J. E. Elias

Rapid QC-MS - Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control

Rapid QC-MS provides an automated dashboard for real-time quality control of LC-MS/MS data, improving efficiency and accuracy in untargeted workflows.

Spatio-temporal analysis of Vaccinia virus infection and host response dynamics using single-cell transcriptomics and proteomics

This study uses single-cell transcriptomics and proteomics to analyze Vaccinia virus infection dynamics and host response heterogeneity in HeLa and fibroblast cells.

Global organelle profiling reveals subcellular localization and remodeling at proteome scale

The paper maps subcellular localization of human proteins and shows proteome remodeling during viral infection by combining organelle immuno-capture with mass spectrometry.

Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells

The paper shows that increasing cell size leads to proteome remodeling similar to starvation, driven by genome dilution in mammalian and yeast cells.

Metabolomic rearrangement controls the intrinsic microbial response to temperature changes

The paper shows that metabolomic rearrangements, not stress responses, control bacterial temperature adaptation, with a model explaining growth dynamics under temperature shifts.

Cell size contributes to single-cell proteome variation

The paper shows that cell size significantly affects protein concentration variation in single-cell proteomics data.

Tuning DO:DM ratios modulates MHC class II immunopeptidomes

This study investigates how varying DO:DM ratios affect MHC-II immunopeptidomes by analyzing HLA-DR4-expressing cell lines with different ratios, revealing peptide characteristics influencing presentation.

mTOR activation induces endolysosomal remodeling and nonclassical secretion of IL-32 via exosomes in inflammatory reactive astrocytes

Gut Microbiota-Targeted Diets Modulate Human Immune Status

This study examines how plant-based fiber and fermented food diets affect the gut microbiome and immune system in healthy adults over 17 weeks.

Increasing cell size remodels the proteome and promotes senescence

The paper shows that increasing cell size remodels the proteome and promotes senescence, but polyploidization can prevent this by altering the DNA-to-ploidy ratio.

An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease

The paper develops a urine peptidomics workflow to identify chemically defined dietary gluten peptides in celiac disease patients, revealing differences from controls.

Starvation induces shrinkage of the bacterial cytoplasm

This study shows that starvation causes E. coli to shrink its inner membrane and cytoplasm, driven by water loss, and that the Tol-Pal system is essential for recovery.

High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota

This study develops a high-throughput method to cultivate diverse, stable fecal-derived microbial communities in vitro, demonstrating their utility for modeling the intestinal microbiota and predicting in vivo responses to antibiotics.

Inter-domain dynamics drive cholesterol transport by NPC1 and NPC1L1 proteins

The paper investigates the role of inter-domain dynamics in cholesterol transport by NPC1 and NPC1L1 proteins, showing that domain movement is essential and that Ezetimibe inhibits NPC1L1 by binding to multiple domains.

Multiple layers of phospho-regulation coordinate metabolism and the cell cycle in budding yeast

This study identifies cell cycle-dependent phosphorylation and dephosphorylation of metabolic enzymes in budding yeast, revealing mechanisms linking the cell cycle to metabolic regulation.

Immuno-proteomic interrogation of dengue infection reveals novel HLA haplotype-specific MHC-I antigens

This study identifies novel MHC-I antigens specific to dengue virus infection using an immuno-proteomics approach, revealing ligands associated with distinct HLA haplotypes and T-cell recognition.

Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites

The paper combines proteomics and machine learning to generate a high-confidence apicoplast proteome in malaria parasites, identifying 346 proteins and validating novel functions.