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Publications

Preprints

  • 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
  • Xu K, Reatini B (in review) The role of self-fertilization in plant colony establishment. preprint

Publications

  1. Gabrielson P, Smith A, Vision TJ, Bruno J, Brandt M (2024) Taxonomic assessment of blade-forming Ulva species (Ulvales, Chlorophyta) in the Galápagos Archipelago, Ecuador using DNA sequencing. Botanica Marina  https://doi.org/10.1515/bot-2023-0079, preprint
  2. Reatini B, Vision TJ (2024) The two faces of secondary contact on islands: Introgressive hybridization between endemics and reproductive interference between endemics and introduced species. Journal of Biogeography 51, 483-498. https://doi.org/10.1111/jbi.14759, preprint
  3. Porto DS, Tarasov S, Charpentier C, Lapp H, Balhoff JP, Vision TJ, Dahdul WM, Mabee PM, Uyeda J (2023) rphenoscate: An R package for semantic-aware evolutionary analyses of anatomical traits. Methods in Ecology and Evolution 14, 2531-2540. https://doi.org/10.1111/2041-210X.14210, preprint
  4. Torres MdL, Urquía D, Moyle L, Gibson M, Vision T, Reatini B (2023) Unravelling the interactions between endemic and invasive plant species in the Galápagos islands, in Walsh SJ, Mena CF, Stewart JR, Muñoz-Pérez, JP (eds.) Island Ecosystems: Challenges to Sustainability. Springer Nature. https://doi.org/10.1007/978-3-031-28089-4_12 
  5. Xu K, Vision TJ, Servedio MR (2023) Evolutionary rescue under demographic and environmental stochasticity. Journal of Evolutionary Biology 36, 1525-1538. https://doi.org/10.1111/jeb.14224, preprint
  6. Porto DS, Dahdul W, Lapp H, Balhoff J, Vision T, Mabee P, Uyeda J (2022) Assessing Bayesian phylogenetic information content of morphological data using knowledge from anatomy ontologies. Systematic Biology 7, 1290-1306. https://doi.org/10.1093/sysbio/syac022
  7. 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. https://doi.org/10.1016/j.respol.2020.104069
  8. Christian T-M, Gooch A, Vision T, Hull E (2020) Journal data policies: Exploring how the understanding of editors and authors corresponds to the policies themselves. PLoS ONE 15(3): e0230281. https://doi.org/10.1371/journal.pone.0230281 data.
  9. Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CD, Vision TJ (2020) A logical model of homology for comparative biology. Systematic Biology 69, 345–362. https://doi.org/10.1093/sysbio/syz067
  10. Reatini B, Vision TJ. (2020) Genetic architecture influences when and how hybridization contributes to colonization. Evolution 74, 1590-1602. https://doi.org/10.1111/evo.13972
  11. Manda P, Hahn A, Lamm K, Provan S, Vision TJ (2019) Avoiding “conflicts of interest”: A computational approach to scheduling parallel conference tracks and its human evaluation. PeerJ Computer Science 5:e234 https://doi.org/10.7717/peerj-cs.234. 
  12. 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, http://doi.org/10.3233/978-1-61499-854-9-187  PDF
  13. 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 https://doi.org/10.1093/database/bay110 
  14. 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: https://doi.org/10.7287/peerj.preprints.26988v1
  15. 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: https://doi.org/10.1101/327833
  16. Reatini B, Torres ML, Valdebenito H, Vision T (2018) Complete plastome sequences of two Psidium species from the Galápagos Islands, F1000 Research 7, 1361, https://f1000research.com/articles/7-1361/v1
  17. Manda P, Vision TJ. (2017) Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. Proceedings of The International Workshop on Semantic Big Data (SBD ’17) doi:10.1145/3066911.3066919, preprint
  18. 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
  19.  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 http://ceur-ws.org/Vol-1747/, preprint
  20. 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
  21. 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 
  22. 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 
  23. 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 
  24. 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 
  25. 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 
  26. 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
  27. 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 
  28. 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 
  29. 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 
  30. Piwowar HA, Vision TJ. (2013) Data reuse and the open data citation advantage. PeerJ 1:e175 doi:10.7717/peerj.175 
  31. 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 
  32. 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
  33. Czabarka E, Székely L, Vision T (2012) Minimizing the number of episodes and Gallai’s theorem on intervals. (preprint: arXiv:1209.5699)
  34. Piwowar HA, Vision TJ, Whitlock MC (2011) Data archiving is a good investment. Nature 473 (7347), 285.  doi:10.1038/473285a
  35. 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 
  36. 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 
  37. 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 
  38. 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 
  39. 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 age. Systematic Biology 59(4):369-83. 
  40. 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 
  41. 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. 
  42. 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
  43. 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/bioinformatic/btp015 
  44. 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
  45. 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 
  46. Knies JL, Dang KK, Vision TJ, Hoffman N, Swanstrom RI, Burch CL (2008) Compensatory evolution in RNA secondary structures increases substitution rate variation among sites. Molecular Biology and Evolution 25, 1778-1787 
  47. Xu X, Martin B, Comstock JP, Vision TJ, Tauer CG, Zhao B, Pausch R, Knapp S (2008) Fine mapping a QTL for carbon isotope composition in tomato. Theoretical and Applied Genetics 117, 221-233. doi:10.1007/s00122-008-0767-6
  48. 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 
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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 
  54. 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 
  55. 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. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167193 
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. Huan J, Prins J, Wang W, Vision TJ (2003) Reconstruction of ancestral gene order following segmental duplication and gene loss.  Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB), pp. 484-485  PDF
  65. 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) 
  66. Zhang L, Vision TJ, Gaut BS (2002) Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana.  Molecular Biology and Evolution 19, 1464-1473.
  67. Carmon A, Vision TJ, Mitchell SE, Thannhauser TW, Muller U, Kresovich S (2002)  Solid-phase PCR in microwells: optimization for high-throughput, fluorescence-based detection.  Biotechniques 32, 410-420  PDF
  68. 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
  69. Zhang L, Gaut BS, Vision TJ (2001) Gene duplication and evolution.  Science 293, 1551-1552  PDF
  70. 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
  71. Vision TJ, Brown DG, Tanksley SD  (2000) The origins of genomic duplications in Arabidopsis.  Science 290:2114-2117. (4 pages).doi:10.1126/science.290.5499.2114 Reprinted in Ridley M, editor Evolution, 2nd ed., Oxford University Press  PDF
  72. 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
  73. 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
  74. 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.
  75. Simms EL, Vision TJ (1995) Pathogen-induced systemic resistance in Ipomoea purpurea.  Oecologia 102:494-500.
  76. Vision TJ, Dillon MO (1996)  Sinopsis de Senecio L. (Senecioneae, Asteraceae) para el Perú.  Arnaldoa 4:24-46.

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