Research Output

2017

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

Vasilevsky, N. A., Minnier, J., Haendel, M. A. & Champieux, R. E., Jan 1 2017, In : PeerJ. 2017, 4, e3208.

Research output: Contribution to journalArticle

25 Scopus citations

Systemic pharmacologic therapies for low back pain: A systematic review for an American College of physicians clinical practice guideline

Chou, R., Deyo, R. R., Friedly, J., Skelly, A., Weimer, M., Fu, R. R., Dana, T., Kraegel, P., Griffin, J. & Grusing, S., Apr 4 2017, In : Annals of Internal Medicine. 166, 7, p. 480-492 13 p.

Research output: Contribution to journalReview article

93 Scopus citations

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

341 Scopus citations

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. A., Jan 1 2017, In : Nucleic acids research. 45, D1, p. D712-D722

Research output: Contribution to journalArticle

84 Scopus citations

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

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

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

Smedley, D., Schubach, M., Jacobsen, JO. O. B., Köhler, S., Zemojtel, T., Spielmann, M., Jäger, M., Hochheiser, H., Washington, NL. L., McMurry, JA. A., Haendel, MA. A., Mungall, CJ. J., Lewis, SE. E., Groza, T., Valentini, G. & Robinson, PN. N., Sep 1 2016, In : American Journal of Human Genetics. 99, 3, p. 595-606 12 p.

Research output: Contribution to journalArticle

70 Scopus citations

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

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

44 Scopus citations

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
1 Scopus citations

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., Jan 1 2016, In : CEUR Workshop Proceedings. 1747

Research output: Contribution to journalConference article

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

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

Innovative approaches to combining genotype, phenotype, epigenetic, and exposure data for precision diagnostics

Haendel, M., Kann, M. G. & Washington, N. L., 2016, Pacific Symposium on Biocomputing 2016, PSB 2016. World Scientific Publishing Co. Pte Ltd, p. 93-95 3 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Intranasal or transdermal nicotine for the treatment of postoperative pain

Matthews, A., Fu, R. R., Dana, T. & Chou, R., Jan 12 2016, In : Cochrane Database of Systematic Reviews. 2016, 1, CD009634.

Research output: Contribution to journalReview article

8 Scopus citations

Laying a community-based foundation for data-driven semantic standards in environmental health sciences

Mattingly, C. J., Boyles, R., Lawler, C. P., Haugen, A. C., Dearry, A. & Haendel, M., 2016, In : Environmental Health Perspectives. 124, 8, p. 1136-1140 5 p.

Research output: Contribution to journalReview article

8 Scopus citations

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. A., 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 2016, In : PloS one. 11, 2, e0149102.

Research output: Contribution to journalArticle

3 Scopus citations

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. A., Aug 2016, In : Genetics. 203, 4, p. 1491-1495 5 p.

Research output: Contribution to journalArticle

24 Scopus citations

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, In : Applied and Translational Genomics. 9, p. 23-29 7 p.

Research output: Contribution to journalArticle

7 Scopus citations

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

2 Scopus citations

Screening for dyslipidemia in younger adults: A systematic review for the U.S. Preventive services task force

Chou, R., Dana, T., Blazina, I., Daeges, M., Bougatsos, C. & Jeanne, T. L., Oct 18 2016, In : Annals of Internal Medicine. 165, 8, p. 560-564 5 p.

Research output: Contribution to journalReview article

15 Scopus citations

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

26 Scopus citations

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

2 Scopus citations

Statins for prevention of cardiovascular disease in adults: Evidence report and systematic review for the US preventive services task force

Chou, R., Dana, T., Blazina, I., Daeges, M. & Jeanne, T. L., Nov 15 2016, In : JAMA - Journal of the American Medical Association. 316, 19, p. 2008-2024 17 p.

Research output: Contribution to journalReview article

183 Scopus citations

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

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. A., Blake, J. A. & Mungall, C. J., Jan 1 2016, In : Journal of Biomedical Semantics. 7, 1, 44.

Research output: Contribution to journalArticle

35 Scopus citations

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., Jan 1 2016, In : PeerJ. 2016, 8, e2331.

Research output: Contribution to journalArticle

13 Scopus citations

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. A., 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 2016, In : PloS one. 11, 4, e0154556.

Research output: Contribution to journalArticle

100 Scopus citations

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., Washington, N., Zudilova-Seinstra, E. & Vasilevsky, N., Jan 1 2016, In : Journal of Comparative Neurology. 524, 1, p. 8-22 15 p.

Research output: Contribution to journalArticle

16 Scopus citations

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. S., Washington, N., Zudilova-Seinstra, E. & Vasilevsky, N., Apr 1 2016, In : Neuroinformatics. 14, 2, p. 169-182 14 p.

Research output: Contribution to journalArticle

8 Scopus citations

The Resource Identification Initiative: A cultural shift in publishing

RINL Resource Identification Initiative, Jan 1 2016, In : Brain and Behavior. 6, 1, p. 1-14 14 p.

Research output: Contribution to journalEditorial

13 Scopus citations
2015

Achieving human and machine accessibility of cited data in scholarly publications

Starr, J., Castro, E., Crosas, M., Dumontier, M., Downs, R. R., Duerr, R., Haak, L. L., Haendel, M., Herman, I., Hodson, S., Hourclé, J., Kratz, J. E., Lin, J., Nielsen, L. H., Nurnberger, A., Proell, S., Rauber, A., Sacchi, S., Smith, A., Taylor, M. & 1 others, Clark, T., Jan 1 2015, In : PeerJ Computer Science. 2015, 5, e1.

Research output: Contribution to journalArticle

50 Scopus citations

Epidural corticosteroid injections for radiculopathy and spinal stenosis: A systematic review and meta-analysis

Chou, R., Hashimoto, R., Friedly, J., Fu, R., Bougatsos, C., Dana, T., BScPharm, S. D. S. & Jarvik, J., Sep 1 2015, In : Annals of internal medicine. 163, 5, p. 373-381 9 p.

Research output: Contribution to journalArticle

84 Scopus citations

Finding Our Way through Phenotypes

Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., Burleigh, J. G., Chanet, B., Cooper, L. D., Courtot, M., Csösz, S., Cui, H., Dahdul, W., Das, S., Dececchi, T. A., Dettai, A., Diogo, R., Druzinsky, R. E. & 54 others, Dumontier, M., Franz, N. M., Friedrich, F., Gkoutos, G. V., Haendel, M., Harmon, L. J., Hayamizu, T. F., He, Y., Hines, H. M., Ibrahim, N., Jackson, L. M., Jaiswal, P., James-Zorn, C., Köhler, S., Lecointre, G., Lapp, H., Lawrence, C. J., Le Novère, N., Lundberg, J. G., Macklin, J., Mast, A. R., Midford, P. E., Mikó, I., Mungall, C. J., Oellrich, A., Osumi-Sutherland, D., Parkinson, H., Ramírez, M. J., Richter, S., Robinson, P. N., Ruttenberg, A., Schulz, K. S., Segerdell, E., Seltmann, K. C., Sharkey, M. J., Smith, A. D., Smith, B., Specht, C. D., Squires, R. B., Thacker, R. W., Thessen, A., Fernandez-Triana, J., Vihinen, M., Vize, P. D., Vogt, L., Wall, C. E., Walls, R. L., Westerfeld, M., Wharton, R. A., Wirkner, C. S., Woolley, J. B., Yoder, M. J., Zorn, A. M. & Mabee, P., Jan 1 2015, In : PLoS Biology. 13, 1

Research output: Contribution to journalArticle

116 Scopus citations
2 Scopus citations

Librarian readiness for research partnerships

Mazure, E. S. & Alpi, K. M., Jan 1 2015, In : Journal of the Medical Library Association. 103, 2, p. 91-95 5 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Meeting report: Identifying practical applications of ontologies for biodiversity informatics

Deck, J., Guralnick, R., Walls, R., Blum, S., Haendel, M., Matsunaga, A. & Wieczorek, J., May 1 2015, In : Standards in Genomic Sciences. 10, MAY2015

Research output: Contribution to journalArticle

3 Scopus citations

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., Bone, W. P., Haendel, M. A. & Robinson, P. N., Dec 1 2015, In : Nature protocols. 10, 12, p. 2004-2015 12 p.

Research output: Contribution to journalArticle

83 Scopus citations

PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases

Buske, O. J., Girdea, M., Dumitriu, S., Gallinger, B., Hartley, T., Trang, H., Misyura, A., Friedman, T., Beaulieu, C., Bone, W. P., Links, A. E., Washington, N. L., Haendel, M. A., Robinson, P. N., Boerkoel, C. F., Adams, D., Gahl, W. A., Boycott, K. M. & Brudno, M., Oct 1 2015, In : Human mutation. 36, 10, p. 931-940 10 p.

Research output: Contribution to journalArticle

61 Scopus citations

Q / How well do antivirals shorten genital herpes pain duration?

Yip, S. T., Liu, R., Warrington, T., Webb, C. W., Hamilton, A. & Vincent, E. C., Mar 1 2015, In : Journal of Family Practice. 64, 3, p. 190-191 2 p.

Research output: Contribution to journalComment/debate

1 Scopus citations

Routine iron supplementation and screening for iron deficiency anemia in pregnancy: A systematic review for the U.S. preventive services task force

Cantor, A. G., Bougatsos, C., Dana, T., Blazina, I. & McDonagh, M., Apr 21 2015, In : Annals of internal medicine. 162, 8, p. 566-576 11 p.

Research output: Contribution to journalReview article

59 Scopus citations

Screening and routine supplementation for iron deficiency anemia: A systematic review

McDonagh, M. S., Blazina, I., Dana, T., Cantor, A. & Bougatsos, C., Apr 1 2015, In : Pediatrics. 135, 4, p. 723-733 11 p.

Research output: Contribution to journalReview article

35 Scopus citations

Screening for type 2 diabetes mellitus: A systematic review for the U.S. preventive services task force

Selph, S., Dana, T., Blazina, I., Bougatsos, C., Patel, H. & Chou, R., Jun 2 2015, In : Annals of internal medicine. 162, 11, p. 765-776 12 p.

Research output: Contribution to journalReview article

62 Scopus citations

Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network

Ochs, C., Perl, Y., Geller, J., Haendel, M., Brush, M., Arabandi, S. & Tu, S., Aug 1 2015, In : Journal of Biomedical Informatics. 56, p. 127-144 18 p.

Research output: Contribution to journalArticle

14 Scopus citations

The effectiveness and risks of long-term opioid therapy for chronic pain: A systematic review for a national institutes of health pathways to prevention workshop

Chou, R., Turner, J. A., Devine, E. B., Hansen, R. N., Sullivan, S. D., Blazina, I., Dana, T., Bougatsos, C. & Deyo, R. A., Feb 17 2015, In : Annals of internal medicine. 162, 4, p. 276-286 11 p.

Research output: Contribution to journalReview article

642 Scopus citations

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

Groza, T., Köhler, S., Moldenhauer, D., Vasilevsky, N., Baynam, G., Zemojtel, T., Schriml, L. M., Kibbe, W. A., Schofield, P. N., Beck, T., Vasant, D., Brookes, A. J., Zankl, A., Washington, N. L., Mungall, C. J., Lewis, S. E., Haendel, M. A., Parkinson, H. & Robinson, P. N., Jan 1 2015, In : American Journal of Human Genetics. 97, 1, p. 111-124 14 p.

Research output: Contribution to journalArticle

101 Scopus citations

The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

Philippakis, A. A., Azzariti, D. R., Beltran, S., Brookes, A. J., Brownstein, C. A., Brudno, M., Brunner, H. G., Buske, O. J., Carey, K., Doll, C., Dumitriu, S., Dyke, S. O. M., den Dunnen, J. T., Firth, H. V., Gibbs, R. A., Girdea, M., Gonzalez, M., Haendel, M. A., Hamosh, A., Holm, I. A. & 18 others, Huang, L., Hurles, M. E., Hutton, B., Krier, J. B., Misyura, A., Mungall, C. J., Paschall, J., Paten, B., Robinson, P. N., Schiettecatte, F., Sobreira, N. L., Swaminathan, G. J., Taschner, P. E., Terry, S. F., Washington, N. L., Züchner, S., Boycott, K. M. & Rehm, H. L., Oct 1 2015, In : Human mutation. 36, 10, p. 915-921 7 p.

Research output: Contribution to journalArticle

174 Scopus citations

The Resource Identification Initiative: A cultural shift in publishing

Resource Identification Initiative Members, May 29 2015, In : F1000Research. 4, 134.

Research output: Contribution to journalArticle

23 Scopus citations

Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery

Mungall, C. J., Washington, N. L., Nguyen-Xuan, J., Condit, C., Smedley, D., Köhler, S., Groza, T., Shefchek, K., Hochheiser, H., Robinson, P. N., Lewis, S. E. & Haendel, M. A., Oct 1 2015, In : Human mutation. 36, 10, p. 979-984 6 p.

Research output: Contribution to journalArticle

23 Scopus citations