A. Murat Eren

The paper introduces the Ocean Microbiomics Database (OMDB) to analyze microbial thermal niches and predict their response to ocean warming, showing richness declines faster than abundance.

The paper introduces synteny-aware pangenome graphs to visualize genomic variation in marine bacteria, revealing structured continua of variability across genomes.

This study shows auxotrophy is a conserved genomic lifestyle feature, not a transient response to nutrients, challenging the Black Queen Hypothesis.

This study shows microbial communities converge on similar metabolic functions under controlled environmental conditions, revealing the role of both imposed and emergent environmental filters.

The paper describes 81 new SAR11 isolate genomes and identifies 29 monophyletic ecotypes within the Pelagibacterales, providing a classification system correlated with ecology and evolution.

The paper presents a high-resolution multi-omics dataset of surface ocean metagenomes, metatranscriptomes, and tRNA transcripts collected over 48 hours to study microbial responses to environmental change.

This study generates 50 complete Mtb genomes, identifies core and accessory gene clusters, and proposes a new pangenome reference resource to improve TB research.

The study identifies chemosynthetic bacteria in the gills of Hypoplectrus reef fishes, revealing their metabolic potential and geographic distribution.

This study identifies distinct habitat preferences for Magnimaribacterales bacteria across marine environments using metagenomic and amplicon data from the tropical Pacific Ocean.

The paper evaluates errors in long-read metagenome assemblers and identifies common issues like chimeras and phantom sequences.

The paper introduces EcoPhylo, a computational workflow to assess genome recovery rates in microbial communities using ribosomal protein phylogeography, applied to human gut and oral cavity data.

This study identifies habitat-specific genes in SAR11 bacteria using new genomes and metagenomes, showing ecological and genetic segregation into ecotypes.

The paper improves microbial gene annotations by adaptively adjusting significance thresholds, enhancing sensitivity without sacrificing accuracy, especially for non-model organisms and underrepresented protein families.

The paper discovers a new group of DNA viruses, egoviruses, found in the digestive systems of humans and animals, closely related to poxviruses and suggesting an evolutionary link between gut-infecting viruses and animal pathogens.

The paper introduces Digital Microbes, an integrative framework for collaborative research on microbes, demonstrating its application with two case studies involving genomic and transcriptomic data.

proovframe corrects frameshift errors in long-read (meta)genomics data using protein-to-nucleotide alignments, improving data quality without requiring high sequencing depth.

The paper develops PlasX to identify plasmids in human gut metagenomes and reveals their ecological and evolutionary patterns across populations.

STRONG identifies strains de novo from metagenome samples using coassembly, binning, and a Bayesian algorithm to resolve haplotypes and abundances.

The paper links comparative genomics with environmental distribution patterns of microbial populations using metagenomics to study the Deepwater Horizon oil spill impact.