Travis J. Wheeler

Integrated genotyping, annotation and epigenetic characterization of transposable elements with GraffiTE

GraffiTE v1.1 is a Nextflow pipeline that genotypes structural variants, annotates polymorphic mobile elements, and maps epigenetic data to transposable elements using pangenome graphs, revealing hypomethylated elements and age-related demethylation.

Updated Transposable Element Libraries for Drosophila melanogaster in Dfam 4.0

The paper updates Drosophila melanogaster transposable element (TE) libraries in Dfam 4.0 by integrating new data, resolving redundancies, and improving consensus sequences.

Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant microbe interactions

The paper reduces a sorghum synthetic microbial community to identify a stable, growth-promoting variant that enhances flavonoid production and plant growth through dynamic gene expression and metabolomic changes.

MDCompress: better, faster compression of molecular dynamics simulation trajectories

MDCompress introduces a new trajectory compression format and software that reduces file size and improves compression/decompression speed for molecular dynamics simulations.

Alternatively Spliced Dual-Coding Regions Contribute to the Human Gene Regulatory Program

The paper identifies 1296 human genes with dual-coding regions (DCRs) and shows their conservation in mice, tissue-specific expression, and functional implications in gene regulation.

DIPLOMAT: multi-animal tracking with efficient manual editing

A hidden Markov model trace over DeepLabCut or SLEAP confidence maps reduced identity swaps versus both tools on 54 MABe mouse-triplet videos; retained probabilities also guide manual editing.

NEAR: Neural Embeddings for Amino acid Relationships

NEAR improves homology detection speed and accuracy by using neural embeddings trained with contrastive learning, outperforming existing methods as a pre-filter for protein sequence annotation.

Simpatico: accurate and ultra-fast virtual drug screening with atomic embeddings

Simpatico improves virtual drug screening by using atomic-level embeddings to rapidly and accurately identify potential ligands for protein targets.

Phenome-Wide Association of APOE Alleles in the All of Us Research Program

This study performs a phenome-wide association analysis of APOE alleles in the All of Us Research Program, identifying significant associations with various health outcomes and highlighting sex and ancestry differences.

Snekmer Learn/Apply: A kmer-based vector similarity approach to proteinclassification suitable for metagenomic datasets

The paper introduces an extension to the Snekmer tool that uses kmer libraries to annotate protein sequences with functional annotations, showing improved sensitivity over HMMs in metagenomic datasets.

Inhibition of PIM kinase in tumor associated macrophages suppresses inflammasome 1 activation and sensitizes prostate cancer to immunotherapy

This study shows that inhibiting PIM kinases in tumor-associated macrophages reduces inflammasome activation and improves response to immunotherapy in prostate cancer.

MDRepo - an open environment for data warehousing and knowledge discovery from molecular dynamics simulations

MDRepo provides an open repository for storing and analyzing molecular dynamics simulations to support drug discovery and structural biology research.

A Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Genome-graphs

GraffiTE analyzes transposable element insertion polymorphisms using genome-graphs, achieving high precision and recall across multiple species and sequencing technologies.

An FPGA-based hardware accelerator supporting sensitivesequence homology filtering with profile hidden Markovmodels

The paper introduces an FPGA-based accelerator for speeding up the SSV algorithm in pHMM alignment, achieving significant speed and energy efficiency improvements.

ULTRA-Effective Labeling of Repetitive Genomic Sequence

The paper introduces ULTRA, a tool for identifying and annotating repetitive genomic sequences, providing reliable coverage and interpretable statistics for use in annotation pipelines.

Diviner uncovers hundreds of novel human (and other) exons though comparative analysis of proteins

Diviner identifies novel exons across species by comparing isoforms, finding hundreds of new exons in human, mouse, rat, and ferret genomes.

MetaPathPredict: A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes

MetaPathPredict predicts KEGG module presence in incomplete bacterial genomes using machine learning models.

VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes

VIBES automates prophage annotation in bacterial genomes and provides visualization tools, demonstrating its utility across 1,072 Pseudomonas genomes.

nail: software for high-speed sequence annotation with profile hidden Markov models

nail provides a fast and accurate sequence annotation tool using profile hidden Markov models, outperforming HMMER3 in speed while maintaining high recall.

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

The paper shows that reversed biological sequences in benchmarks can overstate false match rates due to palindromic structures, affecting sensitivity and tool evaluation.

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

BATH improves protein-coding DNA annotation by detecting frameshift errors, outperforming existing tools on sequences with indels.

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

DISCO is a deep learning tool for segmenting acoustic signals with confidence estimates, demonstrated on beetle courtships and whale songs.

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

Mirage2 improves MSA accuracy for isoforms by enhancing protein-to-genome mappings and usability.

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

The paper presents the first de novo repeat discovery and annotation of a complete human reference genome, identifying novel satellite arrays and characterizing new classes of complex repeats.

Complete genomic and epigenetic maps of human centromeres

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

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

The paper evaluates MSA accuracy for transposable element sequences and finds Refiner outperforms other aligners for high-divergent and fragmented sequences.

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

The paper introduces an optimized FM-index library for nucleotide and amino acid sequence search, showing improved speed and scalability over existing implementations.

PolyA: a tool for adjudicating competing annotations of biological sequences

PolyA adjudicates competing sequence annotations by computing confidence estimates and identifying optimal alignments with rearrangements.