The sponge microbiome project

L Moitinho-Silva, S Nielsen, A Amir, A Gonzalez… - …, 2017 - academic.oup.com
Rhododendron delavayi Franch. is globally famous as an ornamental plant. Its distribution in
southwest China covers several different habitats and environments. However, not much …

Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation

J Chen, B Goudey, N Geard, K Verspoor - Bioinformatics, 2024 - academic.oup.com
Motivation Biological background knowledge plays an important role in the manual quality
assurance (QA) of biological database records. One such QA task is the detection of …

EcoGene 3.0

J Zhou, KE Rudd - Nucleic acids research, 2012 - academic.oup.com
Abstract EcoGene (http://ecogene. org) is a database and website devoted to continuously
improving the structural and functional annotation of Escherichia coli K-12, one of the most …

ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

DV Veres, DM Gyurkó, B Thaler, KZ Szalay… - Nucleic acids …, 2015 - academic.oup.com
Here we present ComPPI, a cellular compartment-specific database of proteins and their
interactions enabling an extensive, compartmentalized protein–protein interaction network …

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space

AM Schnoes, DC Ream, AW Thorman… - PLoS computational …, 2013 - journals.plos.org
The ongoing functional annotation of proteins relies upon the work of curators to capture
experimental findings from scientific literature and apply them to protein sequence and …

Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes

TF Mitterboeck, S Liu, SJ Adamowicz, J Fu… - …, 2017 - academic.oup.com
The evolution of powered flight is a major innovation that has facilitated the success of
insects. Previously, studies of birds, bats, and insects have detected molecular signatures of …

Soft-prompt tuning to predict lung cancer using primary care free-text Dutch medical notes

A Elfrink, I Vagliano, A Abu-Hanna, I Calixto - International Conference on …, 2023 - Springer
We examine the use of large Transformer-based pretrained language models (PLMs) for the
problem of early prediction of lung cancer using free-text patient medical notes of Dutch …

Extracting cross-ontology weighted association rules from gene ontology annotations

G Agapito, M Milano, PH Guzzi… - IEEE/ACM transactions …, 2015 - ieeexplore.ieee.org
Gene Ontology (GO) is a structured repository of concepts (GO Terms) that are associated to
one or more gene products through a process referred to as annotation. The analysis of …

[HTML][HTML] Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO …

P Manda, F McCarthy, SM Bridges - Journal of biomedical informatics, 2013 - Elsevier
Abstract The Gene Ontology (GO), a set of three sub-ontologies, is one of the most popular
bio-ontologies used for describing gene product characteristics. GO annotation data …

GSAn: an alternative to enrichment analysis for annotating gene sets

A Ayllon-Benitez, R Bourqui, P Thébault… - NAR Genomics and …, 2020 - academic.oup.com
The revolution in new sequencing technologies is greatly leading to new understandings of
the relations between genotype and phenotype. To interpret and analyze data that are …