A5012019245- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Protist diversity and phylogeny
- Chromosomal and Genetic Variations
- Congenital heart defects research
- Microbial Community Ecology and Physiology
- Prenatal Screening and Diagnostics
- Genetic diversity and population structure
- Plant Pathogens and Fungal Diseases
- Genomics and Chromatin Dynamics
- Biological and pharmacological studies of plants
- Bioinformatics and Genomic Networks
- Sarcoma Diagnosis and Treatment
- Genomics and Rare Diseases
- Forensic and Genetic Research
- Metabolomics and Mass Spectrometry Studies
- Tissue Engineering and Regenerative Medicine
- Gene expression and cancer classification
- Advanced biosensing and bioanalysis techniques
- Plant Diversity and Evolution
- Genetic Syndromes and Imprinting
- Plant and Fungal Species Descriptions
- Plant and animal studies
- Botanical Studies and Applications
- Algorithms and Data Compression
Okinawa Institute of Science and Technology Graduate University
2024-2025
KU Leuven
2020-2024
Sun Yat-sen University
2020
Vrije Universiteit Brussel
2016-2019
Université Libre de Bruxelles
2016-2019
The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few them focus on assembling organelle genomes. These genomes are used phylogenetic studies, food identification and most deposited eukaryotic GenBank. Producing genome from whole (WGS) data would be accurate least laborious approach, a tool specifically designed for this task is lacking. We developed seed-and-extend algorithm that assembles data, starting...
Orchidaceae is one of the largest families angiosperms. Considering large number species in this family and its symbiotic relationship with fungi, provide an ideal model to study evolution plant mitogenomes. However, date, there only draft mitochondrial genome available. Here, we present a fully assembled annotated sequence (mitogenome) Paphiopedilum micranthum, high economic ornamental value. The mitogenome P. micranthum was 447,368 bp length comprised 26 circular subgenomes ranging size...
COLOMBOS is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. Compared to the previous version it has more than doubled in size, both terms of species and available. The manually curated condition annotation been overhauled as well, giving complete information about samples' experimental conditions their differences. Functionality-wise cross-species analyses now enable users analyse expression all simultaneously, identify candidate...
Abstract Heteroplasmy, the existence of multiple mitochondrial haplotypes within an individual, has been studied across different scientific fields. Mitochondrial genome polymorphisms have linked to severe disorders and are interest evolutionary studies forensic science. Before development massive parallel sequencing (MPS), most variation were limited short fragments heteroplasmic variants associated with a relatively high frequency (>10%). By utilizing ultra-deep sequencing, it now...
Accurate simulations of structural variation distributions and sequencing data are crucial for the development benchmarking new tools. We develop Sim-it, a straightforward tool simulation both long-read data. These from Sim-it reveal strengths weaknesses current available callers platforms. With these findings, we method (combiSV) that can combine results into superior call set with increased recall precision, which is also observed latest benchmark developed by GIAB Consortium.
During normal zygotic division, two haploid parental genomes replicate, unite and segregate into biparental diploid blastomeres.
Abstract Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of globe. The genome single male individual collected from Okinawa, Japan was sequenced using single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. mitogenome 39,268 bp long, featuring large control region around 22,000 bp. We annotated proteins atp6, cob, cox1, cox2, cox3, nad1, nad4, nad5, one more open reading frame that did not match any known gene. This study...
<ns3:p>Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies available for appendicularians, both cryptic species of <ns3:italic>Oikopleura dioica.</ns3:italic> This underrepresentation appendicularian genomes limits environmental DNA sequencing (eDNA) studies that rely on markers as a taxonomic barcode. We report assembly and annotation an unknown isolated from Amami Oshima island, Kagoshima prefecture,...
Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of globe. The genome single male individual collected from Okinawa, Japan was sequenced using single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. mitogenome 39,268 bp long, featuring large control region around 22,000 bp. We annotated proteins atp6, cob, cox1, cox2, cox3, nad1, nad4 nad5, one more open reading frame that did not match any known gene. This study marks...
Segmental duplications or low copy repeats (LCRs) constitute duplicated regions interspersed in the human genome, currently neglected standard analyses due to their extreme complexity. Recent functional studies have indicated potential of genes within LCRs synaptogenesis, neuronal migration, and neocortical expansion lineage. One with highest proportion sequence is 22q11.2 locus, carrying eight (LCR22-A until LCR22-H), rearrangements between them cause deletion syndrome. The LCR22-A block...
The 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. Why incidence of 22q11.2DS much greater than that other genomic disorders remains unknown. Short read sequencing cannot resolve complex segmental duplicon structure to provide direct confirmation hypothesis rearrangements are caused by nonallelic homologous recombination between low copy repeats on Chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping in LCR22 regions, we...
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss heterozygosity (CN-LOH) landscape PMBL which distinguishes this tumor from other malignancies, including the biologically related diffuse large lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, cohort showed...
The 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. Why incidence of 22q11.2DS much greater than that other genomic disorders remains unknown. Short read sequencing cannot resolve complex segmental duplicon structure to provide direct confirmation hypothesis rearrangements are caused by non-allelic homologous recombination between low copy repeats on chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping in LCR22 regions, we...
1. ABSTRACT Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies available for appendicularians, both cryptic species of Oikopleura dioica . This underrepresentation appendicularian genomes limits environmental DNA sequencing (eDNA) studies that rely on markers as a taxonomic barcode. We report assembly and annotation an unknown isolated from Amami Oshima island, Kagoshima prefecture, Japan, has...
<ns4:p>Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies available for appendicularians, both cryptic species of <ns4:italic>Oikopleura dioica.</ns4:italic> This underrepresentation appendicularian genomes limits environmental DNA sequencing (eDNA) studies that rely on markers as a taxonomic barcode. We report assembly and annotation an unknown isolated from Amami Oshima island, Kagoshima prefecture,...
ABSTRACT Despite the rapid evolution of new sequencing technologies, structural variation detection remains poorly ascertained. The high discrepancy between results variant analysis programs makes it difficult to assess their performance on real datasets. Accurate simulations distributions and data human genome are crucial for development benchmarking tools. In order gain a better insight into with long reads, we created realistic simulated model thoroughly compare SV methods impact chosen...
Abstract Segmental duplications or low copy repeats (LCRs) constitute complex regions interspersed in the human genome. They have contributed significantly to evolution by stimulating neo- sub-functionalization of duplicated transcripts. The 22q11.2 region carries eight LCRs (LCR22s). One these LCR22s was recently reported be hypervariable population. It remains unknown whether this variability exists also non-human primates. To assess inter- and intra-species variability, we de novo...
Abstract The zygotic division enables two haploid genomes to segregate into biparental diploid blastomeres. This fundamental tenet was challenged by the observation that blastomeres with different genome ploidy or parental genotypes can coexist within individual embryos. We hypothesized whole distinct blastomere lineages during first through “heterogoneic division”. Here, we map genomic landscape of 82 from 25 embryos underwent multipolar division. coexistence androgenetic and polyploid...