Pouria Dasmeh

AlphaVaR: an R framework for the statistical interpretation of AlphaGenome variant-effect predictions

AlphaVaR structures AlphaGenome's per-track variant scores in R and adds multiple-testing-corrected enrichment and shift tests, a tissue-specificity index and transparent ranking; on rs1427407 it recovers BCL11A erythroid-enhancer biology.

Negative Autoregulation Promotes the Evolution of Strong Environmental Switching

This study shows that negative autoregulation in gene circuits enables stronger environmental switching by favoring alleles that create strong molecular switches in E. coli.

Single cell analysis of Barrett's esophagus and carcinoma reveals cell types conferring risk via genetic predisposition

The paper uses single cell RNA-sequencing and genome-wide association study data to identify cell types and processes involved in Barrett's esophagus and esophageal adenocarcinoma risk.

Gene Interaction Network Architecture of Human Polygenic Traits Reveals Domain-Specific Connectivity and Evolutionary Pressures

The paper analyzes gene interaction networks across polygenic traits, finding higher connectivity in trait-associated genes and weaker selective constraints in highly connected networks, and develops an online portal for hypothesis generation.

Yeast proteins reversibly aggregate like amphiphilic molecules

The paper identifies sequence features of aggregation-prone regions in yeast proteins using machine learning on proteolysis-mass spectrometry data.

Positive selection in the Ebola virus proteome

The paper analyzes amino acid substitutions in Ebola virus proteomes to identify evolutionary hotspots and positive selection across different lineages and outbreaks.

IFNβ and TNFα cooperate to induce a STAT1-independent antiviral and immunoregulatory program via non-canonical STAT2 and IRF9 pathway

The paper shows that IFNβ and TNFα together induce a STAT1-independent antiviral program via non-canonical STAT2 and IRF9 pathways.

Estimating The Contribution Of Folding Stability To Non-Specific Epistasis In Protein Evolution

The paper estimates how much folding stability contributes to epistasis in protein evolution, finding that ~30-60% of amino acid substitutions involve epistasis.

Inferring the selection window in antimicrobial resistance using deep mutational scanning data and biophysics-based fitness models

The paper estimates the mutant-selection window for antimicrobial resistance using a biophysics-based fitness model and deep mutational scanning data.