Institute for Advanced Biosciences,
Systems Biology Program,
Graduate School of Media and Governance,
Faculty of Environment and Information Studies,
Systems Biology Program, Graduate School of Media and Governance
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KEGG-based pathway visualization tool for complex omics data.
In silico biology , 2005 | Pubmed ID: 16268787
A comprehensive software suite for the analysis of cDNAs.
Genomics, proteomics & bioinformatics Aug, 2005 | Pubmed ID: 16487083
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes.
BMC bioinformatics Mar, 2006 | Pubmed ID: 16553966
GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness.
In silico biology , 2006 | Pubmed ID: 16789913
On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli.
FEBS letters Dec, 2006 | Pubmed ID: 17156778
Noise-reduction filtering for accurate detection of replication termini in bacterial genomes.
FEBS letters Jan, 2007 | Pubmed ID: 17188685
Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli.
Gene May, 2007 | Pubmed ID: 17270364
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.
RNA (New York, N.Y.) May, 2007 | Pubmed ID: 17369313
Multiple high-throughput analyses monitor the response of E. coli to perturbations.
Science (New York, N.Y.) Apr, 2007 | Pubmed ID: 17379776
MEGU: pathway mapping web-service based on KEGG and SVG.
In silico biology , 2006 | Pubmed ID: 17518769
Restauro-G: a rapid genome re-annotation system for comparative genomics.
Genomics, proteomics & bioinformatics Feb, 2007 | Pubmed ID: 17572364
Comparative study of circadian oscillatory network models of Drosophila.
Artificial life , 2008 | Pubmed ID: 18171129
Genome Projector: zoomable genome map with multiple views.
BMC bioinformatics Jan, 2009 | Pubmed ID: 19166610
Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes.
Evolutionary bioinformatics online Oct, 2007 | Pubmed ID: 19461975
The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.
Evolutionary bioinformatics online Sep, 2007 | Pubmed ID: 19461976
A web server for interactive and zoomable Chaos Game Representation images.
Source code for biology and medicine Sep, 2009 | Pubmed ID: 19761591
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
PloS one Nov, 2009 | Pubmed ID: 19907644
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index.
BMC genomics Dec, 2009 | Pubmed ID: 20042086
G-language genome analysis environment with REST and SOAP web service interfaces.
Nucleic acids research Jul, 2010 | Pubmed ID: 20439313
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes.
BMC genomics Jan, 2011 | Pubmed ID: 21223577
KBWS: an EMBOSS associated package for accessing bioinformatics web services.
Source code for biology and medicine Apr, 2011 | Pubmed ID: 21529350
Metabolic flux analysis and visualization.
Journal of proteome research Aug, 2011 | Pubmed ID: 21815690
Validation of bacterial replication termination models using simulation of genomic mutations.
PloS one , 2012 | Pubmed ID: 22509315
Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade.
PloS one , 2012 | Pubmed ID: 22937162
Measures of compositional strand bias related to replication machinery and its applications.
Current genomics Mar, 2012 | Pubmed ID: 22942671
Merging multiple omics datasets in silico: statistical analyses and data interpretation.
Methods in molecular biology (Clifton, N.J.) , 2013 | Pubmed ID: 23417818
Quantitative assay for TALEN activity at endogenous genomic loci.
Biology open Apr, 2013 | Pubmed ID: 23616919
Analysis of DNA repair and protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after exposure to UVC radiation.
PloS one , 2013 | Pubmed ID: 23762256
GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses.
Source code for biology and medicine Aug, 2013 | Pubmed ID: 23987304
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Journal of biomedical semantics Feb, 2014 | Pubmed ID: 24495517
Undesigned selection for replication termination of bacterial chromosomes.
Journal of molecular biology Aug, 2014 | Pubmed ID: 24946150
Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes.
BMC genomics Aug, 2014 | Pubmed ID: 25142801
Novel mitochondria-targeted heat-soluble proteins identified in the anhydrobiotic Tardigrade improve osmotic tolerance of human cells.
PloS one , 2015 | Pubmed ID: 25675104
Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly.
Molecular ecology resources May, 2016 | Pubmed ID: 26561354
G-Links: a gene-centric link acquisition service.
F1000Research , 2014 | Pubmed ID: 26673001
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions.
BMC genomics Mar, 2016 | Pubmed ID: 26939900
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 May, 2016 | Pubmed ID: 27173901
Genome sequencing of a single tardigrade Hypsibius dujardini individual.
Scientific data 08, 2016 | Pubmed ID: 27529330
Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein.
Nature communications Sep, 2016 | Pubmed ID: 27649274
Rearing and observation of immature stages of the hoverfly (Diptera, Syrphidae).
Biodiversity data journal , 2016 | Pubmed ID: 28174503
Glucan synthase-like 2 is indispensable for paramylon synthesis in Euglena gracilis.
FEBS letters 05, 2017 | Pubmed ID: 28423179
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus.
PLoS biology Jul, 2017 | Pubmed ID: 28749982
Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins.
PloS one , 2017 | Pubmed ID: 28832627
eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria.
BMC genomics Oct, 2017 | Pubmed ID: 29029602
Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago.
Journal of plant research Jul, 2018 | Pubmed ID: 29460198
An integrative description of Macrobiotus shonaicus sp. nov. (Tardigrada: Macrobiotidae) from Japan with notes on its phylogenetic position within the hufelandi group.
PloS one , 2018 | Pubmed ID: 29489835
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