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  • Porto DS, Dahdul W, Lapp H, Balhoff J, Vision T, Mabee P, Uyeda J (in press) Assessing Bayesian phylogenetic information content of morphological data using knowledge from anatomy ontologies. Systematic Biology (preprint: biorXiv).
  • Reatini B, Torres MdL, Vision TJ (in review) Local exclusion and regional decline of an endemic Galápagos tree species (Psidium galapageium) by an invasive relative (P. guajava). (preprint: biorxiv)
  • Reatini B, Vision TJ (in review) The two faces of secondary contact. (preprint: Carolina Digital Repository)
  • Torres MdL, Urquía D, Moyle L, Gibson M, Vision T, Reatini B (in press) Unravelling the interactions between endemic and invasive plant species in the Galápagos islands, in Walsh SJ, Mena CF (eds.) Island Ecosystems: Challenges to Sustainability. Springer Nature.

  • Hackett EJ, Leahey E, Parker JN, Rafols I, Hampton S, Corte U, Drake JM, Penders B, Sheble L, Vermeulen N, Vision T. (2020) Do synthesis centers synthesize? A semantic analysis of diversity and performance. Research Policy 50, 104069. (preprint: bioRxiv).




  • Braun I, Balhoff JP, Berardini TZ, Cooper L, Gkoutos G, Harper L, Huala E, Jaiswal P, Kazic T, Lapp H, Macklin JA, Specht CD, Vision T, Walls RL, Lawrence-Dill CJ (2018) ‘Computable’ phenotypes enable comparative and predictive phenomics among plant species and across domains of life. pp 187-205 in Application of Semantic Technologies in Biodiversity Science, A. Thessen, editor,  IOS Press, Berlin,  PDF
  • Dahdul W, Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Vision T, Mabee, PM (2018) Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems. Database (preprint:
  • Mabee PM, Dahdul W, Balhoff JP, Lapp H, Manda P, Uyeda J, Vision TJ, Westerfield M (2018) Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology, pp 207-224 in Application of Semantic Technologies in Biodiversity Science, A. Thessen, editor,  IOS Press, Berlin. (preprint:
  • Manda P, Vision T (2018) On the statistical sensitivity of semantic similarity metrics. Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018) PDF (preprint:
  • Reatini B, Torres ML, Valdebenito H, Vision T (2018) Complete plastome sequences of two Psidium species from the Galápagos Islands, F1000 Research,



  • Mayo C, Hull EA, Vision TJ (2016) The location of the citation: changing practices in how publications cite original data in the Dryad Digital Repository. International Journal of Digital Curation 11, 150-155. doi:10.2218/ijdc.v11i1.400  (preprint doi:10.5281/zenodo.32412)
  • Manda P, Balhoff JP, Vision TJ (2016) Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. Proceedings of the Joint International Conference on Biological Ontology and BioCreative,  and (preprint: doi:10.1101/086306)
  • Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Proceedings of the Pacific Symposium on Biocomputing 2016, doi:10.1142/9789814749411_0013  (preprint doi:10.1101/028449)


  • Edmunds RC, Su B, Balhoff JP, Eames BF, Dahdul WM, Lapp H, Lundberg JG, Vision TJ, Dunham RA, Mabee PM, Westerfield M (2015) Phenoscape: Identifying candidate genes for evolutionary phenotypes. Molecular Biology and Evolution doi:10.1093/molbev/msv223 
  • Nunn CL, Alberts, SC, McClain CR, Meshnick SR, Vision TJ, Weigmann MB, Rodrigo AG (2015) Linking Evolution, Ecology, and Health: TriCEM. BioScience 65, 748-749. doi:10.1093/biosci/biv086 
  • Manda P, Balhoff JP, Lapp H, Mabee P, Vision TJ (2015) Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53, 561-571. doi:10.1002/dvg.22878 
  • Swauger S, Vision TJ (2015) What Factors Influence Where Researchers Deposit their Data? A Survey of Researchers Submitting to Data Repositories. International Journal of Digital Curation 10, 68-81. doi:10.2218/ijdc.v10i1.289 


  • Balhoff JP, Dahdul WM, Dececchi TA, Lapp H, Mabee PM, Vision TJ (2014) Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5, 45.  doi:10.1186/2041-1480-5-45 
  • Fenner M, Haak L, Thorisson G, Ruiz S, Vision TJ, Brase J (2014) ODIN: the ORCID and DataCite interoperability network. Int. J. of Knowledge and Learning 9, 305-325. doi:10.1504/IJKL.2014.069537  PDF
  • Flagel LE, Willis LE, Vision TJ (2014) The standing pool of genomic structural variation in a natural population of Mimulus guttatus. Genome Biology and Evolution 6, 53-64. doi:10.1093/gbe/evt199 
  • Vision TJ, Cranston K (2014) Open data for evolutionary synthesis: an introduction to the NESCent collection. Scientific Data 1, 140030 doi:10.1038/sdata.2014.30 


  • Midford PE, Dececchi A, Balhoff JP, Dahdul WM, Ibrahim N, Lapp H, Lundberg JG, Mabee, PM, Sereno PC, Westerfield M, Vision TJ, Blackburn DC (2013) The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics, 4:34  doi:10.1186/2041-1480-4-34 
  • Piwowar HA, Vision TJ. (2013) Data reuse and the open data citation advantage. PeerJ 1:e175 doi:10.7717/peerj.175 
  • Rodrigo A, Alberts S, Cranston K, Kingsolver J, Lapp H, McClain C, Smith R, Vision T, Weintraub J, Wiegmann B (2013) Science Incubators: Synthesis Centers and Their Role in the Research Ecosystem. PLoS Biology 11(1): e1001468. doi:10.1371/journal.pbio.1001468 


  • Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, Westerfield M (2012) 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Icthyology 28, 300-305. doi:10.1111/j.1439-0426.2012.01985.x  PDF
  • Czabarka E, Székely L, Vision T (2012) Minimizing the number of episodes and Gallai’s theorem on intervals. (preprint: arXiv:1209.5699)


  • Piwowar HA, Vision TJ, Whitlock MC (2011) Data archiving is a good investment. Nature 473 (7347), 285.  doi:10.1038/473285a
  • Michener W, Vision T, Cruse P, Vieglais D, Kunze J, Janée G (2010) DataONE: Data Observation Network for Earth — Preserving Data and Enabling Innovation in the Biological and Environmental Sciences. D-Lib Magazine 17 (1/2), doi: 10.1045/january2011-michener 
  • 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, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim S, Kvilekval K, Manjunath B, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston K, Soltis P, Soltis D, O’Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D (2011) The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Sciences 2, 34. doi:10.3389/fpls.2011.00034 
  • Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ (2011) Genome-scale phylogenetics: Inferring the plant tree of life from 18,896 discordant gene trees. Systematic Biology 60, 117-125. doi:10.1093/sysbio/syq072 


  • Balhoff JP, Dahdul WM, Kothari CR, Lapp D, Lundberg JG, Mabee PM, Midford PE, Westerfield M, Vision TJ (2010) Phenex: Ontological annotation of phenotypic data. PLoS ONE 5, e10500. doi:10.1371/journal.pone.0010500 
  • Dahdul WM Mabee PM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M (2010) The Teleost Anatomy Ontology: Anatomical representation for the genomic ageSystematic Biology 59(4):369-83. 
  • Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, Kothari C, Lapp H, Lundberg JG, Midford PE, Vision TJ, Westerfield M, Mabee PM (2010) Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS ONE 5, e10708. doi:10.1371/journal.pone.0010708 
  • 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, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci USA 107, 11889-94. 
  • Vision TJ (2010) Open Data and the Social Contract of Scientific Publishing. BioScience 60, 330-330. doi:10.1525/bio.2010.60.5.2 (perspectives) doi:10.1525/bio.2010.60.5.2


  • Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ (2009) A hierarchical model for incomplete alignments in phylogenetic inference. Bioinformatics 25, 592-598. doi:10.1093/bioinformatics/btp015 
  • Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann, FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ (2009) Systematic identification of balanced transposition polymorphisms in yeast. PLoS Genetics 5. e1000502. doi:10.1371/journal.pgen.1000502
  • Hartmann S, Vision TJ (2008) Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evolutionary Biology 8, 95. doi:10.1186/1471-2148-8-95 



  • Bouck A, Vision TJ (2007) The molecular ecologist’s guide to expressed sequence tags. Molecular Ecology 16, 907-924. doi:10.1111/j.1365-294X.2006.03195.x 
  • Gaulton KJ, Mohlke KL, Vision TJ (2007) A computational system to select candidate genes for complex human traits. Bioinformatics 23, 1132-1140. doi:10.1093/bioinformatics/btm001
  • Ganko EW, Meyers BC, Vision TJ (2007) Divergence in expression between duplicated genes in Arabidopsis. Molecular Biology and Evolution 24, 2298-2309. doi:10.1093/molbev/msm158
  • Hemminger BM, Saelim B, Sullivan PF, Vision TJ (2007) 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 (JASIST) 58, 2341-2352. doi:10.1002/asi.20708
  • Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis PO, Mackey AJ, Osborne BO, Piel WH, Kosakovsky Pond SL, Poon AFY, Qiu W-G, Stajich JE, Stoltzfus A, Thierer T, Vilella A, Vos R, Zmasek CM, Zwickl DJ, Vision TJ (2007) The 2006 NESCent Phyloinformatics Hackathon: a field report. Evolutionary Bioinformatics 3, 287-296 


  • Crayton ME, Powell B, Vision TJ, Giddings MC (2006) Tracking the evolution of alternatively spliced exons within the Dscam gene family. BMC Evolutionary Biology 6, 16. doi:10.1186/1471-2148-6-16 
  • Hartmann S, Lu D, Phillips J, Vision TJ (2006) Phytome: a platform for plant comparative genomics.  Nucleic Acids Research 34, D724-D730. doi:10.1093/nar/gkj045 
  • Leebens-Mack, Vision TJ, Brenner E, Bowers JE, Cannon S and 21 others (2006) Taking the first steps towards a standard for reporting in phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA). OMICS 10, 231-237. 
  • Zou F, Xu Z, Vision TJ (2006) Assessing the significance of quantitative trait loci in replicable mapping populations. Genetics 174, 1063-1068. doi:10.1534/genetics.106.059469


  • Comstock JP, McCouch SR, Martin BC, Tauer CG, Vision TJ, Xu Y, Pausch RC (2005) 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 PDF
  • Xu Z, Zou F, Vision TJ (2005) Improving QTL mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics 170, 401-408. doi:10.1534/genetics.104.033746
  • Vision TJ (2005) Gene order evolution in plants: a slow but sure shuffle.  New Phytologist 168, 51-60. (review) doi:10.1111/j.1469-8137.2005.01537.x  PDF


  • Remington DL, Vision TJ, Guilfoyle TJ, Reed JW (2004)  Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiology 135, 1738-1752. doi:10.1104/pp.104.039669
  • Vision TJ, McLaysaght A (2004) Computational tools and resources for plant genomics.  In Christou P, Klee H, editors, Handbook of Plant Biotechnology.  John Wiley & Sons, Ltd.  Chichester, United Kingdom.  PDF


  • Calabrese P, Chakravarty S, Vision TJ (2003) Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 19, i74-i80. doi:10.1093/bioinformatics/btg1008
  • Hoekenga OA, Vision TJ, Shaff JE, Monforte AJ, Howell SH, Kochian LV (2003) Identi fication and characterization of Al-tolerance loci in Arabidopsis thaliana (Landsberg x Columbia ) by quantitative trait locus mapping: a physiologically simple but genetically complex trait. Plant Physiology 132, 936-948. doi:10.1104/pp.103.023085
  • Huan J, Prins J, Wang W, Vision TJ (2003) Reconstruction of ancestral gene order following segmental duplication and gene lossProceedings of the IEEE Computer Society Bioinformatics Conference (CSB), pp. 484-485  PDF
  • Vision T (2003) An international showcase of bioinformatics research. (A review of the Proceedings of the 11th Annual Intelligent Systems in Molecular Biology Conference, Brisbane, Australia). Genome Biology 4, 335-336. (conference report) 



  • Vision TJ, Xu Y, Van Eck N, Brown DG, Tanskley SD (2001) A Lycopersicon esculentum x L. pennellii backcross recombinant inbred population. Report of the Tomato Genetics Cooperative 51, 15-16. PDF
  • Zhang L, Gaut BS, Vision TJ (2001) Gene duplication and evolution.  Science 293, 1551-1552  PDF


  • Vision TJ, Brown DG (2000)  Genome Archaeology: Detecting the descendants of ancient polyploids in contemporary genomes. pp. 479-491 in Sankoff D, Nadeau JH, editors Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families. Kluwer Academic Publishers, Dordrecht, Netherlands  PDF
  • Vision TJ, Brown DG, Tanksley SD  (2000) The origins of genomic duplications in ArabidopsisScience 290:2114-2117. (4 pages).doi:10.1126/science.290.5499.2114 Reprinted in Ridley M, editor Evolution, 2nd ed., Oxford University Press  PDF
  • Ku, H-M, Vision T, Liu J, Tanksley SD (2000) 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 USA 97:9121-9126. doi:10.1073/pnas.160271297
  • Brown DG, Vision TJ, Tanksley, SD (2000) Selective mapping: a discrete optimization approach to faster, cheaper genetic mapping experiments. Proceedings of the Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms. 419-428  PDF
  • Vision TJ, Brown DG, Shmoys DB, Durrett RT, Tanksley SD (2000) Selective mapping: a strategy for optimizing the construction of high-density linkage map. Genetics 155:407-420.

20th Century


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