Samuel Martin

DGM Is Dead; Long Live DGM-Star! A Quantization-Theoretic Approach to Gamma Rate Discretization

The paper introduces a new method to discretize Gamma rate distributions in phylogenetics, reducing branch length bias compared to the standard DGM.

City life: airborne DNA metagenomic biodiversity monitoring reveals dynamic changes across time and space

This study uses airborne DNA metagenomics to monitor biodiversity across time and space, revealing seasonal and spatial shifts in species composition.

Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics

This paper introduces a site-specific mutation model (SSM) for pandemic-scale phylogenetics, showing it better captures mutation patterns in SARS-CoV-2 genomes than classical models.

CMAPLE 2: Fast and Accurate Phylogenetic Inference for Millions of Pathogen Genomes

CMAPLE 2 improves phylogenetic inference speed and memory efficiency for large pathogen genome datasets, enabling analysis of nearly four million SARS-CoV-2 genomes in 12 days.

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics

The paper improves pandemic-scale phylogenetic analysis by addressing mutation rate variation and sequence errors, reconstructing a reliable phylogenetic tree of over 2 million SARS-CoV-2 genomes.

MARTi: a real-time analysis and visualisation tool for nanopore metagenomics

MARTi provides real-time metagenomic analysis and visualization using open-source tools, supporting classification methods like BLAST and Kraken2 for taxonomic and AMR gene identification.

Squirrel: Reconstructing semi-directed phylogenetic level-1 networks from four-leaved networks or sequence alignments

This paper introduces an algorithm to reconstruct semi-directed phylogenetic level-1 networks from four-leaved networks or sequence alignments, demonstrating its performance on simulated and real data.

A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flow cell

The paper evaluates nanopore sequencing and assembly improvements for Arabidopsis genome assembly and methylation analysis using a single MinION flow cell.

Capturing variation in metagenomic assembly graphs with MetaCortex

MetaCortex improves metagenomic assembly by capturing intra-species diversity, achieving higher coverage and contiguity in simulated and mock communities.

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

This paper demonstrates how adaptive sampling in nanopore sequencing can enrich low-abundance species in metagenomic samples, with efficiency improving with longer read lengths and a mathematical model to predict outcomes.

How low can you go? Driving down the DNA input requirements for nanopore sequencing

This paper demonstrates a low-input DNA extraction and library preparation method for nanopore sequencing, enabling rapid de novo genome assembly from minimal DNA samples.

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

Alvis visualizes alignments and detects chimeric reads to improve assembly contiguity.

Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics

This study uses nanopore sequencing to rapidly profile preterm infant gut microbiota, enabling pathogen detection and antimicrobial resistance profiling within one hour.