Jason McDermott
A5020608405- Methane Hydrates and Related Phenomena
- Seismic Waves and Analysis
- Earthquake Detection and Analysis
- Ionosphere and magnetosphere dynamics
- Geophysics and Gravity Measurements
- Superconducting Materials and Applications
- Seismology and Earthquake Studies
- Geophysical Methods and Applications
- GNSS positioning and interference
- Bioinformatics and Genomic Networks
- Solar and Space Plasma Dynamics
- Astrophysics and Cosmic Phenomena
- Bacteriophages and microbial interactions
- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Metabolomics and Mass Spectrometry Studies
- Bacterial Genetics and Biotechnology
- Gene expression and cancer classification
- Machine Learning in Bioinformatics
- Gene Regulatory Network Analysis
- Microbial infections and disease research
- Plant Virus Research Studies
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Biology Techniques and Applications
Pacific Northwest National Laboratory
2016-2025
Oregon Health & Science University
2015-2025
Environmental Molecular Sciences Laboratory
2008-2025
Mercy University Hospital
2025
University of California, San Diego
2024
Manchester University NHS Foundation Trust
2024
Government of the United States of America
2023
Stanford Synchrotron Radiation Lightsource
2022
Lawrence Berkeley National Laboratory
2022
Mammoth Biosciences (United States)
2022
Abstract Identifying tumor antigen-specific T cells from cancer patients has important implications for immunotherapy diagnostics and therapeutics. Here, we show that CD103 + CD39 tumor-infiltrating CD8 (CD8 TIL) are enriched tumor-reactive both in primary metastatic tumors. This TIL subset is found across six different malignancies displays an exhausted tissue-resident memory phenotype. TILs have a distinct T-cell receptor (TCR) repertoire, with clones expanded the but present at low...
The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this "proteogenomics" approach was applied to 122 treatment-naive primary breast cancers accrued preserve post-translational modifications, including protein phosphorylation acetylation. Proteogenomics challenged standard cancer diagnoses, provided detailed analysis the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint...
Proteomic and lipidomic profiling was performed over a time course of acute hepatitis C virus (HCV) infection in cultured Huh-7.5 cells to gain new insights into the intracellular processes influenced by this virus. Our proteomic data suggest that HCV induces early perturbations glycolysis, pentose phosphate pathway, citric acid cycle, which favor host biosynthetic activities supporting viral replication propagation. This is followed compensatory shift metabolism aimed at maintaining energy...
ABSTRACT Diet can influence the composition of human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on functional potential microbiome. Dietary resistant starch (RS) has shown health benefits, but we lack a mechanistic understanding metabolic processes that occur in gut during digestion RS. Here, collected samples crossover study diets containing large or small amounts We determined RS microbiome pathways gut, using...
Historically neglected by microbial ecologists, soil viruses are now thought to be critical global biogeochemical cycles. However, our understanding of their distribution, activities and interactions with the microbiome remains limited. Here we present Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced metagenomes composed 616,935 uncultivated viral genomes 38,508 unique operational taxonomic units. Rarefaction curves Atlas indicate that most diversity...
INTRODUCTION: The advent of high throughput technologies capable comprehensive analysis genes, transcripts, proteins and other significant biological molecules has provided an unprecedented opportunity for the identification molecular markers disease processes. However, it simultaneously complicated problem extracting meaningful signatures processes from these complex datasets. process biomarker discovery characterization provides opportunities more sophisticated approaches to integrating...
The type III secretion system is an essential component for virulence in many Gram-negative bacteria. Though components of the apparatus are conserved, its substrates--effector proteins--are not. We have used a novel computational approach to confidently identify new secreted effectors by integrating protein sequence-based features, including evolutionary measures such as pattern homologs range other organisms, G+C content, amino acid composition, and N-terminal 30 residues sequence. method...
To cause a systemic infection, Salmonella must respond to many environmental cues during mouse infection and express specific subsets of genes in temporal spatial manner, but the regulatory pathways are poorly established. unravel how micro-environmental signals processed integrated into coordinated action, we constructed in-frame non-polar deletions 83 regulators inferred play role enteriditis Typhimurium (STM) virulence tested them three assays (intraperitoneal [i.p.], intragastric [i.g.]...
Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality their gene products despite well-known limitations this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome data can outperform transcriptome for coexpression based function prediction has not been systematically investigated. Here, we address question by...
Various genetic mutations associated with cancer are known to alter cell signaling, but it is not clear whether they dysregulate signaling pathways by altering the abundance of pathway proteins. Using a combination RNA sequencing and ultrasensitive targeted proteomics, we defined primary components-16 core proteins 10 feedback regulators-of epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) in normal human mammary epithelial cells then quantified their absolute...
ABSTRACT The twentieth century was marked by extraordinary advances in our understanding of microbes and infectious disease, but pandemics remain, food waterborne illnesses are frequent, multidrug-resistant on the rise, needed drugs vaccines have not been developed. scientific approaches past—including intense focus individual genes proteins typical molecular biology—have sufficient to address these challenges. first decade twenty-first has seen remarkable innovations technology...
Many gene products exhibit great structural heterogeneity because of an array modifications. These modifications are not directly encoded in the genomic template but often affect functionality proteins. Protein glycosylation plays a vital role proper protein functions. However, analysis glycoproteins has been challenging compared with other modifications, such as phosphorylation. Here, we perform integrated proteomic and glycoproteomic 83 prospectively collected high-grade serous ovarian...
Our study details the stepwise evolution of gilteritinib resistance in FLT3-mutated acute myeloid leukemia (AML). Early is mediated by bone marrow microenvironment, which protects residual cells. Over time, cells evolve intrinsic mechanisms resistance, or late resistance. We mechanistically define both early and integrating whole-exome sequencing, CRISPR-Cas9, metabolomics, proteomics, pharmacologic approaches. resistant undergo metabolic reprogramming, grow more slowly, are dependent upon...
Abstract Motivation: Biological system behaviors are often the outcome of complex interactions among a large number cells and their biotic abiotic environment. Computational biologists attempt to understand, predict manipulate biological behavior through mathematical modeling computer simulation. Discrete agent-based (in combination with high-resolution grids model extracellular environment) is popular approach for building models. However, computational complexity this forces resort coarser...
In the absence of a dominant driving mutation other than uniformly present TP53 mutations, deeper understanding biology ovarian high-grade serous cancer (HGSC) requires analysis at functional level, including post-translational modifications. Comprehensive proteogenomic and phosphoproteomic characterization 83 prospectively collected HGSC appropriate normal precursor tissue samples (fallopian tube) under strict control ischemia time reveals pathways that significantly differentiate between...
Circadian disruption has been identified as a risk factor for health disorders such obesity, cardiovascular disease, and cancer. Although epidemiological studies suggest an increased of various cancers associated with circadian misalignment due to night shift work, the underlying mechanisms have yet be elucidated. We sought investigate potential mechanistic role that cancer hallmark pathway genes may play in workers. In controlled laboratory study, we investigated transcriptome biological...
Metagenomics is unearthing the previously hidden world of soil viruses. Many viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with replication. Here, we establish AMGs on viruses actually produce functional, active proteins. We focus potentially encode chitosanase enzymes metabolize chitin - a common carbon polymer. express and functionally screen several identified from environmental metagenomes. One expressed protein showing...
Bacteriophages are abundant in soils. However, the majority uncharacterized, and their hosts unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly phage-host relationships. Some have high centralities bacterial community co-occurrence networks, suggesting phage infections an important impact on soil interactions. We observe increased average viral copies per host (VPH) decreased transcriptional activity following a two-week soil-drying incubation,...
Salmonella enterica serovar Typhimurium is a leading cause of acute gastroenteritis throughout the world. This pathogen has two type III secretion systems (TTSS) encoded in pathogenicity islands 1 and 2 (SPI-1 SPI-2) that deliver virulence factors (effectors) to host cell cytoplasm are required for virulence. While many effectors have been identified at least partially characterized, full repertoire not catalogued. In this proteomic study, we effector proteins secreted into defined minimal...