Travis J. Wheeler

22 papers A* 1B 2C 1Journal 13Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
NEAR: neural embeddings for amino acid relationships.
Bioinform.
Daniel Olson, Thomas Colligan, Daphne Demekas, Jack W. Roddy, Ken Youens-Clark, Travis J. Wheeler
2024 J jnl
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models.
BMC Bioinform.
Tim Anderson, Travis J. Wheeler
2024 J jnl
Exploring the Impact of a Transformer's Latent Space Geometry on Downstream Task Performance.
CoRR
Anna C. Marbut, John W. Chandler, Travis J. Wheeler
2023 A* conf
Reliable Measures of Spread in High Dimensional Latent Spaces.
ICML
Anna C. Marbut, Katy McKinney-Bock, Travis J. Wheeler
2022 J jnl
Reliable Measures of Spread in High Dimensional Latent Spaces.
CoRR
Anna C. Marbut, Katy McKinney-Bock, Travis J. Wheeler
2021 — ed.
Algorithms for Computational Biology - 8th International Conference, AlCoB 2021, Missoula, MT, USA, June 7-11, 2021, Proceedings
AlCoB
Carlos Martín-Vide, Miguel A. Vega-Rodríguez, Travis J. Wheeler
2021 J jnl
An optimized FM-index library for nucleotide and amino acid search.
Algorithms Mol. Biol.
Tim Anderson, Travis J. Wheeler
2020 — ed.
Algorithms for Computational Biology - 7th International Conference, AlCoB 2020, Missoula, MT, USA, April 13-15, 2020, Proceedings.
AlCoB
Carlos Martín-Vide, Miguel A. Vega-Rodríguez, Travis J. Wheeler
2019 J jnl
15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms.
Nucleic Acids Res.
Peter V. Hornbeck, Jon M. Kornhauser, Vaughan Latham, Beth Murray, Vidhisha Nandhikonda, Alex S. Nord, Elzbieta Skrzypek, Travis J. Wheeler, Bin Zhang, Florian Gnad
2018 — conf
Splice-Aware Multiple Sequence Alignment of Protein Isoforms.
BCB
Alex S. Nord, Peter V. Hornbeck, Kaitlin Carey, Travis J. Wheeler
2018 — conf
ULTRA: A Model Based Tool to Detect Tandem Repeats.
BCB
Daniel Olson, Travis J. Wheeler
2016 J jnl
The Dfam database of repetitive DNA families.
Nucleic Acids Res.
Robert Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler
2015 J jnl
HMMER web server: 2015 update.
Nucleic Acids Res.
Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy
2014 J jnl
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
BMC Bioinform.
Travis J. Wheeler, Jody Clements, Robert D. Finn
2013 J jnl
Dfam: a database of repetitive DNA based on profile hidden Markov models.
Nucleic Acids Res.
Travis J. Wheeler, Jody Clements, Sean R. Eddy, Robert Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit, Robert D. Finn
2013 J jnl
nhmmer: DNA homology search with profile HMMs.
Bioinform.
Travis J. Wheeler, Sean R. Eddy
2012 B conf
Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising.
RECOMB
Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu
2010 J jnl
Aligning Protein Sequences with Predicted Secondary Structure.
J. Comput. Biol.
John D. Kececioglu, Eagu Kim, Travis J. Wheeler
2009 C conf
Large-Scale Neighbor-Joining with NINJA.
WABI
Travis J. Wheeler
2009 B conf
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure.
RECOMB
Eagu Kim, Travis J. Wheeler, John D. Kececioglu
2007 — conf
Multiple alignment by aligning alignments.
ISMB/ECCB (Supplement of Bioinformatics)
Travis J. Wheeler, John D. Kececioglu
2005 J jnl
Evaluating and improving cDNA sequence quality with cQC.
Bioinform.
Celine A. Hayden, Travis J. Wheeler, Richard A. Jorgensen