Paula Mabee - Publications

Affiliations: 
University of South Dakota, Vermillion, SD, United States 

57 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
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  0.48
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  0.48
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  0.48
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  0.48
2016 Dececchi TA, Mabee PM, Blackburn DC. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. Plos One. 11: e0155680. PMID 27191170 DOI: 10.1371/Journal.Pone.0155680  0.48
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  0.48
2015 Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, ... ... Mabee PM, et al. Emerging semantics to link phenotype and environment. Peerj. 3: e1470. PMID 26713234 DOI: 10.7717/Peerj.1470  0.48
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  0.48
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  0.48
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  0.48
2015 Dahdul W, Dececchi TA, Ibrahim N, Lapp H, Mabee P. Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. Database : the Journal of Biological Databases and Curation. 2015: bav040. PMID 25972520 DOI: 10.1093/database/bav040  0.48
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, ... ... Mabee P, et al. Finding our way through phenotypes. Plos Biology. 13: e1002033. PMID 25562316 DOI: 10.1371/Journal.Pbio.1002033  0.48
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  0.48
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  0.48
2014 Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5: 34. PMID 25140222 DOI: 10.1186/2041-1480-5-34  0.48
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  0.48
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  0.48
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  0.48
2013 Druzinsky R, Mungall C, Haendel M, Lapp H, Mabee P. What is an anatomy ontology? Anatomical Record (Hoboken, N.J. : 2007). 296: 1797-9. PMID 24127438 DOI: 10.1002/Ar.22805  0.48
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, 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  0.48
2012 Mabee P, Deans A, Huala E, Lewis SE. Phenotype Ontology Research Coordination Network meeting report: creating a community network for comparing and leveraging phenotype-genotype knowledge across species. Standards in Genomic Sciences. 6: 440-3. PMID 23409218 DOI: 10.4056/Sigs.2926219  0.48
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  0.48
2012 Block AJ, Mabee PM. Development of the mandibular, hyoid arch and gill arch skeleton in the Chinese barb Puntius semifasciolatus: comparisons of ossification sequences among Cypriniformes. Journal of Fish Biology. 81: 54-80. PMID 22747804 DOI: 10.1111/j.1095-8649.2012.03307.x  0.48
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  0.48
2012 Grey EA, Mabee PM. Gill-arch musculature of the quillback Carpiodes cyprinus (Cypriniformes: Catostomidae) with a comparison to cyprinids. Journal of Morphology. 273: 909-18. PMID 22610546 DOI: 10.1002/jmor.20030  0.48
2012 Engeman JM, Mabee PM. Segmentation and fusion on the midline: basibranchial homologies in cypriniform fishes. Journal of Morphology. 273: 725-36. PMID 22460806 DOI: 10.1002/jmor.20017  0.48
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.  0.48
2011 Mabee PM, Grey EA, Arratia G, Bogutskaya N, Boron A, Coburn MM, Conway KW, He S, Naseka A, Rios N, Simons A, Szlachciak J, Wang X. Gill arch and hyoid arch diversity and cypriniform phylogeny: Distributed integration of morphology and web-based tools Zootaxa. 1-40.  0.48
2011 Vision T, Blake J, Lapp H, Mabee P, Westerfield M. Similarity between semantic description sets: Addressing needs beyond data integration Ceur Workshop Proceedings. 783.  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2009 Engeman JM, Aspinwall N, Mabee PM. Development of the pharyngeal arch skeleton in Catostomus commersonii (Teleostei: Cypriniformes). Journal of Morphology. 270: 291-305. PMID 19034917 DOI: 10.1002/jmor.10688  0.48
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  0.48
2007 Crotwell PL, Mabee PM. Gene expression patterns underlying proximal-distal skeletal segmentation in late-stage zebrafish, Danio rerio. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 236: 3111-28. PMID 17948314 DOI: 10.1002/Dvdy.21352  0.48
2007 Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, Westerfield M. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 308: 655-68. PMID 17599725 DOI: 10.1002/Jez.B.21181  0.48
2007 Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology & Evolution. 22: 345-50. PMID 17416439 DOI: 10.1016/J.Tree.2007.03.013  0.48
2007 Grünbaum T, Cloutier R, Mabee PM, Le François NR. Early developmental plasticity and integrative responses in arctic charr (Salvelinus alpinus): effects of water velocity on body size and shape. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 308: 396-408. PMID 17358017 DOI: 10.1002/Jez.B.21163  0.48
2006 Mabee PM. Integrating evolution and development: The need for bioinformatics in evo-devo Bioscience. 56: 301-309. DOI: 10.1641/0006-3568(2006)56[301:IEADTN]2.0.CO;2  0.48
2004 Crotwell PL, Sommervold AR, Mabee PM. Expression of bmp2a and bmp2b in late-stage zebrafish median fin development. Gene Expression Patterns : Gep. 5: 291-6. PMID 15567728 DOI: 10.1016/J.Modgep.2004.07.001  0.48
2004 Mabee PM, Noordsy M. Development of the paired fins in the paddlefish, Polyodon spathula. Journal of Morphology. 261: 334-44. PMID 15281061 DOI: 10.1002/jmor.10253  0.48
2003 Bird NC, Mabee PM. Developmental morphology of the axial skeleton of the zebrafish, Danio rerio (Ostariophysi: Cyprinidae). Developmental Dynamics : An Official Publication of the American Association of Anatomists. 228: 337-57. PMID 14579374 DOI: 10.1002/Dvdy.10387  0.48
2002 Mabee PM, Crotwell PL, Bird NC, Burke AC. Evolution of median fin modules in the axial skeleton of fishes. The Journal of Experimental Zoology. 294: 77-90. PMID 12210109 DOI: 10.1002/Jez.10076  0.48
2001 Richardson M, Keynes R, Mabee P, Selwood L. Founding editorial: embryology--an integrated approach. Thescientificworldjournal. 1: 602-4. PMID 12805856 DOI: 10.1100/Tsw.2001.298  0.48
2001 Crotwell PL, Clark TG, Mabee PM. Gdf5 is expressed in the developing skeleton of median fins of late-stage zebrafish, Danio rerio. Development Genes and Evolution. 211: 555-8. PMID 11862461 DOI: 10.1007/S00427-001-0186-Z  0.48
2000 Mabee PM, Olmstead KL, Cubbage CC. An experimental study of intraspecific variation, developmental timing, and heterochrony in fishes. Evolution; International Journal of Organic Evolution. 54: 2091-106. PMID 11209785  0.48
2000 Burian R, Gilbert S, Mabee P, Swalla B. General introduction to the symposium on-evolutionary developmental biology: Paradigms, problems, and prospects American Zoologist. 40: 711-717.  0.48
2000 Mabee PM. Developmental data and phylogenetic systematics: Evolution of the vertebrate limb American Zoologist. 40: 789-800.  0.48
1998 Mabee PM, Cua DS, Barlow SB, Helvik JV. Morphology of the hatching glands in Betta splendens (Teleostei: Perciformes) Copeia. 1021-1026.  0.48
1998 Mabee PM, Aldridge E, Warren E, Helenurm K. Effect of clearing and staining on fish length Copeia. 346-353.  0.48
1996 Cubbage CC, Mabee PM. Development of the cranium and paired fins in the zebrafish Danio rerio (Ostariophysi, Cyprinidae) Journal of Morphology. 229: 121-160. DOI: 10.1002/(SICI)1097-4687(199608)229:2<121::AID-JMOR1>3.0.CO;2-4  0.48
1996 Mabee PM, Trendler TA. Development of the cranium and paired fins in Betta splendens (Teleostei: Percomorpha): Intraspecific variation and interspecific comparisons Journal of Morphology. 227: 249-287. DOI: 10.1002/(SICI)1097-4687(199603)227:3<249::AID-JMOR1>3.0.CO;2-1  0.48
1995 Mabee PM. Evolution of pigment pattern development in centrarchid fishes Copeia. 586-607.  0.48
1994 Collazo A, Fraser SE, Mabee PM. A dual embryonic origin for vertebrate mechanoreceptors. Science (New York, N.Y.). 264: 426-30. PMID 8153631 DOI: 10.1126/Science.8153631  0.48
1993 Mabee PM. Phylogenetic interpretation of ontogenetic change: sorting out the actual and artefactual in an empirical case study of centrarchid fishes Zoological Journal of the Linnean Society. 107: 175-291. DOI: 10.1006/zjls.1993.1013  0.48
1993 Mabee PM, Humphries J. Coding polymorphic data: Examples from allozymes and ontogeny Systematic Biology. 42: 166-181.  0.48
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