Travis Wheeler

Address
Department of Computer Science
University of Montana
Social Sciences Bldg. Room 412
Missoula MT 59812
USA
Telephone
(406) 530-8585
Email
Curriculum Vitae
pdf

Research

I am an Assistant Professor in the Department of Computer Science at the University of Montana, in Missoula. I am also an Associated Faculty member of the Cellular, Molecular, and Microbial Biology Program

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.

Recent News (from my blog)

Students

PhD students
Walt Shands (Computer Science)
Translated search in HMMER
Masters students
Rutger Evans (Computer Science)
Sequence search in HMMER (esp. FM index for protein search)

Alex Nord (Computer Science)
Sequence search in HMMER (esp. applications of spaced seed)

Angela Gross (Computer Science; jointly advised with Michael Cassens)
Video game development
Undergraduate students
Adam Clemons (Computer Science)
Software Plagiarism Detection

Nic Lavance (Computer Science)
Conserved Non-coding Elements

Gilia Patterson (Biology)
Transposable Element Annotation

Courses

CSCI 323 (Design and Analysis of Algorithms)
Spring 2015
CSCI 491 / CSCI 595 (Applied Parallel Computing)
Spring 2015
CSCI 451 / CSCI 558 (Computational Biology / Bioinformatics)
Fall 2014
Contact me if you wish to see material from past classes.

Papers

HMMER web server: 2015 update. (2015) [link]
Finn, R.D., Clements, J., Arndt, W., Miller, B.L., Wheeler, T.J., Schreiber, F., Bateman, A., and Eddy, S.R. Nucleic Acids Research 43:gkv397.
(doi:10.1093/nar/gkv397)
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. (2014) [link]
Wheeler, T.J., Clements, J., and 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
HMMER webserver, and 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