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

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.

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

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

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

Vaccines, 2023

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

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

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

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

Nature, 2022

Keywords: T cell receptor cancer cell therapy clinical

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

Front. Oncol., 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

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

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

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

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

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

Cell, 2021

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