Research Output 2006 2019

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2019

An analysis and metric of reusable data licensing practices for biomedical resources

Carbon, S., Champieux, R., McMurry, J. A., Winfree, L., Wyatt, L. R. & Haendel, M., Mar 1 2019, In : PloS one. 14, 3, e0213090.

Research output: Contribution to journalArticle

Open Access
research support
biomedical research
Licensure
drugs
Reusability

Bi-allelic Variants in TONSL Cause SPONASTRIME Dysplasia and a Spectrum of Skeletal Dysplasia Phenotypes

University of Washington Center for Mendelian Genomics & Undiagnosed Diseases Network, Mar 7 2019, In : American Journal of Human Genetics. 104, 3, p. 422-438 17 p.

Research output: Contribution to journalArticle

Zebrafish
Coxa Vara
Phenotype
Tooth Root
Recombinational DNA Repair

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

Köhler, S., Øien, N. C., Buske, O. J., Groza, T., Jacobsen, J. O. B., McNamara, C., Vasilevsky, N., Carmody, L. C., Gourdine, J. P., Gargano, M., McMurry, J. A., Danis, D., Mungall, C. J., Smedley, D., Haendel, M. & Robinson, P. N., Jan 1 2019, In : Current protocols in human genetics. 103, 1, e92.

Research output: Contribution to journalArticle

Exome
Differential Diagnosis
Phenotype
Inborn Genetic Diseases
Rare Diseases
1 Citation (Scopus)

Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay

Undiagnosed Diseases Network, Jan 3 2019, In : American Journal of Human Genetics. 104, 1, p. 164-178 15 p.

Research output: Contribution to journalArticle

Intellectual Disability
Hypertrichosis
Genes
Exome
Eyebrows
16 Citations (Scopus)

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., Osumi-Sutherland, D., Cipriani, V., Balhoff, J. P., Conlin, T., Blau, H., Baynam, G., Palmer, R., Gratian, D., Dawkins, H., Segal, M. & 49 others, Jansen, A. C., Muaz, A., Chang, W. H., Bergerson, J., Laulederkind, S. J. F., Yüksel, Z., Beltran, S., Freeman, A. F., Sergouniotis, P. I., Durkin, D., Storm, A. L., Hanauer, M., Brudno, M., Bello, S. M., Sincan, M., Rageth, K., Wheeler, M. T., Oegema, R., Lourghi, H., Della Rocca, M. G., Thompson, R., Castellanos, F., Priest, J., Cunningham-Rundles, C., Hegde, A., Lovering, R. C., Hajek, C., Olry, A., Notarangelo, L., Similuk, M., Zhang, X. A., Gómez-Andrés, D., Lochmüller, H., Dollfus, H., Rosenzweig, S., Marwaha, S., Rath, A., Sullivan, K., Smith, C., Milner, J. D., Leroux, D., Boerkoel, C. F., Klion, A., Carter, M. C., Groza, T., Smedley, D., Haendel, M., Mungall, C. & Robinson, P. N., Jan 8 2019, In : Nucleic Acids Research. 47, D1, p. D1018-D1027

Research output: Contribution to journalArticle

Knowledge Bases
Phenotype
Exome
Vocabulary
Electronic Health Records

Extracutaneous manifestations in phacomatosis cesioflammea and cesiomarmorata: Case series and literature review

Undiagnosed Diseases Network, Jun 1 2019, In : American Journal of Medical Genetics, Part A. 179, 6, p. 966-977 12 p.

Research output: Contribution to journalArticle

Neurocutaneous Syndromes
Blood Vessels
Mutation
Nervous System Malformations
Skin

Lysosomal Storage and Albinism Due to Effects of a De Novo CLCN7 Variant on Lysosomal Acidification

Undiagnosed Diseases Network, Jun 6 2019, In : American Journal of Human Genetics. 104, 6, p. 1127-1138 12 p.

Research output: Contribution to journalArticle

Albinism
Hypopigmentation
Fibroblasts
Vacuoles
Osteopetrosis
3 Citations (Scopus)

Preexposure prophylaxis for the prevention of HIV infection: Evidence report and systematic review for the US preventive services task force

Chou, R., Evans, C., Hoverman, A., Sun, C., Dana, T., Bougatsos, C., Grusing, S. & Korthuis, P. T., Jun 11 2019, In : JAMA - Journal of the American Medical Association. 321, 22, p. 2214-2230 17 p.

Research output: Contribution to journalArticle

Advisory Committees
Tenofovir
HIV Infections
Numbers Needed To Treat
Placebos

The Global academic research organization network: Data sharing to cure diseases and enable learning health systems

Fukushima, M., Austin, C., Sato, N., Maruyama, T., Navarro, E., Rocca, M., Demotes, J., Haendel, M., Volchenboum, S. L., Cowperthwaite, M., Silverstein, J. C., Webb, C., Sim, I., Chase, M., Speakman, J., Augustine, E., Ford, D. E. & Kush, R., Jan 1 2019, In : Learning Health Systems. 3, 1, e10073.

Research output: Contribution to journalArticle

Open Access
Information Dissemination
Learning
Health
Research
Japan
2018
6 Citations (Scopus)

A comprehensive iterative approach is highly effective in diagnosing individuals who are exome negative

Undiagnosed Diseases Network, Jun 15 2018, (Accepted/In press) In : Genetics in Medicine. p. 1-12 12 p.

Research output: Contribution to journalArticle

Exome
Genome
Computational Biology
Genetic Association Studies
Phenotype
7 Citations (Scopus)

Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder

Undiagnosed Diseases Network, Mar 1 2018, In : American Journal of Human Genetics. 102, 3, p. 494-504 11 p.

Research output: Contribution to journalArticle

Mitochondrial Diseases
Adenosine Triphosphate
Mitochondrial Proton-Translocating ATPases
Head
Hyperammonemia

Biocuration: Distilling data into knowledge

International Society for Biocuration, Apr 16 2018, In : PLoS Biology. 16, 4, e2002846.

Research output: Contribution to journalArticle

assets
researchers
Research Personnel
Medicine
Costs

Characteristics of undiagnosed diseases network applicants: Implications for referring providers

Walley, N. M., Pena, L. D. M., Hooper, S. R., Cope, H., Jiang, Y. H., McConkie-Rosell, A., Sanders, C., Schoch, K., Spillmann, R. C., Strong, K., McCray, A. T., Mazur, P., Esteves, C., Leblanc, K., Adams, D. R., Alejandro, M. E., Allard, P., Ashley, E. A., Azamian, M. S., Bacino, C. A. & 166 others, Balasubramanyam, A., Barseghyan, H., Batzli, G. F., Beggs, A. H., Bellen, H. J., Bernstein, J. A., Bican, A., Bick, D. P., Birch, C. L., Bonner, D., Boone, B. E., Bostwick, B. L., Briere, L. C., Brown, D. M., Brush, M., Burke, E. A., Burrage, L. C., Chen, S., Clark, G. D., Coakley, T. R., Cogan, J. D., Cooper, C. M., Craigen, W. J., D'Souza, P., Davids, M., Davidson, J. M., Dayal, J. G., Dell'Angelica, E. C., Dhar, S. U., Dillon, A., Dipple, K. M., Donnell-Fink, L. A., Dorrani, N., Dorset, D. C., Douine, E. D., Draper, D. D., Dries, A. M., Eckstein, D. J., Emrick, L. T., Eng, C. M., Enns, G. M., Eskin, A., Estwick, T., Fernandez, L., Fisher, P. G., Fogel, B. L., Friedman, N. D., Gahl, W. A., Glanton, E., Godfrey, R. A., Goldstein, D. B., Gould, S. E., Gourdine, J. P. F., Groden, C. A., Gropman, A. L., Haendel, M., Hamid, R., Hanchard, N. A., Handley, L. H., Herzog, M. R., Holm, I. A., Hom, J., Howerton, E. M., Huang, Y., Jacob, H. J., Jain, M., Johnston, J. M., Jones, A. L., Koeller, D., Kohane, I. S., Kohler, J. N., Krasnewich, D. M., Krieg, E. L., Krier, J. B., Kyle, J. E., Lalani, S. R., Christopher Lau, C., Lazar, J., Lee, B. H., Lee, H., Levy, S. E., Lewis, R. A., Lincoln, S. A., Lipson, A., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Majcherska, M. M., Malicdan, M. C. V., Mamounas, L. A., Manolio, T. A., Markello, T. C., Marom, R., Martínez-Agosto, J. A., Marwaha, S., May, T., McCormack, C. E., Merker, J. D., Metz, T. O., Might, M., Moretti, P. M., Mulvihill, J. J., Murphy, J. L., Muzny, D. M., Nehrebecky, M. E., Nelson, S. F., Scott Newberry, J., Newman, J. H., Nicholas, S. K., Novacic, D., Orange, J. S., Carl Pallais, J., Palmer, C. G. S., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Postlethwait, J. H., Potocki, L., Pusey, B. N., Reuter, C. M., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Sampson, J. B., Samson, S. L., Schroeder, M. C., Scott, D. A., Sharma, P., Silverman, E. K., Sinsheimer, J. S., Smith, K. S., Soldatos, A. G., Stoler, J. M., Stong, N., Sullivan, J. A., Sweetser, D. A., Tifft, C. J., Toro, C., Tran, A. A., Urv, T. K., Valivullah, Z. M., Vilain, E., Vogel, T. P., Waggott, D. M., Wahl, C. E., Walsh, C. A., Wangler, M. F., Ward, P. A., Waters, K. M., Webb-Robertson, B. J. M., Westerfield, M., Wheeler, M. T., Wolfe, L. A., Worthey, E. A., Yamamoto, S., Yang, Y., Yu, G., Zastrow, D. B., Zhao, C., Zheng, A., Wise, A. L. & Shashi, V., Aug 22 2018, In : BMC Health Services Research. 18, 1, 652.

Research output: Contribution to journalArticle

Referral and Consultation
Demography
Primary Care Physicians
Signs and Symptoms
Fatigue
24 Citations (Scopus)

Classification, ontology, and precision medicine

Haendel, M., Chute, C. G. & Robinson, P. N., Oct 11 2018, In : New England Journal of Medicine. 379, 15, p. 1452-1462 11 p.

Research output: Contribution to journalArticle

Precision Medicine
Patient Care Management
Translational Medical Research
Research Personnel
Therapeutics
4 Citations (Scopus)

ClinGen advancing genomic data-sharing standards as a GA4GH driver project

Dolman, L., Page, A., Babb, L., Freimuth, R. R., Arachchi, H., Bizon, C., Brush, M., Fiume, M., Haendel, M., Hansen, D. P., Milosavljevic, A., Patel, R. Y., Pawliczek, P., Yates, A. D. & Rehm, H. L., Nov 1 2018, In : Human Mutation. 39, 11, p. 1686-1689 4 p.

Research output: Contribution to journalArticle

Information Dissemination
Genome
Genomics
Insurance Pools
Precision Medicine

From museum to archives: managing the Panama Canal Museum Collection

Nemmers, J. R., Duckworth, S., Marcetti, J. B. & Santamaría-Wheeler, L., Jan 2 2018, In : Archives and Records. 39, 1, p. 42-56 15 p.

Research output: Contribution to journalArticle

Canals
Museum Collections
Panama
Artifact
Archivists
3 Citations (Scopus)

IRF2BPL Is Associated with Neurological Phenotypes

Program for Undiagnosed Diseases (UD-PrOZA) & Undiagnosed Diseases Network, Aug 2 2018, In : American Journal of Human Genetics. 103, 2, p. 245-260 16 p.

Research output: Contribution to journalArticle

Interferon Regulatory Factor-2
Carrier Proteins
Phenotype
Ataxia
Diptera
9 Citations (Scopus)

Looking beyond the exome: A phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases

Undiagnosed Diseases Network Members, Apr 1 2018, In : Genetics in Medicine. 20, 4, p. 464-469 6 p.

Research output: Contribution to journalArticle

Exome
Molecular Pathology
Rare Diseases
Phenotype
Systemic Hyalinosis
2 Citations (Scopus)

matchbox: An open-source tool for patient matching via the Matchmaker Exchange

Arachchi, H., Wojcik, M. H., Weisburd, B., Jacobsen, J. O. B., Valkanas, E., Baxter, S., Byrne, A. B., O'Donnell-Luria, A. H., Haendel, M., Smedley, D., MacArthur, D. G., Philippakis, A. A. & Rehm, H. L., Jan 1 2018, (Accepted/In press) In : Human Mutation.

Research output: Contribution to journalArticle

Rare Diseases
Research Personnel
Databases
Genetic Association Studies
Causality
3 Citations (Scopus)

The First National Institutes of Health Institutional Training Program in Emergency Care Research: Productivity and Outcomes

Newgard, C., Morris, C., Smith, L., Cook, J. N. B., Yealy, D. M., Collins, S., Holmes, J. F., Kuppermann, N., Richardson, L. D., Kimmel, S., Becker, L. B., Scott, J. D., Lowe, R. B., Callaway, C. W., Gowen, L. K., Baren, J., Storrow, A. B., Vasilevsky, N., White, M. & Zell, A., Jan 1 2018, (Accepted/In press) In : Annals of Emergency Medicine.

Research output: Contribution to journalArticle

Organized Financing
National Institutes of Health (U.S.)
Emergency Medical Services
Outcome Assessment (Health Care)
Education
2017
28 Citations (Scopus)

A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3

Undiagnosed Diseases Network, Jan 5 2017, In : American Journal of Human Genetics. 100, 1, p. 128-137 10 p.

Research output: Contribution to journalArticle

B-Lymphocytes
Homeobox Genes
Nervous System
Intellectual Disability
Transcription Factors
8 Citations (Scopus)

Defining disease, diagnosis, and translational medicine within a homeostatic perturbation paradigm: The National Institutes of Health undiagnosed diseases program experience

Gall, T., Valkanas, E., Bello, C., Markello, T., Adams, C., Bone, W. P., Brandt, A. J., Brazill, J. M., Carmichael, L., Davids, M., Davis, J., Diaz-Perez, Z., Draper, D., Elson, J., Flynn, E. D., Godfrey, R., Groden, C., Hsieh, C. K., Fischer, R., Golas, G. A. & 31 others, Guzman, J., Huang, Y., Kane, M. S., Lee, E., Li, C., Links, A. E., Maduro, V., Malicdan, M. C. V., Malik, F. S., Nehrebecky, M., Park, J., Pemberton, P., Schaffer, K., Simeonov, D., Sincan, M., Smedley, D., Valivullah, Z., Wahl, C., Washington, N., Wolfe, L. A., Xu, K., Zhu, Y., Gahl, W. A., Tifft, C. J., Toro, C., Adams, D. R., He, M., Robinson, P. N., Haendel, M., Grace Zhai, R. & Boerkoel, C. F., Jan 1 2017, In : Frontiers in Medicine. 4, MAY, 62.

Research output: Contribution to journalArticle

Open Access
Translational Medical Research
National Institutes of Health (U.S.)
Genetic Association Studies
Patient Care
Genotype
60 Citations (Scopus)

Disease model discovery from 3,328 gene knockouts by the International Mouse Phenotyping Consortium

Meehan, T. F., Conte, N., West, D. B., Jacobsen, J. O., Mason, J., Warren, J., Chen, C. K., Tudose, I., Relac, M., Matthews, P., Karp, N., Santos, L., Fiegel, T., Ring, N., Westerberg, H., Greenaway, S., Sneddon, D., Morgan, H., Codner, G. F., Stewart, M. E. & 43 others, Brown, J., Horner, N., Haendel, M., Washington, N., Mungall, C. J., Reynolds, C. L., Gallegos, J., Gailus-Durner, V., Sorg, T., Pavlovic, G., Bower, L. R., Moore, M., Morse, I., Gao, X., Tocchini-Valentini, G. P., Obata, Y., Cho, S. Y., Seong, J. K., Seavitt, J., Beaudet, A. L., Dickinson, M. E., Herault, Y., Wurst, W., De Angelis, M. H., Kent Lloyd, K. C., Flenniken, A. M., Nutter, L. M. J., Newbigging, S., McKerlie, C., Justice, M. J., Murray, S. A., Svenson, K. L., Braun, R. E., White, J. K., Bradley, A., Flicek, P., Wells, S., Skarnes, W. C., Adams, D. J., Parkinson, H., Mallon, A. M., Brown, S. D. M. & Smedley, D., Aug 1 2017, In : Nature Genetics. 49, 8, p. 1231-1238 8 p.

Research output: Contribution to journalArticle

Gene Knockout Techniques
Knockout Mice
Genes
Genome
Arrhythmogenic Right Ventricular Dysplasia

Do oral decongestants have a clinically significant effect on BP in patients with hypertension?

Hollander-Rodriguez, J., Montjoy, H. L., Smedra, B., Prouty, J. P., Hamilton, A. & Guthmann, R., Jun 1 2017, In : Journal of Family Practice. 66, 6, p. E1-E2

Research output: Contribution to journalArticle

Pseudoephedrine
Nasal Decongestants
Blood Pressure
Hypertension
23 Citations (Scopus)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

McMurry, J. A., Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D. K., Gonzalez-Beltran, A., Gormanns, P., Grethe, J., Hastings, J., Hériché, J. K., Hermjakob, H., Ison, J. C., Jimenez, R. C., Jupp, S., Kunze, J. & 24 others, Laibe, C., Le Novère, N., Malone, J., Martin, M. J., McEntyre, J. R., Morris, C., Muilu, J., Müller, W., Rocca-Serra, P., Sansone, S. A., Sariyar, M., Snoep, J. L., Soiland-Reyes, S., Stanford, N. J., Swainston, N., Washington, N., Williams, A. R., Wimalaratne, S. M., Winfree, L. M., Wolstencroft, K., Goble, C., Mungall, C. J., Haendel, M. & Parkinson, H., Jun 29 2017, In : PLoS Biology. 15, 6, e2001414.

Research output: Contribution to journalArticle

Biological Science Disciplines
Databases
bricks
Knowledge Bases
Data integration
32 Citations (Scopus)
Genetic Models
Human Genome
Databases
Genetic Databases
Biological Phenomena
16 Citations (Scopus)

Matchmaker Exchange

Matchmaker Exchange Consortium, Oct 18 2017, In : Current Protocols in Human Genetics. 95, p. 9.31.1-9.31.15

Research output: Contribution to journalArticle

Rare Diseases
Insurance Pools
Communication
Databases
Mosaicism
12 Citations (Scopus)

PDX-MI: Minimal information for patient-derived tumor xenograft models

Meehan, T. F., Conte, N., Goldstein, T., Inghirami, G., Murakami, M. A., Brabetz, S., Gu, Z., Wiser, J. A., Dunn, P., Begley, D. A., Krupke, D. M., Bertotti, A., Bruna, A., Brush, M. H., Byrne, A. T., Caldas, C., Christie, A. L., Clark, D. A., Dowst, H., Dry, J. R. & 34 others, Doroshow, J. H., Duchamp, O., Evrard, Y. A., Ferretti, S., Frese, K. K., Goodwin, N. C., Greenawalt, D., Haendel, M., Hermans, E., Houghton, P. J., Jonkers, J., Kemper, K., Khor, T. O., Lewis, M. T., Lloyd, K. C. K., Mason, J., Medico, E., Neuhauser, S. B., Olson, J. M., Peeper, D. S., Rueda, O. M., Seong, J. K., Trusolino, L., Vinolo, E., Wechsler-Reya, R. J., Weinstock, D. M., Welm, A., Weroha, S. J., Amant, F., Pfister, S. M., Kool, M., Parkinson, H., Butte, A. J. & Bult, C. J., Nov 1 2017, In : Cancer Research. 77, 21, p. e62-e66

Research output: Contribution to journalArticle

Heterografts
Neoplasms
Research
Computer Communication Networks
Aptitude
14 Citations (Scopus)

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

Vasilevsky, N. A., Minnier, J., Haendel, M. & Champieux, R. E., 2017, In : PeerJ. 2017, 4, e3208.

Research output: Contribution to journalArticle

Information Dissemination
Research
Proteins
Journal Impact Factor
reproducibility
253 Citations (Scopus)

The human phenotype ontology in 2017

Köhler, S., Vasilevsky, N. A., Engelstad, M., Foster, E., McMurry, J., Aymé, S., Baynam, G., Bello, S. M., Boerkoel, C. F., Boycott, K. M., Brudno, M., Buske, O. J., Chinnery, P. F., Cipriani, V., Connell, L. E., Dawkins, H. J. S., DeMare, L. E., Devereau, A. D., De Vries, B. B. A., Firth, H. V. & 39 others, Freson, K., Greene, D., Hamosh, A., Helbig, I., Hum, C., Jähn, J. A., James, R., Krause, R., Laulederkind, S. J. F., Lochmüller, H., Lyon, G. J., Ogishima, S., Olry, A., Ouwehand, W. H., Pontikos, N., Rath, A., Schaefer, F., Scott, R. H., Segal, M., Sergouniotis, P. I., Sever, R., Smith, C. L., Straub, V., Thompson, R., Turner, C., Turro, E., Veltman, M. W. M., Vulliamy, T., Yu, J., Von Ziegenweidt, J., Zankl, A., Züchner, S., Zemojtel, T., Jacobsen, J. O. B., Groza, T., Smedley, D., Mungall, C. J., Haendel, M. & Robinson, P. N., Jan 1 2017, In : Nucleic Acids Research. 45, D1, p. D865-D876

Research output: Contribution to journalArticle

Phenotype
Precision Medicine
Translational Medical Research
Vocabulary
Nucleic Acid Databases
58 Citations (Scopus)

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

Mungall, C. J., McMurry, J. A., Kohler, S., Balhoff, J. P., Borromeo, C., Brush, M., Carbon, S., Conlin, T., Dunn, N., Engelstad, M., Foster, E., Gourdine, J. P., Jacobsen, J. O. B., Keith, D., Laraway, B., Lewis, S. E., Xuan, J. N., Shefchek, K., Vasilevsky, N., Yuan, Z. & 6 others, Washington, N., Hochheiser, H., Groza, T., Smedley, D., Robinson, P. N. & Haendel, M., Jan 1 2017, In : Nucleic Acids Research. 45, D1, p. D712-D722

Research output: Contribution to journalArticle

Genotype
Phenotype
Precision Medicine
Informatics
Genetic Association Studies

Tools for exploring mouse models of human disease

Haendel, M., Papatheodorou, I., Oellrich, A., Mungall, C. J., Washington, N., Lewis, S. E., Robinson, P. N. & Smedley, D., 2017, (Accepted/In press) In : Drug Discovery Today: Disease Models.

Research output: Contribution to journalArticle

Validation Studies
Genetic Association Studies
Pharmaceutical Preparations
Therapeutics

Translating technobabble: All you really need to know about uris, linked data, and FRBR

Banerjee, J., Dec 1 2017, Computers in Libraries, 37, 10, p. 21-24 4 p.

Research output: Contribution to specialist publicationArticle

2016
54 Citations (Scopus)

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., Haendel, M., Mungall, C. J., Lewis, S. E., Groza, T., Valentini, G. & Robinson, P. N., Apr 4 2016, (Accepted/In press) In : American Journal of Human Genetics.

Research output: Contribution to journalArticle

Genome
Gene Frequency
Nucleotides
Machine Learning

Building a molecular glyco-phenotype ontology to decipher undiagnosed diseases

Gourdine, J. P., Koeller, D., Brush, M. H., Haendel, M. & Metz, T. O., 2016, In : CEUR Workshop Proceedings. 1747

Research output: Contribution to journalArticle

Ontology
Genes
Textbooks
Pattern matching
Computational methods
38 Citations (Scopus)

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency

Bone, W. P., Washington, N. L., Buske, O. J., Adams, D. R., Davis, J., Draper, D., Flynn, E. D., Girdea, M., Godfrey, R., Golas, G., Groden, C., Jacobsen, J., Köhler, S., Lee, E. M. J., Links, A. E., Markello, T. C., Mungall, C. J., Nehrebecky, M., Robinson, P. N., Sincan, M. & 13 others, Soldatos, A. G., Tifft, C. J., Toro, C., Trang, H., Valkanas, E., Vasilevsky, N., Wahl, C., Wolfe, L. A., Boerkoel, C. F., Brudno, M., Haendel, M., Gahl, W. A. & Smedley, D., Jun 1 2016, In : Genetics in Medicine. 18, 6, p. 608-617 10 p.

Research output: Contribution to journalArticle

Exome
Phenotype
Genes
Benchmarking
Inborn Genetic Diseases
1 Citation (Scopus)

Distributed cognition and process management enabling individualized translational research: The NIH undiagnosed diseases program experience

Links, A. E., Draper, D., Lee, E., Guzman, J., Valivullah, Z., Maduro, V., Lebedev, V., Didenko, M., Tomlin, G., Brudno, M., Girdea, M., Dumitriu, S., Haendel, M., Mungall, C. J., Smedley, D., Hochheiser, H., Arnold, A. M., Coessens, B., Verhoeven, S., Bone, W. & 4 others, Adams, D., Boerkoel, C. F., Gahl, W. A. & Sincan, M., Jan 1 2016, In : Frontiers in Medicine. 3, OCT, 39.

Research output: Contribution to journalArticle

Open Access
Translational Medical Research
Cognition
Uridine Diphosphate
National Institutes of Health (U.S.)
Research

Enhancing SciENcv through semantic research profile integration with the VIVO-ISF ontology

White, M., Brush, M., Essaid, S., Champieux, R., Zell, A., Haendel, M., Grove, C., Tabish, S. M. & Eichmann, D., 2016, In : CEUR Workshop Proceedings. 1747

Research output: Contribution to journalArticle

Ontology
Semantics

Enhancing the human phenotype ontology for use by the layperson

Vasilevsky, N. A., Engelstad, M., Foster, E. D., Haendel, M., Mungall, C. J., Robinson, P. & Köhler, S., 2016, In : CEUR Workshop Proceedings. 1747

Research output: Contribution to journalArticle

Ontology
Terminology
Labels

Gold-standard ontology-based annotation of concepts in biomedical text in the CRAFT corpus: Updates and extensions

Bada, M., Hunter, L., Vasilevsky, N. & Haendel, M., 2016, In : CEUR Workshop Proceedings. 1747

Research output: Contribution to journalArticle

Ontology
Gold
Semantics
3 Citations (Scopus)

Muscle logic: New knowledge resource for anatomy enables comprehensive searches of the literature on the feeding muscles of mammals

Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M., Herrel, A., Herring, S. W., Lapp, H., Mabee, P. M., Muller, H. M., Mungall, C. J., Sternberg, P. W., Van Auken, K., Vinyard, C. J., Williams, S. H. & Wall, C. E., Feb 1 2016, In : PLoS One. 11, 2, e0149102.

Research output: Contribution to journalArticle

Mammals
Ontology
Muscle
Anatomy
mammals
19 Citations (Scopus)

Navigating the phenotype frontier: The monarch initiative

McMurry, J. A., Köhler, S., Washington, N. L., Balhoff, J. P., Borromeo, C., Brush, M., Carbon, S., Conlin, T., Dunn, N., Engelstad, M., Foster, E., Gourdine, J. P., Jacobsen, J. O. B., Keith, D., Laraway, B., Xuan, J. N., Shefchek, K., Vasilevsky, N. A., Yuan, Z., Lewis, S. E. & 6 others, Hochheiser, H., Groza, T., Smedley, D., Robinson, P. N., Mungall, C. J. & Haendel, M., Aug 1 2016, In : Genetics. 203, 4, p. 1491-1495 5 p.

Research output: Contribution to journalArticle

Phenotype
Precision Medicine
Genomics
Genotype
Health
4 Citations (Scopus)

Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease

Mulder, N., Nembaware, V., Adekile, A., Anie, K. A., Inusa, B., Brown, B., Campbell, A., Chinenere, F., Chunda-Liyoka, C., Derebail, V. K., Geard, A., Ghedira, K., Hamilton, C. M., Hanchard, N. A., Haendel, M., Huggins, W., Ibrahim, M., Jupp, S., Kamga, K. K., Knight-Madden, J. & 17 others, Lopez-Sall, P., Mbiyavanga, M., Munube, D., Nirenberg, D., Nnodu, O., Ofori-Acquah, S. F., Ohene-Frempong, K., Opap, K. B., Panji, S., Park, M., Pule, G., Royal, C., Sangeda, R., Tayo, B., Treadwell, M., Tshilolo, L. & Wonkam, A., Mar 1 2016, (Accepted/In press) In : Applied and Translational Genomics.

Research output: Contribution to journalArticle

Sickle Cell Anemia
Education
Quality of Life
Africa South of the Sahara
Infant Mortality
2 Citations (Scopus)

Reproducibility and conflicts in immune epitope data

Vita, R., Vasilevsky, N., Bandrowski, A., Haendel, M., Sette, A. & Peters, B., Mar 1 2016, In : Immunology. 147, 3, p. 349-354 6 p.

Research output: Contribution to journalArticle

Epitopes
Research
Publications
Research Personnel
Databases
17 Citations (Scopus)

Screening for impaired visual acuity in older adults: Updated evidence report and systematic review for the US preventive services task force

Chou, R., Dana, T., Bougatsos, C., Grusing, S. & Blazina, I., Mar 1 2016, In : JAMA - Journal of the American Medical Association. 315, 9, p. 915-933 19 p.

Research output: Contribution to journalArticle

Advisory Committees
Visual Acuity
Macular Degeneration
Refractive Errors
Cataract
1 Citation (Scopus)

SEPIO: A semantic model for the integration and analysis of scientific evidence

Brush, M. H., Shefchek, K. & Haendel, M., 2016, In : CEUR Workshop Proceedings. 1747

Research output: Contribution to journalArticle

Ontology
Semantics
Data integration
Metadata
Data mining

Systemic corticosteroids for radicular and non-radicular low back pain

Chou, R., Pinto, R. Z., Fu, R. R., Lowe, R. B., Henschke, N. & Dana, T., Dec 5 2016, In : Cochrane Database of Systematic Reviews. 2016, 12, CD012450.

Research output: Contribution to journalArticle

Low Back Pain
Adrenal Cortex Hormones
Placebos
25 Citations (Scopus)

The cell ontology 2016: Enhanced content, modularization, and ontology interoperability

Diehl, A. D., Meehan, T. F., Bradford, Y. M., Brush, M. H., Dahdul, W. M., Dougall, D. S., He, Y., Osumi-Sutherland, D., Ruttenberg, A., Sarntivijai, S., Van Slyke, C. E., Vasilevsky, N. A., Haendel, M., Blake, J. A. & Mungall, C. J., 2016, In : Journal of Animal Science and Biotechnology. 7, 1, 44.

Research output: Contribution to journalArticle

Interoperability
Ontology
cells
Foundries
Biological Ontologies
8 Citations (Scopus)

The health care and life sciences community profile for dataset descriptions

Dumontier, M., Gray, A. J. G., Marshall, M. S., Alexiev, V., Ansell, P., Bader, G., Baran, J., Bolleman, J. T., Callahan, A., Cruz-Toledo, J., Gaudet, P., Gombocz, E. A., Gonzalez-Beltran, A. N., Groth, P., Haendel, M., Ito, M., Jupp, S., Juty, N., Katayama, T., Kobayashi, N. & 10 others, Krishnaswami, K., Laibe, C., Le Novère, N., Lin, S., Malone, J., Miller, M., Mungall, C. J., Rietveld, L., Wimalaratne, S. M. & Yamaguchi, A., 2016, In : PeerJ. 2016, 8, e2331.

Research output: Contribution to journalArticle

Biological Science Disciplines
Metadata
Health care
health services
Vocabulary
78 Citations (Scopus)

The Ontology for Biomedical Investigations

Bandrowski, A., Brinkman, R., Brochhausen, M., Brush, M. H., Bug, B., Chibucos, M. C., Clancy, K., Courtot, M., Derom, D., Dumontier, M., Fan, L., Fostel, J., Fragoso, G., Gibson, F., Gonzalez-Beltran, A., Haendel, M., He, Y., Heiskanen, M., Hernandez-Boussard, T., Jensen, M. & 24 others, Lin, Y., Lister, A. L., Lord, P., Malone, J., Manduchi, E., McGee, M., Morrison, N., Overton, J. A., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S. A., Scheuermann, R. H., Schober, D., Smith, B., Soldatova, L. N., Stoeckert, C. J., Taylor, C. F., Torniai, C., Turner, J. A., Vita, R., Whetzel, P. L. & Zheng, J., Apr 1 2016, In : PLoS One. 11, 4, e0154556.

Research output: Contribution to journalArticle

Biological Ontologies
Ontology
Strigiformes
immunology
planning