AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

H Hu, YR Miao, LH Jia, QY Yu, Q Zhang… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to
provide the most comprehensive and accurate information for animal transcription factors …

The fecal metabolome as a functional readout of the gut microbiome

J Zierer, MA Jackson, G Kastenmüller, M Mangino… - Nature …, 2018 - nature.com
The human gut microbiome plays a key role in human health 1, but 16S characterization
lacks quantitative functional annotation 2. The fecal metabolome provides a functional …

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

AM Altenhoff, CM Train, KJ Gilbert… - Nucleic acids …, 2021 - academic.oup.com
OMA is an established resource to elucidate evolutionary relationships among genes from
currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise …

Systematic integration of biomedical knowledge prioritizes drugs for repurposing

DS Himmelstein, A Lizee, C Hessler, L Brueggeman… - Elife, 2017 - elifesciences.org
The ability to computationally predict whether a compound treats a disease would improve
the economy and success rate of drug approval. This study describes Project Rephetio to …

BP180/Collagen XVII: A molecular view

J Tuusa, N Kokkonen, K Tasanen - International journal of molecular …, 2021 - mdpi.com
BP180 is a type II collagenous transmembrane protein and is best known as the major
autoantigen in the blistering skin disease bullous pemphigoid (BP). The BP180 trimer is a …

New and continuing developments at PROSITE

CJA Sigrist, E De Castro, L Cerutti… - Nucleic acids …, 2012 - academic.oup.com
Abstract PROSITE (http://prosite. expasy. org/) consists of documentation entries describing
protein domains, families and functional sites, as well as associated patterns and profiles to …

TISSUES 2.0: an integrative web resource on mammalian tissue expression

O Palasca, A Santos, C Stolte, J Gorodkin… - Database, 2018 - academic.oup.com
Physiological and molecular similarities between organisms make it possible to translate
findings from simpler experimental systems—model organisms—into more complex ones …

Wikidata as a knowledge graph for the life sciences

A Waagmeester, G Stupp, S Burgstaller-Muehlbacher… - Elife, 2020 - elifesciences.org
Wikidata is a community-maintained knowledge base that has been assembled from
repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical …

Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage

AM Liaci, B Steigenberger, PCT de Souza, S Tamara… - Molecular cell, 2021 - cell.com
The signal peptidase complex (SPC) is an essential membrane complex in the endoplasmic
reticulum (ER), where it removes signal peptides (SPs) from a large variety of secretory pre …

Enzyme annotation in UniProtKB using Rhea

A Morgat, T Lombardot, E Coudert, K Axelsen… - …, 2020 - academic.oup.com
Motivation To provide high quality computationally tractable enzyme annotation in
UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical …