Kazuharu Arakawa

Institute for Advanced Biosciences, Keio University

Research Area

Genetics

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title	2018

Other Publications

Article	Year
KEGG-based pathway visualization tool for complex omics data. In silico biology\| PubMed ID: 16268787	2005
A comprehensive software suite for the analysis of cDNAs. Genomics, proteomics & bioinformatics\| PubMed ID: 16487083	2005
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC bioinformatics\| PubMed ID: 16553966	2006
GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness. In silico biology\| PubMed ID: 16789913	2006
On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli. FEBS letters\| PubMed ID: 17156778	2006
Noise-reduction filtering for accurate detection of replication termini in bacterial genomes. FEBS letters\| PubMed ID: 17188685	2007
Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli. Gene\| PubMed ID: 17270364	2007
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA (New York, N.Y.)\| PubMed ID: 17369313	2007
Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (New York, N.Y.)\| PubMed ID: 17379776	2007
MEGU: pathway mapping web-service based on KEGG and SVG. In silico biology\| PubMed ID: 17518769	2006
Restauro-G: a rapid genome re-annotation system for comparative genomics. Genomics, proteomics & bioinformatics\| PubMed ID: 17572364	2007
Comparative study of circadian oscillatory network models of Drosophila. Artificial life\| PubMed ID: 18171129	2008
Genome Projector: zoomable genome map with multiple views. BMC bioinformatics\| PubMed ID: 19166610	2009
Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes. Evolutionary bioinformatics online\| PubMed ID: 19461975	2007
The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection. Evolutionary bioinformatics online\| PubMed ID: 19461976	2007
A web server for interactive and zoomable Chaos Game Representation images. Source code for biology and medicine\| PubMed ID: 19761591	2009
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PloS one\| PubMed ID: 19907644	2009
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index. BMC genomics\| PubMed ID: 20042086	2009
G-language genome analysis environment with REST and SOAP web service interfaces. Nucleic acids research\| PubMed ID: 20439313	2010
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. BMC genomics\| PubMed ID: 21223577	2011
KBWS: an EMBOSS associated package for accessing bioinformatics web services. Source code for biology and medicine\| PubMed ID: 21529350	2011
Metabolic flux analysis and visualization. Journal of proteome research\| PubMed ID: 21815690	2011
Validation of bacterial replication termination models using simulation of genomic mutations. PloS one\| PubMed ID: 22509315	2012
Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade. PloS one\| PubMed ID: 22937162	2012
Measures of compositional strand bias related to replication machinery and its applications. Current genomics\| PubMed ID: 22942671	2012
Merging multiple omics datasets in silico: statistical analyses and data interpretation. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 23417818	2013
Quantitative assay for TALEN activity at endogenous genomic loci. Biology open\| PubMed ID: 23616919	2013
Analysis of DNA repair and protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after exposure to UVC radiation. PloS one\| PubMed ID: 23762256	2013
GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses. Source code for biology and medicine\| PubMed ID: 23987304	2013
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of biomedical semantics\| PubMed ID: 24495517	2014
Undesigned selection for replication termination of bacterial chromosomes. Journal of molecular biology\| PubMed ID: 24946150	2014
Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes. BMC genomics\| PubMed ID: 25142801	2014
Novel mitochondria-targeted heat-soluble proteins identified in the anhydrobiotic Tardigrade improve osmotic tolerance of human cells. PloS one\| PubMed ID: 25675104	2015
Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly. Molecular ecology resources\| PubMed ID: 26561354	2016
G-Links: a gene-centric link acquisition service. F1000Research\| PubMed ID: 26673001	2014
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions. BMC genomics\| PubMed ID: 26939900	2016
No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 27173901	2016
Genome sequencing of a single tardigrade Hypsibius dujardini individual. Scientific data\| PubMed ID: 27529330	2016
Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nature communications\| PubMed ID: 27649274	2016
Rearing and observation of immature stages of the hoverfly (Diptera, Syrphidae). Biodiversity data journal\| PubMed ID: 28174503	2016
Glucan synthase-like 2 is indispensable for paramylon synthesis in Euglena gracilis. FEBS letters\| PubMed ID: 28423179	2017
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLoS biology\| PubMed ID: 28749982	2017
Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins. PloS one\| PubMed ID: 28832627	2017
eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria. BMC genomics\| PubMed ID: 29029602	2017
Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago. Journal of plant research\| PubMed ID: 29460198	2018
An integrative description of Macrobiotus shonaicus sp. nov. (Tardigrada: Macrobiotidae) from Japan with notes on its phylogenetic position within the hufelandi group. PloS one\| PubMed ID: 29489835	2018