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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
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58 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
2024 Matentzoglu N, Bello SM, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff JP, Balk MA, Bradford YM, Bridges Y, Callahan TJ, Caufield H, Cuzick A, Carmody LC, Caron AR, de Souza V, et al. The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics. Biorxiv : the Preprint Server For Biology. PMID 39345458 DOI: 10.1101/2024.09.18.613276  0.383
2023 Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, et al. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Research. PMID 37953324 DOI: 10.1093/nar/gkad1005  0.335
2023 Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, et al. The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. Mammalian Genome : Official Journal of the International Mammalian Genome Society. PMID 37076585 DOI: 10.1007/s00335-023-09992-1  0.385
2023 Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, et al. The Gene Ontology knowledgebase in 2023. Genetics. 224. PMID 36866529 DOI: 10.1093/genetics/iyad031  0.343
2023 Stefancsik R, Balhoff JP, Balk MA, Ball R, Bello SM, Caron AR, Chessler E, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, et al. The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences. Biorxiv : the Preprint Server For Biology. PMID 36747660 DOI: 10.1101/2023.01.26.525742  0.397
2022 Porto DS, Dahdul WM, Lapp H, Balhoff JP, Vision TJ, Mabee PM, Uyeda J. Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies. Systematic Biology. PMID 35285502 DOI: 10.1093/sysbio/syac022  0.661
2021 Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, et al. OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database : the Journal of Biological Databases and Curation. 2021. PMID 34697637 DOI: 10.1093/database/baab069  0.346
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  0.368
2020 Cox S, Ahalt SC, Balhoff J, Bizon C, Fecho K, Kebede Y, Morton K, Tropsha A, Wang P, Xu H. Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface. Jmir Medical Informatics. 8: e17964. PMID 33226347 DOI: 10.2196/17964  0.359
2019 Bizon C, Cox S, Balhoff J, Kebede Y, Wang P, Morton K, Fecho K, Tropsha A. ROBOKOP KG AND KGB: Integrated Knowledge Graphs from Federated Sources. Journal of Chemical Information and Modeling. PMID 31769676 DOI: 10.1021/Acs.Jcim.9B00683  0.369
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  0.348
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  0.702
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  0.433
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  0.427
2019 Matentzoglu N, Osumi-Sutherland D, Balhoff JP, Bello S, Bradford Y, Cardmody L, Grove C, Harris MA, Harris N, Köhler S, McMurry J, Mungall C, Munoz-Torres M, Pilgrim C, Robb S, et al. uPheno 2: Framework for standardised representation of phenotypes across species F1000research. 8. DOI: 10.7490/F1000Research.1116540.1  0.362
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  0.771
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  0.441
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  0.413
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  0.327
2017 Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C. Dead simple OWL design patterns. Journal of Biomedical Semantics. 8: 18. PMID 28583177 DOI: 10.1186/S13326-017-0126-0  0.374
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  0.325
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  0.326
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  0.723
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  0.484
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  0.406
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  0.348
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  0.772
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  0.693
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  0.787
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  0.488
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  0.45
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  0.754
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  0.694
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  0.501
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  0.304
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  0.312
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  0.734
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  0.7
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  0.474
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  0.364
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  0.392
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  0.469
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  0.378
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  0.728
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  0.455
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  0.394
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  0.406
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.  0.635
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  0.742
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  0.741
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  0.729
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  0.412
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  0.62
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  0.6
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  0.734
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  0.555
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  0.719
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