Matthew D. Clark
A5100643965- Genomics and Phylogenetic Studies
- Environmental DNA in Biodiversity Studies
- Plant Disease Resistance and Genetics
- Microbial Community Ecology and Physiology
- Chromosomal and Genetic Variations
- Wheat and Barley Genetics and Pathology
- Molecular Biology Techniques and Applications
- Genetic Mapping and Diversity in Plants and Animals
- Gene expression and cancer classification
- Forest Insect Ecology and Management
- Plant Virus Research Studies
- Plant-Microbe Interactions and Immunity
- Genetic diversity and population structure
- RNA and protein synthesis mechanisms
- Plant and Fungal Interactions Research
- Insect-Plant Interactions and Control
- Bacteriophages and microbial interactions
- Plant Pathogenic Bacteria Studies
- Plant and animal studies
- Click Chemistry and Applications
- Genetic and phenotypic traits in livestock
- Algorithms and Data Compression
- Nanopore and Nanochannel Transport Studies
- Animal Genetics and Reproduction
- Protein Degradation and Inhibitors
University of California, San Francisco
2024-2025
Natural History Museum
2017-2025
German Oceanographic Museum
2024-2025
City College of San Francisco
2025
Earlham Institute
2013-2024
St James's University Hospital
2024
Norwich Research Park
2013-2023
University of Cambridge
2019-2023
Chester Zoo
2023
University of Nottingham
2017-2023
A high-quality sequence assembly of the zebrafish genome reveals largest gene set any vertebrate and provides information on key genomic features, comparison to human reference shows that approximately 70% protein-coding genes have at least one clear orthologue. The — a model organism for study development disease has now been sequenced published as well-annotated genome. Zebrafish turns out so far sequenced, few pseudogenes. Importantly studies, between sequences obvious second paper...
Cereal grasses of the Triticeae tribe have been major food source in temperate regions since dawn agriculture. Their large genomes are characterized by a high content repetitive elements and pericentromeric that virtually devoid meiotic recombination. Here we present high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive linear order sequences across space investigate spatial organization chromatin nucleus at megabase...
Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts wheat ( Triticum spp.) been more challenging. This is largely owing to size and complexity genome 1 , lack genome-assembly data for multiple lines 2,3 . Here we generated ten chromosome pseudomolecule five scaffold assemblies hexaploid explore genomic diversity among from global breeding programs. Comparative analysis revealed extensive structural rearrangements,...
Advances in genome sequencing and assembly technologies are generating many high-quality sequences, but assemblies of large, repeat-rich polyploid genomes, such as that bread wheat, remain fragmented incomplete. We have generated a new wheat whole-genome shotgun sequence using combination optimized data types an algorithm designed to deal with large complex genomes. The represents >78% the scaffold N50 88.8 kb has high fidelity input data. Our annotation combines strand-specific Illumina...
The genome of the Southern Ocean phytoplankton Fragilariopsis cylindrus differs markedly from genomes its more temperate relatives, with divergent alleles being differentially expressed in environmentally specific conditions such as freezing and darkness. Diatoms are main primary producers Ocean, but how they have adapted to an environment extremes light temperature has remained unknown. Here Thomas Mock et al. report sequence a cold-adapted diatom cylindrus, compare this 'psychrophile'...
Abstract Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries up to 12 kb. The LMP are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization structural variants. However, intrinsically noisy maximize their value, post-sequencing data analysis is required. Standardizing laboratory protocols selection sequenced reads non-trivial tasks. NextClip a tool...
Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. To test its potential for rarer species within metagenomic samples, we create synthetic mock community and construct libraries with range mean read lengths. Enrichment up 13.87-fold the least abundant in longest length library; factoring reduced yields from rejecting molecules calculated efficiency raises this 4.93-fold. Finally, introduce mathematical model based on molecule relative...
The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used coupled to NanoOK RT software package perform shotgun metagenomic and profile mock communities faecal samples from healthy ill preterm infants. Using Nanopore data, we reliably classified a 20-species community captured diversity immature gut microbiota over time response interventions such as probiotic supplementation,...
Abstract Barley ( Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by International Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report experimental computational procedures to (i) assemble more than 80,000 bacterial artificial chromosome (BAC) clones along minimum tiling path genome-wide physical map, (ii) find...
Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal that has been moving across continents hosts from Asian to European ash. Most common trees (Fraxinus excelsior) are highly susceptible H. although minority (~5%) have partial resistance dieback. Here, we assemble annotate fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity Europe in Japan,...
Abstract Zoo populations of threatened species are a valuable resource for the restoration wild populations. However, their small effective population size poses risk to long‐term viability, especially in with high genetic load. Recent bioinformatic developments can identify harmful variants genome data. Here, we advance this approach, analysing load pink pigeon ( Nesoenas mayeri ). We lifted mutation‐impact scores that had been calculated chicken Gallus gallus ) estimate six pigeons....
Abstract: Security infrastructure along international boundaries threatens to degrade connectivity for wildlife. To explore potential effects of a fence under construction the U.S.–Mexico border on wildlife, we assessed movement behavior two species with different life histories whose regional persistence may depend transboundary movements. We used radiotelemetry assess how vegetation and landscape structure affect flight natal dispersal behaviors Ferruginous Pygmy‐Owls ( Glaucidium...
A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow expensive, whereas faster, cheaper short-read-only assemblies can be incomplete highly fragmented, which minimizes their usefulness. The last few years have seen the introduction many new technologies assembly. These associated algorithms typically benchmarked on microbial genomes or, if they scale appropriately, larger (e.g., human) genomes....
The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after severe population bottleneck in the 1970s to early 1990s. Prior this bottleneck, ex situ was established from which captive-bred individuals were released into free-living subpopulations increase size and genetic variation. This conservation rescue led rapid 400-480 individuals, twice downlisted on International Union for Conservation Nature (IUCN) Red List. We analyzed impacts...
Abstract Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the Access Programme (MAP), promises long reads real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q base calling output and provide basic yield statistics. However, no single tool yet exists comprehensive alignment-based quality control error profile analysis—something that is extremely important given speed with which platform evolving. Results:...
Abstract Automated phenotyping technologies are capable of providing continuous and precise measurements traits that key to today’s crop research, breeding agronomic practices. In additional monitoring developmental changes, high-frequency high-precision phenotypic analysis can enable both accurate delineation the genotype-to-phenotype pathway identification genetic variation influencing environmental adaptation yield potential. Here, we present an automated scalable field platform called...
Abstract The ability to identify and quantify the constituent plant species that make up a mixed‐species sample of pollen has important applications in ecology, conservation, agriculture. Recently, metabarcoding protocols have been developed for can species, but there are strong reasons doubt accurately their relative abundances. A PCR‐free, shotgun metagenomics approach greater potential quantifying abundances, applying eukaryotes is challenging due low numbers reference genomes. We...
Zebrafish (Danio rerio) is a popular vertebrate model organism largely deployed using outbred laboratory animals. The nonisogenic nature of the zebrafish as system offers opportunity to understand natural variations and their effect in modulating phenotype. In an effort better characterize range variation this complement reference genome project, whole sequence wild at 39-fold coverage was determined. Comparative analysis with revealed approximately 5.2 million single nucleotide over 1.6...