Travis J. Wheeler

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 9

Top Topics

Profile Hidden Markov Models

High Dimensional

Top Venues

Nucleic Acids Res.

Publications

Tim Anderson, Travis J. Wheeler
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models. BMC Bioinform. 25 (1) (2024)
Anna C. Marbut, John W. Chandler, Travis J. Wheeler
Exploring the Impact of a Transformer's Latent Space Geometry on Downstream Task Performance. CoRR (2024)
Anna C. Marbut, Katy McKinney-Bock, Travis J. Wheeler
Reliable Measures of Spread in High Dimensional Latent Spaces. ICML (2023)
Anna C. Marbut, Katy McKinney-Bock, Travis J. Wheeler
Reliable Measures of Spread in High Dimensional Latent Spaces. CoRR (2022)
Tim Anderson, Travis J. Wheeler
An optimized FM-index library for nucleotide and amino acid search. Algorithms Mol. Biol. 16 (1) (2021)
Peter V. Hornbeck, Jon M. Kornhauser, Vaughan Latham, Beth Murray, Vidhisha Nandhikonda, Alex S. Nord, Elzbieta Skrzypek, Travis J. Wheeler, Bin Zhang, Florian Gnad
15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. Nucleic Acids Res. 47 (Database-Issue) (2019)
Daniel Olson, Travis J. Wheeler
ULTRA: A Model Based Tool to Detect Tandem Repeats. BCB (2018)
Alex S. Nord, Peter V. Hornbeck, Kaitlin Carey, Travis J. Wheeler
Splice-Aware Multiple Sequence Alignment of Protein Isoforms. BCB (2018)
Robert Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler
The Dfam database of repetitive DNA families. Nucleic Acids Res. 44 (Database-Issue) (2016)
Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy
HMMER web server: 2015 update. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Travis J. Wheeler, Jody Clements, Robert D. Finn
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. BMC Bioinform. 15 (2014)
Travis J. Wheeler, Jody Clements, Sean R. Eddy, Robert Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit, Robert D. Finn
Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res. 41 (Database-Issue) (2013)
Travis J. Wheeler, Sean R. Eddy
nhmmer: DNA homology search with profile HMMs. Bioinform. 29 (19) (2013)
Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu
Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. RECOMB (2012)
John D. Kececioglu, Eagu Kim, Travis J. Wheeler
Aligning Protein Sequences with Predicted Secondary Structure. J. Comput. Biol. 17 (3) (2010)
Travis J. Wheeler
Large-Scale Neighbor-Joining with NINJA. WABI (2009)
Eagu Kim, Travis J. Wheeler, John D. Kececioglu
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. RECOMB (2009)
Travis J. Wheeler, John D. Kececioglu
Multiple alignment by aligning alignments. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Celine A. Hayden, Travis J. Wheeler, Richard A. Jorgensen
Evaluating and improving cDNA sequence quality with cQC. Bioinform. 21 (24) (2005)