Laboratory of Todd Vision
Department of Biology
University of North Carolina at Chapel Hill

Selected Publications

2008

• Hartmann S, Vision TJ (2008) Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Bio 8, 95. doi:10.1186/1471-2148-8-95
• Knies JL, Dank KK, Vision TJ, Hoffman N, Swanstrom RI, Burch CL (2008) Compensatory evolution in RNA secondary structures increases substitution rate variation among sites. Molecular Biology & Evolution. doi:10.1093/molbev/msn130
• 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. doi:10.1007/s00122-008-0767-6

2007

• 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 et al (2007) The 2006 NESCent Phyloinformatics Hackathon: a field report. Evolutionary Bioinformatics 3, 357. link

2006

• Crayton ME, Powell B, Vision TJ, Giddings MC (2006) Tracking the evolution of alternatively spliced exons in 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 J, Vision T, 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. doi:10.1089/omi.2006.10.231
• Zou F, Xu Z, Vision TJ (2006) Assessing the significance of QTL in replicated mapping populations. Genetics 174, 1063-1068. doi:10.1534/genetics.106.059469

2005

• 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. doi:10.1071/FP05117
• Vision TJ (2005) Gene order evolution in plants: a slow but sure shuffle. New Phytologist 168, 51-60. doi:10.1111/j.1469-8137.2005.01537.x
• 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

2004

• 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, McLysaght A (2004) Computational Tools and Resources in Plant Genome Informatics. Handbook of Plant Biotechnology. Wiley and Sons.

2003

• Calabrese PP, Chakravarty S, Vision TJ  (2003) Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 19, i74-i80. doi:1010.93/bioinformatics/btg1008
• Hoekenga OA, Vision TJ, Shaff JE, Monforte AJ, Howell SH, Kochian LV (2003) Identification 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

2002

• 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. abstract
• Carmon A, Vision TJ, Mitchell SE, Thannhauser TW, Muller U, Kresovich S (2002) Solid-phase PCR in microwells: effects of linker length and composition on tethering, hybridization and extension.  Biotechniques 32, 410-420. abstract

2001

• Zhang L, Gaut BS, Vision TJ (2001) Gene duplication and evolution. Science 293, 1551-1552.

2000

• 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. abstract
• Vision TJ, Brown DG (2000) Genome archaeology: Detecting ancient polyploidy in contemporary genomes. pp. 479-492 in Sankoff D, Nadeau JH (eds.) Comparative Genomics, Kluwer Academic Publishers.
• Vision TJ, Brown DG, Shmoys DS, Durrett RT, Tanksley SD (2000) Selective mapping: a strategy for optimizing the construction of high-density linkage maps. Genetics 155, 407-420. abstract
• Vision TJ, Brown DG and Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290, 2114-7. abstract, supplementary material