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Todd J. Vision, PhD - Publications

Biology University of North Carolina, Chapel Hill, Chapel Hill, NC 
evolutionary genetics, bioinformatics

61 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 Manda P, Hahn A, Beekman K, Vision TJ. Avoiding "conflicts of interest": a computational approach to scheduling parallel conference tracks and its human evaluation. Peerj. Computer Science. 5: e234. PMID 33816887 DOI: 10.7717/peerj-cs.234  0.4
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  0.4
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
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  0.4
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  0.4
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  0.96
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  0.96
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  0.4
2015 Fenner M, Haak LL, Thorisson GA, Ruiz S, Vision TJ, Brase J. ODIN: The ORCID and DataCite interoperability network International Journal of Knowledge and Learning. 9: 305-325. DOI: 10.1504/IJKL.2014.069537  0.96
2015 Nunn CL, Alberts SC, McClain CR, Meshnick SR, Vision TJ, Wiegmann BM, Rodrigo AG. Linking Evolution, Ecology, and Health: TriCEM Bioscience. 65: 748-749. DOI: 10.1093/Biosci/Biv086  0.96
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  0.96
2014 Flagel LE, Willis JH, Vision TJ. The standing pool of genomic structural variation in a natural population of Mimulus guttatus. Genome Biology and Evolution. 6: 53-64. PMID 24336482 DOI: 10.1093/Gbe/Evt199  0.96
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  0.96
2013 Piwowar HA, Vision TJ. Data reuse and the open data citation advantage. Peerj. 1: e175. PMID 24109559 DOI: 10.7717/peerj.175  0.96
2013 Rodrigo A, Alberts S, Cranston K, Kingsolver J, Lapp H, McClain C, Smith R, Vision T, Weintraub J, Wiegmann B. Science incubators: synthesis centers and their role in the research ecosystem. Plos Biology. 11: e1001468. PMID 23335860 DOI: 10.1371/Journal.Pbio.1001468  0.96
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  0.96
2011 Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, ... ... Vision TJ, et al. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science. 2: 34. PMID 22645531 DOI: 10.3389/Fpls.2011.00034  0.96
2011 Piwowar HA, Vision TJ, Whitlock MC. Data archiving is a good investment. Nature. 473: 285. PMID 21593852 DOI: 10.1038/473285A  0.96
2011 Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ. Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Systematic Biology. 60: 117-25. PMID 21186249 DOI: 10.1093/Sysbio/Syq072  0.96
2011 Michener W, Vieglais D, Vision T, Kunze J, Cruse P, Janée G. DataONE: Data observation network for earth - preserving data and enabling innovation in the biological and environmental sciences D-Lib Magazine. 17. DOI: 10.1045/January2011-Michener  0.96
2011 Piwowar HA, Carlson JD, Vision TJ. Beginning to track 1000 datasets from public repositories into the published literature Proceedings of the Asist Annual Meeting. 48. DOI: 10.1002/meet.2011.14504801337  0.96
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.  0.96
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.  0.96
2010 Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, ... ... Vision TJ, et al. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proceedings of the National Academy of Sciences of the United States of America. 107: 11889-94. PMID 20547848 DOI: 10.1073/Pnas.1003391107  0.96
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  0.96
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  0.96
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  0.96
2010 Vision TJ. Open data and the social contract of scientific publishing Bioscience. 60: 330-331. DOI: 10.1525/bio.2010.60.5.2  0.96
2010 Burleigh JG, Bansal MS, Eulenstein O, Vision TJ. Inferring species trees from gene duplication episodes 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 198-203. DOI: 10.1145/1854776.1854806  0.96
2010 Enriquez V, Judson SW, Walker N, Allard S, Cook R, Piwowar H, Sandusky R, Vision T, Wilson B. Data citation in the wild Nature Precedings. 1-1. DOI: 10.1038/Npre.2010.5452.1  0.4
2010 Vision T. The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem Nature Precedings. 5: 1-1. DOI: 10.1038/Npre.2010.4595.1  0.4
2010 Weber NM, Piwowar HA, Vision TJ. Evaluating data citation and sharing policies in the environmental sciences Proceedings of the Asist Annual Meeting. 47. DOI: 10.1002/meet.14504701445  0.96
2009 Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ. Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. Plos Genetics. 5: e1000502. PMID 19503594 DOI: 10.1371/Journal.Pgen.1000502  0.96
2009 Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ. A hierarchical model for incomplete alignments in phylogenetic inference. Bioinformatics (Oxford, England). 25: 592-8. PMID 19147663 DOI: 10.1093/Bioinformatics/Btp015  0.96
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  0.4
2008 Xu X, Martin B, Comstock JP, Vision TJ, Tauer CG, Zhao B, Pausch RC, Knapp S. Fine mapping a QTL for carbon isotope composition in tomato. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 117: 221-33. PMID 18542914 DOI: 10.1007/S00122-008-0767-6  0.96
2008 Knies JL, Dang KK, Vision TJ, Hoffman NG, Swanstrom R, Burch CL. Compensatory evolution in RNA secondary structures increases substitution rate variation among sites. Molecular Biology and Evolution. 25: 1778-87. PMID 18535013 DOI: 10.1093/Molbev/Msn130  0.96
2008 Hartmann S, Vision TJ. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? Bmc Evolutionary Biology. 8: 95. PMID 18366758 DOI: 10.1186/1471-2148-8-95  0.96
2008 O'Meara B, Alfaro M, Bell C, Bolker B, Butler M, Cowan P, Vienne Dd, Desper R, Felsenstein J, Harmon L, Heibl C, Hipp A, Hunt G, Jombart T, Kembel S, ... ... Vision T, et al. Comparative methods in R hackathon Nature Precedings. DOI: 10.1038/Npre.2008.2126.1  0.4
2007 Ganko EW, Meyers BC, Vision TJ. Divergence in expression between duplicated genes in Arabidopsis. Molecular Biology and Evolution. 24: 2298-309. PMID 17670808 DOI: 10.1093/Molbev/Msm158  0.96
2007 Bouck A, Vision T. The molecular ecologist's guide to expressed sequence tags. Molecular Ecology. 16: 907-24. PMID 17305850 DOI: 10.1111/J.1365-294X.2006.03195.X  0.96
2007 Gaulton KJ, Mohlke KL, Vision TJ. A computational system to select candidate genes for complex human traits. Bioinformatics (Oxford, England). 23: 1132-40. PMID 17237041 DOI: 10.1093/Bioinformatics/Btm001  0.96
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, ... ... Vision TJ, et al. The 2006 NESCent phyloinformatics hackathon: A field report Evolutionary Bioinformatics. 3: 287-296. DOI: 10.4137/Ebo.S0  0.96
2007 Hemminger BM, Saelim B, Sullivan PF, Vision TJ. Comparison of full-text searching to metadata searching for genes in two biomedical literature cohorts Journal of the American Society For Information Science and Technology. 58: 2341-2352. DOI: 10.1002/Asi.V58:14  0.96
2006 Zou F, Xu Z, Vision T. Assessing the significance of quantitative trait loci in replicable mapping populations Genetics. 174: 1063-1068. PMID 16888335 DOI: 10.1534/Genetics.106.059469  0.96
2006 Crayton ME, Powell BC, Vision TJ, Giddings MC. Tracking the evolution of alternatively spliced exons within the Dscam family. Bmc Evolutionary Biology. 6: 16. PMID 16483367 DOI: 10.1186/1471-2148-6-16  0.96
2006 Hartmann S, Lu D, Phillips J, Vision TJ. Phytome: a platform for plant comparative genomics. Nucleic Acids Research. 34: D724-30. PMID 16381967 DOI: 10.1093/Nar/Gkj045  0.96
2005 Vision TJ. Gene order in plants: a slow but sure shuffle. The New Phytologist. 168: 51-60. PMID 16159320 DOI: 10.1111/j.1469-8137.2005.01537.x  0.96
2005 Xu Z, Zou F, Vision TJ. Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics. 170: 401-8. PMID 15781710 DOI: 10.1534/Genetics.104.033746  0.96
2005 Comstock JP, McCouch SR, Martin BC, Tauer CG, Vision TJ, Xu Y, Pausch RC. The effects of resource availability and environmental conditions on genetic rankings for carbon isotope discrimination during growth in tomato and rice Functional Plant Biology. 32: 1089-1105. DOI: 10.1071/FP05117  0.96
2003 Vision T. An international showcase of bioinformatics research Genome Biology. 4. PMID 12952531 DOI: 10.1186/Gb-2003-4-9-337  0.96
2003 Calabrese PP, Chakravarty S, Vision TJ. Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics (Oxford, England). 19: i74-80. PMID 12855440 DOI: 10.1093/Bioinformatics/Btg1008  0.96
2002 Zhang L, Vision TJ, Gaut BS. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Molecular Biology and Evolution. 19: 1464-73. PMID 12200474 DOI: 10.1093/Oxfordjournals.Molbev.A004209  0.96
2002 Carmon A, Vision TJ, Mitchell SE, Thannhauser TW, Müller U, Kresovich S. Solid-phase PCR in microwells: effects of linker length and composition on tethering, hybridization, and extension. Biotechniques. 32: 410, 412, 414-8, 420. PMID 11848417  0.96
2001 Zhang L, Gaut BS, Vision TJ. Gene duplication and evolution. Science (New York, N.Y.). 293: 1551. PMID 11550701  0.96
2000 Vision TJ, Brown DG, Tanksley SD. The origins of genomic duplications in Arabidopsis. Science (New York, N.Y.). 290: 2114-7. PMID 11118139 DOI: 10.1126/Science.290.5499.2114  0.96
2000 Ku HM, Vision T, Liu J, Tanksley SD. Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proceedings of the National Academy of Sciences of the United States of America. 97: 9121-6. PMID 10908680 DOI: 10.1073/Pnas.160271297  0.96
2000 Vision TJ, Brown DG, Shmoys DB, Durrett RT, Tanksley SD. Selective mapping: a strategy for optimizing the construction of high-density linkage maps. Genetics. 155: 407-20. PMID 10790413  0.96
2000 Brown DG, Vision TJ, Tanksley SD. Selective mapping: A discrete optimization approach to selecting a population subset for use in a high-density genetic mapping project Proceedings of the Annual Acm-Siam Symposium On Discrete Algorithms. 419-428.  0.96
1995 Simms EL, Vision TJ. Pathogen-induced systemic resistance in Ipomoea purpurea. Oecologia. 102: 494-500. PMID 28306893 DOI: 10.1007/BF00341362  1
1995 Simms EL, Vision TJ. Pathogen-induced systemic resistance in Ipomoea purpurea Oecologia. 102: 494-500. DOI: 10.1007/BF00341362  0.96
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