Biology OA

Global detection of human variants and isoforms by deep proteome sequencing - Nature Biotechnology Deep proteome sequencing achieves ~80% coverage of the human proteome.

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.

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species - Nature Communications Root exudates display a diurnal signature, change with growth environment, and can be divided into a core metabolome common to multiple plant species, and specialized exudates produced by distinct spe...

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.

High-throughput microbial culturomics using automation and machine learning - Nature Biotechnology A machine learning isolation and genotyping platform enable high-throughput bacterial culture generation.

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 are valuable hypotheses and accelerate but do not replace experimental structure determination - Nature Methods An analysis of AlphaFold protein structure predictions shows that while in many cases the predictions are highly accurate, there are also many instances where the predicted structures or parts of pred...

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 unifies microbial data in a single reference tree - Nature Biotechnology A comprehensive microbial resource reconciles genomic and 16S rRNA data in a single tree.

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.

Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources Abstract. As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community sinc

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.

Ancient gene linkages support ctenophores as sister to other animals - Nature Deeply conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of the comb jellies (ctenophores)—placing ctenophores as t...

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.

Quantifying the local adaptive landscape of a nascent bacterial community - Nature Communications Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial commu...

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.

Identification of mobile genetic elements with geNomad - Nature Biotechnology geNomad identifies mobile genetic elements in sequencing data.

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.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain - Nature  A transcriptomic cell-type atlas of the whole adult mouse brain with ~5,300 clusters built from single-cell and spatial transcriptomic datasets with more than eight million cells reveals remarka...

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.

On the limits of fitting complex models of population history to f-statistics Many published findings about population history that rely on inference of admixture graph models fitted to f-statistics are not robust since the method is generally inappropriate for extracting new i...

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.

Global detection of human variants and isoforms by deep proteome sequencing - Nature Biotechnology Deep proteome sequencing achieves ~80% coverage of the human proteome.

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.

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species - Nature Communications Root exudates display a diurnal signature, change with growth environment, and can be divided into a core metabolome common to multiple plant species, and specialized exudates produced by distinct spe...

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.

High-throughput microbial culturomics using automation and machine learning - Nature Biotechnology A machine learning isolation and genotyping platform enable high-throughput bacterial culture generation.

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 are valuable hypotheses and accelerate but do not replace experimental structure determination - Nature Methods An analysis of AlphaFold protein structure predictions shows that while in many cases the predictions are highly accurate, there are also many instances where the predicted structures or parts of pred...

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 unifies microbial data in a single reference tree - Nature Biotechnology A comprehensive microbial resource reconciles genomic and 16S rRNA data in a single tree.

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.

Ancient gene linkages support ctenophores as sister to other animals - Nature Deeply conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of the comb jellies (ctenophores)—placing ctenophores as t...

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.

Quantifying the local adaptive landscape of a nascent bacterial community - Nature Communications Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial commu...

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.

Identification of mobile genetic elements with geNomad - Nature Biotechnology geNomad identifies mobile genetic elements in sequencing data.

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.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain - Nature  A transcriptomic cell-type atlas of the whole adult mouse brain with ~5,300 clusters built from single-cell and spatial transcriptomic datasets with more than eight million cells reveals remarka...

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.