Thomas Abeel

Evaluating Few-Shot Meta-Learning using STUNT for Microbiome-Based Disease Classification

This study evaluates STUNT, a meta-learning framework for microbiome-based disease classification, finding that its benefits are limited under data scarcity and diminish with more samples.

Comparing metabolic engineering scenarios using simulated design-build-test-learn-cycles

This study uses in-silico DBTL cycles to evaluate how process parameters affect strain optimization outcomes in metabolic engineering.

Predicted meta-omics: a potential solution to multi-omics data scarcity in microbiome studies

The paper predicts other meta-omics data from metagenomics using machine learning, showing reliable predictions for transcript and metabolite abundances but challenges in protein profiles, and demonstrates utility for inflammatory bowel disease classification.

Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species

This study benchmarks plasmid detection and reconstruction tools on short-read assemblies from diverse bacterial species, finding performance varies with database coverage and assembly quality.

Machine Learning-Assisted Pathway Optimization in Large Combinatorial Design Spaces: a p-Coumaric Acid Case Study

This paper applies a machine learning-assisted recommendation strategy with exploration-exploitation balance to optimize p-coumaric acid production in yeast, achieving a 137% increase over parent strains.

Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions

This study uses long-term multi-meta-omics to identify the ecophysiological controls of seasonal N2O emissions in wastewater treatment systems.

A comparative metagenomic analysis of antibiotic resistance in the fecal microbiome of pigs raised with and without antibiotics

This study compares the fecal microbiome of pigs with and without antibiotic exposure to assess changes in microbial communities and antibiotic resistance genes.

Fast and exact gap-affine partial order alignment with POASTA

POASTA is an optimal algorithm for partial order alignment that improves speed and memory efficiency, enabling larger alignments in bacterial gene datasets.

Neural Ordinary Differential Equations Inspired Parameterization of Kinetic Models

The paper introduces a framework for training metabolic kinetic models using neural ODEs, demonstrating efficient parameterization on SBML models and glycolysis data.

Portable In-Field DNA Sequencing for Rapid Detection of Pathogens and Antimicrobial Resistance: A Proof-of-Concept Study

This study evaluates portable in-field DNA sequencing for pathogen and antimicrobial resistance detection, finding it feasible and comparable to traditional lab methods.

A Metagenomic Study of Antibiotic Resistance Across Diverse Soil Types and Geographical Locations

This study analyzes antibiotic resistance patterns in soil metagenomes across different types and locations, identifying key resistance genes and their environmental influences.

SAP: Synteny-aware gene function prediction for bacteria using protein embeddings

SAP improves bacterial gene function prediction using protein embeddings and conserved synteny, identifying novel toxins in enterococci.

The effect of removing repeat-induced overlaps in de novo assembly

This study evaluates the impact of removing repeat-induced overlaps on de novo genome assembly performance using simulated datasets.

When do longer reads matter? A benchmark of long read de novo assembly tools for eukaryotic genomes

The paper benchmarks long-read de novo assemblers for eukaryotic genomes, finding that Flye performs best overall, and longer reads can improve assembly quality depending on genome complexity.

HAT: Haplotype Assembly Tool using short and error-prone long reads

HAT reconstructs haplotypes using short and long reads with a reference genome, outperforming existing tools on yeast and simulated polyploid data.

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

StrainGE identifies low-abundance microbial strains from metagenomic data with higher sensitivity and resolution than existing tools.

A novel method to isolate free-floating extracellular DNA from wastewater for quantitation and metagenomic profiling of mobile genetic elements and antibiotic resistance genes

QuantTB - A method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data

QuantTB classifies mixed Mycobacterium tuberculosis infections in whole genome sequencing data, accurately quantifying strains and detecting resistance mutations.

Nanopore sequencing and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

The paper uses nanopore sequencing and a new method to show lager-brewing yeasts originated from a single hybridization event, with Group 1 and 2 strains diverging after this event.

Alpaca: a kmer-based approach for investigating mosaic structures in microbial genomes

Alpaca identifies mosaic structures in microbial genomes by analyzing kmer similarity across sequencing datasets to map evolutionary origins.

Laboratory evolution of a Saccharomyces cerevisiae x S. eubayanus hybrid under simulated lager-brewing conditions: genetic diversity and phenotypic convergence

This study evolves a Saccharomyces cerevisiae x S. eubayanus hybrid under brewing conditions, showing phenotypic diversity and limited aneuploidy, with specific mutations linked to industrial traits.

Variants in RNA-Seq data show a continued mutation rate during strain preservation of Schizophyllum commune

The paper analyzes RNA-seq data from Schizophyllum commune to show that spontaneous mutations accumulate during strain preservation, with a mutation rate of 1.923×10^-8 per haploid genome per base per generation.

Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D

This paper presents a near-complete genome assembly of Saccharomyces cerevisiae strain CEN.PK113-7D using Nanopore sequencing, revealing new genes and a chromosomal translocation.