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Items: 37

1.

A Logical Model of Homology for Comparative Biology.

Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CJ, Vision TJ.

Syst Biol. 2020 Mar 1;69(2):345-362. doi: 10.1093/sysbio/syz067.

PMID:
31596473
3.

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.

Edmunds RC, Su B, Balhoff JP, Eames BF, Dahdul WM, Lapp H, Lundberg JG, Vision TJ, Dunham RA, Mabee PM, Westerfield M.

Mol Biol Evol. 2016 Jan;33(1):13-24. doi: 10.1093/molbev/msv223. Epub 2015 Oct 24.

4.

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.

Manda P, Balhoff JP, Lapp H, Mabee P, Vision TJ.

Genesis. 2015 Aug;53(8):561-71. doi: 10.1002/dvg.22878. Epub 2015 Aug 11. Review.

PMID:
26220875
5.

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

Balhoff JP, Dahdul WM, Dececchi TA, Lapp H, Mabee PM, Vision TJ.

J Biomed Semantics. 2014 Nov 5;5(1):45. doi: 10.1186/2041-1480-5-45. eCollection 2014.

6.

Open data for evolutionary synthesis: an introduction to the NESCent collection.

Vision TJ, Cranston K.

Sci Data. 2014 Sep 2;1:140030. doi: 10.1038/sdata.2014.30. eCollection 2014. No abstract available.

7.

The standing pool of genomic structural variation in a natural population of Mimulus guttatus.

Flagel LE, Willis JH, Vision TJ.

Genome Biol Evol. 2014 Jan;6(1):53-64. doi: 10.1093/gbe/evt199.

8.

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

Midford PE, Dececchi TA, Balhoff JP, Dahdul WM, Ibrahim N, Lapp H, Lundberg JG, Mabee PM, Sereno PC, Westerfield M, Vision TJ, Blackburn DC.

J Biomed Semantics. 2013 Nov 22;4(1):34. doi: 10.1186/2041-1480-4-34.

9.

Data reuse and the open data citation advantage.

Piwowar HA, Vision TJ.

PeerJ. 2013 Oct 1;1:e175. doi: 10.7717/peerj.175. eCollection 2013.

10.

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.

Mabee BP, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, Westerfield M.

J Appl Ichthyol. 2012 Jun 1;28(3):300-305. Epub 2012 May 21.

11.

Data archiving is a good investment.

Piwowar HA, Vision TJ, Whitlock MC.

Nature. 2011 May 19;473(7347):285. doi: 10.1038/473285a. No abstract available.

PMID:
21593852
12.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology.

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 SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, 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.

Front Plant Sci. 2011 Jul 25;2:34. doi: 10.3389/fpls.2011.00034. eCollection 2011.

13.

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.

Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ.

Syst Biol. 2011 Mar;60(2):117-25. doi: 10.1093/sysbio/syq072. Epub 2010 Dec 24.

14.

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

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.

Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11889-94. doi: 10.1073/pnas.1003391107. Epub 2010 Jun 14.

15.

The teleost anatomy ontology: anatomical representation for the genomics age.

Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM.

Syst Biol. 2010 Jul;59(4):369-83. doi: 10.1093/sysbio/syq013. Epub 2010 Mar 29.

16.

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, Kothari C, Lapp H, Lundberg JG, Midford PE, Vision TJ, Westerfield M, Mabee PM.

PLoS One. 2010 May 20;5(5):e10708. doi: 10.1371/journal.pone.0010708.

17.

Phenex: ontological annotation of phenotypic diversity.

Balhoff JP, Dahdul WM, Kothari CR, Lapp H, Lundberg JG, Mabee P, Midford PE, Westerfield M, Vision TJ.

PLoS One. 2010 May 5;5(5):e10500. doi: 10.1371/journal.pone.0010500.

18.

Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae.

Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ.

PLoS Genet. 2009 Jun;5(6):e1000502. doi: 10.1371/journal.pgen.1000502. Epub 2009 Jun 5.

19.

A hierarchical model for incomplete alignments in phylogenetic inference.

Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ.

Bioinformatics. 2009 Mar 1;25(5):592-8. doi: 10.1093/bioinformatics/btp015. Epub 2009 Jan 15.

20.

Fine mapping a QTL for carbon isotope composition in tomato.

Xu X, Martin B, Comstock JP, Vision TJ, Tauer CG, Zhao B, Pausch RC, Knapp S.

Theor Appl Genet. 2008 Jul;117(2):221-33. doi: 10.1007/s00122-008-0767-6. Epub 2008 Apr 30.

PMID:
18542914
21.

Compensatory evolution in RNA secondary structures increases substitution rate variation among sites.

Knies JL, Dang KK, Vision TJ, Hoffman NG, Swanstrom R, Burch CL.

Mol Biol Evol. 2008 Aug;25(8):1778-87. doi: 10.1093/molbev/msn130. Epub 2008 Jun 4.

22.

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Hartmann S, Vision TJ.

BMC Evol Biol. 2008 Mar 26;8:95. doi: 10.1186/1471-2148-8-95.

23.

Divergence in expression between duplicated genes in Arabidopsis.

Ganko EW, Meyers BC, Vision TJ.

Mol Biol Evol. 2007 Oct;24(10):2298-309. Epub 2007 Aug 1.

PMID:
17670808
24.

A computational system to select candidate genes for complex human traits.

Gaulton KJ, Mohlke KL, Vision TJ.

Bioinformatics. 2007 May 1;23(9):1132-40. Epub 2007 Jan 19.

PMID:
17237041
25.

Tracking the evolution of alternatively spliced exons within the Dscam family.

Crayton ME 3rd, Powell BC, Vision TJ, Giddings MC.

BMC Evol Biol. 2006 Feb 16;6:16.

26.

Phytome: a platform for plant comparative genomics.

Hartmann S, Lu D, Phillips J, Vision TJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D724-30.

27.

Gene order in plants: a slow but sure shuffle.

Vision TJ.

New Phytol. 2005 Oct;168(1):51-60. Review.

28.
29.

Contrasting modes of diversification in the Aux/IAA and ARF gene families.

Remington DL, Vision TJ, Guilfoyle TJ, Reed JW.

Plant Physiol. 2004 Jul;135(3):1738-52. Epub 2004 Jul 9.

30.

Fast identification and statistical evaluation of segmental homologies in comparative maps.

Calabrese PP, Chakravarty S, Vision TJ.

Bioinformatics. 2003;19 Suppl 1:i74-80.

PMID:
12855440
31.
32.

Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana.

Zhang L, Vision TJ, Gaut BS.

Mol Biol Evol. 2002 Sep;19(9):1464-73.

PMID:
12200474
33.

Solid-phase PCR in microwells: effects of linker length and composition on tethering, hybridization, and extension.

Carmon A, Vision TJ, Mitchell SE, Thannhauser TW, Müller U, Kresovich S.

Biotechniques. 2002 Feb;32(2):410, 412, 414-8, 420.

34.

Gene duplication and evolution.

Zhang L, Gaut BS, Vision TJ.

Science. 2001 Aug 31;293(5535):1551. No abstract available.

PMID:
11550701
35.

The origins of genomic duplications in Arabidopsis.

Vision TJ, Brown DG, Tanksley SD.

Science. 2000 Dec 15;290(5499):2114-7.

36.

Selective mapping: a strategy for optimizing the construction of high-density linkage maps.

Vision TJ, Brown DG, Shmoys DB, Durrett RT, Tanksley SD.

Genetics. 2000 May;155(1):407-20.

37.

Pathogen-induced systemic resistance in Ipomoea purpurea.

Simms EL, Vision TJ.

Oecologia. 1995 Jun;102(4):494-500. doi: 10.1007/BF00341362.

PMID:
28306893

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