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2016

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

Research engagement of health sciences librarians: A survey of research-related activities and attitudes

Lessick, S., Perryman, C., Billman, B. L., Alpi, K. M., De Groote, S. L. & Babin, T. D., Apr 1 2016, In : Journal of the Medical Library Association. 104, 2, p. 166-173 8 p.

Research output: Contribution to journalArticle

Open Access
16 Scopus citations

Scanning technology selection impacts acceptability and usefulness of image-rich content

Alpi, K. M., Brown, J. C., Neel, J. A., Grindem, C. B., Linder, K. E. & Harper, J. B., Jan 1 2016, In : Journal of the Medical Library Association. 104, 1, p. 15-23 9 p.

Research output: Contribution to journalArticle

Open Access

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

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., 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. 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

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
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., 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
1 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 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
2014

A sea of standards for omics data: Sink or swim?

Tenenbaum, J. D., Sansone, S. A. & Haendel, M., Feb 21 2014, In : Journal of the American Medical Informatics Association. 21, 2, p. 200-203 4 p.

Research output: Contribution to journalArticle

39 Scopus citations

Clinical interpretation of CNVs with cross-species phenotype data

Köhler, S., Schoeneberg, U., Czeschik, J. C., Doelken, S. C., Hehir-Kwa, J. Y., Ibn-Salem, J., Mungall, C. J., Smedley, D., Haendel, M. A. & Robinson, P. N., Jan 1 2014, In : Journal of medical genetics. 51, 11, p. 766-772 7 p.

Research output: Contribution to journalArticle

13 Scopus citations

CLO: The cell line ontology

Sarntivijai, S., Lin, Y., Xiang, Z., Meehan, T. F., Diehl, A. D., Vempati, U. D., Schürer, S. C., Pang, C., Malone, J., Parkinson, H., Liu, Y., Takatsuki, T., Saijo, K., Masuya, H., Nakamura, Y., Brush, M. H., Haendel, M. A., Zheng, J., Stoeckert, C. J., Peters, B. & 5 others, Mungall, C. J., Carey, T. E., States, D. J., Athey, B. D. & He, Y., Aug 13 2014, In : Journal of Biomedical Semantics. 5, 1, 37.

Research output: Contribution to journalArticle

47 Scopus citations

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

Zemojtel, T., Köhler, S., Mackenroth, L., Jäger, M., Hecht, J., Krawitz, P., Graul-Neumann, L., Doelken, S., Ehmke, N., Spielmann, M., Øien, N. C., Schweiger, M. R., Krüger, U., Frommer, G., Fischer, B., Kornak, U., Flöttmann, R., Ardeshirdavani, A., Moreau, Y., Lewis, S. E. & 5 others, Haendel, M., Smedley, D., Horn, D., Mundlos, S. & Robinson, P. N., Sep 3 2014, In : Science translational medicine. 6, 252, 252ra123.

Research output: Contribution to journalArticle

138 Scopus citations

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

Robinson, P. N., Köhler, S., Oellrich, A., Genetics, S. M., Wang, K., Mungall, C. J., Lewis, S. E., Washington, N., Bauer, S., Seelow, D., Krawitz, P., Gilissen, C., Haendel, M. & Smedley, D., Feb 1 2014, In : Genome Research. 24, 2, p. 340-348 9 p.

Research output: Contribution to journalArticle

162 Scopus citations
35 Scopus citations

Nose to tail, roots to shoots: Spatial descriptors for phenotypic diversity in the Biological Spatial Ontology

Dahdul, W. M., Cui, H., Mabee, P. M., Mungall, C. J., Osumi-Sutherland, D., Walls, R. L. & Haendel, M. A., Aug 11 2014, In : Journal of Biomedical Semantics. 5, 1, 34.

Research output: Contribution to journalArticle

18 Scopus citations
4 Scopus citations

The Human Phenotype Ontology project: Linking molecular biology and disease through phenotype data

Köhler, S., Doelken, S. C., Mungall, C. J., Bauer, S., Firth, H. V., Bailleul-Forestier, I., Black, G. C. M., Brown, D. L., Brudno, M., Campbell, J., Fitzpatrick, D. R., Eppig, J. T., Jackson, A. P., Freson, K., Girdea, M., Helbig, I., Hurst, J. A., Jähn, J., Jackson, L. G., Kelly, A. M. & 27 others, Ledbetter, D. H., Mansour, S., Martin, C. L., Moss, C., Mumford, A., Ouwehand, W. H., Park, S. M., Riggs, E. R., Scott, R. H., Sisodiya, S., Vooren, S. V., Wapner, R. J., Wilkie, A. O. M., Wright, C. F., Vulto-Van Silfhout, A. T., Leeuw, N. D., De Vries, B. B. A., Washingthon, N. L., Smith, C. L., Westerfield, M., Schofield, P., Ruef, B. J., Gkoutos, G. V., Haendel, M., Smedley, D., Lewis, S. E. & Robinson, P. N., Jan 1 2014, In : Nucleic acids research. 42, D1, p. D966-D974

Research output: Contribution to journalArticle

462 Scopus citations

The influence of disease categories on gene candidate predictions from model organism phenotypes

Oellrich, A., Koehler, S., Washington, N., Mungall, C., Lewis, S., Haendel, M., Robinson, P. N., Smedley, D. & Sanger Mouse Genetic Project, M. G. P., Jan 1 2014, In : Journal of Biomedical Semantics. 5, S4.

Research output: Contribution to journalArticle

5 Scopus citations

Thematic series on biomedical ontologies in JBMS: Challenges and new directions

Hoehndorf, R., Haendel, M., Stevens, R. & Rebholz-Schuhmann, D., Mar 6 2014, In : Journal of Biomedical Semantics. 5, 1, 15.

Research output: Contribution to journalArticle

8 Scopus citations

The Porifera Ontology (PORO): Enhancing sponge systematics with an anatomy ontology

Thacker, R. W., Díaz, M. C., Kerner, A., Vignes-Lebbe, R., Segerdell, E., Haendel, M. A. & Mungall, C. J., Sep 8 2014, In : Journal of Biomedical Semantics. 5, 1, 39.

Research output: Contribution to journalArticle

3 Scopus citations

The zebrafish anatomy and stage ontologies: Representing the anatomy and development of Danio rerio

van Slyke, C. E., Bradford, Y. M., Westerfield, M. & Haendel, M. A., Feb 25 2014, In : Journal of Biomedical Semantics. 5, 1, 12.

Research output: Contribution to journalArticle

27 Scopus citations

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Haendel, M. A., Balhoff, J. P., Bastian, F. B., Blackburn, D. C., Blake, J. A., Bradford, Y., Comte, A., Dahdul, W. M., Dececchi, T. A., Druzinsky, R. E., Hayamizu, T. F., Ibrahim, N., Lewis, S. E., Mabee, P. M., Niknejad, A., Robinson-Rechavi, M., Sereno, P. C. & Mungall, C. J., May 19 2014, In : Journal of Biomedical Semantics. 5, 1, 21.

Research output: Contribution to journalArticle

58 Scopus citations

Use of animal models for exome prioritization of rare disease genes

Sanger Mouse Genetics Project, Nov 11 2014, In : Orphanet journal of rare diseases. 9, 1, O19.

Research output: Contribution to journalArticle

2013

An overview of the BioCreative 2012 Workshop Track III: Interactive text mining task

Arighi, C. N., Carterette, B., Cohen, K. B., Krallinger, M., Wilbur, W. J., Fey, P., Dodson, R., Cooper, L., Van Slyke, C. E., Dahdul, W., Mabee, P., Li, D., Harris, B., Gillespie, M., Jimenez, S., Roberts, P., Matthews, L., Becker, K., Drabkin, H., Bello, S. & 21 others, Licata, L., Chatr-aryamontri, A., Schaeffer, M. L., Park, J., Haendel, M., Van Auken, K., Li, Y., Chan, J., Muller, H. M., Cui, H., Balhoff, J. P., Wu, J. C. Y., Lu, Z., Wei, C. H., Tudor, C. O., Raja, K., Subramani, S., Natarajan, J., Cejuela, J. M., Dubey, P. & Wu, C., 2013, In : Database. 2013, bas056.

Research output: Contribution to journalArticle

42 Scopus citations
13 Scopus citations

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, In : PeerJ. 2013, 1, e148.

Research output: Contribution to journalArticle

130 Scopus citations

Ontology based molecular signatures for immune cell types via gene expression analysis

Meehan, T. F., Vasilevsky, N. A., Mungall, C. J., Dougall, D. S., Haendel, M. A., Blake, J. A. & Diehl, A. D., Aug 30 2013, In : BMC bioinformatics. 14, 1, 263.

Research output: Contribution to journalArticle

8 Scopus citations

Subject matter expert and public evaluations of a veterinary toxicology course brochure-writing assignment

Dorman, D. C., Alpi, K. M. & Chappell, K. H., Jan 1 2013, In : Journal of Veterinary Medical Education. 40, 1, p. 19-28 10 p.

Research output: Contribution to journalArticle

5 Scopus citations

Using Facebook Page Insights Data to Determine Posting Best Practices in an Academic Health Sciences Library

Houk, K. M. & Thornhill, K., Dec 19 2013, In : Journal of Web Librarianship. 7, 4, p. 372-388 17 p.

Research output: Contribution to journalArticle

6 Scopus citations
2012

A Unified Anatomy Ontology of the Vertebrate Skeletal System

Dahdul, W. M., Balhoff, J. P., Blackburn, D. C., Diehl, A. D., Haendel, M. A., Hall, B. K., Lapp, H., Lundberg, J. G., Mungall, C. J., Ringwald, M., Segerdell, E., van Slyke, C. E., Vickaryous, M. K., Westerfield, M. & Mabee, P. M., Dec 10 2012, In : PloS one. 7, 12, e51070.

Research output: Contribution to journalArticle

31 Scopus citations

Dealing with data: A case study on information and data management literacy

Haendel, M. A., Vasilevsky, N. A. & Wirz, J. A., May 2012, In : PLoS Biology. 10, 5, e1001339.

Research output: Contribution to journalArticle

32 Scopus citations
Open Access

Research resources: Curating the new eagle-i discovery system

Vasilevsky, N., Johnson, T., Corday, K., Torniai, C., Brush, M., Segerdell, E., Wilson, M., Shaffer, C., Robinson, D. & Haendel, M., 2012, In : Database. 2012, bar067.

Research output: Contribution to journalArticle

24 Scopus citations