Travis Wheeler

Address
Department of Computer Science
University of Montana
Social Sciences Bldg. Room 412
Missoula MT 59812
USA
Telephone
(571) 449-6401
Email
Curriculum Vitae
pdf

Research

I am an Assistant Professor in the Department of Computer Science at the University of Montana, in Missoula.

My group develops methods in computational biology, with an emphasis on sequence analysis - (1) development of algorithms that increase the speed and power of homology search using profile hidden Markov models, (2) implementation of those methods in the highly-used HMMER homology search toolkit, and (3) application of these methods to biology-motivated topics, especially those involving transposable elements and regulatory elements.

The lab has open positions for motivated postdocs and PhD students. Please drop me a line if you'd like to discuss possibilities.

Papers

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. (2014) [link]
Wheeler, T.J., Clements, J., Finn, R.D. BMC Bioinformatics, 15:7.
(doi:10.1186/1471-2105-15-7)
Distinguished as a “Highly Accessed Article”.
nhmmer: DNA homology search with profile HMMs. (2013) [link]
Wheeler, T.J., Eddy, S.R. Bioinformatics, 29(19):2487–2489.
(doi: 10.1093/bioinformatics/btt403)
In the top 20 most-read Bioinformatics articles during September 2013.
Dfam: a database of repetitive DNA based on profile hidden Markov models. (2013) [link]
Wheeler, T.J., Clements, J., Eddy, S.R., Hubley, R., Jones, T.A., Jurka, J., Smit, A.F.A, and Finn, R.D. Nucleic Acids Research 41:D70–D82.
(doi: 10.1093/nar/gks1265)
Selected as an NAR Featured Article.
Estimating the accuracy of multiple alignments and its use in parameter advising. (2012) [link]
DeBlasio, D., Wheeler, T., and Kececioglu, J. Proceedings of the 16th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics, 7262: 45-59.
(doi: 10.1007/978-3-642-29627-7_5)
Complete nucleomorph genome sequence of the non-photosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set. (2010) [link]
Tanifuji, G. Onodera, N.T., Wheeler, T.J., Dlutek, M., Donaher, N., and Archibald, J.M. Genome Biology and Evolution, 3: 44-54.
(doi: 10.1093/gbe/evq082)
Aligning protein sequences with predicted secondary structure. (2010) [link]
Kececioglu, J., Kim, E., and Wheeler, T. Journal of Computational Biology, 17(3): 561-580.
(doi:10.1089/cmb.2009.0222)
Selected as a "recommended read" for Faculty of 1000 Biology.
Efficient construction of accurate multiple alignments and large-scale phylogenies. (2009) [link]
Wheeler, T.J.
Ph.D. dissertation
Department of Computer Science, University of Arizona, Tucson, Arizona.
Large-scale neighbor-joining with NINJA. (2009) [link, preprint]
Wheeler, T.J. Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI), 375-389.
(doi: 10.1007/978-3-642-04241-6_31)
Learning models for aligning protein sequence with predicted secondary structure. (2009) [link]
Kim, E., Wheeler, T.J., and Kececioglu, J.D. Proceedings of the 13th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics, 5541: 586-605.
(doi: 10.1007/978-3-642-02008-7_36)
Multiple alignment by aligning alignments. (2007) [link]
Wheeler, T.J. and Kececioglu, J.D. Proceedings of the 15th ISCB Conference on Intelligent Systems for Molecular Biology, Bioinformatics, 23: i559-i568.
(doi: 10.1093/bioinformatics/btm226)
Adaptive protein evolution and regulatory divergence in Drosophila. (2006) [link]
Good, J.M., Hayden, C.A., and Wheeler T.J. Molecular Biology and Evolution, 23(6): 1101-1103.
(doi: 10.1093/molbev/msk002)
Evaluating and improving cDNA sequence quality with cQC. (2005) [link]
Hayden, C.A., Wheeler, T.J., and Jorgensen R.A. Bioinformatics, 21(24): 4414-4415.
(doi: 10.1093/bioinformatics/bti709)
Transposable element orientation bias in the Drosophila melanogaster genome. (2005) [link]
Cutter, A.D, Good, J.M., Pappas, C.T., Saunders, M.A., Starrett, D.M., Wheeler T.J. Journal of Molecular Evolution, 61(6): 733-741.
(doi: 10.1007/s00239-004-0243-0)

Software and databases

Skylign Logo server [link]
A tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
Wheeler, T.J., Clements, J., Finn, R.D.
2013
HMMER3.1 [link]
Biological sequence analysis using profile hidden Markov models.
Eddy, S.R. and Wheeler, T.J.
2013
nhmmer [link] (within HMMER3.1)
A DNA-DNA sequence homology search tool based on profile hidden Markov models, in the HMMER3 framework.
Wheeler, T.J. and Eddy, S.R.
2012
Dfam [link]
A Database of Repetitive DNA Based on Profile Hidden Markov Models.
Wheeler, T.J., Clements, J., Eddy, S.R., Hubley, R., Jones, T.A., Jurka, J., Smit, A.F.A, Finn, R.D.
2012
Ninja [link].
A Mesquite package for fast neighbor-joining phylogeny inference.
Wheeler, T.J. and Maddison, D.R.
2010
NINJA [link]
Software for large-scale neighbor-joining phylogeny inference.
Wheeler ,T.J.
2009
Opalescent [link]
A Mesquite package for multiple sequence alignment.
Wheeler, T.J. and Maddison, D.R.
2009
Opal [link]
Software for multiple sequence alignment by optimally aligning alignments.
Wheeler ,T.J. and Kececioglu. J.D.
2006
Align [link]
A Mesquite package for aligning sequence data.
Maddison, D.R., Wheeler, T.J., and Maddison, W.P.
2006
AlignAlign [link]
Software for optimally aligning alignments.
Starrett, D.M., Wheeler, T.J., and Kececioglu, J.D.
2005
cQC - cDNA Quality Control [link]
A tool for resolving putative sequencing errors in single-pass cDNA, based on genomic sequence.
Hayden, C.A. and Wheeler, T.J.
2005