Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

(2019) Nathaniel D. Chu et al.   BMC IMMUNOLOGY

Dependence of CD8 T Cell Response upon Antigen Load During Primary Infection

(2019) James R. Moore et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Killer-like receptors and GPR56 progressive expression defines cytokine production of human CD4+ memory T cells

(2019) Kim-Long Truong et al.   Nature Communications

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

High-throughput determination of the antigen specificities of T cell receptors in single cells

(2018) Shu-Qi Zhang et al.   NATURE BIOTECHNOLOGY

Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins

(2018) Mikhail V. Pogorelyy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Origin and differentiation of human memory CD8 T cells after vaccination

(2017) Rama S. Akondy et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes

(2017) Tyler Borrman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

(2017) Mikhail V. Pogorelyy et al.   PLoS Computational Biology

Adaptive immune responses to booster vaccination against yellow fever virus are much reduced compared to those after primary vaccination

(2017) Michael Kongsgaard et al.   Scientific Reports

CCR7 expression alters memory CD8 T-cell homeostasis by regulating occupancy in IL-7– and IL-15–dependent niches

(2016) Yong Woo Jung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Single 17D Yellow Fever Vaccination Provides Lifelong Immunity; Characterization of Yellow-Fever-Specific Neutralizing Antibody and T-Cell Responses after Vaccination

(2016) Rosanne W. Wieten et al.   PLoS One

Dynamics of the Cytotoxic T Cell Response to a Model of Acute Viral Infection

(2015) William S. DeWitt et al.   JOURNAL OF VIROLOGY

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Initial viral load determines the magnitude of the human CD8 T cell response to yellow fever vaccination

(2015) Rama S. Akondy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-lasting stem cell–like memory CD8 + T cells with a naïve-like profile upon yellow fever vaccination

(2015) Silvia A. Fuertes Marraco et al.   Science Translational Medicine

Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life

(2014) Joseph J.C. Thome et al.   CELL

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

Temporal Dynamics of the Primary Human T Cell Response to Yellow Fever Virus 17D As It Matures from an Effector- to a Memory-Type Response

(2013) K. Blom et al.   JOURNAL OF IMMUNOLOGY

Yellow Fever Vaccination Elicits Broad Functional CD4+T Cell Responses That Recognize Structural and Nonstructural Proteins

(2013) Eddie A. James et al.   JOURNAL OF VIROLOGY

T-Cell Memory Responses Elicited by Yellow Fever Vaccine are Targeted to Overlapping Epitopes Containing Multiple HLA-I and -II Binding Motifs

(2013) Andréa Barbosa de Melo et al.   PLoS Neglected Tropical Diseases

The early cellular signatures of protective immunity induced by live viral vaccination

(2012) Siegfried Kohler et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Distribution and Compartmentalization of Human Circulating and Tissue-Resident Memory T Cell Subsets

(2012) Taheri Sathaliyawala et al.   IMMUNITY

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

A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes

(2012) Brian G. Pierce et al.   PROTEIN SCIENCE

Differentiation and Persistence of Memory CD8+ T Cells Depend on T Cell Factor 1

(2010) Xinyuan Zhou et al.   IMMUNITY

Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory

(2010) G. Jeannet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The Yellow Fever Virus Vaccine Induces a Broad and Polyfunctional Human Memory CD8+ T Cell Response

(2009) R. S. Akondy et al.   JOURNAL OF IMMUNOLOGY

Distinct Profiles of Cytotoxic Granules in Memory CD8 T Cells Correlate with Function, Differentiation Stage, and Antigen Exposure

(2009) A. Harari et al.   JOURNAL OF VIROLOGY

Phenotype and function of human T lymphocyte subsets: Consensus and issues

(2008) Victor Appay et al.   CYTOMETRY PART A

Human Effector and Memory CD8+ T Cell Responses to Smallpox and Yellow Fever Vaccines

(2008) Joseph D. Miller et al.   IMMUNITY

The RosettaDock server for local protein-protein docking

(2008) S. Lyskov et al.   NUCLEIC ACIDS RESEARCH