Machine learning approaches and databases for prediction of drug–target interaction: a survey paper

M Bagherian, E Sabeti, K Wang… - Briefings in …, 2021 - academic.oup.com
The task of predicting the interactions between drugs and targets plays a key role in the
process of drug discovery. There is a need to develop novel and efficient prediction …

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

C Manzoni, DA Kia, J Vandrovcova… - Briefings in …, 2018 - academic.oup.com
Advances in the technologies and informatics used to generate and process large biological
data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While …

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

BT Sherman, M Hao, J Qiu, X Jiao… - Nucleic acids …, 2022 - academic.oup.com
DAVID is a popular bioinformatics resource system including a web server and web service
for functional annotation and enrichment analyses of gene lists. It consists of a …

WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

P Davis, M Zarowiecki, V Arnaboldi, A Becerra… - Genetics, 2022 - academic.oup.com
Abstract WormBase (www. wormbase. org) is the central repository for the genetics and
genomics of the nematode Caenorhabditis elegans. We provide the research community …

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

D Szklarczyk, AL Gable, KC Nastou, D Lyon… - Nucleic acids …, 2021 - academic.oup.com
Cellular life depends on a complex web of functional associations between biomolecules.
Among these associations, protein–protein interactions are particularly important due to their …

The IntAct database: efficient access to fine-grained molecular interaction data

N Del Toro, A Shrivastava, E Ragueneau… - Nucleic acids …, 2022 - academic.oup.com
The IntAct molecular interaction database (https://www. ebi. ac. uk/intact) is a curated
resource of molecular interactions, derived from the scientific literature and from direct data …

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

M Efremova, M Vento-Tormo, SA Teichmann… - Nature protocols, 2020 - nature.com
Cell–cell communication mediated by ligand–receptor complexes is critical to coordinating
diverse biological processes, such as development, differentiation and inflammation. To …

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

D Szklarczyk, AL Gable, D Lyon, A Junge… - Nucleic acids …, 2019 - academic.oup.com
Proteins and their functional interactions form the backbone of the cellular machinery. Their
connectivity network needs to be considered for the full understanding of biological …

UniProt: a worldwide hub of protein knowledge

UniProt Consortium - Nucleic acids research, 2019 - academic.oup.com
Abstract The UniProt Knowledgebase is a collection of sequences and annotations for over
120 million proteins across all branches of life. Detailed annotations extracted from the …