sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes

(2023) Kun Wang et al.   NATURE BIOTECHNOLOGY

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

(2023) Adam Gayoso et al.   NATURE METHODS

Germinal centre-driven maturation of B cell response to mRNA vaccination

(2022) Wooseob Kim et al.   NATURE

CellRank for directed single-cell fate mapping

(2022) Marius Lange et al.   NATURE METHODS

Single-cell genomics identifies distinct B1 cell developmental pathways and reveals aging-related changes in the B-cell receptor repertoire

(2022) Yao Luo et al.   Cell and Bioscience

Pandemic, Epidemic, Endemic: B Cell Repertoire Analysis Reveals Unique Anti-Viral Responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus

(2022) Alexander Stewart et al.   Frontiers in Immunology

The humoral response and antibodies against SARS-CoV-2 infection

(2022) Hai Qi et al.   NATURE IMMUNOLOGY

Single-cell profiling of the antigen-specific response to BNT162b2 SARS-CoV-2 RNA vaccine

(2022) Kevin J. Kramer et al.   Nature Communications

Single cell clonal analysis identifies an AID ‐dependent pathway of plasma cell differentiation

(2022) Carmen Gómez‐Escolar et al.   EMBO REPORTS

Lineage tracing reveals B cell antibody class switching is stochastic, cell-autonomous, and tuneable

(2022) Miles B. Horton et al.   IMMUNITY

Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics

(2021) Hamish W. King et al.   Science Immunology

Single-cell multi-omics analysis of the immune response in COVID-19

(2021) Emily Stephenson et al.   NATURE MEDICINE

Pseudocell Tracer—A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination

(2021) Derek Reiman et al.   PLoS Computational Biology

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways

(2021) Alexander Stewart et al.   Frontiers in Immunology

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

RNA velocity—current challenges and future perspectives

(2021) Volker Bergen et al.   Molecular Systems Biology

Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells

(2021) Nimitha R. Mathew et al.   Cell Reports

Integrated single-cell transcriptomics and epigenomics reveals strong germinal center–associated etiology of autoimmune risk loci

(2021) Hamish W. King et al.   Science Immunology

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

Longitudinal Isolation of Potent Near-Germline SARS-CoV-2-Neutralizing Antibodies from COVID-19 Patients

(2020) Christoph Kreer et al.   CELL

An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity

(2020) David R. Glass et al.   IMMUNITY

IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to IgG2b in BXD2 Mice

(2020) Huixian Hong et al.   JOURNAL OF IMMUNOLOGY

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

B Cell Responses: Cell Interaction Dynamics and Decisions

(2019) Jason G. Cyster et al.   CELL

Class-Switch Recombination Occurs Infrequently in Germinal Centers

(2019) Jonathan A. Roco et al.   IMMUNITY

Conformational and Dynamical Effects of Tyr32 Phosphorylation in K-Ras: Molecular Dynamics Simulation and Markov State Models Analysis

(2019) Mohammed Khaled et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE

(2016) Yee Ling Wu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transition path theory analysis of c-Src kinase activation

(2016) Yilin Meng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyester: simulating RNA-seq datasets with differential transcript expression

(2015) Alyssa C. Frazee et al.   BIOINFORMATICS

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

IgH Chain Class Switch Recombination: Mechanism and Regulation

(2014) Janet Stavnezer et al.   JOURNAL OF IMMUNOLOGY

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads

(2012) Wei Li et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Role of Germline Promoters and I Exons in Cytokine-Induced Gene-Specific Class Switch Recombination

(2010) W. A. Dunnick et al.   JOURNAL OF IMMUNOLOGY

The transmembrane activator TACI triggers immunoglobulin class switching by activating B cells through the adaptor MyD88

(2010) Bing He et al.   NATURE IMMUNOLOGY

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis

(2008) X. Brochet et al.   NUCLEIC ACIDS RESEARCH