

Migrant memory B cells secrete luminal antibody in the vagina

Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4 + Cell Properties during Viral Infection

Polycomb Repressive Complex 2-Mediated Chromatin Repression Guides Effector CD8+ T Cell Terminal Differentiation and Loss of Multipotency

Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations

Germinal Center B Cell and T Follicular Helper Cell Development Initiates in the Interfollicular Zone

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

Dynamic expression profiling of type I and type III interferon‐stimulated hepatocytes reveals a stable hierarchy of gene expression

Cutting Edge: Ig H Chains Are Sufficient to Determine Most B Cell Clonal Relationships

B cell phylogenetics in the single cell era

The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection

Alignment free identification of clones in B cell receptor repertoires

B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes

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

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)

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