Haendel, Melissa A

Uberon, an integrative multi-species anatomy ontology

Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., & Haendel, M. A. (2012) · Genome biology

Biomedical Text Mining and OntologiesSemantic Web and Ontologies

Cited by 732

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

Köhler, S., Carmody, L., Vasilevsky, N., Jacobsen, J. O. B., Danis, D., Gourdine, J.-P., Gargano, M., Harris, N. L., Matentzoglu, N., McMurry, J. A., et al. (2019) · Nucleic Acids Research

Biomedical Text Mining and OntologiesGenomics and Rare Diseases

Cited by 677

How many rare diseases are there?

Haendel, M., Vasilevsky, N., Unni, D., Bologa, C., Harris, N., Rehm, H., Hamosh, A., Baynam, G., Groza, T., McMurry, J., et al. (2020) · Nature Reviews Drug Discovery

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 554

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment

Haendel, M. A., Chute, C. G., Bennett, T. D., Eichmann, D. A., Guinney, J., Kibbe, W. A., Payne, P. R. O., Pfaff, E. R., Robinson, P. N., Saltz, J. H., et al. (2021) · Journal of the American Medical Informatics Association

Research Data Management PracticesElectronic Health Records Systems

Cited by 553

Next-generation diagnostics and disease-gene discovery with the Exomiser

Smedley, D., Jacobsen, J. O. B., Jäger, M., Köhler, S., Holtgrewe, M., Schubach, M., Siragusa, E., Zemojtel, T., Buske, O. J., Washington, N. L., et al. (2015) · Nature Protocols

Genomics and Rare DiseasesBioinformatics and Genomic Networks

Cited by 445

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

Mungall, C. J., McMurry, J. A., Köhler, S., Balhoff, J. P., Borromeo, C., Brush, M., Carbon, S., Conlin, T., Dunn, N., Engelstad, M., et al. (2017) · Nucleic Acids Research

Biomedical Text Mining and OntologiesBioinformatics and Genomic Networks

Cited by 441

The Human Phenotype Ontology in 2024: phenotypes around the world

Gargano, M. A., Matentzoglu, N., Coleman, B., Addo-Lartey, E. B., Anagnostopoulos, A. V., Anderton, J., Avillach, P., Bagley, A. M., Bakštein, E., Balhoff, J. P., et al. (2024) · Nucleic Acids Research

Biomedical Text Mining and OntologiesGenomics and Rare Diseases

Cited by 410

Improved exome prioritization of disease genes through cross-species phenotype comparison

Robinson, P. N., Köhler, S., Oellrich, A., Sanger Mouse Genetics Project, Wang, K., Mungall, C. J., Lewis, S. E., Washington, N., Bauer, S., Seelow, D., et al. (2014) · Genome Research

Genomics and Rare DiseasesBioinformatics and Genomic Networks

Cited by 375

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

Smedley, D., Schubach, M., Jacobsen, J. O. B., Köhler, S., Zemojtel, T., Spielmann, M., Jäger, M., Hochheiser, H., Washington, N. L., McMurry, J. A., et al. (2016) · The American Journal of Human Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 283

On the reproducibility of science: unique identification of research resources in the biomedical literature

Vasilevsky, N. A., Brush, M. H., Paddock, H., Ponting, L., Tripathy, S. J., LaRocca, G. M., & Haendel, M. A. (2013) · PeerJ

Research Data Management PracticesAcademic Publishing and Open Access

Cited by 271

Characterizing long COVID: deep phenotype of a complex condition

Deer, R. R., Rock, M. A., Vasilevsky, N., Carmody, L., Rando, H., Anzalone, A. J., Basson, M. D., Bennett, T. D., Bergquist, T., Boudreau, E. A., et al. (2021) · EBioMedicine

Long-Term Effects of COVID-19Biomedical Text Mining and Ontologies

Cited by 200

Reproducible and reusable research: are journal data sharing policies meeting the mark?

Vasilevsky, N. A., Minnier, J., Haendel, M. A., & Champieux, R. E. (2017) · PeerJ

Research Data Management PracticesAcademic Publishing and Open Access

Cited by 165

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

Variant Interpretation for Cancer Consortium, Wagner, A. H., Walsh, B., Mayfield, G., Tamborero, D., Sonkin, D., Krysiak, K., Deu-Pons, J., Duren, R. P., Gao, J., et al. (2020) · Nature Genetics

Genomics and Rare DiseasesCancer Genomics and Diagnostics

Cited by 164

Deletions of chromosomal regulatory boundaries are associated with congenital disease

Ibn-Salem, J., Köhler, S., Love, M. I., Chung, H.-R., Huang, N., Hurles, M. E., Haendel, M., Washington, N. L., Smedley, D., Mungall, C. J., et al. (2014) · Genome Biology

Genomic variations and chromosomal abnormalitiesGenomics and Chromatin Dynamics

Cited by 143

Mondo: Unifying diseases for the world, by the world

Vasilevsky, N. A., Matentzoglu, N. A., Toro, S., Flack, J. E., Hegde, H., Unni, D. R., Alyea, G. F., Amberger, J. S., Babb, L., Balhoff, J. P., et al. (2022) · medRxiv

Biomedical Text Mining and OntologiesSemantic Web and Ontologies

Cited by 107

The Resource Identification Initiative: A cultural shift in publishing

Bandrowski, A., Brush, M., Grethe, J. S., Haendel, M. A., Kennedy, D. N., Hill, S., Hof, P. R., Martone, M. E., Pols, M., Tan, S., et al. (2015) · F1000Research

Research Data Management PracticesAcademic Publishing and Open Access

Cited by 80

The resource identification initiative: a cultural shift in publishing

Bandrowski, A., Brush, M., Grethe, J. S., Haendel, M. A., Kennedy, D. N., Hill, S., Hof, P. R., Martone, M. E., Pols, M., Tan, S., et al. (2015) · F1000Research

Research Data Management PracticesAcademic Publishing and Open Access

Cited by 50

A Census of Disease Ontologies

Haendel, M. A., McMurry, J. A., Relevo, R., Mungall, C. J., Robinson, P. N., & Chute, C. G. (2018) · Annual Review of Biomedical Data Science

Biomedical Text Mining and OntologiesSemantic Web and Ontologies

Cited by 49

The Resource Identification Initiative: a cultural shift in publishing

Bandrowski, A., Brush, M., Grethe, J. S., Haendel, M. A., Kennedy, D. N., Hill, S., Hof, P. R., Martone, M. E., Pols, M., Tan, S. C., et al. (2016) · Journal of Comparative Neurology

Research Data Management PracticesAcademic Publishing and Open Access

Cited by 41

Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools

Reese, J. T., Chimirri, L., Bridges, Y., Danis, D., Caufield, J. H., Gargano, M. A., Kroll, C., Schmeder, A., Liu, F., Wissink, K., et al. (2024) · medRxiv

Artificial Intelligence in Healthcare and EducationGenomics and Rare Diseases

Cited by 8