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You've reached Travis Wheeler's academic home on the web.
I'm a postdoctoral research associate in the Eddy
lab
at Janelia Farm
in Northern Virginia. My recent doctoral work was done at
the University of Arizona
with John Kececioglu
and Mike Sanderson.
I spend most of my academic time designing and implementing algorithms for problems motivated by data from molecular biology. The overarching theme of my work is identifying patterns in molecular sequences based on models of sequence evolution. I've worked on multiple sequence alignment, phylogeny inference, and now homology search.
Curriculum Vitae
:
(pdf)
(MS Word)
Publications
Kececioglu, J., Kim, E., and Wheeler, T. 2010.
Aligning protein sequences with predicted secondary structure.
Journal of Computational Biology, 17(3): 561-580.
[link]
Wheeler, T.J. 2009. Efficient construction of accurate multiple alignments and large-scale phylogenies. Ph.D. dissertation, Department of Computer Science, University of Arizona, Tucson, Arizona. [link] Wheeler, T.J. 2009. Large-scale neighbor-joining with NINJA. Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI), 375-389. [link, preprint] Kim, E., Wheeler, T.J., and Kececioglu, J.D. 2009. Learning models for aligning protein sequence with predicted secondary structure. Proceedings of the 13th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics 5541: 586-605. [link] Wheeler, T.J. and Kececioglu, J.D. 2007. Multiple alignment by aligning alignments. Proceedings of the 15th ISCB Conference on Intelligent Systems for Molecular Biology, Bioinformatics, 23: i559-i568. [link] Good, J.M., Hayden, C.A., and Wheeler T.J. 2006. Adaptive protein evolution and regulatory divergence in Drosophila. Molecular Biology and Evolution, 23(6): 1101-1103. [link] Hayden, C.A., Wheeler, T.J., and Jorgensen R.A. 2005. Evaluating and improving cDNA sequence quality with cQC. Bioinformatics, 21(24): 4414-4415. [link] Cutter, A.D, Good, J.M., Pappas, C.T., Saunders, M.A., Starrett, D.M., Wheeler T.J. 2005. Transposable element orientation bias in the Drosophila melanogaster genome. Journal of Molecular Evolution, 61(6): 733-741. [link]
Software Wheeler, T.J. and Maddison, D.R. 2010. Ninja: a Mesquite package for fast neighbor-joining phylogeny inference. http://mesquiteproject.org. Wheeler ,T.J. 2009. NINJA: software for large-scale neighbor-joining phylogeny inference. http://nimbletwist.com/software/ninja Wheeler, T.J. and Maddison, D.R. 2009. Opalescent: a Mesquite package for multiple sequence alignment. http://mesquiteproject.org Wheeler ,T.J. and Kececioglu. J.D. 2006. Opal: software for multiple sequence alignment by optimally aligning alignments. http://opal.cs.arizona.edu Maddison, D.R., Wheeler, T.J., and Maddison, W.P. 2006. Align: a Mesquite package for aligning sequence data. http://mesquiteproject.org Starrett, D.M., Wheeler, T.J., and Kececioglu, J.D. 2005. AlignAlign: software for optimally aligning alignments. http://alignalign.cs.arizona.edu Hayden, C.A. and Wheeler, T.J. 2005. cQC - cDNA Quality Control: A tool for resolving putative sequencing errors in single-pass cDNA, based on genomic sequence. Version 1.0. http://genomics.arizona.edu/software/cQC/
Contact info Wheeler, Travis HHMI Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA.(See my my personal page, if you must) |