[HTML][HTML] Ontology map** for semantically enabled applications

I Harrow, R Balakrishnan, E Jimenez-Ruiz, S Jupp… - Drug discovery today, 2019 - Elsevier
Highlights•Ontology map** enables data analytics through interoperability and
integration.•Map** between ontologies expands coverage across large domains such as …

Computational aspects underlying genome to phenome analysis in plants

AM Bolger, H Poorter, K Dumschott… - The Plant …, 2019 - Wiley Online Library
Recent advances in genomics technologies have greatly accelerated the progress in both
fundamental plant science and applied breeding research. Concurrently, high‐throughput …

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction

FZ Smaili, X Gao, R Hoehndorf - Bioinformatics, 2019 - academic.oup.com
Motivation Ontologies are widely used in biology for data annotation, integration and
analysis. In addition to formally structured axioms, ontologies contain meta-data in the form …

DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes

W Liu-Wei, Ş Kafkas, J Chen, NJ Dimonaco… - …, 2021 - academic.oup.com
Motivation Infectious diseases caused by novel viruses have become a major public health
concern. Rapid identification of virus–host interactions can reveal mechanistic insights into …

Predicting candidate genes from phenotypes, functions and anatomical site of expression

J Chen, A Althagafi, R Hoehndorf - Bioinformatics, 2021 - academic.oup.com
Motivation Over the past years, many computational methods have been developed to
incorporate information about phenotypes for disease–gene prioritization task. These …

DeepPVP: phenotype-based prioritization of causative variants using deep learning

I Boudellioua, M Kulmanov, PN Schofield… - BMC …, 2019 - Springer
Background Prioritization of variants in personal genomic data is a major challenge.
Recently, computational methods that rely on comparing phenotype similarity have shown to …

Biomedical ontology alignment: an approach based on representation learning

P Kolyvakis, A Kalousis, B Smith, D Kiritsis - Journal of biomedical …, 2018 - Springer
Background While representation learning techniques have shown great promise in
application to a number of different NLP tasks, they have had little impact on the problem of …

Semantic disease gene embeddings (smudge): phenotype-based disease gene prioritization without phenotypes

M Alshahrani, R Hoehndorf - Bioinformatics, 2018 - academic.oup.com
Motivation In the past years, several methods have been developed to incorporate
information about phenotypes into computational disease gene prioritization methods …

Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project

SL Stenton, MC O'Leary, G Lemire, GE VanNoy… - Human Genomics, 2024 - Springer
Background A major obstacle faced by families with rare diseases is obtaining a genetic
diagnosis. The average" diagnostic odyssey" lasts over five years and causal variants are …

NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks

M Abdellah, J Hernando, S Eilemann, S Lapere… - …, 2018 - academic.oup.com
Motivation From image stacks to computational models, processing digital representations of
neuronal morphologies is essential to neuroscientific research. Workflows involve various …