Travis Wheeler's academic home

Research

I'm a postdoctoral researcher in Sean Eddy's lab at HHMI Janelia Farm Research Campus in Northern Virginia. I work on methods in computational biology, with an emphasis on sequence analysis; the primary focus of my postdoctoral work has been on (1) algorithms for accelerating and increasing the power of homology search, (2) implementation of those methods in DNA homology search software called nhmmer, and (3) application of nhmmer to the search for DNA cis-regulatory elements and the genomic remnants of transposable elements. I completed my Ph.D. in 2009 at the University of Arizona, focused on algorithms for efficient construction of accurate multiple sequence alignments and large-scale phylogenies, co-advised by John Kececioglu (Computer Science) and Mike Sanderson (Evolutionary Biology) at the University of Arizona.

My continued research largely focuses on extending my current work in homology search and on related biology-motivated topics, especially those involving transposable elements and regulatory elements. I am also interested in the broader fields of algorithm design and genomics, and will gladly collaborate on other interesting problems.

Publications

nhmmer: DNA homology search with profile HMMs. (2013): Wheeler, T.J., Eddy, S.R. Bioinformatics (submitted).
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.
(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

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