Publications

Indexed Online

You can easily access our publications online via PubMed or Google Scholar.

Detailed lists can also be found on some of the personal pages of our lab members, as well as the page of Dr. Jim Heath.

Recent Publications

A large-scale database of T-cell receptor beta sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Frontiers in Immunology, 2025

Keywords: COVID-19 SARS-CoV-2 T cel TCR repertoire cellular immunity immune response

Disease diagnostics using machine learning of B cell and T cell receptor sequences

Science, 2025

Keywords: Immune receptors B cells T cells BCR TCR machine learning Mal-ID autoimmune disorders vaccine responses COVID-19 HIV lupus flu type 1 diabetes

CITE-Seq Analysis Reveals a Differential Natural Killer Cell SPON2 Expression in Cardiovascular Disease Patients Impacted by Human-Cytomegalovirus Serostatus and Diabetes

Intl. Journal of Molecular Sciences, 2025

Keywords: SPON2 cardiovascular disease cytomegalovirus diabetes natural killer cells

APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence

Nature Communications, 2025

Keywords: CD8 T cell antigen-TCR pairing APMAT multiomic analysis physicochemical T cell phenotype antigen stimulation COVID-19 SARS-CoV-2

Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels.

Frontiers in Immunology, 2025

Keywords: COVID-19 SARS-CoV-2 T cell TCR repertoire cellular immunity immune response

Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma

Cancer Discovery, 2024

Keywords: Ovarian cancer fallopian tube p53 signatures Serous Tubal Intraepithelial Carcinoma antigen presentation innate immune system Natural Killer cells preneoplasia cancer progression High Grade Serous Ovarian Carcinoma spatial transcriptomics single cell tumor immune interaction multiplex imaging tumor microenvironment homologous recombinant deficient tumor cancer progression

Kinetic Trajectories of Glucose Uptake in Single Cancer Cells Reveal a Drug-Induced Cell-State Change Within Hours of Drug Treatment

The Journal of Physical Chemistry B, 2024

Keywords: cancer carbohydrates cells computational chemistry genetics

Integrated Antigenic and Nucleic Acid Detection in Single Virions and Extracellular Vesicles with Viral Content.

Advanced Healthcare Materials, 2024

Keywords: COVID‐19 multiparametric SARS‐CoV‐2 single extracellular vesicle single virion

Multi-Omic characterization of the effects of Ocrelizumab in patients with relapsing-remitting multiple sclerosis

Neurological Sciences, 2024

Keywords: B-cell activating factor CD20 Ceramide Cytokine signaling Lysophosphatidylcholine Metabolome Multi-omics Neurofilament Ocrelizumab Proteome Relapsing-remitting multiple sclerosis

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Genome Medicine, 2024

Keywords: Rare variants COVID-19 Immunity Type I interferon

Integrative systems biology reveals NKG2A-biased immune responses correlate with protection in infectious disease, autoimmune disease, and cancer

Cell Reports, 2024

Keywords: CD8(+) T cells NKG2A cancer autoimmune disease infectious disease multi-disease plasma proteomics single-cell multi-omics systems immunology

T cell receptor sequences are the dominant factor contributing to the phenotype of CD8⁺ T cells with specificities against immunogenic viral antigensReport

Cell Reports, 2023

Keywords: CD8(+) T cells T cell receptor single-cell multi-omics systems immunology

Organ-specific immunity: A tissue analysis framework for investigating local immune responses to SARS-CoV-2

Cell Reports, 2023

Keywords: COVID-19 SARS-CoV-2 biomarker dendritic cells digital pathology local immunity macrophages mucosal lymphoid tissues post-mortem tissue injury

Non-Mass Spectrometric Targeted Single-Cell Metabolomics

Trends in Analytical Chemistry, 2023

Keywords: Raman microscopy Single-cell metabolism fluorescent metabolic tracer microfluidic chip single-cell amperometry surface chemistry

Researching COVID to Enhance Recovery (RECOVER) adult study protocol: Rationale, objectives, and design

PLOS ONE, 2023

Keywords: SARS-CoV-2 infection PASC long COVID

Effects of HLA single chain trimer design on peptide presentation and stability

Frontiers in Immunology, 2023

Keywords: HLA single-chain trimers X-ray crystallography human class I leukocyte antigens pan-anti-class I antibodies peptide presentation

Stereochemical engineering yields a multifunctional peptide macrocycle inhibitor of Akt2 by fine-tuning macrocycle-cell membrane interactions

Communications Chemistry, 2023

Keywords: Peptides Screening Kinases Chemical tools Computational chemistry

Prediction of HLA genotypes from single-cell transcriptome data

Frontiers in Immunology, 2023

Keywords: HLA genotype HLA typing algorithm allele specific expression human leukocyte antigen (HLA) major histocompatibility (MHC) next-generation sequencing data (NGS) single-cell sequencing (scRNA-seq)

Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities

Cell Systems, 2023

Keywords: T cell receptor CDR3 TCR motif Entropy

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Genome Medicine, 2023

Keywords: COVID-19 Immunity Rare variants Type I interferon

Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy

Nature, 2023

Keywords: T cell receptor neoantigen CD8 PD-1 cancer cell therapy clinical

Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae

Nature Medicine, 2023

Keywords: Gene ontology Infectious diseases Transcriptomics Viral infection Gene regulation in immune cells

Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report

Vaccines, 2023

Keywords: SARS-CoV-2 COVID-19 reinfection Humoral immunity

Angiotensin-Converting Enzyme (ACE) Inhibitors May Moderate COVID-19 Hyperinflammatory Response: An Observational Study with Deep Immunophenotyping

Health Data Science, 2022

Keywords: COVID-19 angiotensin-converting enzyme 2 (ACE2) Angiotensin-converting enzyme inhibitors ACEi) angiotensin-II receptor blockers (ARB) renin-angiotensin-aldosterone system (RAAS)

Non-viral precision T cell receptor replacement for personalized cell therapy

Nature, 2022

Keywords: T cell receptor cancer cell therapy clinical

Diminished cell proliferation promotes natural killer cell adaptive-like phenotype by limiting FcεRIγ expression

Journal of Experimental Medicine, 2022

Keywords: COVID-19 natural killer (NK) cells innate immunity inflammation FcεRIγ expression

Physical and in silico immunopeptidomic profiling of a cancer antigen prostatic acid phosphatase reveals targets enabling TCR isolation

Proceedings of the National Academy of Sciences, 2022

Keywords: T cell receptor (TCR) immunopeptidome major histocompatibility complexes (MHC) prostate cancer prostatic acid phosphatase

The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies

Proceedings of the National Academy of Sciences, 2022

Keywords: COVID-19 autoantibodies infection fatality rate relative risk type I IFNs

KIR⁺CD8⁺ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19

Science, 2022

Keywords: COVID-19 KIR⁺CD8⁺ T cells autoimmune disease Ly49⁺CD8⁺ regulatory T cells

Multiple Early Factors Anticipate Post-Acute COVID-19 Sequelae

Cell, 2022

Keywords: Post-acute sequelae of COVID-19 (PASC) Multi-omic Type 2 diabetes SARS-CoV-2 RNAemia Epstein-Barr virus viremia Autoantibodies

Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer

Frontiers in Oncology, 2022

Keywords: metabolic model python cancer

Large libraries of single-chain trimer peptide-MHCs enable rapid antigen-specific CD8+ T cell discovery and analysis

Preprint, 2022

Keywords: pMHC COVID-19 single-chain-trimer CD8 T cell

HLA-A^∗02:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses

Cell Reports, 2021

Keywords: CD8 COVID-19 SARS-CoV-2 T cells TCR antigen cell therapy immune response single-cell

Characteristics and Factors Associated With Coronavirus Disease 2019 Infection, Hospitalization, and Mortality Across Race and Ethnicity

Clinical Infectious Diseases, 2021

Keywords: COVID-19 SARS-CoV-2 health disparity public health race/ethnicity

Angiotensin II receptor I auto-antibodies following SARS-CoV-2 infection

PLOS ONE, 2021

Keywords: COVID-19 endothelial activation coagulopathy pro-thrombotic autoantibodies angiotensin II type I receptor (AT1R-Ab)

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Immunity, 2021

Keywords: COVID-19 NK cells TNF antiviral lung fibrosis moderate proteomics scRNA-seq severe type 1 IFN

Protein Catalyzed Capture (PCC) Agents for Antigen Targeting

Methods in Molecular Biology, 2021

Keywords: combinatorial chemistry Epitope targeted in situ click chemistry Macrocyclic peptides One-bead one-compound libraries

Microfluidic Single-Cell Proteomics Assay Chip: Lung Cancer Cell Line Case Study

Micromachines, 2021

Keywords: cancer heterogeneity lung cancer microfluidics proteomics

Autoantibodies neutralizing type I IFNs are present in ~ 4% of uninfected individuals over 70 years old and account for ~ 20% of COVID-19 deaths

Science Immunology, 2021

Keywords: COVID-19 SARS-CoV-2 autoantibodies neutralizing type I IFNs IFN-α IFN-β

Case Study: A Precision Medicine Approach to Multifactorial Dementia and Alzheimer’s Disease

Journal of Alzheimers Disease & Parkinsonism, 2021

Keywords: Alzheimer dementia dementia-multifactorial lifestyle multimodal multimorbidity neuroplasticity primary biliary cholangitis

X-linked recessive TLR7 deficiency in~ 1% of men under 60 years old with life-threatening COVID-19

Science Immunology, 2021

Keywords: Immune response COVID-19 patients X Chromosome genetic risk

Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths

Science Immunology, 2021

Keywords: Immune response COVID-19 Type I interferons autoantibodies

Resolution of tissue signatures of therapy response in patients with recurrent GBM treated with neoadjuvant anti-PD1

Nature Communications, 2021

Keywords: gioblastoma multimore (GBM) neoadjuvant checkpoint blockade cancer microenvironment melanoma immunology systems biology intra-tumor heterogeneity

Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19

Nature Biotechnology, 2021

Keywords: Immune response multi-omics COVID-19 infection proteomics metabolomics single-cell TCR-seq single-cell RNA-seq CITE-seq single-cell secretome

Resolution of tissue signatures of therapy response in patients with recurrent GBM treated with neoadjuvant anti-PD1

Nature communications, 2021

Keywords: GBM anti-PD1 Tissue imaging machine-learning based image analysis immune response

Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses

Immunity, 2021

Keywords: pan-virus analysis conserved host response to viruses systems immunology multi-cohort analysis covid-19

Unique challenges for glioblastoma immunotherapy-discussions across neuro-oncology and non-neuro-oncology experts in cancer immunology. Meeting Report from the 2019 SNO Immuno-Oncology Think Tank

Journal of Neuro-Oncology, 2021

Keywords: clinical trial conference report glioblastoma immunosuppression immunotherapy

Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19

Cell, 2020

Keywords: Immune response multi-omics COVID-19 infection proteomics metabolomics single-cell TCR-seq single-cell RNA-seq CITE-seq single-cell secretome

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

Nature communications, 2020

Keywords: Multi-omic melanoma cell trajectories drug-tolerant

Visualizing Subcellular Enrichment of Glycogen in Live Cancer Cells by Stimulated Raman Scattering

Anal. Chem., 2020

Keywords: Raman scattering microscopy Glycogen melanoma metabolism

Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells

Nature communications, 2020

Keywords: Raman spectro-microscopy metabolomics melanoma lipidomics transcriptomics

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Cell, 2020

Keywords: immunotherapy neoantigen immunogenomics epitope TESLA immunogenicity

Antibody-recruiting protein-catalyzed capture agents to combat antibiotic-resistant bacteria

Chem. Sci., 2020

Keywords: Antibiotic resistant antibody-recruiting protein‐catalyzed capture agents (AR-PCCs)

Inhibition of heme sequestration of histidine‐rich protein 2 using multiple epitope‐targeted peptides

J Pep Sci., 2019

Keywords: Plasmodium falciparum HRP2 protein‐catalyzed capture agents (PCCs)

4D electron microscopy of T cell activation

PNAS, 2019

Keywords: T cell activation | PINEM | electron microscopy | electron-photon coupling | T cell receptor

Development of Hematopoietic Stem Cell-Engineered Invariant Natural Killer T Cell Therapy for Cancer

Cell Stem Cell, 2019

Keywords: hematopoietic stem cell HSC TCR gene therapy cell therapy stem cell therapy cancer immunotherapy sr39TK suicide gene preclinical development