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Jim Balhoff's Publications

Bioinformatics specialist , National Evolutionary Synthesis Center (NESCent)
Durham, North Carolina, United States

Research field: Biological Sciences - Bioinformatics
No research interests added yet.
Conference Proceedings (1) | Journal Article (21)

Journal Article

Melissa a Haendel, James P Balhoff, Frederic B Bastian, David C Blackburn, Judith a Blake, Yvonne Bradford, Aurelie Comte, Wasila M Dahdul, Thomas a Dececchi, Robert E Druzinsky, Terry F Hayamizu, Nizar Ibrahim, Suzanna E Lewis, Paula M Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C Sereno, Christopher J Mungall (2014) Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon., 21. In Journal of Biomedical Semantics 5 (1).
James P. Balhoff, István Mikó, Matthew J. Yoder, Patricia L. Mullins, Andrew R. Deans (2013) A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia., 639-659. In Systematic biology 62 (5).
Cecilia N Arighi, Ben Carterette, K Bretonnel Cohen, Martin Krallinger, W John Wilbur, Petra Fey, Robert Dodson, Laurel Cooper, Ceri E Van Slyke, Wasila Dahdul, Paula Mabee, Donghui Li, Bethany Harris, Marc Gillespie, Silvia Jimenez, Phoebe Roberts, Lisa Matthews, Kevin Becker, Harold Drabkin, Susan Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L Schaeffer, Julie Park, Melissa Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Muller, Hong Cui, James P Balhoff, Johnny Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy Wu (2013) An overview of the BioCreative 2012 Workshop Track III: interactive text mining task., bas056. In Database : the journal of biological databases and curation.
Matthew A. Bertone, István Mikó, Matthew J. Yoder, Katja C. Seltmann, James P. Balhoff, Andrew R. Deans (2013) Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment., bas057. In Database : the journal of biological databases and curation.
Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O'Meara, Matthew W Pennell, Siavash Mirarab, Michael S Rosenberg, James P Balhoff, Holly M Bik, Tracy a Heath, Peter E Midford, Joseph W Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E Alfaro, Aaron Steele, Greg Jordan (2013) Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient, 158. In BMC Bioinformatics 14 (1).
Peter E. Midford, Thomas Alex Dececchi, James P. Balhoff, Wasila M. Dahdul, Nizar Ibrahim, Hilmar Lapp, John G. Lundberg, Paula M. Mabee, Paul C. Sereno, Monte Westerfield, Todd J. Vision, David C. Blackburn (2013) The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes., 34. In Journal of Biomedical Semantics 4 (1).
P. Mabee, J. P. Balhoff, W. M. Dahdul, H. Lapp, P. E. Midford, T. J. Vision, M. Westerfield (2012) 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton, 300-305. In Journal of Applied Ichthyology 28 (3).
Katja Seltmann, Matthew Yoder, Istvan Miko, Mattias Forshage, Matthew Bertone, Donat Agosti, Andrew Austin, James Balhoff, Marek Borowiec, Seán Brady, Gavin Broad, Denis Brothers, Roger Burks, Matthew Buffington, Heather Campbell, Kelly Dew, Andrew Ernst, Jose Fernandez-Triana, Michael Gates, Gary Gibson, John Jennings, Norman Johnson, Dave Karlsson, Ricardo Kawada, Lars Krogmann, Robert Kula, Patricia Mullins, Michael Ohl, Claus Rasmussen, Fredrick Ronquist, Susanne Schulmeister, Michael Sharkey, Elijah Talamas, Erika Tucker, Lars Vilhelmsen, Philip S. Ward, Robert Wharton, Andrew Deans (2012) A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions, 67-88. In Journal of Hymenoptera Research.
Wasila M Dahdul, James P Balhoff, David C Blackburn, Alexander D Diehl, Melissa A Haendel, Brian K Hall, Hilmar Lapp, John G Lundberg, Christopher J Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K Vickaryous, Monte Westerfield, Paula M Mabee (2012) A Unified Anatomy Ontology of the Vertebrate Skeletal System, e51070. In PLoS ONE 7 (12).
R. A. Vos, J. P. Balhoff, J. A. Caravas, M. T. Holder, H. Lapp, W. P. Maddison, P. E. Midford, A. Priyam, J. Sukumaran, X. Xia, A. Stoltzfus (2012) NeXML: rich, extensible, and verifiable representation of comparative data and metadata, sys025-. In Systematic Biology.
Andrew R. Deans, Matthew J. Yoder, James P. Balhoff (2012) Time to change how we describe biodiversity., 78-84. In Trends in Ecology & Evolution 27 (2).
Wasila M. Dahdul, James P. Balhoff, Jeffrey Engeman, Terry Grande, Eric J. Hilton, Cartik Kothari, Hilmar Lapp, John G. Lundberg, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee (2010) Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature., e10708. In PloS one 5 (5).
James P. Balhoff, Wasila M. Dahdul, Cartik R. Kothari, Hilmar Lapp, John G. Lundberg, Paula Mabee, Peter E. Midford, Monte Westerfield, Todd J. Vision (2010) Phenex: ontological annotation of phenotypic diversity., e10500. In PloS one 5 (5).
Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield, Paula M. Mabee (2010) The teleost anatomy ontology: anatomical representation for the genomics age., 369-83. In Systematic biology 59 (4).
Julie E Horvath, David W Weisrock, Stephanie L Embry, Isabella Fiorentino, James P Balhoff, Peter Kappeler, Gregory A Wray, Huntington F Willard, Anne D Yoder (2008) Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs., 489-99. In Genome research 18 (3).
H Lapp, S Bala, J P Balhoff, A Bouck, N Goto, M Holder, R Holland, A Holloway, T Katayama, P O Lewis, Aaron J Mackey, Brian I Osborne, William H Piel, Sergei L Kosakovsky Pond, Art F Y Poon, Wei-Gang Qiu, Jason E Stajich, Arlin Stoltzfus, Tobias Thierer, Albert J Vilella, Rutger A Vos, Christian M Zmasek, Derrick J Zwickl, Todd J Vision (2007) The 2006 NESCent Phyloinformatics Hackathon: A Field Report, 287-296. In Evolutionary Bioinformatics Online.
James P Balhoff, Gregory A Wray (2005) Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites., 8591-6. In Proceedings of the National Academy of Sciences of the United States of America 102 (24).
Gregory A Wray, Matthew W Hahn, Ehab Abouheif, James P Balhoff, Margaret Pizer, Matthew V Rockman, Laura A Romano (2003) The evolution of transcriptional regulation in eukaryotes., 1377-419. In Molecular Biology and Evolution 20 (9).
J P Balhoff, J M Stephens (1998) Highly specific and quantitative activation of STATs in 3T3-L1 adipocytes., 894-900. In Biochemical and biophysical research communications 247 (3).