Controllable protein design with language models
The twenty-first century is presenting humankind with unprecedented environmental and
medical challenges. The ability to design novel proteins tailored for specific purposes would …
medical challenges. The ability to design novel proteins tailored for specific purposes would …
Linking metagenomics to aquatic microbial ecology and biogeochemical cycles
Microbial communities are essential components of aquatic ecosystems through their
contribution to food web dynamics and biogeochemical processes. Aquatic microbial …
contribution to food web dynamics and biogeochemical processes. Aquatic microbial …
Mutant phenotypes for thousands of bacterial genes of unknown function
MN Price, KM Wetmore, RJ Waters, M Callaghan… - Nature, 2018 - nature.com
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a
function. Here, to investigate the functions of these genes, we present genome-wide mutant …
function. Here, to investigate the functions of these genes, we present genome-wide mutant …
Using deep learning to annotate the protein universe
Understanding the relationship between amino acid sequence and protein function is a long-
standing challenge with far-reaching scientific and translational implications. State-of-the-art …
standing challenge with far-reaching scientific and translational implications. State-of-the-art …
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning
J Hong, Y Luo, Y Zhang, J Ying, W Xue… - Briefings in …, 2020 - academic.oup.com
Functional annotation of protein sequence with high accuracy has become one of the most
important issues in modern biomedical studies, and computational approaches of …
important issues in modern biomedical studies, and computational approaches of …
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
Experimental studies of Escherichia coli K-12 MG1655 often implicate poorly annotated
genes in cellular phenotypes. However, we lack a systematic understanding of these genes …
genes in cellular phenotypes. However, we lack a systematic understanding of these genes …
Bacillus subtilis, the model Gram‐positive bacterium: 20 years of annotation refinement
Genome annotation is, nowadays, performed via automatic pipelines that cannot
discriminate between right and wrong annotations. Given their importance in increasing the …
discriminate between right and wrong annotations. Given their importance in increasing the …
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
Y Gao, JT Yurkovich, SW Seo… - Nucleic Acids …, 2018 - academic.oup.com
Transcriptional regulation enables cells to respond to environmental changes. Of the
estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 …
estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 …
PaperBLAST: text mining papers for information about homologs
Large-scale genome sequencing has identified millions of protein-coding genes whose
function is unknown. Many of these proteins are similar to characterized proteins from other …
function is unknown. Many of these proteins are similar to characterized proteins from other …
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1. 3.15 enzyme class
E Rembeza, MKM Engqvist - PLoS computational biology, 2021 - journals.plos.org
Only a small fraction of genes deposited to databases have been experimentally
characterised. The majority of proteins have their function assigned automatically, which can …
characterised. The majority of proteins have their function assigned automatically, which can …