Research Output

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

Preface

Brochhausen, M., Haendel, M., Stoeckert, C. & Zheng, J., Jan 1 2014, In : CEUR Workshop Proceedings. 1309, 1 p.

Research output: Contribution to journalEditorial

4 Scopus citations

Screening for hepatitis B virus infection in adolescents and adults: A systematic review to update the U.S. Preventive Services Task Force recommendation

Chou, R., Dana, T., Bougatsos, C., Blazina, I., Khangura, J. & Zakher, B., Jul 1 2014, In : Annals of internal medicine. 161, 1, p. 31-45 15 p.

Research output: Contribution to journalReview article

31 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., Dec 1 2013, In : Database. 2013, bas056.

Research output: Contribution to journalArticle

42 Scopus citations

Eaglei-i: Ontology-driven federated search and data entry tools for discovering biomedical research resources

Haendel, M., Torniai, C., Vasilevsky, N., Hoffmann, S. & Bourges-Waldegg, D., Jan 1 2013, In : CEUR Workshop Proceedings. 1060, p. 130-131 2 p.

Research output: Contribution to journalConference article

Enabling semantic search in a biospecimen repository

Essaid, S., Torniai, C. & Haendel, M. A., Jan 1 2013, In : CEUR Workshop Proceedings. 1060, p. 50-53 4 p.

Research output: Contribution to journalConference article

Finding common ground: Integrating the eagle-i and VIVO ontologies

Torniai, C., Essaid, S., Lowe, B., Corson-Rikert, J. & Haendel, M., Jan 1 2013, In : CEUR Workshop Proceedings. 1060, p. 46-49 4 p.

Research output: Contribution to journalConference article

2 Scopus citations

Interinstitutional library collaboration: Support for a joint master of public health program

Ford, E. R. & Zeigen, L., Dec 9 2013, Mergers and Alliances: The Operational View and Cases. Woodsworth, A. & Penniman, D. (eds.). p. 59-79 21 p. (Advances in Librarianship; vol. 37).

Research output: Chapter in Book/Report/Conference proceedingChapter

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., Oct 14 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

Pressure ulcer risk assessment and prevention: A systematic comparative effectiveness review

Chou, R., Dana, T., Bougatsos, C., Blazina, I., Starmer, A. J., Reitel, K. & Buckley, D. I., Jul 2 2013, In : Annals of internal medicine. 159, 1, p. 28-38 11 p.

Research output: Contribution to journalReview article

73 Scopus citations

Screening for hypertension in children and adolescents to prevent cardiovascular disease

Thompson, M., Dana, T., Bougatsos, C., Blazina, I. & Norris, S. L., Mar 2013, In : Pediatrics. 131, 3, p. 490-525 36 p.

Research output: Contribution to journalReview article

72 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

Treatments for symptoms of the common cold

Livingston, C., Cozzens, J. & Hamilton, A., Dec 15 2013, In : American family physician. 88, 12, p. 864C

Research output: Contribution to journalComment/debate

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

What is an anatomy ontology?

Druzinsky, R., Mungall, C., Haendel, M., Lapp, H. & Mabee, P., Dec 1 2013, In : Anatomical Record. 296, 12, p. 1797-1799 3 p.

Research output: Contribution to journalLetter

1 Scopus citations

What's in a genotype? An ontological characterization for integration of genetic variation data

Brush, M. H., Mungall, C., Washington, N. & Haendel, M. A., Jan 1 2013, In : CEUR Workshop Proceedings. 1060, p. 105-108 4 p.

Research output: Contribution to journalConference article

4 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 1 2012, In : PLoS Biology. 10, 5, e1001339.

Research output: Contribution to journalArticle

32 Scopus citations

Lost and Found in Behavioral Informatics

Haendel, M. A. & Chesler, E. J., 2012, International Review of Neurobiology. Academic Press Inc., p. 1-18 18 p. (International Review of Neurobiology; vol. 103).

Research output: Chapter in Book/Report/Conference proceedingChapter

Preface

Chesler, E. J. & Haendel, M. A., Dec 4 2012, In : International review of neurobiology. 103, p. xi-xii

Research output: Contribution to journalEditorial

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., Jul 25 2012, In : Database. 2012, bar067.

Research output: Contribution to journalArticle

24 Scopus citations

Review: PSA-based screening does not reduce prostate cancer mortality or all-cause mortality

Chou, R., Croswell, J. M. & Dana, T., Apr 19 2012, In : Annals of internal medicine. 156, 8, p. JC4-2

Research output: Contribution to journalComment/debate

Screening for HIV: Systematic review to update the 2005 U.S. Preventive Services Task Force recommendation

Chou, R., Selph, S., Dana, T., Bougatsos, C., Zakher, B., Blazina, I. & Todd Korthuis, P., Nov 20 2012, In : Annals of internal medicine. 157, 10, p. 706-718 13 p.

Research output: Contribution to journalReview article

24 Scopus citations

The field of bioinformatics. Preface.

Chesler, E. J. & Haendel, M. A., Dec 1 2012, In : International review of neurobiology. 103, p. xi-xii

Research output: Contribution to journalEditorial

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
2011

Aligning research resource and researcher representation: The eagle-i and VIVO use case

Mitchell, S., Torniai, C., Lowe, B., Corson-Rikert, J., Wilson, M., Ahmed, M., Chen, S., Ding, Y., Rejack, N. & Haendel, M., Dec 1 2011, In : CEUR Workshop Proceedings. 833, p. 260-262 3 p.

Research output: Contribution to journalConference article

1 Scopus citations

An ontology-based approach to linking model organisms and resources to human diseases

Mungall, C. J., Anderson, D., Bandrowski, A., Canada, B., Chatyr-Aryamontri, A., Cheng, K., Conn, P. M., Dolinski, K., Ellisman, M., Eppig, J., Grethe, J. S., Kemnitz, J., Iadonato, S., Larson, S. D., Magness, C., Martone, M. E., Tyers, M., Torniai, C., Troyanskaya, O., Turner, J. & 2 others, Westerfield, M. & Haendel, M. A., Dec 1 2011, In : CEUR Workshop Proceedings. 833, p. 263-265 3 p.

Research output: Contribution to journalConference article

Connecting knowledge resources to the veterinary electronic health record: Opportunities for learning at point of care

Alpi, K. M., Burnett, H. A., Bryant, S. J. & Anderson, K. M., Jan 1 2011, In : Journal of Veterinary Medical Education. 38, 2, p. 110-122 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

Crystal structure of the human collagen XV trimerization domain: A potent trimerizing unit common to multiplexin collagens

Wirz, J. A., Boudko, S. P., Lerch, T. F., Chapman, M. S. & Bächinger, H. P., Jan 1 2011, In : Matrix Biology. 30, 1, p. 9-15 7 p.

Research output: Contribution to journalArticle

12 Scopus citations

Developing an application ontology for biomedical resource annotation and retrieval: Challenges and lessons learned

Torniai, C., Brush, M., Vasilevsky, N., Segerdell, E., Wilson, M., Johnson, T., Corday, K., Shaffer, C. & Haendel, M., Dec 1 2011, In : CEUR Workshop Proceedings. 833, p. 101-108 8 p.

Research output: Contribution to journalConference article

4 Scopus citations

Developing a reagent application ontology within the OBO foundry framework

Brush, M. H., Vasilevsky, N., Torniai, C., Johnson, T., Shaffer, C. & Haendel, M. A., Dec 1 2011, In : CEUR Workshop Proceedings. 833, p. 234-236 3 p.

Research output: Contribution to journalConference article

1 Scopus citations

Integrated methods for teaching population health

Sistrom, M. G., Zeigen, L., Jones, M., Durham, K. F. & Boudrot, T., Jan 1 2011, In : Journal of Nursing Education. 50, 1, p. 35-39 5 p.

Research output: Contribution to journalArticle

3 Scopus citations

Modularization for the cell ontology

Mungall, C. J., Haendel, M., Ireland, A., Manzoor, S., Meehan, T., Osumi-Sutherland, D., Torniai, C. & Diehl, A. D., Dec 1 2011, In : CEUR Workshop Proceedings. 833, p. 370-376 7 p.

Research output: Contribution to journalConference article

1 Scopus citations