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Realising the potential impact of artificial intelligence for rare diseases – A framework

Rare
2025 | Journal article
Contributors: Tudor Groza; Chun-Hung Chan; David A. Pearce; Gareth Baynam
Source: check_circle
Crossref

FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology

Bioinformatics
2024-07-01 | Journal article
Contributors: Tudor Groza; Dylan Gration; Gareth Baynam; Peter N Robinson; Jonathan Wren
Source: check_circle
Crossref

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts

Bioinformatics
2023-12-01 | Journal article
Contributors: Tudor Groza; Honghan Wu; Marcel E Dinger; Daniel Danis; Coleman Hilton; Anita Bagley; Jon R Davids; Ling Luo; Zhiyong Lu; Peter N Robinson et al.
Source: check_circle
Crossref

PDCM Finder: an open global research platform for patient-derived cancer models.

Nucleic acids research
2023-01 | Journal article
Contributors: Perova Z; Martinez M; Mandloi T; Gomez FL; Halmagyi C; Follette A; Mason J; Newhauser S; Begley DA; Krupke DM et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease

Nucleic Acids Research
2023-01-06 | Journal article
Contributors: Tudor Groza; Federico Lopez Gomez; Hamed Haseli Mashhadi; Violeta Muñoz-Fuentes; Osman Gunes; Robert Wilson; Pilar Cacheiro; Anthony Frost; Piia Keskivali-Bond; Bora Vardal et al.
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Crossref

The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource

Nucleic Acids Research
2023-01-06 | Journal article
Contributors: Elliot Sollis; Abayomi Mosaku; Ala Abid; Annalisa Buniello; Maria Cerezo; Laurent Gil; Tudor Groza; Osman Güneş; Peggy Hall; James Hayhurst et al.
Source: check_circle
Crossref

A consensus score to combine inferences from multiple centres

2022-11 | Preprint
Contributors: Haselimashhadi H; Babalola K; Wilson R; Groza T; Muñoz-Fuentes V
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

A consensus score to combine inferences from multiple centres

2022-11-14 | Preprint
Contributors: Hamed Haselimashhadi; Kolawole Babalola; Robert Wilson; Tudor Groza; Violeta Muñoz-Fuentes
Source: check_circle
Crossref

The GA4GH Phenopacket schema defines a computable representation of clinical data.

Nature biotechnology
2022-06 | Journal article
Contributors: Jacobsen JOB; Baudis M; Baynam GS; Beckmann JS; Beltran S; Buske OJ; Callahan TJ; Chute CG; Courtot M; Danis D et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Mondo: Unifying diseases for the world, by the world

2022-04 | Preprint
Contributors: Vasilevsky NA; Matentzoglu NA; Toro S; Flack JE; Hegde H; Unni DR; Alyea GF; Amberger JS; Babb L; Balhoff JP et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Cell genomics
2021-11 | Other
Contributors: Rehm HL; Page AJH; Smith L; Adams JB; Alterovitz G; Babb LJ; Barkley MP; Baudis M; Beauvais MJS; Beck T et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

2021-11 | Preprint
Contributors: Jacobsen JOB; Baudis M; Baynam GS; Beckmann JS; Beltran S; Callahan TJ; Chute CG; Courtot M; Danis D; Elemento O et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

A flexible computational pipeline for research analyses of unsolved clinical exome cases.

NPJ genomic medicine
2020-12 | Journal article
Contributors: Lassmann T; Francis RW; Weeks A; Tang D; Jamieson SE; Broley S; Dawkins HJS; Dreyer L; Goldblatt J; Groza T et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

BioHackathon 2015: Semantics of data for life sciences and reproducible research

2020-02 | Preprint
Contributors: Vos RA; Katayama T; Mishima H; Kawano S; Kawashima S; Kim J; Moriya Y; Tokimatsu T; Yamaguchi A; Yamamoto Y et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

How many rare diseases are there?

Nature reviews. Drug discovery
2020-02 | Journal article
Contributors: Haendel M; Vasilevsky N; Unni D; Bologa C; Harris N; Rehm H; Hamosh A; Baynam G; Groza T; McMurry J et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Impacts of genomics on the health and social costs of intellectual disability.

Journal of medical genetics
2020-01 | Journal article
Contributors: Doble B; Schofield D; Evans CA; Groza T; Mattick JS; Field M; Roscioli T
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Nucleic acids research
2020-01 | Journal article
Contributors: Shefchek KA; Harris NL; Gargano M; Matentzoglu N; Unni D; Brush M; Keith D; Conlin T; Vasilevsky N; Zhang XA et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.

Current protocols in human genetics
2019-09 | Journal article
Contributors: Köhler S; Øien NC; Buske OJ; Groza T; Jacobsen JOB; McNamara C; Vasilevsky N; Carmody LC; Gourdine JP; Gargano M et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative.

Frontiers in genetics
2019-07 | Journal article
Contributors: Nellåker C; Alkuraya FS; Baynam G; Bernier RA; Bernier FPJ; Boulanger V; Brudno M; Brunner HG; Clayton-Smith J; Cogné B et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Nucleic acids research
2019-01 | Journal article
Contributors: Köhler S; Carmody L; Vasilevsky N; Jacobsen JOB; Danis D; Gourdine JP; Gargano M; Harris NL; Matentzoglu N; McMurry JA et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Cancer Care Treatment Outcome Ontology: A Novel Computable Ontology for Profiling Treatment Outcomes in Patients With Solid Tumors.

JCO clinical cancer informatics
2018-12 | Journal article
Contributors: Lin FP; Groza T; Kocbek S; Antezana E; Epstein RJ
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Building interpretable models for polypharmacy prediction in older chronic patients based on drug prescription records.

PeerJ
2018-10 | Journal article
Contributors: Kocbek S; Kocbek P; Stozer A; Zupanic T; Groza T; Stiglic G
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

CogStack - experiences of deploying integrated information retrieval and extraction services in a large National Health Service Foundation Trust hospital.

BMC medical informatics and decision making
2018-06 | Journal article
Contributors: Jackson R; Kartoglu I; Stringer C; Gorrell G; Roberts A; Song X; Wu H; Agrawal A; Lui K; Groza T et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Plain-language medical vocabulary for precision diagnosis.

Nature genetics
2018-04 | Journal article
Contributors: Vasilevsky NA; Foster ED; Engelstad ME; Carmody L; Might M; Chambers C; Dawkins HJS; Lewis J; Della Rocca MG; Snyder M et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Harmonising phenomics information for a better interoperability in the rare disease field.

European journal of medical genetics
2018-02 | Journal article
Contributors: Maiella S; Olry A; Hanauer M; Lanneau V; Lourghi H; Donadille B; Rodwell C; Köhler S; Seelow D; Jupp S et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Matchmaker Exchange.

Current protocols in human genetics
2017-10 | Journal article
Contributors: Sobreira NLM; Arachchi H; Buske OJ; Chong JX; Hutton B; Foreman J; Schiettecatte F; Groza T; Jacobsen JOB; Haendel MA et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Initiating an undiagnosed diseases program in the Western Australian public health system.

Orphanet journal of rare diseases
2017-05 | Journal article
Contributors: Baynam G; Broley S; Bauskis A; Pachter N; McKenzie F; Townshend S; Slee J; Kiraly-Borri C; Vasudevan A; Hawkins A et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

CogStack - Experiences Of Deploying Integrated Information Retrieval And Extraction Services In A Large National Health Service Foundation Trust Hospital

2017-04 | Preprint
Contributors: Jackson R; Kartoglu IE; Agrawal A; Lui K; Wu H; Groza T; Roberts A; Gorrell G; Song X; Lewsley D et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework.

Advances in experimental medicine and biology
2017-01 | Journal article
Contributors: Baynam G; Bowman F; Lister K; Walker CE; Pachter N; Goldblatt J; Boycott KM; Gahl WA; Kosaki K; Adachi T et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.

Journal of biomedical semantics
2016-12 | Journal article
Contributors: Verspoor K; Oellrich A; Collier N; Groza T; Rocca-Serra P; Soldatova L; Dumontier M; Shah N
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

The Human Phenotype Ontology in 2017.

Nucleic acids research
2016-11 | Journal article
Contributors: Köhler S; Vasilevsky NA; Engelstad M; Foster E; McMurry J; Aymé S; Baynam G; Bello SM; Boerkoel CF; Boycott KM et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species

2016-11 | Preprint
Contributors: Mungall CJ; McMurry JA; Köhler S; Balhoff JP; Borromeo C; Brush M; Carbon S; Conlin T; Dunn N; Engelstad M et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Nucleic acids research
2016-11 | Journal article
Contributors: Mungall CJ; McMurry JA; Köhler S; Balhoff JP; Borromeo C; Brush M; Carbon S; Conlin T; Dunn N; Engelstad M et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

American journal of human genetics
2016-08 | Journal article
Contributors: Smedley D; Schubach M; Jacobsen JOB; Köhler S; Zemojtel T; Spielmann M; Jäger M; Hochheiser H; Washington NL; McMurry JA et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Navigating the Phenotype Frontier: The Monarch Initiative.

Genetics
2016-08 | Journal article
Contributors: McMurry JA; Köhler S; Washington NL; Balhoff JP; Borromeo C; Brush M; Carbon S; Conlin T; Dunn N; Engelstad M et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Navigating the phenotype frontier: The Monarch Initiative

2016-06 | Preprint
Contributors: McMurry JA; Köhler S; Balhoff JP; Borromeo C; Brush M; Carbon S; Conlin T; Dunn N; Engelstad M; Foster E et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Special issue on bio-ontologies and phenotypes.

Journal of biomedical semantics
2015-12 | Journal article
Contributors: Soldatova LN; Collier N; Oellrich A; Groza T; Verspoor K; Rocca-Serra P; Dumontier M; Shah NH
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

PhenoMiner: from text to a database of phenotypes associated with OMIM diseases.

Database : the journal of biological databases and curation
2015-10 | Journal article
Contributors: Collier N; Groza T; Smedley D; Robinson PN; Oellrich A; Rebholz-Schuhmann D
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

The digital revolution in phenotyping.

Briefings in bioinformatics
2015-09 | Journal article
Contributors: Oellrich A; Collier N; Groza T; Rebholz-Schuhmann D; Shah N; Bodenreider O; Boland MR; Georgiev I; Liu H; Livingston K et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Use of model organism and disease databases to support matchmaking for human disease gene discovery.

Human mutation
2015-09 | Journal article
Contributors: Mungall CJ; Washington NL; Nguyen-Xuan J; Condit C; Smedley D; Köhler S; Groza T; Shefchek K; Hochheiser H; Robinson PN et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Modelling expertise at different levels of granularity using semantic similarity measures in the context of collaborative knowledge-curation platforms.

Journal of intelligent information systems
2015-08 | Journal article
Contributors: Ziaimatin H; Groza T; Tudorache T; Hunter J
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

A supervised approach to quantifying sentence similarity: with application to evidence based medicine.

PloS one
2015-06 | Journal article
Contributors: Hassanzadeh H; Groza T; Nguyen A; Hunter J
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Concept selection for phenotypes and diseases using learn to rank.

Journal of biomedical semantics
2015-06 | Journal article
Contributors: Collier N; Oellrich A; Groza T
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

American journal of human genetics
2015-06 | Journal article
Contributors: Groza T; Köhler S; Moldenhauer D; Vasilevsky N; Baynam G; Zemojtel T; Schriml LM; Kibbe WA; Schofield PN; Beck T et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Capturing domain knowledge from multiple sources: the rare bone disorders use case.

Journal of biomedical semantics
2015-04 | Journal article
Contributors: Groza T; Tudorache T; Robinson PN; Zankl A
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.

PloS one
2015-03 | Journal article
Contributors: Groza T; Verspoor K
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Automatic concept recognition using the human phenotype ontology reference and test suite corpora.

Database : the journal of biological databases and curation
2015-02 | Journal article
Contributors: Groza T; Köhler S; Doelken S; Collier N; Oellrich A; Smedley D; Couto FM; Baynam G; Zankl A; Robinson PN
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

PloS one
2015-01 | Journal article
Contributors: Oellrich A; Collier N; Smedley D; Groza T
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Phenotyping: targeting genotype's rich cousin for diagnosis.

Journal of paediatrics and child health
2014-08 | Journal article
Contributors: Baynam G; Walters M; Claes P; Kung S; LeSouef P; Dawkins H; Bellgard M; Girdea M; Brudno M; Robinson P et al.
Source: Self-asserted source
Tudor Groza via Europe PubMed Central

Identifying scientific artefacts in biomedical literature: the Evidence Based Medicine use case.

Journal of biomedical informatics
2014-02 | Journal article
Contributors: Hassanzadeh H; Groza T; Hunter J
Source: Self-asserted source
Tudor Groza via Europe PubMed Central
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