dbDEMC 3.0: functional exploration of differentially expressed miRNAs in cancers of human and model organisms

F Xu, Y Wang, Y Ling, C Zhou, H Wang… - … and Bioinformatics, 2022 - academic.oup.com
… Here we report an update of the dbDEMC to version 3.0, … ” or “miRNA” to conduct an exhaustive
search for the microarray-… to find a candidate miRNA list which links to an individual type …

jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population

S Tadaka, E Hishinuma, S Komaki… - … acids research, 2021 - academic.oup.com
… the UK Biobank are being conducted by deCODE genetics Inc. … population, we constructed
a web-based database of data … The 'Chain' dropdown list can be used to highlight the …

[HTML][HTML] SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

S Volant, P Lechat, P Woringer, L Motreff… - … bioinformatics, 2020 - Springer
… the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. … other
web interfaces designed for metataxonomic analyses (see Table 1). We first defined a list of …

TransmiR v2. 0: an updated transcription factor-microRNA regulation database

Z Tong, Q Cui, J Wang, Y Zhou - Nucleic acids research, 2019 - academic.oup.com
… are likely to regulate a miRNA list of interest. In conclusion, … motif matrices of human TFs
do not specify the action type (ie … better applications of this dataset for bioinformatics analysis. …

hypeR: an R package for geneset enrichment workflows

A Federico, S Monti - Bioinformatics, 2020 - academic.oup.com
… one or more signatures and a list of genesets to test for either … to cluster their first degree
connections, allowing for dynamic … of performing geneset enrichment workflows for a variety of …

The BioGRID interaction database: 2019 update

R Oughtred, C Stark, BJ Breitkreutz, J Rust… - … acids research, 2019 - academic.oup.com
… existing applications via our web service platforms. BioGRID … These statistics do not include
the widespread dissemination … The ranked publications are then curated, and the gene list

MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks

H Fu, F Huang, X Liu, Y Qiu, W Zhang - Bioinformatics, 2022 - academic.oup.com
… (NIA) layer to update node embeddings in each view of the … In this section, we conduct case
studies to exhibit the … For each of the three diseases, we list the top five predicted candidate …

WormBase: a modern model organism information resource

TW Harris, V Arnaboldi, S Cain, J Chan… - … acids research, 2020 - academic.oup.com
… of the web interface and options for users wishing to conduct … ’ allows users to enter or upload
a list of genes from one of the … -year effort to upgrade the software driving the website, we …

The Pfam protein families database in 2019

S El-Gebali, J Mistry, A Bateman, SR Eddy… - … acids research, 2019 - academic.oup.com
… The Pfam website has been updated to provide a link to … , rather than the concatenated list
previously provided. This is an … of the EMBL-European Bioinformatics Institute training team for …

[HTML][HTML] In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR

G Pawar, JC Madden, D Ebbrell, JW Firman… - Frontiers in …, 2019 - frontiersin.org
study was to provide a comprehensive and consolidated list … on clinical studies (summary
and protocols) are updated by … The Ensembl database provides a bioinformatics framework to …