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Author: Robert Hoehndorf

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  • All-time downloads: 13,581 (rank: 5,262 (tie) out of 393,295)
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    • bioinformatics: 12,891 (rank: 375 out of 33,499)
    • systems biology: 690 (rank: 4,633 (tie) out of 11,532)

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Preprints

FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation.

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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

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Drug repurposing through joint learning on knowledge graphs and literature

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Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings

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

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Machine learning with biomedical ontologies

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DeepGOPlus: Improved protein function prediction from sequence

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Notions of similarity for computational biology models

systems biology more details view paper
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DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier

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Taxonomic propagation of phenotypic features predict host pathogen interactions

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Formal axioms in biomedical ontologies improve analysis and interpretation of associated data

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Ontology-based prediction of cancer driver genes

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Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

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VSIM: Visualization and simulation of variants in personal genomes with an application to premarital testing

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Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies

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    • In bioinformatics: 6,469 out of 8,636
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OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

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Prediction of novel virus-host interactions by integrating clinical symptoms and protein sequences

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Ontology-based validation and identification of regulatory phenotypes

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Ontology based mining of pathogen-disease associations from literature

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

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DDIEM: Drug Database for Inborn Errors of Metabolism

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PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research

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D4: Deep Drug-drug interaction Discovery and Demystification

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Self-normalizing learning on biomedical ontologies using a deep Siamese neural network

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A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text

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Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies

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Improved characterisation of clinical text through ontology-based vocabulary expansion

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