C. Titus Brown

This study compares TDH and TRH in Vibrio parahaemolyticus using sequence, structure, and function analysis to show their conserved core function with divergent evolutionary paths driven by accumulated mutations.

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

This paper predicts the pathogenic potential of Vibrio parahaemolyticus using pangenome data and machine learning, achieving high AUC scores with Random Forest and Convolutional Neural Network.

The Great Genotyper efficiently genotypes structural variants in large populations using a graph-based method, improving precision and recall while reducing computational time.

The paper benchmarks taxonomic classification and profiling methods for long-read metagenomic datasets, finding long-read methods outperform short-read ones in precision and recall.

The paper introduces branchwater, a tool for fast petabase-scale sequence search across public metagenomes using FracMinHash k-mer sketching.

The paper identifies five bacterial strains associated with Crohn's disease using a novel method combining machine learning and assembly graphs for metagenomic analysis.

This paper introduces a method using protein k-mers to perform metapangenomics without assembly, identifying strain fluctuations in stool metagenomes during antibiotic treatment.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Greedy minimum set cover over FracMinHash k-mer sketches selects a small set of reference genomes explaining a metagenome, supporting species-level taxonomic profiling and choice of genomes for read mapping.

The paper describes the development of a metadata federation system for NIH Common Fund data to improve discoverability without data movement.

This paper introduces Kmermaid and Orpheum to enable scRNA-seq analysis in species without reference genomes by detecting cell type-specific sequences without gene annotations.

The paper introduces MQF and buffered MQF, efficient data structures for storing k-mers with counts and metadata, improving space efficiency and speed over existing methods.

The paper assembles and annotates a reference genome for Culex tarsalis, identifies genetic clusters, and estimates divergence time from Culex quinquefasciatus.

The paper provides strategies for using workflow systems to streamline biological data analysis, emphasizing reproducibility and scalability in high-throughput sequencing projects.

The paper characterizes the genomic features of diazotrophic microbes associated with maize aerial root mucilage, identifying diverse nitrogen fixation gene configurations.

The paper introduces a system to recover missing genomic content from metagenomic data by analyzing subgraphs in assembly graphs.

The paper presents draft genome assemblies for four Fundulus killifish species using Illumina and Oxford Nanopore sequencing data, with contig N50 values ranging from 0.4 Mb to 2.7 Mb and BUSCO scores above 90%.

FAIRshake evaluates the FAIRness of research digital resources through community-driven metrics, automated assessments, and visualization tools, revealing opportunities for improvement.

Kevlar identifies de novo variants without mapping reads to a reference genome, achieving high sensitivity and specificity in simulated and real pedigrees.

The paper introduces sourmash, a software package that uses MinHash to create compressed sequence signatures for efficient large-scale sequence comparison and database searching.

The paper identifies microbial contamination in the domesticated olive genome, primarily from Aureobasidium pullulans, and notes its potential impact on downstream analyses.

The paper re-assembles and annotates 678 microbial eukaryotic transcriptomes using new tools and compares them to previous assemblies, finding novel gene content and taxon-specific trends.

The paper identifies a FGF4 retrogene on CFA12 as the cause of chondrodystrophy and intervertebral disc disease in dogs, with a high odds ratio for IVDD.

The paper evaluates metagenome assemblers on a mock community with 64 genomes, finding MEGAHIT performs best and recovers more strain variants.

The paper constructs a refined equine transcriptome using RNA-seq data from multiple tissues, improving gene structure and isoform resolution.

The paper introduces an open-source implementation of the HyperLogLog algorithm for efficiently estimating k-mer counts in large DNA sequencing datasets.