James P. Balhoff, Ph.D. - Publications

Affiliations: 
2005-2015 Informatics NESCent, Durham, NC, United States 
 2017- Renaissance Computing Institute University of North Carolina, Chapel Hill, Chapel Hill, NC 
Area:
evolutionary biology, bioinformatics

51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Good BM, Van Auken K, Hill DP, Mi H, Carbon S, Balhoff JP, Albou LP, Thomas PD, Mungall CJ, Blake JA, D'Eustachio P. Reactome and the Gene Ontology: Digital convergence of data resources. Bioinformatics (Oxford, England). PMID 33964129 DOI: 10.1093/bioinformatics/btab325  1
2020 Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Transforming the study of organisms: Phenomic data models and knowledge bases. Plos Computational Biology. 16: e1008376. PMID 33232313 DOI: 10.1371/journal.pcbi.1008376  1
2020 Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, et al. KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. Patterns (New York, N.Y.). 100155. PMID 33196056 DOI: 10.1016/j.patter.2020.100155  1
2019 Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, et al. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research. PMID 31701156 DOI: 10.1093/nar/gkz997  1
2019 Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CJ, Vision TJ. A Logical Model of Homology for Comparative Biology. Systematic Biology. PMID 31596473 DOI: 10.1093/Sysbio/Syz067  1
2019 Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ. Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Nature Genetics. PMID 31548717 DOI: 10.1038/S41588-019-0500-1  1
2019 Jackson RC, Balhoff JP, Douglass E, Harris NL, Mungall CJ, Overton JA. ROBOT: A Tool for Automating Ontology Workflows. Bmc Bioinformatics. 20: 407. PMID 31357927 DOI: 10.1186/S12859-019-3002-3  0.4
2019 Stucky BJ, Balhoff JP, Barve N, Barve V, Brenskelle L, Brush MH, Dahlem GA, Gilbert JDJ, Kawahara AY, Keller O, Lucky A, Mayhew PJ, Plotkin D, Seltmann KC, Talamas E, et al. Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions. Biodiversity Data Journal. 7: e33303. PMID 30918448 DOI: 10.3897/Bdj.7.E33303  1
2018 Dahdul W, Manda P, Cui H, Balhoff JP, Dececchi TA, Ibrahim N, Lapp H, Vision T, Mabee PM. Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. Database : the Journal of Biological Databases and Curation. 2018. PMID 30576485 DOI: 10.1093/Database/Bay110  1
2018 Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, et al. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Research. PMID 30476213 DOI: 10.1093/Nar/Gky1105  1
2018 Jackson LM, Fernando PC, Hanscom JS, Balhoff JP, Mabee PM. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. Systematic Biology. PMID 29325126 DOI: 10.1093/Sysbio/Syx098  1
2018 Balhoff JP, Good BM, Carbon S, Mungall CJ. Arachne: an OWL RL reasoner applied to gene ontology causal activity models (and beyond) F1000research. 7. DOI: 10.7490/F1000Research.1116194.1  0.4
2017 Fernando P, Jackson L, Balhoff J, Zeng E, Mabee P. A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies F1000research. 6. DOI: 10.7490/F1000Research.1114056.1  1
2017 Jackson LM, Fernando PC, Hanscom JS, Balhoff JP, Mabee PM. A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life F1000research. 6. DOI: 10.7490/F1000Research.1113878.1  1
2017 Dahdul W, Manda P, Cui H, Balhoff J, Dececchi TA, Ibrahim N, Lapp H, Mabee P, Vision T. Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes F1000research. 6. DOI: 10.7490/F1000Research.1113805.1  1
2016 Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, et al. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research. PMID 27899636 DOI: 10.1093/Nar/Gkw1128  1
2016 McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, et al. Navigating the Phenotype Frontier: The Monarch Initiative. Genetics. 203: 1491-5. PMID 27516611 DOI: 10.1534/Genetics.116.188870  1
2016 Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H, Mabee PM, Muller HM, Mungall CJ, Sternberg PW, Van Auken K, Vinyard CJ, et al. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. Plos One. 11: e0149102. PMID 26870952 DOI: 10.1371/Journal.Pone.0149102  1
2016 Manda P, Mungall CJ, Balhoff JP, Lapp H, Vision TJ. INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 21: 132-43. PMID 26776180  1
2015 Edmunds RC, Su B, Balhoff JP, Eames BF, Dahdul WM, Lapp H, Lundberg JG, Vision TJ, Dunham RA, Mabee PM, Westerfield M. Phenoscape: Identifying candidate genes for evolutionary phenotypes. Molecular Biology and Evolution. PMID 26500251 DOI: 10.1093/Molbev/Msv223  1
2015 Manda P, Balhoff JP, Lapp H, Mabee P, Vision TJ. Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis (New York, N.Y. : 2000). 53: 561-71. PMID 26220875 DOI: 10.1002/Dvg.22878  1
2015 Dececchi TA, Balhoff JP, Lapp H, Mabee PM. Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. Systematic Biology. PMID 26018570 DOI: 10.1093/Sysbio/Syv031  1
2015 Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, et al. Finding our way through phenotypes. Plos Biology. 13: e1002033. PMID 25562316 DOI: 10.1371/Journal.Pbio.1002033  1
2015 Balhoff J, Manda P, Lapp H, Mabee P, Vision T. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation F1000research. 4. DOI: 10.7490/F1000Research.1000199.1  1
2014 Balhoff JP, Dahdul WM, Dececchi TA, Lapp H, Mabee PM, Vision TJ. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics. 5: 45. PMID 25411634 DOI: 10.1186/2041-1480-5-45  1
2014 Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, et al. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Journal of Biomedical Semantics. 5: 21. PMID 25009735 DOI: 10.1186/2041-1480-5-21  1
2014 Mikó I, Copeland RS, Balhoff JP, Yoder MJ, Deans AR. Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania). Plos One. 9: e94056. PMID 24787704 DOI: 10.1371/Journal.Pone.0094056  1
2014 Balhoff J, Dececchi A, Lapp H, Mabee P. Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data F1000research. 5. DOI: 10.7490/F1000Research.1095873.1  1
2013 Midford PE, Dececchi TA, Balhoff JP, Dahdul WM, Ibrahim N, Lapp H, Lundberg JG, Mabee PM, Sereno PC, Westerfield M, Vision TJ, Blackburn DC. The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4: 34. PMID 24267744 DOI: 10.1186/2041-1480-4-34  1
2013 Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, ... ... Balhoff JP, et al. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. Bmc Bioinformatics. 14: 158. PMID 23668630 DOI: 10.1186/1471-2105-14-158  1
2013 Balhoff JP, Mikó I, Yoder MJ, Mullins PL, Deans AR. A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia. Systematic Biology. 62: 639-59. PMID 23652347 DOI: 10.1093/Sysbio/Syt028  1
2013 Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, ... ... Balhoff JP, et al. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database : the Journal of Biological Databases and Curation. 2013: bas056. PMID 23327936 DOI: 10.1093/Database/Bas056  1
2013 Bertone MA, Mikó I, Yoder MJ, Seltmann KC, Balhoff JP, Deans AR. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment. Database : the Journal of Biological Databases and Curation. 2013: bas057. PMID 23303300 DOI: 10.1093/Database/Bas057  1
2012 Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. A unified anatomy ontology of the vertebrate skeletal system. Plos One. 7: e51070. PMID 23251424 DOI: 10.1371/Journal.Pone.0051070  1
2012 Mullins PL, Kawada R, Balhoff JP, Deans AR. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. Zookeys. 1-38. PMID 23166458 DOI: 10.3897/Zookeys.223.3572  1
2012 Mabee BP, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, Westerfield M. 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. Zeitschrift Fur Angewandte Ichthyologie = Journal of Applied Ichthyology. 28: 300-305. PMID 22736877 DOI: 10.1111/J.1439-0426.2012.01985.X  1
2012 Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology. 61: 675-89. PMID 22357728 DOI: 10.1093/Sysbio/Sys025  1
2012 Deans AR, Yoder MJ, Balhoff JP. Time to change how we describe biodiversity. Trends in Ecology & Evolution. 27: 78-84. PMID 22189359 DOI: 10.1016/J.Tree.2011.11.007  1
2012 Seltmann KC, Yoder MJ, Mikó I, Forshage M, Bertone MA, Agosti D, Austin AD, Balhoff JP, Borowiec ML, Brady SG, Broad GR, XBrothers GR, Burks RA, Buffington ML, Campbell HM, et al. A hymenopterists' guide to the Hymenoptera Anatomy Ontology: Utility, clarification, and future directions Journal of Hymenoptera Research. 27: 67-88. DOI: 10.3897/Jhr.27.2961  1
2011 Dahdul W, Balhoff J, Lapp H, Midford P, Vision T, Westerfield M, Mabee P. Phenoscape: Use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes Ceur Workshop Proceedings. 833: 428-429.  1
2011 Balhoff JP, Midford PE, Lapp H. Integrating anatomy and phenotype ontologies with taxonomic hierarchies Ceur Workshop Proceedings. 833: 426-427.  1
2010 Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM. The teleost anatomy ontology: anatomical representation for the genomics age. Systematic Biology. 59: 369-83. PMID 20547776 DOI: 10.1093/Sysbio/Syq013  1
2010 Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, Kothari C, Lapp H, Lundberg JG, Midford PE, Vision TJ, Westerfield M, Mabee PM. Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. Plos One. 5: e10708. PMID 20505755 DOI: 10.1371/Journal.Pone.0010708  1
2010 Balhoff JP, Dahdul WM, Kothari CR, Lapp H, Lundberg JG, Mabee P, Midford PE, Westerfield M, Vision TJ. Phenex: ontological annotation of phenotypic diversity. Plos One. 5: e10500. PMID 20463926 DOI: 10.1371/Journal.Pone.0010500  1
2010 Midford PE, Balhoff JP, Dahdul W, Kothari CR, Lapp H, Lundberg J, Mabee P, Westerfield M. The Teleost Taxonomy Ontology Nature Precedings. DOI: 10.1038/Npre.2010.4629.1  1
2009 Midford P, Mabee P, Vision T, Lapp H, Balhoff J, Dahdul W, Kothari C, Lundberg J, Westerfield M. Phenoscape: Ontologies for Large Multi-species Phenotype Datasets Nature Precedings. DOI: 10.1038/Npre.2009.3594.1  1
2008 Horvath JE, Weisrock DW, Embry SL, Fiorentino I, Balhoff JP, Kappeler P, Wray GA, Willard HF, Yoder AD. Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs. Genome Research. 18: 489-99. PMID 18245770 DOI: 10.1101/Gr.7265208  1
2007 Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis PO, Mackey AJ, Osborne BI, Piel WH, Pond SLK, Poon AFY, et al. The 2006 NESCent phyloinformatics hackathon: A field report Evolutionary Bioinformatics. 3: 287-296. DOI: 10.4137/Ebo.S0  1
2005 Balhoff JP, Wray GA. Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. Proceedings of the National Academy of Sciences of the United States of America. 102: 8591-6. PMID 15937122 DOI: 10.1073/Pnas.0409638102  1
2003 Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA. The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution. 20: 1377-419. PMID 12777501 DOI: 10.1093/Molbev/Msg140  1
1998 Balhoff JP, Stephens JM. Highly specific and quantitative activation of STATs in 3T3-L1 adipocytes. Biochemical and Biophysical Research Communications. 247: 894-900. PMID 9647789 DOI: 10.1006/Bbrc.1998.8890  1
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