Evaluating and improving cDNA sequence quality with cQC. - Celine A. Hayden; Travis J. Wheeler; Richard A. Jorgensen (Bioinform., 2005)

Multiple alignment by aligning alignments. - Travis J. Wheeler; John D. Kececioglu (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. - Eagu Kim; Travis J. Wheeler; John D. Kececioglu (RECOMB, 2009)

Large-Scale Neighbor-Joining with NINJA. - Travis J. Wheeler (WABI, 2009)

Efficient Construction of accurate Multiple alignments and Large-Scale phylogenies. - Travis John Wheeler (2009)

Aligning Protein Sequences with Predicted Secondary Structure. - John D. Kececioglu; Eagu Kim; Travis J. Wheeler (J. Comput. Biol., 2010)

Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. - Dan F. DeBlasio; Travis J. Wheeler; John D. Kececioglu (RECOMB, 2012)

nhmmer: DNA homology search with profile HMMs. - Travis J. Wheeler; Sean R. Eddy (Bioinform., 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)

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)

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)

The Dfam database of repetitive DNA families. - Robert Hubley; Robert D. Finn; Jody Clements; Sean R. Eddy; Thomas A. Jones; Weidong Bao 004; Arian F. A. Smit; Travis J. Wheeler (Nucleic Acids Res., 2016)

Splice-Aware Multiple Sequence Alignment of Protein Isoforms. - Alex S. Nord; Peter V. Hornbeck; Kaitlin Carey; Travis J. Wheeler (BCB, 2018)

ULTRA: A Model Based Tool to Detect Tandem Repeats. - Daniel Olson; Travis J. Wheeler (BCB, 2018)

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)

An optimized FM-index library for nucleotide and amino acid search. - Tim Anderson; Travis J. Wheeler (Algorithms Mol. Biol., 2021)

Reliable Measures of Spread in High Dimensional Latent Spaces. - Anna C. Marbut; Katy McKinney-Bock; Travis J. Wheeler (ICML, 2023)

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)

An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models. - Tim Anderson; Travis J. Wheeler (BMC Bioinform., 2024)