[Acta Biotheoretica] The scientific restlessness surrounding the question of what life is (expressed in the provocations of Feynman and Schrödinger) guides this review article by integrating physics, chemistry, and biology […]
genomics
Posted inGenomics, Proteomics, Bioinformatics
Deep Shifts In Evolutionary Rate Trajectories Of Ancient Bacterial Genes
[biorxiv.org] Reconstruction of ancestral gene repertoires from extant genomes captures only the genes that survived; those lost from the record are invisible. Among the genes that did persist, selective pressures […]
Posted inGenomics, Proteomics, Bioinformatics
A Genomic Catalog Of Earth’s Bacterial And Archaeal Symbionts
[Nature Biotechnology] Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth yet remains underexplored because of culturing challenges.
Posted inBiophysics
How A Deep-sea Protein Adapts To An Extreme Environment
[Kyushu University] Life in the deep sea is under immense pressure—literally. Such extreme conditions can disrupt the delicate structures of proteins essential to life. Yet somehow, the proteins in deep-sea […]
Posted inOrigin & Evolution of Life
The History Of Enzyme Evolution Embedded In Metabolism
[PNAS]. Whereas phylogenetic reconstructions are a primary record of protein evolution, it is unknown whether the deep history of enzymes is encoded at higher levels of biological organization.
Posted inNomenclature, Systematics, Natural History
Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions
[biorxiv.org] Asgard archaea are the closest known relatives of eukaryotes and are central to models of eukaryogenesis involving archaeal–bacterial symbiosis, yet the contribution of viruses remains unexplored.
Posted inNanotechnology & SynBio
Advances in Machine Learning for Directed Evolution: A Five-Year Retrospective
[q-bio.BM] The last five-plus years have seen many protein engineering disciplines transformed by advances in machine learning (ML), but the same cannot be said for directed evolution.
Posted inOrigin & Evolution of Life
The Emergence Of Life In The Light Of Evolution
[q-bio.PE] The origin of life is often framed primarily as a chemical problem, yet life s defining feature is evolution.
Posted inOrigin & Evolution of Life
ReactionAtlas: Ab Origine Exploration Of Chemical Reaction Networks With Machine Learning
[cs.LG] Mapping a chemical reaction network, the graph of minima and transition states (TS) and the elementary reactions connecting them, is the natural language of chemistry, from catalysis to combustion […]
Posted inGenomics, Proteomics, Bioinformatics
ExMODE: A Comprehensive Resource For Extremophile Genomic And Functional Exploration
[iMetaOmics] ExMODE (https://db.genomics.cn/exmode/) integrates 3518 samples to build a unified extremophile resource, which hosts 1.35 billion habitat-specific non-redundant genes, 5.25 million representative protein structures, 67,026 metagenome-assembled genomes (MAGs), and 164,132 […]