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Article
Open AccessDonor cord blood aging accelerates in recipients after transplantation
Cord blood stem cell transplantation is an important alternative for patients needing hematopoietic stem cell transplantation. However, it is unclear how cord blood cells, which are 0 years old, age in the rec...
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Protocol
Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System
With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species...
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Article
Open AccessRapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance p...
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Article
Open AccessComprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains
Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become e...
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Article
Molecular characterization of feline paramyxovirus in Japanese cat populations
Feline paramyxovirus (FPaV) is a member of the family Paramyxoviridae that has been reported only in Germany and the United Kingdom. We detected FPaV for the first time in Japan by transcriptome sequencing of cat...
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Article
Identification of a distinct lineage of aviadenovirus from crane feces
Viruses are believed to be ubiquitous; however, the diversity of viruses is largely unknown because of the bias of previous research toward pathogenic viruses. Deep sequencing is a promising and unbiased appro...
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Article
Open AccessReal-time diagnostic analysis of MinION™-based metagenomic sequencing in clinical microbiology evaluation: a case report
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Article
Open AccessNanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy
Subtelomeric macrosatellite repeats are difficult to sequence using conventional sequencing methods owing to the high similarity among repeat units and high GC content. Sequencing these repetitive regions is c...
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Article
Open AccessThe efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
Accurate quantification of biomolecules in system-wide measurements is in high demand, especially for systems with limited sample amounts such as single cells. Because of this, digital quantification of nuclei...
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Article
Open AccessA portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial composition...
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Chapter
Protein-Coding and Noncoding RNA Genes
During the last decade, our understanding about human genes has gradually but drastically changed. When the human genome-sequencing project announced its completion in 2004, they reported the number of human p...
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Article
Selection pressure on human STR loci and its relevance in repeat expansion disease
Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units...
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Article
Open AccessPCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-Invitational protein-protein interactions integrative dataset
Proteins interact with other proteins or biomolecules in complexes to perform cellular functions. Existing protein-protein interaction (PPI) databases and protein complex databases for human proteins are not o...
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Article
Open AccessAbundance of ultramicro inversions within local alignments between human and chimpanzee genomes
Chromosomal inversion is one of the most important mechanisms of evolution. Recent studies of comparative genomics have revealed that chromosomal inversions are abundant in the human genome. While such previou...
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Article
CIPRO 2.5: Ciona intestinalis Protein Database - a unique integrated repository of large-scale omics data, bioinformatic analyses, and curated annotation, with ability for user rating and comments
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Article
Open AccessA comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing
Alternative splicing (AS) is a key molecular process that endows biological functions with diversity and complexity. Generally, functional redundancy leads to the generation of new functions through relaxation...
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Article
Characteristics of the β-Globin Gene Cluster Haplotypes of Three Han Chinese Populations at Bei**g, **’an, and Kunming as Compared with Those of Other Asian Populations
Haplotype frequencies of the β-globin gene cluster of Han Chinese at Bei**g, **’an, and Kunming were estimated, and their mutual genetic relationships were examined and compared to those of Buryats, Khalkhs, ...
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Article
Open AccessTwo different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions
It is essential in modern biology to understand how transcriptional regulatory regions are composed of cis-elements, yet we have limited knowledge of, for example, the combinational uses of these elements and the...
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Article
Open AccessA genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group
Changes in protein evolutionary rates among lineages have been frequently observed during periods of notable phenotypic evolution. It is also known that, following gene duplication and loss, the protein evolut...
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Article
Isolation and characterization of a pig major histocompatibility complex (SLA) class II DNA cDNA clone
