1. Whole exome sequencing in Thai patients with retinitis pigmentosa reveals novel mutations in six genes.

    Investigative Ophthalmology & Visual Science 55(4):2259 (2014) PMID 24618324

    To identify disease-causing mutations and describe genotype-phenotype correlations in Thai patients with nonsyndromic retinitis pigmentosa (RP). Whole exome sequencing was performed in 20 unrelated patients. Eighty-six genes associated with RP, Leber congenital amaurosis, and cone-rod dystrophy ...
  2. Whole exome sequencing in Thai patients with retinitis pigmentosa reveals novel mutations in six genes.

    Investigative Ophthalmology & Visual Science 55(4):2259 (2014) PMID 24618324

    To identify disease-causing mutations and describe genotype-phenotype correlations in Thai patients with nonsyndromic retinitis pigmentosa (RP). Whole exome sequencing was performed in 20 unrelated patients. Eighty-six genes associated with RP, Leber congenital amaurosis, and cone-rod dystrophy ...
  3. Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater.

    BMC Microbiology 14(1):318 (2014) PMID 25539583 PMCID PMC4326521

    Special features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. ...
  4. Comparative analysis of DNA word abundances in four yeast genomes using a novel statistical background model.

    PLoS ONE 8(3):e58038 (2013) PMID 23472131 PMCID PMC3589456

    Previous studies have shown that the identification and analysis of both abundant and rare k-mers or "DNA words of length k" in genomic sequences using suitable statistical background models can reveal biologically significant sequence elements. Other studies have investigated the uni/multimodal...
  5. Comparative analysis of DNA word abundances in four yeast genomes using a novel statistical background model.

    PLoS ONE 8(3):e58038 (2013) PMID 23472131 PMCID PMC3589456

    Previous studies have shown that the identification and analysis of both abundant and rare k-mers or "DNA words of length k" in genomic sequences using suitable statistical background models can reveal biologically significant sequence elements. Other studies have investigated the uni/multimodal...
  6. Functional assignment of metagenomic data: challenges and applications.

    Briefings in Bioinformatics 13(6):711 (2012) PMID 22772835 PMCID PMC3504928

    Metagenomic sequencing provides a unique opportunity to explore earth's limitless environments harboring scores of yet unknown and mostly unculturable microbes and other organisms. Functional analysis of the metagenomic data plays a central role in projects aiming to explore the most essential q...
  7. Functional assignment of metagenomic data: challenges and applications.

    Briefings in Bioinformatics 13(6):711 (2012) PMID 22772835 PMCID PMC3504928

    Metagenomic sequencing provides a unique opportunity to explore earth's limitless environments harboring scores of yet unknown and mostly unculturable microbes and other organisms. Functional analysis of the metagenomic data plays a central role in projects aiming to explore the most essential q...
  8. Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping.

    Open Biology 2(4):120043 (2012) PMID 22724063 PMCID PMC3376729

    We present findings on the nucleosomal arrangement in the genome of the basidiomycete Mixia osmundae, focusing on nucleosomal linker DNA regions. We have assembled the genomic sequences of M. osmundae, annotated genes and transcription start sites (TSSs) on the genome, and created a detailed nuc...
  9. Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping.

    Open Biology 2(4):120043 (2012) PMID 22724063 PMCID PMC3376729

    We present findings on the nucleosomal arrangement in the genome of the basidiomycete Mixia osmundae, focusing on nucleosomal linker DNA regions. We have assembled the genomic sequences of M. osmundae, annotated genes and transcription start sites (TSSs) on the genome, and created a detailed nuc...
  10. Acetate-producing bifidobacteria protect the host from enteropathogenic infection via carbohydrate transporters.

    Gut Microbes 3(5):449 (2012) PMID 22825494

    The human gut harbors a large and diverse community of commensal bacteria. Among them, Bifidobacterium is known to exhibit various probiotic effects including protection of hosts from infectious diseases. We recently discovered that genes encoding an ATP-binding-cassette-type carbohydrate transp...
  11. Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.

    PLoS ONE 7(4):e34030 (2012) PMID 22496776 PMCID PMC3319535

    Taxonomic assignment of sequence reads is a challenging task in metagenomic data analysis, for which the present methods mainly use either composition- or homology-based approaches. Though the homology-based methods are more sensitive and accurate, they suffer primarily due to the time needed to...
  12. Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.

    PLoS ONE 7(4):e34030 (2012) PMID 22496776 PMCID PMC3319535

    Taxonomic assignment of sequence reads is a challenging task in metagenomic data analysis, for which the present methods mainly use either composition- or homology-based approaches. Though the homology-based methods are more sensitive and accurate, they suffer primarily due to the time needed to...
  13. Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp. strain L, both isolated from a microbial fuel cell.

    Journal of Bacteriology 193(22):6411 (2011) PMID 22038970 PMCID PMC3209197

    Arcobacter butzleri strain ED-1 is an exoelectrogenic epsilonproteobacterium isolated from the anode biofilm of a microbial fuel cell. Arcobacter sp. strain L dominates the liquid phase of the same fuel cell. Here we report the finished and annotated genome sequences of these organisms.
  14. Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp. strain L, both isolated from a microbial fuel cell.

    Journal of Bacteriology 193(22):6411 (2011) PMID 22038970 PMCID PMC3209197

    Arcobacter butzleri strain ED-1 is an exoelectrogenic epsilonproteobacterium isolated from the anode biofilm of a microbial fuel cell. Arcobacter sp. strain L dominates the liquid phase of the same fuel cell. Here we report the finished and annotated genome sequences of these organisms.
  15. Complete Genome Sequences of Rat and Mouse Segmented Filamentous Bacteria, a Potent Inducer of Th17 Cell Differentiation

    Cell Host & Microbe 10(3):273 (2011)

    Segmented filamentous bacteria (SFB) are noncultivable commensals inhabiting the gut of various vertebrate species and have been shown to induce Th17 cells in mice. We present the complete genome sequences of both rat and mouse SFB isolated from SFB-monocolonized hosts. The rat and mou...
  16. Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation.

    Cell Host & Microbe 10(3):273 (2011) PMID 21925114

    Segmented filamentous bacteria (SFB) are noncultivable commensals inhabiting the gut of various vertebrate species and have been shown to induce Th17 cells in mice. We present the complete genome sequences of both rat and mouse SFB isolated from SFB-monocolonized hosts. The rat and mouse SFB gen...
  17. Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation.

    Cell Host & Microbe 10(3):273 (2011) PMID 21925114

    Segmented filamentous bacteria (SFB) are noncultivable commensals inhabiting the gut of various vertebrate species and have been shown to induce Th17 cells in mice. We present the complete genome sequences of both rat and mouse SFB isolated from SFB-monocolonized hosts. The rat and mouse SFB gen...
  18. Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient.

    Journal of Bacteriology 193(13):3385 (2011) PMID 21515762 PMCID PMC3133283

    The diverse clinical outcomes of colonization by Helicobacter pylori reflect the need to understand the genomic rearrangements enabling the bacterium to adapt to host niches and exhibit varied colonization/virulence potential. We describe the genome sequences of the two serial isolates, H. pylor...
  19. Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient.

    Journal of Bacteriology 193(13):3385 (2011) PMID 21515762 PMCID PMC3133283

    The diverse clinical outcomes of colonization by Helicobacter pylori reflect the need to understand the genomic rearrangements enabling the bacterium to adapt to host niches and exhibit varied colonization/virulence potential. We describe the genome sequences of the two serial isolates, H. pylor...
  20. Bifidobacteria can protect from enteropathogenic infection through production of acetate.

    Nature 469(7331):543 (2011) PMID 21270894

    The human gut is colonized with a wide variety of microorganisms, including species, such as those belonging to the bacterial genus Bifidobacterium, that have beneficial effects on human physiology and pathology. Among the most distinctive benefits of bifidobacteria are modulation of host defenc...