This paper advances deep proteome sequencing, improving detection of protein variants & isoforms beyond standard shotgun proteomics. By analyzing six human cell lines, it identifies a million unique peptides from 17,717 protein groups, highlighting translation of most alternatively spliced isoforms.

This paper examines root exudation dynamics in Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula. It finds exudate collection should happen in hours, not days, highlights growth-driven profile differences, and identifies a core metabolome shared across species.

This research introduces an open-source robotic platform for isolating bacterial strains, integrating machine learning to enhance microbial diversity. It generated a biobank of 26,997 isolates from human fecal samples, highlighting microbial interactions, strain evolution, and gene transfer.

AlphaFold predictions accelerate protein structure determination but require experimental validation. Many align with crystallographic maps, but discrepancies occur, highlighting the importance of confidence assessment & verification for accurate structural insights.

Greengenes2 is a new reference tree integrating genomic and 16S rRNA databases, resolving discrepancies from PCR biases. It shows that 16S rRNA and shotgun metagenomics data from the same samples align in principal coordinates space, taxonomy, and phenotype effect size.

The Saccharomyces Genome Database (SGD) has been updated with improvements in software architecture & gene nomenclature, enhancing support for researchers. These upgrades provide a comprehensive S. cerevisiae pan-genome, ensuring SGD remains a top resource for the scientific community.

Chromosome-scale gene linkages support ctenophores (comb jellies) as the sister group to all animals. They share ancestral metazoan patterns with unicellular eukaryotes, unlike sponges, bilaterians, & cnidarians, which show derived chromosomal rearrangements—robust evidence for this phylogeny.

This research investigates how a nascent bacterial community adapts over time, focusing on two E. coli ecotypes. It analyzes gene knockouts in different conditions, revealing fitness patterns and correlations with evolution, highlighting environmental and epistatic factors in adaptation.

Introducing geNomad, a framework to identify and characterize plasmids and viruses in sequencing data. With a dataset of 200k+ protein profiles and a conditional random field model, geNomad has processed 2.7T base pairs, discovering millions of new viruses and plasmids.

Created using single-cell RNA sequencing and spatial transcriptomics, this high-res atlas of the adult mouse brain reveals cell-type differences between dorsal and ventral regions. This study is a key resource for future brain research.

This research develops a method to systematically explore admixture graphs (AGs), integrating non-genetic data via topology constraints. Findings show many alternative models fit better than published AGs, suggesting that strong population history claims require shared topological features.

This paper advances deep proteome sequencing, improving detection of protein variants & isoforms beyond standard shotgun proteomics. By analyzing six human cell lines, it identifies a million unique peptides from 17,717 protein groups, highlighting translation of most alternatively spliced isoforms.

This paper examines root exudation dynamics in Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula. It finds exudate collection should happen in hours, not days, highlights growth-driven profile differences, and identifies a core metabolome shared across species.

This research introduces an open-source robotic platform for isolating bacterial strains, integrating machine learning to enhance microbial diversity. It generated a biobank of 26,997 isolates from human fecal samples, highlighting microbial interactions, strain evolution, and gene transfer.

AlphaFold predictions accelerate protein structure determination but require experimental validation. Many align with crystallographic maps, but discrepancies occur, highlighting the importance of confidence assessment & verification for accurate structural insights.

Greengenes2 is a new reference tree integrating genomic and 16S rRNA databases, resolving discrepancies from PCR biases. It shows that 16S rRNA and shotgun metagenomics data from the same samples align in principal coordinates space, taxonomy, and phenotype effect size.

Chromosome-scale gene linkages support ctenophores (comb jellies) as the sister group to all animals. They share ancestral metazoan patterns with unicellular eukaryotes, unlike sponges, bilaterians, & cnidarians, which show derived chromosomal rearrangements—robust evidence for this phylogeny.

This research investigates how a nascent bacterial community adapts over time, focusing on two E. coli ecotypes. It analyzes gene knockouts in different conditions, revealing fitness patterns and correlations with evolution, highlighting environmental and epistatic factors in adaptation.

Introducing geNomad, a framework to identify and characterize plasmids and viruses in sequencing data. With a dataset of 200k+ protein profiles and a conditional random field model, geNomad has processed 2.7T base pairs, discovering millions of new viruses and plasmids.

Created using single-cell RNA sequencing and spatial transcriptomics, this high-res atlas of the adult mouse brain reveals cell-type differences between dorsal and ventral regions. This study is a key resource for future brain research.