Matthew Dunn
A5002299527- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Developmental Biology and Gene Regulation
- Genomics and Chromatin Dynamics
- Marine Ecology and Invasive Species
- RNA Research and Splicing
- Genomic variations and chromosomal abnormalities
- Genetic diversity and population structure
- Marine Invertebrate Physiology and Ecology
- RNA and protein synthesis mechanisms
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetics and Neurodevelopmental Disorders
- Congenital Ear and Nasal Anomalies
- Insect symbiosis and bacterial influences
- Plant Disease Resistance and Genetics
- RNA regulation and disease
- Hedgehog Signaling Pathway Studies
- Plant Pathogenic Bacteria Studies
- Parasitic Diseases Research and Treatment
- Bacteriophages and microbial interactions
- Plant-Microbe Interactions and Immunity
- Livestock and Poultry Management
- Marine and environmental studies
- Probiotics and Fermented Foods
- Evolution and Paleontology Studies
Brigham Young University
2022
Marine Biological Laboratory
2021
Wellcome Sanger Institute
2003-2019
St. John's University
2016
Stony Brook University
2011-2013
Max Planck Institute for Developmental Biology
2013
Cornell University
2008-2009
Harvard University
2001
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...
I have read the journal's policy and following conflicts: Paul Flicek is married to deputy editor of PLoS Medicine, Melissa Norton. Evan Eichler on board Pacific Biosciences. Support for this work came from Intramural Research Program NIH, The National Library European Molecular Biology Laboratory, Wellcome Trust (grant number 077198), Howard Hughes Medical Institute (EEE). funders had no role in study design, data collection analysis, decision publish or preparation manuscript.
Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced isolates, representing 273 species (105 novel species) from 31 families found in human gastrointestinal microbiota. The HBC increases number genomes derived microbiota by 37%....
Abstract Human onchocerciasis is a serious neglected tropical disease caused by the filarial nematode Onchocerca volvulus that can lead to blindness and chronic disability. Control of relies largely on mass administration single drug, development new drugs vaccines depends better knowledge parasite biology. Here, we describe chromosomes O. its Wolbachia endosymbiont. We provide highest-quality sequence assembly for any parasitic date, giving glimpse into evolution proteomes. This resource...
Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies Mus caroli pahari genomes. Together musculus Rattus norvegicus genomes, this set rodent genomes is divergence times to Hominidae (human-chimpanzee-gorilla-orangutan). By comparing evolutionary dynamics between Muridae Hominidae,...
Despite the rapid development of sequencing technologies, assembly mammalian-scale genomes into complete chromosomes remains one most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout 2, a reference-assisted tool that works for large and complex genomes. By taking or more target assemblies (generated from an NGS assembler) multiple related reference genomes, 2 infers evolutionary relationships between builds final using genome rearrangement...
Editorial on the Research Topic Food safety in low-and middle-income countriesThis is first special edition food informal markets low-and-middle income countries (LMICs).Despite their important public health and socio-economic impacts, foodborne diseases have only recently gained attention of development institutes initiatives (Grace, 2023).The result growing appreciation enormous burden disease LMICs: comparable to that malaria, HIV/AIDs or tuberculosis economic cost more than 100 billion...
An antimicrobial activity screen of Burkholderia gladioli BCC0238, a clinical isolate from cystic fibrosis patient, led to the discovery gladiolin, novel macrolide antibiotic with potent against Mycobacterium tuberculosis H37Rv. Gladiolin is structurally related etnangien, highly unstable Sorangium cellulosum that also active Mycobacteria. Like gladiolin was found inhibit RNA polymerase, validated drug target in M. tuberculosis. However, lacks labile hexaene moiety etnangien and thus possess...
As the sea anemone Nematostella vectensis emerges as a model for studying regeneration, new tools will be needed to assess its regenerative processes and describe perturbations resulting from experimental investigation. Chief among these is need universal set of staging criteria establish morphological landmarks that provide common format discussion investigators.We have established stages rapidly assessing regeneration aboral end (physa) Nematostella. Using this system, we observed rates...
The notochord is a defining feature of the chordate body plan. Experiments in ascidian, frog and mouse embryos have shown that co-expression Brachyury FoxA class transcription factors required for development. However, studies on cis-regulatory sequences mediating synergistic effects these are complicated by limited knowledge genes modules (CRMs) directly targeted both. We identified an easily testable model such investigations 155-bp notochord-specific CRM from ascidian Ciona intestinalis....
Abstract The notochord is a defining character of the chordates, and T‐box transcription factor Brachyury has been shown to be required for development in all chordates examined. In ascidian Ciona intestinalis , at least 44 genes have identified as bona fide transcriptional targets Brachyury. We examined embryonic expression subset murine orthologs target assess its conservation throughout chordate evolution. focused on analyzing Leprecan gene family, which mouse composed three genes,...
Abstract Despite the rapid development of sequencing technologies, assembly mammalian-scale genomes into complete chromosomes remains one most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout, a reference-assisted tool that now works for large and complex genomes. Taking or more target assemblies (generated from an NGS assembler) multiple related reference genomes, Ragout infers evolutionary relationships between builds final using genome...
Here, the full genome sequences of 22 T1-like bacteriophages isolated from wastewater are reported. Eight (BlueShadow, Brooksby, Devorator, ElisaCorrea, Reinasaurus, SorkZaugg, Supreme284, ZeroToHero) were on Citrobacter, six Klebsiella (Chell, FairDinkum, HazelMika, Opt-817, P528, PeteCarol), and eight Escherichia (Fulano1, Mishu, Opt-719, PhleaSolo, Punny, Poky, Phunderstruck, Sadiya).
How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load the putative ancient ostracod Darwinula stevensoni. examined long contiguous stretches DNA clones from a genomic fosmid library, totaling about 2.5 Mb, supplemented these data with results on abundance Illumina draft genome. In contrast to other studies putatively asexuals, which revealed relatively low content, we found that at...
ABSTRACT Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies Mus caroli pahari genomes. Together musculus Rattus norvegicus genomes, this set rodent genomes is divergence times to Hominidae (human-chimpanzee-gorilla-orangutan). By comparing evolutionary dynamics between Muridae...
Background : As the sea anemone Nematostella vectensis emerges as a model for studying regeneration, new tools will be needed to assess its regenerative processes and describe perturbations resulting from experimental investigation. Chief among these is need universal set of staging criteria establish morphological landmarks that provide common format discussion investigators. Results: We have established stages rapidly assessing regeneration aboral end (physa) . Using this system, we...