Antonijo Mrčela

Concomitant suppression of COX-1 and COX-2 is insufficient to induce enteropathy associated with chronic NSAID use

The paper shows that suppressing both COX-1 and COX-2 does not cause intestinal injury in mice unless combined with specific NSAIDs, and that gut microbiome changes amplify NSAID-induced enteropathy.

Sources of non-uniform coverage in short-read RNA-Seq data

This study investigates sources of non-uniform coverage in RNA-Seq data and finds that no single factor explains the issue, contradicting prior claims.

Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms

This study shows that age-related blood-borne factors alter circadian gene expression in cultured fibroblasts, affecting oxidative phosphorylation and cholesterol biosynthesis pathways.

Disruption of the PGE2 synthesis / response pathway restrains atherogenesis in programmed cell death-1 (Pd-1) deficient hyperlipidemic mice

This study shows that disrupting the PGE2 synthesis or response pathway reduces atherogenesis in PD-1 deficient hyperlipidemic mice through different immune mechanisms.

BEERS2: RNA-Seq simulation through high fidelity in silico modeling

BEERS2 simulates RNA-seq reads with high fidelity, incorporating detailed library preparation and sequencing steps, and evaluates its impact on the Salmon pseudoalignment algorithm.

Meta-analysis of diurnal transcriptomics reveals strong patterns of concordance and discordance in mouse liver

This paper performs a meta-analysis of mouse liver transcriptomics data to assess consistency of biological rhythms across studies, finding high concordance for core clock genes but low overlap for other rhythmic genes.

Deep Phenotyping of the Lipidomic Response in COVID and non-COVID Sepsis

The paper identifies lipidomic biomarkers and therapeutic targets in sepsis patients, including those with COVID-19, and develops an interactive network analysis tool for multiomic data exploration.

Comparative evaluation of full-length isoform quantification from RNA-Seq

This study evaluates isoform quantification methods using simulated data, finding that no method significantly outperforms a simple approach on realistic data.