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Todd J. Vision, PhD - Publications

Affiliations: 
Biology University of North Carolina, Chapel Hill, Chapel Hill, NC 
Area:
evolutionary genetics, bioinformatics
Website:
http://visionlab.bio.unc.edu
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41 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
2023 Xu K, Vision TJ, Servedio MR. Evolutionary rescue under demographic and environmental stochasticity. Journal of Evolutionary Biology. 36: 1525-1538. PMID 37776088 DOI: 10.1111/jeb.14224  0.553
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  0.646
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  0.616
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  0.672
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. DOI: 10.7717/Peerj-Cs.234  0.615
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  0.768
2018 Reatini B, Torres ML, Valdebenito H, Vision T. Complete plastome sequences of two species from the Galápagos Islands. F1000research. 7: 1361. PMID 30345032 DOI: 10.12688/F1000Research.15653.1  0.308
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  0.731
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  0.769
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  0.668
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  0.776
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  0.756
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  0.657
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  0.746
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  0.69
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  0.695
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  0.693
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  0.663
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  0.302
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.  0.624
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  0.7
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  0.696
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  0.709
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  0.331
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  0.306
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  0.757
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  0.647
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  0.624
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  0.65
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  0.588
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  0.765
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  0.314
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  0.737
2006 Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, et al. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). Omics : a Journal of Integrative Biology. 10: 231-7. PMID 16901231 DOI: 10.1089/Omi.2006.10.231  0.428
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  0.67
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  0.535
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  0.537
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  0.46
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.  0.453
1995 Simms EL, Vision TJ. Pathogen-induced systemic resistance in Ipomoea purpurea. Oecologia. 102: 494-500. PMID 28306893 DOI: 10.1007/BF00341362  0.455
1995 Simms EL, Vision TJ. Pathogen-induced systemic resistance in Ipomoea purpurea Oecologia. 102: 494-500. DOI: 10.1007/BF00341362  0.438
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