Travis J Wheeler (Travis Wheeler)

Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 38

Top Venues

bioRxiv : the preprint server for biology

Bioinformatics advances

NAR genomics and bioinformatics

PloS one

University of Montana

University of Arizona (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Montana Aug 01 2014

United States

Associate Professor :: Computer Science

Howard Hughes Medical Institute Janelia Farm Research Campus Sep 01 2009 - Jun 30 2014

United States

Research Scientist

Education History

University of Arizona Jan 01 2005 - Aug 01 2009

United States

PHD :: Computer Science

Publications

Vishwesh Venkatraman, Jeremiah Gaiser, Daphne Demekas, Amitava Roy, Rui Xiong, Travis J Wheeler
Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No). Pharmaceuticals (Basel, Switzerland) 17 (8) (2024)
Alexander J Nord, Travis J Wheeler
Diviner uncovers hundreds of novel human (and other) exons though comparative analysis of proteins. bioRxiv : the preprint server for biology (2024)
Conner J Copeland, Jack W Roddy, Amelia K Schmidt, Patrick R Secor, Travis J Wheeler
VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes. NAR genomics and bioinformatics 6 (2) (2024)
Genevieve R Krause, Walt Shands, Travis J Wheeler
Sensitive and error-tolerant annotation of protein-coding DNA with BATH. bioRxiv : the preprint server for biology (2024)
George Glidden-Handgis, Travis J Wheeler
WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences. Bioinformatics advances 4 (1) (2024)
Jack W Roddy, David H Rich, Travis J Wheeler
nail: software for high-speed, high-sensitivity protein sequence annotation. bioRxiv : the preprint server for biology (2024)
Ehsan Khajouei, Valentina Ghisays, Ignazio S Piras, Kiana L Martinez, Marcus Naymik, Preston Ngo, Tam C Tran, Joshua C Denny, Travis J Wheeler, Matthew J Huentelman, Eric M Reiman, Jason H Karnes
Phenome-Wide Association of APOE Alleles in the All of Us Research Program. medRxiv : the preprint server for health sciences (2024)
Alexander J Nord, Travis J Wheeler
Diviner uncovers hundreds of novel human (and other) exons though comparative analysis of proteins. bioRxiv : the preprint server for biology (2024)
Daniel R Olson, Travis J Wheeler
ULTRA-Effective Labeling of Repetitive Genomic Sequence. bioRxiv : the preprint server for biology (2024)
Jack W Roddy, David H Rich, Travis J Wheeler
nail: software for high-speed, high-sensitivity protein sequence annotation. bioRxiv : the preprint server for biology (2024)
Genevieve R Krause, Walt Shands, Travis J Wheeler
Sensitive and error-tolerant annotation of protein-coding DNA with BATH. Bioinformatics advances 4 (1) (2024)
Conner J Copeland, Jack W Roddy, Amelia K Schmidt, Patrick R Secor, Travis J Wheeler
VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes. NAR genomics and bioinformatics 6 (2) (2024)
Genevieve R Krause, Walt Shands, Travis J Wheeler
Sensitive and error-tolerant annotation of protein-coding DNA with BATH. Bioinformatics advances 4 (1) (2024)
Conner J Copeland, Jack W Roddy, Amelia K Schmidt, Patrick R Secor, Travis J Wheeler
VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes. NAR genomics and bioinformatics 6 (2) (2024)
Genevieve R Krause, Walt Shands, Travis J Wheeler
Sensitive and error-tolerant annotation of protein-coding DNA with BATH. bioRxiv : the preprint server for biology (2024)
Daniel R Olson, Travis J Wheeler
ULTRA-Effective Labeling of Repetitive Genomic Sequence. bioRxiv : the preprint server for biology (2024)
Genevieve R Krause, Walt Shands, Travis J Wheeler
Sensitive and error-tolerant annotation of protein-coding DNA with BATH. bioRxiv : the preprint server for biology (2024)
Vishwesh Venkatraman, Jeremiah Gaiser, Daphne Demekas, Amitava Roy, Rui Xiong, Travis J Wheeler
Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No). Pharmaceuticals (Basel, Switzerland) 17 (8) (2024)
George Glidden-Handgis, Travis J Wheeler
WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences. Bioinformatics advances 4 (1) (2024)
Conner J Copeland, Jack W Roddy, Amelia K Schmidt, Patrick R Secor, Travis J Wheeler
VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes. NAR genomics and bioinformatics 6 (2) (2024)
Genevieve R Krause, Walt Shands, Travis J Wheeler
Sensitive and error-tolerant annotation of protein-coding DNA with BATH. Bioinformatics advances 4 (1) (2024)
Genevieve R Krause, Walt Shands, Travis J Wheeler
Sensitive and error-tolerant annotation of protein-coding DNA with BATH. Bioinformatics advances 4 (1) (2024)
Alexander J Nord, Travis J Wheeler
Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms. PloS one 18 (5) (2023)
Thomas Colligan, Kayla Irish, Douglas J Emlen, Travis J Wheeler
DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals. bioRxiv : the preprint server for biology (2023)
Alexander J Nord, Travis J Wheeler
Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms. PloS one 18 (5) (2023)
Alexander J Nord, Travis J Wheeler
Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms. PloS one 18 (5) (2023)
Conner J Copeland, Jack W Roddy, Amelia K Schmidt, Patrick R Secor, Travis J Wheeler
VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes. bioRxiv : the preprint server for biology (2023)
Thomas Colligan, Kayla Irish, Douglas J Emlen, Travis J Wheeler
DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals. bioRxiv : the preprint server for biology (2023)
Thomas Colligan, Kayla Irish, Douglas J Emlen, Travis J Wheeler
DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals. bioRxiv : the preprint server for biology (2023)
Alexander J Nord, Travis J Wheeler
Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms. PloS one 18 (5) (2023)
Thomas Colligan, Kayla Irish, Douglas J Emlen, Travis J Wheeler
DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals. PloS one 18 (7) (2023)
Savannah J Hoyt, Jessica M Storer, Gabrielle A Hartley, Patrick G S Grady, Ariel Gershman, Leonardo Gomes de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J Core, Jennifer L Gerton, Wojciech Makalowski, Daniel R Olson, Jeb Rosen, Arian F A Smit, Aaron F Straight, Mitchell R Vollger, Travis J Wheeler, Michael C Schatz, Evan E Eichler, Adam M Phillippy, Winston Timp, Karen H Miga, Rachel J O'Neill
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science (New York, N.Y.) 376 (6588) (2022)
Jack W Roddy, George T Lesica, Travis J Wheeler
SODA: a TypeScript/JavaScript library for visualizing biological sequence annotation. NAR genomics and bioinformatics 4 (4) (2022)
Nicolas Altemose, Glennis A Logsdon, Andrey V Bzikadze, Pragya Sidhwani, Sasha A Langley, Gina V Caldas, Savannah J Hoyt, Lev I Uralsky, Fedor D Ryabov, Colin J Shew, Michael E G Sauria, Matthew Borchers, Ariel Gershman, Alla Mikheenko, Valery A Shepelev, Tatiana Dvorkina, Olga Kunyavskaya, Mitchell R Vollger, Arang Rhie, Ann M McCartney, Mobin Asri, Ryan Lorig-Roach, Kishwar Shafin, Julian K Lucas, Sergey Aganezov, Daniel R Olson, Leonardo Gomes de Lima, Tamara A Potapova, Gabrielle A Hartley, Marina Haukness, Peter Kerpedjiev, Fedor E Gusev, Kristof Tigyi, Shelise Brooks, Alice C Young, Sergey Nurk, Sergey Koren, Sofie R Salama, Benedict Paten, Evgeny I Rogaev, Aaron Streets, Gary H Karpen, Abby F Dernburg, Beth A Sullivan, Aaron F Straight, Travis J Wheeler, Jennifer L Gerton, Evan E Eichler, Adam M Phillippy, Winston Timp, Megan Y Dennis, Rachel J O'Neill, Justin M Zook, Michael C Schatz, Pavel A Pevzner, Mark E Diekhans, Charles H Langley, Ivan A Alexandrov, Karen H Miga
Complete genomic and epigenetic maps of human centromeres. Science (New York, N.Y.) 376 (6588) (2022)
Tim Anderson, Travis J Wheeler
An optimized FM-index library for nucleotide and amino acid search. Algorithms for molecular biology : AMB 16 (1) (2021)
null null, Tyler A Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, Travis J Wheeler
TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation. Mobile DNA 12 (1) (2021)
Kaitlin M Carey, Gilia Patterson, Travis J Wheeler
Transposable element subfamily annotation has a reproducibility problem. Mobile DNA 12 (1) (2021)
Mark Grimes, Benjamin Hall, Lauren Foltz, Tyler Levy, Klarisa Rikova, Jeremiah Gaiser, William Cook, Ekaterina Smirnova, Travis J Wheeler, Neil R Clark, Alexander Lachmann, Bin Zhang, Peter V Hornbeck, Avi Ma'ayan, Michael Comb
Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. Science signaling 11 (531) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Travis J Wheeler (Travis Wheeler)