Research Output

Filter
Article
2012
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

Uberon, an integrative multi-species anatomy ontology

Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E. & Haendel, M. A., Jan 31 2012, In : Genome biology. 13, 1, R5.

Research output: Contribution to journalArticle

275 Scopus citations
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

44 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

131 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
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

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., Lewis, S. E., Ott, C. E., Bauer, S., Schofield, P. N., Mundlos, S., Spielmann, M. & Robinson, P. N., 2014, In : Genome biology. 15, 9, 1 p., 423.

Research output: Contribution to journalArticle

72 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

139 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

165 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

465 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

59 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

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

117 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
3 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

85 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

102 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

177 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
2016

Access to human, animal, and environmental journals is still limited for the One Health community

Vreeland, C. E., Alpi, K. M., Pike, C. A., Whitman, E. E. & Kennedy-Stoskopf, S., Apr 2016, In : Journal of the Medical Library Association. 104, 2, p. 100-108 9 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

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

71 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. A., 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., 2016, In : Frontiers in Medicine. 3, OCT, 39.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

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

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

8 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