Arkadiy I. Garber

BTEXgenie is a tool that uses profile HMMs to annotate BTEX degradation genes with higher sensitivity than existing methods, supporting pathway visualization and genomic analysis.

MagicLamp provides a toolkit and web server for targeted microbial function annotation using curated HMMs, enabling sensitive and specific gene annotation for specialized processes.

The paper measures transcript and protein abundance in bacterial endosymbionts to understand how they manage pseudogenes, finding that pseudogenes are transcribed but rarely produce proteins, and that tmRNA may target them for degradation.

The paper surveys subseafloor microbial communities in the San Pedro Basin to establish a baseline for ecological and microbiological variation, supporting future monitoring and research.

This study analyzes poxvirus genome architecture across the family, finding correlations between genome size, coding density, GC-content, and protein distribution, with implications for viral evolution and biology.

The paper investigates how paternal genome elimination in citrus mealybugs affects molecular evolution, finding faster evolution in female-biased genes and more adaptation in male-biased genes.

The paper identifies a mealybug with three endosymbionts, one contributing only two genes to produce a single essential nutrient, chorismate, highlighting extreme genome reduction in endosymbionts.

Pseudofinder identifies pseudogenes in prokaryotic genomes, detecting both degraded and newly formed pseudogenes, as well as genes under relaxed selection.

SprayNPray provides a user-friendly tool for taxonomic profiling of genome and metagenome contigs using multiple metrics to classify and analyze sequences.

FeGenie identifies iron-related genes and gene clusters in genomes and metagenomes using a comprehensive HMM database, improving detection of iron oxidation and reduction genes.