A5055160909- Mass Spectrometry Techniques and Applications
- Influenza Virus Research Studies
- Monoclonal and Polyclonal Antibodies Research
- Advanced Proteomics Techniques and Applications
- vaccines and immunoinformatics approaches
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Mosquito-borne diseases and control
- HIV Research and Treatment
- Pancreatic and Hepatic Oncology Research
- Fungal and yeast genetics research
- Immunotherapy and Immune Responses
- Galectins and Cancer Biology
- Peptidase Inhibition and Analysis
- Endoplasmic Reticulum Stress and Disease
- Microbial Inactivation Methods
- Celiac Disease Research and Management
- Lymphoma Diagnosis and Treatment
- Virology and Viral Diseases
- Gene expression and cancer classification
- Prion Diseases and Protein Misfolding
- Hematopoietic Stem Cell Transplantation
- T-cell and B-cell Immunology
- Complement system in diseases
- Probiotics and Fermented Foods
Claremont Graduate University
2023
Stanford University
2016-2022
Stratford University
2016-2017
The University of Sydney
2012-2014
Celiac disease (CeD) is an autoimmune disorder induced by consuming gluten proteins from wheat, barley, and rye. Glutens resist gastrointestinal proteolysis, resulting in peptides that elicit inflammation patients with CeD. Despite well-established connections between glutens CeD, chemically defined, bioavailable produced dietary have never been identified humans unbiased manner. This largely attributable to technical challenges, impeding our knowledge of potentially diverse peptide species...
A new phylogenetics approach and algorithm with which to chart the evolutionary history of organisms is presented. It utilizes mass spectral data produced from proteolytic digestion proteins, rather than partial or complete gene translated sequences. The concept validity demonstrated herein using both theoretical experimental data, together sequences hemagglutinin protein influenza virus. comparison trees conventional sequenced-based phylogenetic trees, two separate tree algorithms, reveals...
A new approach employing mass trees is described and implemented which enables the evolution of influenza neuraminidase across all subtypes (N1–N9) in human animal hosts to be monitored charted without gene or protein sequencing. These are shown congruent with sequence based trees. Such can built solely from masses proteolytic peptide ions viral proteins recorded by a spectrometer. They able correctly chart evolutionary history pandemic viruses, originated hosts, also resolve antiviral...
A matrix-assisted laser desorption ionization (MALDI) mass spectrometry-based approach is applied to identify active site domains within influenza neuraminidase that bind the antiviral inhibitors zanamivir (ZANA) and 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (DANA). Combined data from tryptic Glu-C endoproteinase digests of neuraminidase-inhibitor complexes have identified binding peptides contain residues Arg118, Glu119, Arg156, Glu276, Tyr406. The these was confirmed analysis available...
Graft-versus-host disease (GvHD) is a major complication after allogeneic hematopoietic cell transplantation (HCT). Current strategies to prevent GvHD with immunosuppressive drugs carry significant morbidity and may affect the graft-versus-tumor (GVT) effect. Inflammatory bowel (IBD) an intestinal inflammatory condition that affects more than 2 million people in United States. colitis morbidity. Recently, Repulsive Guidance Molecule b (RGMb) has been identified as part of signaling hub...
Protein aggregation, particularly in its prion-like form, has long been thought to be detrimental. However, recent studies have identified multiple instances where protein aggregation is important for normal physiological functions. Combining mass spectrometry and cell biological approaches, we developed a strategy the identification of aggregates lysates. We used this approach characterize prion-based traits pathogenic strains yeast Saccharomyces cerevisiae isolated from immunocompromised...
Summary Thousands of protein post-translational modifications (PTMs) dynamically impact nearly all cellular functions. Mass spectrometry is well suited to PTM identification, but proteome-scale analyses are biased towards PTMs with existing enrichment methods. To measure the full landscape regulation, software must overcome two fundamental challenges: intractably large search spaces and difficulty distinguishing correct from incorrect identifications. Here, we describe TagGraph, that...
Abstract Pancreatic ductal adenocarcinoma (PDAC) is currently the 3rd leading cause of cancer-related deaths in US. Although all-stage 5-year survival rate ~10%, early-stage markedly superior and excess 40%. Hence, early detection PDAC via blood-based liquid biopsies holds promise to reduce morbidity mortality. PrognomiQ’s multi-omics platform performs deep unbiased molecular profiling blood samples detect proteins, metabolites, lipids, mRNA, miRNA, cfDNA fragmentation copy-number, CpG...
Abstract Broadly effective vaccines against dengue virus (DENV) infection have remained elusive, despite rising rates in the developing world. Infection-specific peptide ligands presented on Major Histocompatibility Complexes (MHC) open new avenues for T-cell-based interventions. Past efforts towards mapping viral MHC epitopes were based computational predictions that only partially reflected actual antigen presentation. To empirically identify DENV-specific ligands, we developed an...
ABSTRACT Celiac disease (CeD) is an autoimmune disorder induced by consuming gluten proteins from wheat, barley, and rye. Glutens resist gastrointestinal proteolysis, resulting in peptides that elicit inflammation patients with CeD. Despite well-established connections between glutens CeD, chemically defined, bioavailable produced dietary have never been identified humans unbiased manner. This largely attributable to technical challenges, impeding our knowledge of potentially diverse peptide...
Abstract Dengue (DEN) virus infection is a leading cause of hospitalization and death in the developing world broadly effective vaccines therapies remain elusive. Identifying infection-specific peptide antigens would open new avenues for T cell based interventions. Past efforts towards mapping viral used computational predictions that only partially reflect actual presented by major histocompatibility complex (MHC). To identify DEN-specific without relying on error prone predictions, we...
Abstract Lung cancer is the leading cause of cancer-related deaths in United States, with estimates 236,740 new cases and 118,830 2022 secondary to disease. Blood-based liquid biopsies hold promise reduce morbidity mortality from lung by enabling early detection downstage disease at diagnosis, theragnostic identification patients most likely be helped or harmed therapy, monitoring therapeutic efficacy, residual PrognomiQ’s multi-omics platform comprehensively profiles proteins, metabolites,...
Abstract Presentation of novel antigenic peptides (neoantigens) that distinguish malignant from normal cells by major histocompatibility complexes (MHC) can serve as potent substrates for specific anti-tumor immune responses. We sought to identify mantle cell lymphoma (MCL) neoantigens taking an integrated genomic and proteomic strategy interrogates antigen presented MHC-class I class II. Peptides bound MHC were purified via immunoprecipitation followed identification using mass...
Abstract The recent outbreak of Zika virus (ZIKV) infection across the Americas has raised dire concerns about its potential long-term health effects including negative impact on neuronal, psychological and motor development in affected individuals. Emerging evidence pointing to Alzheimer’s-like damage adult brain further highlights urgent need for efficacious prophylactic measures. Zika-affected regions are often endemic related Dengue (DENV). Antibodies against two viruses crossreactive...
Abstract Pancreatic cancer is the seventh leading cause of cancer-related death worldwide and third in USA. The low survival rate pancreatic due to challenges early detection disease, highlighting need for diagnostic test development. While signatures are less challenging identify at localized tumor via biopsy, signals found bloodstream cellular leakage, metastasis, signaling, innate immune response, remain key interest reduced invasive sampling. encountered liquid biopsy biomarker discovery...
Abstract Pancreatic cancer is the third leading cause of cancer-related deaths in United States. Disease biomarkers quantified from blood-based assays may help reduce mortality by enabling early detection, treatment selection, or response and resistance assessment. PrognomiQ has developed a multi-omics assay analysis platform that comprehensively profiles blood samples to detect proteins, metabolites, lipids, mRNA, miRNA, cfDNA fragments, methylation at CpG sites. This can provide deep...