Travis Wheeler
Travis Wheeler
Associate Professor, Dept Computer Science, U. Montana
Verified email at - Homepage
Cited by
Cited by
HMMER web server: 2015 update
RD Finn, J Clements, W Arndt, BL Miller, TJ Wheeler, F Schreiber, ...
Nucleic acids research 43 (W1), W30-W38, 2015
nhmmer: DNA homology search with profile HMMs
TJ Wheeler, SR Eddy
Bioinformatics 29 (19), 2487-2489, 2013
The Dfam database of repetitive DNA families
R Hubley, RD Finn, J Clements, SR Eddy, TA Jones, W Bao, AFA Smit, ...
Nucleic acids research 44 (D1), D81-D89, 2016
Multiple alignment by aligning alignments
TJ Wheeler, JD Kececioglu
Bioinformatics 23 (13), i559-i568, 2007
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models
TJ Wheeler, J Clements, RD Finn
BMC Bioinformatics 15 (1), 7, 2014
Dfam: a database of repetitive DNA based on profile hidden Markov models
TJ Wheeler, J Clements, SR Eddy, R Hubley, TA Jones, J Jurka, AFA Smit, ...
Nucleic acids research 41 (D1), D70-D82, 2012
Large-scale neighbor-joining with NINJA
TJ Wheeler
International Workshop on Algorithms in Bioinformatics, 375-389, 2009
A call for benchmarking transposable element annotation methods
DR Hoen, G Hickey, G Bourque, J Casacuberta, R Cordaux, C Feschotte, ...
Mobile DNA 6 (1), 1-9, 2015
15 years of PhosphoSitePlus: integrating post-translationally modified sites, disease variants and isoforms
PV Hornbeck, JM Kornhauser, V Latham, B Murray, V Nandhikonda, ...
Nucleic acids research 47 (D1), D433-D441, 2019
Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set
G Tanifuji, NT Onodera, TJ Wheeler, M Dlutek, N Donaher, JM Archibald
Genome biology and evolution 3, 44-54, 2011
Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks
M Grimes, B Hall, L Foltz, T Levy, K Rikova, J Gaiser, W Cook, E Smirnova, ...
Science Signaling 11 (531), 2018
Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising
D DeBlasio, T Wheeler, J Kececioglu
Research in Computational Molecular Biology, 45-59, 2012
Adaptive protein evolution and regulatory divergence in Drosophila
JM Good, CA Hayden, TJ Wheeler
Molecular biology and evolution 23 (6), 1101-1103, 2006
Transposable element orientation bias in the Drosophila melanogaster genome
AD Cutter, JM Good, CT Pappas, MA Saunders, DM Starrett, TJ Wheeler
Journal of molecular evolution 61 (6), 733-741, 2005
Aligning protein sequences with predicted secondary structure
J Kececioglu, E Kim, T Wheeler
Journal of Computational Biology 17 (3), 561-580, 2010
The Dfam community resource of transposable element families, sequence models, and genome annotations
J Storer, R Hubley, J Rosen, TJ Wheeler, AF Smit
Mobile DNA 12 (1), 1-14, 2021
Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections
PR Secor, EB Burgener, M Kinnersley, LK Jennings, V Roman-Cruz, ...
Frontiers in Immunology 11, 2020
ULTRA: A Model Based Tool to Detect Tandem Repeats
D Olson, T Wheeler
ACM-BCB ’18, 2018
Evaluating and improving cDNA sequence quality with cQC
CA Hayden, TJ Wheeler, RA Jorgensen
Bioinformatics 21 (24), 4414-4415, 2005
A scalable parallel implementation of the neighbor joining algorithm for phylogenetic trees
R McLay, D Stanzione, SJ Mckay, T Wheeler
ICCABS Conference, 2011
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