Travis Wheeler

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Associate Professor

University of Arizona

United States

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About

Travis Wheeler is an Associate Professor at the University of Arizona, USA. His research encompasses a range of topics including neural embeddings, transposable element insertion polymorphisms, and protein-coding DNA annotation. He has contributed significantly to the field through recent publications on viral sequence annotation, deep learning for acoustic signal segmentation, and visualization of biological sequence data.

Recent Grants

Grant: Close

Building Knowledge About Alternatively-spliced Dual-Coding Exons

Open Date: 2022-09-09

Close Date: 2024-08-31

Grant: Close

Machine Learning Approaches for Integrating Multi-Omics Data to Expand Microbiome Annotation

Open Date: 2020-09-15

Close Date: 2023-09-14

Grant: Close

Machine learning approaches for improved accuracy and speed in sequence annotation

Open Date: 2019-09-20

Close Date: 2023-07-31

Grant: Close

Overcoming combinatoric complexity problems in computational mass spectrometry

Open Date: 2019-08-01

Close Date: 2023-07-31

Grant: Close

CC* Compute: Improved Computing for Advanced Research and Education (ICARE)

Open Date: 2019-07-01

Close Date: 2021-06-30

Articles (17)

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2025

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2021

Collaborators (8)

Karen H. Miga

University of California, Santa Cruz

UNITED STATES

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Guillaume Bourque

McGill University

CANADA

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Patrick R. Secor

University of Montana

UNITED STATES

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Beth Sullivan

James B. Duke Distinguished Professor

Duke University

UNITED STATES

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Tony Heitkam

GERMANY

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Amitava Roy

Research Professor

University of Montana Missoula

UNITED STATES

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Rui Xiong

Assistant Professor

University of Arizona

UNITED STATES

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Nicolas Altemose

Assistant Professor

Stanford University

UNITED STATES

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Travis Wheeler

Research Interests

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About

Recent Grants

Articles (17)

NEAR: neural embeddings for amino acid relationships

Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences

A unified framework to analyze transposable element insertion polymorphisms using graph genomes

ULTRA-effective labeling of tandem repeats in genomic sequence

DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals

Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms

Complete genomic and epigenetic maps of human centromeres.

SODA: a TypeScript/JavaScript library for visualizing biological sequence annotation

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families

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

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation

The Dfam community resource of transposable element families, sequence models, and genome annotations

Collaborators (8)

Karen H. Miga

Guillaume Bourque

Patrick R. Secor

Beth Sullivan

Tony Heitkam

Amitava Roy

Rui Xiong

Nicolas Altemose

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