Matthew D. Clark

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

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.

This study investigates how Arabidopsis arenosa adapts to serpentine soils by shaping its associated microbiome, identifying specific microbial variants linked to plant adaptation.

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

The paper introduces a Snakemake toolkit for assembling, annotating, and analyzing mitochondrial genomes and ribosomal genes from low-coverage genome skims of museum specimens.

This study evaluates exome capture and shotgun sequencing for genomic analysis of historical Antarctic krill samples, showing effective variant calling and DNA assembly despite degraded DNA and large genome size.

The paper introduces Air-seq, a method to monitor agricultural ecosystem biodiversity using airborne DNA, showing it can detect pathogens and track their abundance over time.

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.

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.

The paper presents a low-cost genomic DNA extraction method for soil samples, which produces high-quality DNA suitable for amplicon sequencing and downstream applications at a lower cost than commercial kits.

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

This paper introduces Grid-seq, a cost-effective spatial transcriptomics method for plants, and demonstrates its ability to detect immune responses in Arabidopsis thaliana to flagellin-22.

This paper compares genome assembly technologies for the potato species S. verrucosum, evaluating their completeness, accuracy, cost, and computational requirements.

The paper assesses and improves wheat genome assemblies using Fosill jumping libraries, finding that whole genome shotgun assemblies are more accurate than BAC-based ones.

The paper analyzes the genetic diversity of Hymenoscyphus fraxineus, showing the European population was founded by two divergent haplotypes with adaptive potential.

The paper reports on a crowdsourced project analyzing ash dieback fungus data, revealing insights into its genome and biology through community contributions.