Joshua J. Coon

Performance Evaluation of a Quantitative Metabolomics Workflow Incorporating Microchip Capillary Electrophoresis, Indexed Migration Time, and Single-Point External Calibration

This paper evaluates a metabolomics workflow using microchip CE-MS with indexed migration time and single-point external calibration, showing improved accuracy and consistency across biological matrices.

Proteome-wide QTL mapping enables gene-protein-phenotype metabolic network construction in a genetically diverse MASLD mouse model

This study maps proteome-wide QTLs in a MASLD mouse model to construct gene-protein-phenotype metabolic networks, identifying Ubr1 as a central regulator of proteostasis and lipid metabolism.

The Aspergillus fumigatus C2-Domain Protein SppA is required for septal integrity and alters susceptibility to echinocandins and neutrophil killing during infection

This paper identifies SppA as a critical protein for septal integrity in A. fumigatus, showing its role in antifungal tolerance and virulence.

Rapid Peptide Mapping of Monoclonal Antibodies with Direct Infusion Mass Spectrometry

This paper introduces RaPiD-mAb-MS, a direct infusion mass spectrometry method for rapid peptide mapping of monoclonal antibodies, achieving 100-fold faster analysis with high sequence coverage and comparable results to conventional methods.

Multi-omic analysis reveals nitric oxide dependent remodeling in classically activated macrophages and identifies negative regulation mediated by AKR1A1

This study uses multi-omic analysis to show NO* drives controlled remodeling in macrophages, with AKR1A1 mediating negative regulation of metabolic and functional changes during immune response.

UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism

This study identifies UFMylation of PDH as a regulator of mitochondrial metabolism, showing it enhances pyruvate oxidation and TCA cycle activity.

Primate lineage specification requires suppression of Alu hyperediting

The paper identifies ILF2/3 as a regulator of primate cell fate by suppressing Alu element editing, showing its role in preventing aberrant splicing and maintaining epigenetic stability.

Proteotyping reactivant toxoplasmic encephalitis reveals virulence-associated dense granule protein GRA5 polymorphisms

The paper identifies strain-specific GRA5 polymorphisms in T. gondii using proteomic analysis of cerebrospinal fluid from reactivated toxoplasmosis cases, suggesting a proteotype for strain risk stratification.

Atlas of lysine acetylation in the mouse

The paper presents a comprehensive atlas of lysine acetylation in the mouse, identifying 17,952 sites across 15 tissues and highlighting shared and tissue-specific acetylation events.

Regarding Emitter Positioning for Nanoflow Electrospray Ionization

The paper investigates how emitter positioning affects peptide signal intensity in nanoflow electrospray ionization for proteomics, finding consistent signal behavior across m/z range.

Developmentally-specific physiological and metabolic responses support drought resilience in switchgrass and constrains biofuel yield

This study examines how drought at different developmental stages affects switchgrass physiology, metabolism, and biofuel yield, finding that vegetative-stage drought increases resilience but reduces biofuel production.

Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in Zymomonas mobilis

The paper identifies genomic targets for improving anaerobic chemical tolerance in Zymomonas mobilis using orthogonal gene perturbation screens and validates findings through gene deletions.

Tumor-Derived Polyamines Initiate Fat Wasting in Cancer Cachexia

This study identifies polyamine-dependent tumor-adipose crosstalk as an early driver of fat wasting in cancer cachexia, linking polyamine metabolism to adipocyte lipolysis and poor patient survival.

Thermodynamics shape the in vivo enzyme burden of glycolytic pathways

The paper quantifies enzyme burdens in glycolytic pathways of three bacteria, finding that thermodynamically favorable pathways require less enzymatic protein to sustain the same flux.

Adeno-Associated Virus 2 (AAV2) - induced RPA exhaustion generates cellular DNA damage and restricts viral gene expression

This study shows that AAV2 genomes compete with host RPA for binding, causing replication stress and DNA damage, which suppresses viral gene expression.

Machine learning uncovers gene families impacting oxidative stress resistance across yeasts

This study uses machine learning to identify gene families associated with oxidative stress resistance in yeasts and validates their roles experimentally.

Genetic mapping of lifespan and mitochondrial stress response in C. elegans

The paper identifies a UPRmt modulator, fipp-1/FIP1L1, that extends lifespan in C. elegans and is associated with metabolic homeostasis in humans.

IFIT3 RNA-binding activity promotes influenza A virus infection and translation efficiency

This study shows IFIT3 binds RNA and enhances influenza A virus translation, revealing its pro-viral role during infection.

SLX4IP acts in parallel to FANCM to limit BLM-dependent replication stress at ALT telomeres

This study identifies SLX4IP as a suppressor of BLM-driven replication stress at ALT telomeres and reveals its parallel function with FANCM to regulate telomere maintenance.

A Technical Evaluation of Plasma Proteomics Technologies

This paper evaluates six plasma proteomic technologies, finding that Seer Proteograph XT provides the highest proteomic depth and quantification, while Olink Explore HT shows comparable LOD but worse LOQ.

pH adjustment increases biofuel production from inhibitory switchgrass hydrolysates

This study shows that adjusting pH and using SAA pretreatment improves biofuel production from drought-switchgrass hydrolysates.

Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

This study identifies how altering translation in E. coli mitigates the growth inhibition caused by chemically stabilized G-quadruplexes.

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST

This study uses nMOST to profile proteo-lipidomics in lysosomal storage disease mutants, revealing autophagy defects and mitochondrial dysfunction.

SPE-CZE-MS quantifies zeptomole concentrations ofphosphorylated peptides

The paper develops SPE-CZE-MS for quantifying phosphorylated peptides in single-cell equivalent phosphoproteomics, demonstrating improved sensitivity and compatibility with mass spectrometry.

Substrate-directed control of N-glycosylation in the endoplasmic reticulum calibrates signal reception at the cell-surface

The paper identifies an ER pathway that regulates N-glycosylation by modulating OST-A activity, impacting cell-surface signaling and tissue development.

High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan

The paper identifies genetic and molecular regulators of lifespan in C. elegans using a recombinant inbred population and validates their relevance to human age-related diseases.

Deep Learning Predicts Non-Normal Peptide FAIMS Mobility Distributions Directly from Sequence

The paper develops deep learning models to predict FAIMS ion mobility of peptides from sequence, achieving high F2 score on E. coli peptides.

Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer

The paper introduces a method using the Orbitrap Astral mass spectrometer with DIA to rapidly analyze phosphoproteomes, detecting over 80,000 phosphorylation sites in mice.

SCD1 and monounsaturated lipids are required for autophagy and survival of adipocytes

This study shows that SCD1 and monounsaturated lipids are essential for autophagy and survival of adipocytes, with SCD1 deficiency causing autophagosome accumulation and cell death.

PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae

The paper investigates how PKA signaling coordinates growth and metabolism in yeast during anaerobic xylose fermentation by analyzing transcriptomic, lipidomic, and phosphoproteomic data.