Travis J. Wheeler

According to our database, Travis J. Wheeler authored at least 22 papers between 2005 and 2026.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2026

MDCompress: better, faster compression of molecular dynamics simulation trajectories.

Marek Kokot, Amitava Roy, Travis J. Wheeler, Sebastian Deorowicz

Bioinform., 2026

2025

NEAR: neural embeddings for amino acid relationships.

Daniel Olson, Thomas Colligan, Daphne Demekas, Jack W. Roddy, Ken Youens-Clark, Travis J. Wheeler

Bioinform., 2025

2024

An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models.

Tim Anderson, Travis J. Wheeler

BMC Bioinform., December, 2024

A Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Graph Genomes.

Cristian Groza, Xun Chen, Travis J. Wheeler, Guillaume Bourque, Clément Goubert

Dataset, May, 2024

Exploring the Impact of a Transformer's Latent Space Geometry on Downstream Task Performance.

Anna C. Marbut, John W. Chandler, Travis J. Wheeler

CoRR, 2024

2023

Reliable Measures of Spread in High Dimensional Latent Spaces.

Anna C. Marbut, Katy McKinney-Bock, Travis J. Wheeler

Proceedings of the International Conference on Machine Learning, 2023

2021

An optimized FM-index library for nucleotide and amino acid search.

Tim Anderson, Travis J. Wheeler

Algorithms Mol. Biol., 2021

2019

15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms.

Peter V. Hornbeck, Jon M. Kornhauser, Vaughan Latham, Beth Murray, Vidhisha Nandhikonda, Alex S. Nord, Elzbieta Skrzypek, Travis J. Wheeler, Bin Zhang, Florian Gnad

Nucleic Acids Res., 2019

2018

ULTRA: A Model Based Tool to Detect Tandem Repeats.

Daniel Olson, Travis J. Wheeler

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

Splice-Aware Multiple Sequence Alignment of Protein Isoforms.

Alex S. Nord, Peter V. Hornbeck, Kaitlin Carey, Travis J. Wheeler

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2016

The Dfam database of repetitive DNA families.

Robert Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler

Nucleic Acids Res., 2016

2015

HMMER web server: 2015 update.

Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy

Nucleic Acids Res., 2015

2014

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.

Travis J. Wheeler, Jody Clements, Robert D. Finn

BMC Bioinform., 2014

2013

Dfam: a database of repetitive DNA based on profile hidden Markov models.

Travis J. Wheeler, Jody Clements, Sean R. Eddy, Robert Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit, Robert D. Finn

Nucleic Acids Res., 2013

nhmmer: DNA homology search with profile HMMs.

Travis J. Wheeler, Sean R. Eddy

Bioinform., 2013

2012

Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising.

Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu

Proceedings of the Research in Computational Molecular Biology, 2012

2010

Aligning Protein Sequences with Predicted Secondary Structure.

John D. Kececioglu, Eagu Kim, Travis J. Wheeler

J. Comput. Biol., 2010

2009

Efficient Construction of accurate Multiple alignments and Large-Scale phylogenies.

Travis John Wheeler

PhD thesis, 2009

Large-Scale Neighbor-Joining with NINJA.

Travis J. Wheeler

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Learning Models for Aligning Protein Sequences with Predicted Secondary Structure.

Eagu Kim, Travis J. Wheeler, John D. Kececioglu

Proceedings of the Research in Computational Molecular Biology, 2009

2007

Multiple alignment by aligning alignments.

Travis J. Wheeler, John D. Kececioglu

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2005

Evaluating and improving cDNA sequence quality with cQC.

Celine A. Hayden, Travis J. Wheeler, Richard A. Jorgensen

Bioinform., 2005