Daniel H. Huson

A host-directed virulence factor of Clostridium perfringens is modulated by gut commensal strains

The paper investigates how gut commensal strains modulate the growth and virulence of Clostridium perfringens through substrate competition and protein level changes.

Phylogenetic parallelograms: visual comparison of discordant phylogenetic trees

The paper introduces phylogenetic parallelograms to visually compare multiple discordant phylogenetic trees and applies them to study introgression and organellar discordance.

Development of a continuous bioreactor to maintain stable nasal microbiomes from swab specimens and synthetic communities

This paper develops a continuous bioreactor to maintain stable nasal microbiomes from swab specimens and synthetic communities, showing long-term stability and S. aureus decolonization.

Displacement-Optimized Tanglegrams for Trees and Networks

The paper introduces a new method for visualizing phylogenetic trees and networks by minimizing taxon and reticulate displacement, showing improved performance over existing approaches.

MMonitor: Software for Real-Time Monitoring of Microbial Communities Using Long Reads

MMonitor provides real-time analysis and visualization of metagenomic data, enabling dynamic microbiome research through automated pipelines and interactive dashboards.

Sketch, capture and layout phylogenies

The paper introduces PhyloSketch, an app for visualizing and improving the layout of phylogenetic trees and networks, with features for capturing topology from figures and minimizing reticulate edge displacement.

PhyloFusion- Fast and easy fusion of rooted phylogenetic trees into rooted phylogenetic networks

PhyloFusion merges rooted phylogenetic trees into networks, handling unresolved nodes and missing taxa, and is available in SplitsTree.

Toward industrial C8 production: Oxygen intrusion drives renewable n caprylate production from ethanol and acetate via intermediate metabolite production

This study identifies oxygen's role in enabling renewable n-caprylate production from ethanol and acetate via intermediate metabolite synthesis in bioreactors.

The gases H2 and O2 in open-culture reactors influence the performance and microbiota of chain elongation into n-caproate and n-caprylate.

This study investigates how H2 and O2 levels in open-culture reactors affect n-caproate and n-caprylate production and microbiota composition.

mgPGPT: Metagenomic analysis of plant growth-promoting traits

The paper extends the PGPT ontology to analyze metagenomic datasets, introducing mgPGPT-db and integrating it into MEGAN for PGPT-related gene identification.

Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.

MMIP integrates microbiome and metabolome data to identify features and predict metabolite signatures from amplicon sequencing data without requiring initial metabolomic analysis.

Enhanced 5mC-Methylation-Site Recognition in DNA Sequences using Token Classification and a Domain-specific Loss Function

The paper introduces MR-DNA, a deep-learning framework for predicting 5mC-methylation states in DNA sequences with 97.9% accuracy using a domain-specific loss function and a stacked model architecture.

Megan Server: facilitating interactive access to metagenomic data on a server

Megan Server provides web-based interactive access to metagenomic data without requiring full data downloads.

Structural and evolutionary analyses support reclassification of glycopeptide antibiotics as xyclopeptides

The paper reclassifies glycopeptide antibiotics as xyclopeptides based on structural and evolutionary analyses of biosynthetic gene clusters.

MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction

MuLan-Methyl uses five transformer-based models to predict three types of DNA methylation sites, achieving good performance on a benchmark dataset.

DeepToA: An Ensemble Deep-Learning Approach to Predicting the Theater of Activity of a Microbiome

DeepToA predicts the theater of activity of a microbiome using taxonomic and functional profiles with high accuracy.

Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN

The paper analyzes fruit-waste fermentation samples to identify biosurfactant-producing microbes using metagenomic sequencing and integrates BiosurfDB into MEGAN for interactive exploration.

Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis

The paper demonstrates that using AnnoTree improves speed and assignment rates in DIAMOND+MEGAN microbiome analysis compared to NCBI-nr.

Phylogenetic context using phylogenetic outlines

The paper introduces an interactive tool using Mash sketches and SplitsTree5 to determine the phylogenetic context of draft genomes by displaying phylogenetic outlines.

Enhanced COVID-19 data for improved prediction of survival

The paper enhances a COVID-19 dataset by adding weather and research sentiment features, achieving 95% accuracy in survival prediction using XGBoost.

Analysis procedures for assessing recovery of high quality, complete, closed genomes from Nanopore long read metagenome sequencing

The paper describes methods to validate long read assembled genomes using short read metagenome assembled genomes and assesses correction procedures' impact on genome quality, contributing new closed genomes from wastewater bioprocesses.

Enriched environmental conditions modify the gut microbiome composition and fecal markers of inflammation in Parkinson’s disease

This study shows that enriched environments reduce inflammation markers in Parkinson's disease mice by altering gut bacteria.

Human gut mobileome during antibiotic therapy. A trajectory-based approach to analysis of the metagenomic time-series datasets

The paper analyzes metagenomic time-series data to track the spread of antibiotic resistance genes through bacterial chromosomes, plasmids, and phages during antibiotic therapy.

Anti-consensus: detecting trees that have an evolutionary signal that is lost in consensus

The paper introduces an anti-consensus network to highlight significant discrepancies in gene trees, demonstrating its use with Kosakonia species and strains.

Annotated bacterial chromosomes from frame-shift-corrected long read metagenomic data

The paper demonstrates obtaining whole bacterial chromosomes from metagenomic samples using long-read sequencing and presents a pipeline with frame-shift correction.

Human salivary amylase gene copy number impacts oral and gut microbiomes

The paper shows that human AMY1 gene copy number affects oral and gut microbiome composition and function, with low-AMY1 associated with enhanced complex carbohydrate breakdown and high-AMY1 linked to resistant starch fermentation and higher adiposity.

Improving recovery of member genomes from enrichment reactor microbial communities using MinION--based long read metagenomics

The paper demonstrates that MinION long read sequencing can recover near-complete genomes from low-medium complexity microbial communities.

Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico

The paper identifies Salmonella enterica genomes from a 16th-century epidemic cemetery in Mexico, linking them to enteric fever as a cause of population decline.

MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

MEGAN-LR provides new algorithms for taxonomic and functional binning of long reads and contigs, with evaluation on simulated and real datasets.