Advanced model systems and tools for basic and translational human immunology

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes

(2018) Marvin H. Gee et al.   CELL

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

(2018) Peggie Cheung et al.   CELL

Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD

(2018) Renaud Gaujoux et al.   GUT

Modeling the human bone marrow niche in mice: From host bone marrow engraftment to bioengineering approaches

(2018) Ander Abarrategi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

(2018) Etienne Patin et al.   NATURE IMMUNOLOGY

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

Inflammation-on-a-Chip: Probing the Immune System Ex Vivo

(2018) Daniel Irimia et al.   TRENDS IN BIOTECHNOLOGY

Rational Design of Mouse Models for Cancer Research

(2018) Marietta Landgraf et al.   TRENDS IN BIOTECHNOLOGY

A community approach to mortality prediction in sepsis via gene expression analysis

(2018) Timothy E. Sweeney et al.   Nature Communications

The use of humanized mice for studies of viral pathogenesis and immunity

(2018) Florian Douam et al.   Current Opinion in Virology

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

(2018) Victor Ovchinnikov et al.   eLife

Analyzing Immunoglobulin Repertoires

(2018) Neha Chaudhary et al.   Frontiers in Immunology

Modeling Human Antitumor Responses In Vivo Using Umbilical Cord Blood-Engrafted Mice

(2018) Nicholas A. Zumwalde et al.   Frontiers in Immunology

Controlled Human Hookworm Infection: Accelerating Human Hookworm Vaccine Development

(2018) David Diemert et al.   Open Forum Infectious Diseases

Gene annotation bias impedes biomedical research

(2018) Winston A. Haynes et al.   Scientific Reports

Genomic Tools for the Use of Nonhuman Primates in Translational Research

(2017) John D. Harding   ILAR JOURNAL

Elicitation of Robust Tier 2 Neutralizing Antibody Responses in Nonhuman Primates by HIV Envelope Trimer Immunization Using Optimized Approaches

(2017) Matthias Pauthner et al.   IMMUNITY

High-Dimensional Phenotypic Mapping of Human Dendritic Cells Reveals Interindividual Variation and Tissue Specialization

(2017) Marcela Alcántara-Hernández et al.   IMMUNITY

Human Ig knockin mice to study the development and regulation of HIV-1 broadly neutralizing antibodies

(2017) Laurent Verkoczy et al.   IMMUNOLOGICAL REVIEWS

Genetic engineering in nonhuman primates for human disease modeling

(2017) Kenya Sato et al.   JOURNAL OF HUMAN GENETICS

Vaccine-draining lymph nodes of cancer patients for generating anti-cancer antibodies

(2017) Girja S. Shukla et al.   Journal of Translational Medicine

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

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

(2017) Alexander C. Huang et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

(2017) Mikhail Shugay et al.   NUCLEIC ACIDS RESEARCH

Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges

(2017) Barbara Piasecka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Humanized mouse model supports development, function, and tissue residency of human natural killer cells

(2017) Dietmar Herndler-Brandstetter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solving Immunology?

(2017) Yoram Vodovotz et al.   TRENDS IN IMMUNOLOGY

Disease Modeling in Stem Cell-Derived 3D Organoid Systems

(2017) Devanjali Dutta et al.   TRENDS IN MOLECULAR MEDICINE

The in vitro MIMIC® platform reflects age-associated changes in immunological responses after influenza vaccination

(2017) Allison Dauner et al.   VACCINE

The comparative immunology of wild and laboratory mice, Mus musculus domesticus

(2017) Stephen Abolins et al.   Nature Communications

Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids

(2017) Russell W. Jenkins et al.   Cancer Discovery

Mass Cytometry and Topological Data Analysis Reveal Immune Parameters Associated with Complications after Allogeneic Stem Cell Transplantation

(2017) Tadepally Lakshmikanth et al.   Cell Reports

Impact of CD4+ T Cell Responses on Clinical Outcome following Oral Administration of Wild-Type Enterotoxigenic Escherichia coli in Humans

(2017) Monica A. McArthur et al.   PLoS Neglected Tropical Diseases

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Importance of Salmonella Typhi-Responsive CD8+ T Cell Immunity in a Human Typhoid Fever Challenge Model

(2017) Stephanie Fresnay et al.   Frontiers in Immunology

Identifying baseline immune-related biomarkers to predict clinical outcome of immunotherapy

(2017) Sacha Gnjatic et al.   Journal for ImmunoTherapy of Cancer

Modeling Development and Disease with Organoids

(2016) Hans Clevers   CELL

Single-dose Live Oral Cholera Vaccine CVD 103-HgR Protects Against Human Experimental Infection WithVibrio choleraeO1 El Tor

(2016) Wilbur H. Chen et al.   CLINICAL INFECTIOUS DISEASES

Nonhuman primate models of transplant tolerance

(2016) William H. Kitchens et al.   Current Opinion in Organ Transplantation

Standardization and quality control for high-dimensional mass cytometry studies of human samples

(2016) Katja Kleinsteuber et al.   CYTOMETRY PART A

Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability

(2016) Bernhard Mlecnik et al.   IMMUNITY

Inherited CD70 deficiency in humans reveals a critical role for the CD70–CD27 pathway in immunity to Epstein-Barr virus infection

(2016) Kazushi Izawa et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genome editing in nonhuman primates: approach to generating human disease models

(2016) Y. Chen et al.   JOURNAL OF INTERNAL MEDICINE

Using animal models to overcome temporal, spatial and combinatorial challenges in HIV persistence research

(2016) Paul W. Denton et al.   Journal of Translational Medicine

Salmonella Typhi-specific multifunctional CD8+ T cells play a dominant role in protection from typhoid fever in humans

(2016) Stephanie Fresnay et al.   Journal of Translational Medicine

The intercell dynamics of T cells and dendritic cells in a lymph node-on-a-chip flow device

(2016) Patrícia Moura Rosa et al.   LAB ON A CHIP

Normalizing the environment recapitulates adult human immune traits in laboratory mice

(2016) Lalit K. Beura et al.   NATURE

Ageing, neurodegeneration and brain rejuvenation

(2016) Tony Wyss-Coray   NATURE

Highly multiplexed simultaneous detection of RNAs and proteins in single cells

(2016) Andreas P Frei et al.   NATURE METHODS

Immuno-engineered organoids for regulating the kinetics of B-cell development and antibody production

(2016) Alberto Purwada et al.   Nature Protocols

Methods to increase reproducibility in differential gene expression via meta-analysis

(2016) Timothy E. Sweeney et al.   NUCLEIC ACIDS RESEARCH

Priming HIV-1 broadly neutralizing antibody precursors in human Ig loci transgenic mice

(2016) D. Sok et al.   SCIENCE

Diversification of the antigen-specific T cell receptor repertoire after varicella zoster vaccination

(2016) Qian Qi et al.   Science Translational Medicine

The Importance of Understanding MHC-I Diversity in Nonhuman Primate Models of Human Infectious Diseases

(2016) Nicholas J. Maness   TOXICOLOGIC PATHOLOGY

Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade

(2016) P.-L. Chen et al.   Cancer Discovery

Direct Probing of Germinal Center Responses Reveals Immunological Features and Bottlenecks for Neutralizing Antibody Responses to HIV Env Trimer

(2016) Colin Havenar-Daughton et al.   Cell Reports

Using a Human Challenge Model of Infection to Measure Vaccine Efficacy: A Randomised, Controlled Trial Comparing the Typhoid Vaccines M01ZH09 with Placebo and Ty21a

(2016) Thomas C. Darton et al.   PLoS Neglected Tropical Diseases

Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis

(2016) Timothy E Sweeney et al.   Lancet Respiratory Medicine

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

(2016) Greg Finak et al.   Scientific Reports

A multiscale computational model predicts distribution of anti-angiogenic isoform VEGF165b in peripheral arterial disease in human and mouse

(2016) Liang-Hui Chu et al.   Scientific Reports

Effects of endothelial cell proliferation and migration rates in a computational model of sprouting angiogenesis

(2016) Kerri-Ann Norton et al.   Scientific Reports

Multiplex Serum Cytokine Immunoassay Using Nanoplasmonic Biosensor Microarrays

(2015) Pengyu Chen et al.   ACS Nano

Ex vivo engineered immune organoids for controlled germinal center reactions

(2015) Alberto Purwada et al.   BIOMATERIALS

Variation in the Human Immune System Is Largely Driven by Non-Heritable Influences

(2015) Petter Brodin et al.   CELL

Multiparameter analysis of stimulated human peripheral blood mononuclear cells: A comparison of mass and fluorescence cytometry

(2015) Katherine J. Nicholas et al.   CYTOMETRY PART A

Modeling mouse and human development using organoid cultures

(2015) M. Huch et al.   DEVELOPMENT

Immunology studies in non-human primate models of tuberculosis

(2015) JoAnne L. Flynn et al.   IMMUNOLOGICAL REVIEWS

Fine-Needle Aspiration Biopsy of the Lymph Node: A Novel Tool for the Monitoring of Immune Responses after Skin Antigen Delivery

(2015) Danijela Tatovic et al.   JOURNAL OF IMMUNOLOGY

Single-dose attenuated Vesiculovax vaccines protect primates against Ebola Makona virus

(2015) Chad E. Mire et al.   NATURE

Combination cancer immunotherapies tailored to the tumour microenvironment

(2015) Mark J. Smyth et al.   Nature Reviews Clinical Oncology

The laboratory mouse and wild immunology

(2015) M. Viney et al.   PARASITE IMMUNOLOGY

An Ebola whole-virus vaccine is protective in nonhuman primates

(2015) A. Marzi et al.   SCIENCE

Why Build Whole-Cell Models?

(2015) Javier Carrera et al.   TRENDS IN CELL BIOLOGY

Ethical Criteria for Human Challenge Studies in Infectious Diseases: Table 1.

(2015) Ben Bambery et al.   Public Health Ethics

Evaluating Human T-Cell Therapy of Cytomegalovirus Organ Disease in HLA-Transgenic Mice

(2015) Simone Thomas et al.   PLoS Pathogens

Lessons from the analysis of nonhuman primates for understanding human aging and neurodegenerative diseases

(2015) Jean-Michel Verdier et al.   Frontiers in Neuroscience

Individuality and Variation of Personal Regulomes in Primary Human T Cells

(2015) Kun Qu et al.   Cell Systems

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

Spatiotemporal Basis of Innate and Adaptive Immunity in Secondary Lymphoid Tissue

(2014) Hai Qi et al.   Annual Review of Cell and Developmental Biology

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

(2014) Michael E. Birnbaum et al.   CELL

An Outpatient, Ambulant-Design, Controlled Human Infection Model Using Escalating Doses of Salmonella Typhi Challenge Delivered in Sodium Bicarbonate Solution

(2014) Claire S. Waddington et al.   CLINICAL INFECTIOUS DISEASES

Validation of the Wild-type Influenza A Human Challenge Model H1N1pdMIST: An A(H1N1)pdm09 Dose-Finding Investigational New Drug Study

(2014) Matthew J. Memoli et al.   CLINICAL INFECTIOUS DISEASES

Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis

(2014) Johannes Trück et al.   JOURNAL OF IMMUNOLOGY

Controlled Human Malaria Infection

(2014) M. Spring et al.   JOURNAL OF INFECTIOUS DISEASES

A functional microengineered model of the human splenon-on-a-chip

(2014) L. G. Rigat-Brugarolas et al.   LAB ON A CHIP

Preclinical research: Make mouse studies work

(2014) Steve Perrin   NATURE

The present and future role of microfluidics in biomedical research

(2014) Eric K. Sackmann et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Development and function of human innate immune cells in a humanized mouse model

(2014) Anthony Rongvaux et al.   NATURE BIOTECHNOLOGY

Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery

(2014) E-Chiang Lee et al.   NATURE BIOTECHNOLOGY

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Mice are not men

(2014) H. Shaw Warren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models

(2014) Denise E. Kirschner et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

High-throughput detection of miRNAs and gene-specific mRNA at the single-cell level by flow cytometry

(2014) Filippos Porichis et al.   Nature Communications

Modeling Tuberculosis in Nonhuman Primates

(2014) C. A. Scanga et al.   Cold Spring Harbor Perspectives in Medicine

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

An introduction to mass cytometry: fundamentals and applications

(2013) Scott D. Tanner et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Dietary gluten triggers concomitant activation of CD4+ and CD8+    T cells and    T cells in celiac disease

(2013) A. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human lymphohematopoietic reconstitution and immune function in immunodeficient mice receiving cotransplantation of human thymic tissue and CD34+ cells

(2012) Zheng Hu et al.   Cellular & Molecular Immunology

Clinical, scientific and ethnographic studies of influenza in quarantine

(2012) John S Oxford et al.   Expert Review of Vaccines

Maintenance of Peripheral Naive T Cells Is Sustained by Thymus Output in Mice but Not Humans

(2012) Ineke den Braber et al.   IMMUNITY

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

(2012) Taheri Sathaliyawala et al.   IMMUNITY

Three-dimensional microfluidic model for tumor cell intravasation and endothelial barrier function

(2012) I. K. Zervantonakis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A deep profiler's guide to cytometry

(2012) Sean C. Bendall et al.   TRENDS IN IMMUNOLOGY

Follicular Helper CD4 T Cells (TFH)

(2011) Shane Crotty   Annual Review of Immunology

Mice with human immune system components as in vivo models for infections with human pathogens

(2011) Patrick C Rämer et al.   IMMUNOLOGY AND CELL BIOLOGY

In-vitro derived germinal centre B cells differentially generate memory B or plasma cells in vivo

(2011) Takuya Nojima et al.   Nature Communications

Immune regulation of multiple sclerosis by transdermally applied myelin peptides

(2010) Maciej Juryńczyk et al.   ANNALS OF NEUROLOGY

Assessing the human immune system through blood transcriptomics

(2010) Damien Chaussabel et al.   BMC BIOLOGY

Monoclonal antibody TGN1412 trial failure explained by species differences in CD28 expression on CD4+ effector memory T-cells

(2010) D Eastwood et al.   BRITISH JOURNAL OF PHARMACOLOGY

Primate testing of TGN1412: right target, wrong cell

(2010) M Pallardy et al.   BRITISH JOURNAL OF PHARMACOLOGY

Parameters for establishing humanized mouse models to study human immunity: Analysis of human hematopoietic stem cell engraftment in three immunodeficient strains of mice bearing the IL2rγnull mutation

(2010) Michael A. Brehm et al.   CLINICAL IMMUNOLOGY

T cells and follicular dendritic cells in germinal center B-cell formation and selection

(2010) Carola G. Vinuesa et al.   IMMUNOLOGICAL REVIEWS

A model for harmonizing flow cytometry in clinical trials

(2010) Holden T Maecker et al.   NATURE IMMUNOLOGY

Clinical microfluidics for neutrophil genomics and proteomics

(2010) Kenneth T Kotz et al.   NATURE MEDICINE

In vitro antibody response to tetanus in the MIMIC™ system is a representative measure of vaccine immunogenicity

(2009) Anthony M. Byers et al.   BIOLOGICALS

In Situ Cytotoxic and Memory T Cells Predict Outcome in Patients With Early-Stage Colorectal Cancer

(2009) Franck Pagès et al.   JOURNAL OF CLINICAL ONCOLOGY

Clinical Outcomes of Elite Controllers, Viremic Controllers, and Long‐Term Nonprogressors in the US Department of Defense HIV Natural History Study

(2009) Jason F. Okulicz et al.   JOURNAL OF INFECTIOUS DISEASES

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Time Lines of Infection and Disease in Human Influenza: A Review of Volunteer Challenge Studies

(2008) Fabrice Carrat et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Use of humanized severe combined immunodeficient mice for human vaccine development

(2008) Gloria C Koo et al.   Expert Review of Vaccines

Validation and comparison of two multiplex technologies, Luminex® and Mesoscale Discovery, for human cytokine profiling

(2008) Ferdousi Chowdhury et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Tissue-Engineered Spleen Protects Against Overwhelming Pneumococcal Sepsis in a Rodent Model

(2008) Tracy C. Grikscheit et al.   JOURNAL OF SURGICAL RESEARCH

Nonhuman primate models and the failure of the Merck HIV-1 vaccine in humans

(2008) David I Watkins et al.   NATURE MEDICINE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS