Kazuharu Arakawa

Kazuharu Arakawa

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Kazuharu Arakawa

Kazuharu Arakawa

Publications by authors named "Kazuharu Arakawa"

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A new redescription of , supported by transcriptome, provides resources for describing concealed species diversity within the monotypic genus (Eutardigrada).

Zoological Lett 2020 5;6. Epub 2020 Feb 5.

1Department of Entomology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.

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http://dx.doi.org/10.1186/s40851-020-0154-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003491PMC
February 2020

AMPK activity is required for the induction of anhydrobiosis in a tardigrade Hypsibius exemplaris, and its potential up-regulator is PP2A.

Genes Cells 2019 Dec 6;24(12):768-780. Epub 2019 Nov 6.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.

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http://dx.doi.org/10.1111/gtc.12726DOI Listing
December 2019

Comparison of the transcriptomes of two tardigrades with different hatching coordination.

BMC Dev Biol 2019 12 9;19(1):24. Epub 2019 Dec 9.

Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.

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http://dx.doi.org/10.1186/s12861-019-0205-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925440PMC
December 2019

Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii.

Mol Ecol 2019 09 11;28(17):3977-3993. Epub 2019 Sep 11.

Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.

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http://dx.doi.org/10.1111/mec.15193DOI Listing
September 2019

Complete Genome Sequence of Halophilic Deep-Sea Bacterium Halomonas axialensis Strain Althf1.

Microbiol Resour Announc 2019 Aug 1;8(31). Epub 2019 Aug 1.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan

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http://dx.doi.org/10.1128/MRA.00839-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6675999PMC
August 2019

Nanopore sequencing: Review of potential applications in functional genomics.

Dev Growth Differ 2019 Jun 29;61(5):316-326. Epub 2019 Apr 29.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.

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http://dx.doi.org/10.1111/dgd.12608DOI Listing
June 2019

Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue.

Sci Rep 2019 Jun 10;9(1):8380. Epub 2019 Jun 10.

Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.

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http://dx.doi.org/10.1038/s41598-019-44775-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557832PMC
June 2019

The bagworm genome reveals a unique fibroin gene that provides high tensile strength.

Commun Biol 2019 29;2:148. Epub 2019 Apr 29.

1Institute for Advanced Biosciences, Keio University, Yamagata, Japan.

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http://dx.doi.org/10.1038/s42003-019-0412-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6488591PMC
April 2019

Comparison of Sexual Reproductive Behaviors in Two Species of Macrobiotidae (Tardigrada: Eutardigrada).

Zoolog Sci 2019 04;36(2):120-127

School of Fundamental Science and Technology, Graduate School of Science and Technology, Keio University, Kohoku-ku, Yokohama-shi, Kanagawa 223-8522, Japan,

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https://bioone.org/journals/zoological-science/volume-36/iss
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http://dx.doi.org/10.2108/zs180103DOI Listing
April 2019

Ultralow Input Genome Sequencing Library Preparation from a Single Tardigrade Specimen.

J Vis Exp 2018 07 15(137). Epub 2018 Jul 15.

Institute for Advanced Biosciences, Keio University; Systems Biology Program, Graduate School of Media and Governance, Keio University; Faculty of Environment and Information Studies, Keio University;

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http://dx.doi.org/10.3791/57615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126485PMC
July 2018

Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins.

PLoS One 2017 23;12(8):e0183397. Epub 2017 Aug 23.

Enzyme Research Team, Center for Sustainable Resource Science, RIKEN, Wako-shi, Saitama, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183397PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568437PMC
October 2017

eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria.

BMC Genomics 2017 Oct 13;18(1):784. Epub 2017 Oct 13.

Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.

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http://dx.doi.org/10.1186/s12864-017-4162-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640929PMC
October 2017

Glucan synthase-like 2 is indispensable for paramylon synthesis in Euglena gracilis.

FEBS Lett 2017 05 7;591(10):1360-1370. Epub 2017 May 7.

Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan.

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http://dx.doi.org/10.1002/1873-3468.12659DOI Listing
May 2017

Genome sequencing of a single tardigrade Hypsibius dujardini individual.

Sci Data 2016 08 16;3:160063. Epub 2016 Aug 16.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan.

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http://dx.doi.org/10.1038/sdata.2016.63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986543PMC
August 2016

Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly.

Mol Ecol Resour 2016 May 6;16(3):662-72. Epub 2015 Dec 6.

Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.

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http://dx.doi.org/10.1111/1755-0998.12485DOI Listing
May 2016

No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.

Authors:
Kazuharu Arakawa

Proc Natl Acad Sci U S A 2016 May 12;113(22):E3057. Epub 2016 May 12.

Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan

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http://dx.doi.org/10.1073/pnas.1602711113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896722PMC
May 2016

De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions.

BMC Genomics 2016 Mar 3;17:182. Epub 2016 Mar 3.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan.

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http://dx.doi.org/10.1186/s12864-016-2540-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778363PMC
March 2016

G-Links: a gene-centric link acquisition service.

F1000Res 2014 19;3:285. Epub 2014 Nov 19.

Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670005PMC
http://dx.doi.org/10.12688/f1000research.5754.2DOI Listing
December 2015

Undesigned selection for replication termination of bacterial chromosomes.

J Mol Biol 2014 Aug 16;426(16):2918-27. Epub 2014 Jun 16.

Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2014.06.005DOI Listing
August 2014

Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes.

BMC Genomics 2014 Aug 21;15:699. Epub 2014 Aug 21.

Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1186/1471-2164-15-699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159541PMC
August 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses.

Source Code Biol Med 2013 Aug 29;8(1):17. Epub 2013 Aug 29.

Institute for Advanced Biosciences, Keio University, 14-1, Baba town, Tsuruoka city, Yamagata Pref, 997-0035, Japan.

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http://dx.doi.org/10.1186/1751-0473-8-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847652PMC
August 2013

Merging multiple omics datasets in silico: statistical analyses and data interpretation.

Methods Mol Biol 2013 ;985:459-70

Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa, Japan.

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http://dx.doi.org/10.1007/978-1-62703-299-5_23DOI Listing
July 2013

Quantitative assay for TALEN activity at endogenous genomic loci.

Biol Open 2013 Apr 12;2(4):363-7. Epub 2013 Feb 12.

Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center , RIKEN, Furuedai 6-2-3, Suita, Osaka 565-0874 , Japan.

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http://dx.doi.org/10.1242/bio.20133871DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625863PMC
April 2013

Validation of bacterial replication termination models using simulation of genomic mutations.

PLoS One 2012 3;7(4):e34526. Epub 2012 Apr 3.

Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034526PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317982PMC
August 2012

Measures of compositional strand bias related to replication machinery and its applications.

Curr Genomics 2012 Mar;13(1):4-15

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://www.eurekaselect.com/openurl/content.php?genre=articl
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http://dx.doi.org/10.2174/138920212799034749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269016PMC
March 2012

Metabolic flux analysis and visualization.

J Proteome Res 2011 Aug;10(8):3313-23

Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.

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http://dx.doi.org/10.1021/pr2002885DOI Listing
August 2011

KBWS: an EMBOSS associated package for accessing bioinformatics web services.

Source Code Biol Med 2011 Apr 29;6. Epub 2011 Apr 29.

1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan.

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http://dx.doi.org/10.1186/1751-0473-6-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101651PMC
April 2011

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes.

BMC Genomics 2011 Jan 11;12:19. Epub 2011 Jan 11.

Systems Biology Program, Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa 252-8520, Japan.

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http://dx.doi.org/10.1186/1471-2164-12-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025954PMC
January 2011

G-language genome analysis environment with REST and SOAP web service interfaces.

Nucleic Acids Res 2010 Jul 3;38(Web Server issue):W700-5. Epub 2010 May 3.

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://dx.doi.org/10.1093/nar/gkq315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896103PMC
July 2010

A web server for interactive and zoomable Chaos Game Representation images.

Source Code Biol Med 2009 Sep 17;4. Epub 2009 Sep 17.

Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan.

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http://dx.doi.org/10.1186/1751-0473-4-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753581PMC
September 2009

Genome Projector: zoomable genome map with multiple views.

BMC Bioinformatics 2009 Jan 23;10:31. Epub 2009 Jan 23.

Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan.

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http://dx.doi.org/10.1186/1471-2105-10-31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2636772PMC
January 2009

Comparative study of circadian oscillatory network models of Drosophila.

Artif Life 2008 ;14(1):29-48

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://dx.doi.org/10.1162/artl.2008.14.1.29DOI Listing
October 2008

Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes.

Evol Bioinform Online 2007 Oct 9;3:279-86. Epub 2007 Oct 9.

Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684129PMC
October 2007

The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.

Evol Bioinform Online 2007 Sep 6;3:159-68. Epub 2007 Sep 6.

Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684130PMC
September 2007

MEGU: pathway mapping web-service based on KEGG and SVG.

In Silico Biol 2006 ;6(6):621-5

Institute for Advanced Biosciences, Keio University, Fujisawa, Japan.

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June 2007

Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli.

Gene 2007 May 12;392(1-2):239-46. Epub 2007 Jan 12.

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://dx.doi.org/10.1016/j.gene.2006.12.022DOI Listing
May 2007

In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.

RNA 2007 May 16;13(5):671-81. Epub 2007 Mar 16.

Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.

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http://dx.doi.org/10.1261/rna.309507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852824PMC
May 2007

Restauro-G: a rapid genome re-annotation system for comparative genomics.

Genomics Proteomics Bioinformatics 2007 Feb;5(1):53-8

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://dx.doi.org/10.1016/S1672-0229(07)60014-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054091PMC
February 2007

Noise-reduction filtering for accurate detection of replication termini in bacterial genomes.

FEBS Lett 2007 Jan 18;581(2):253-8. Epub 2006 Dec 18.

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://doi.wiley.com/10.1016/j.febslet.2006.12.021
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http://dx.doi.org/10.1016/j.febslet.2006.12.021DOI Listing
January 2007

On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli.

FEBS Lett 2006 Dec 30;580(30):6909-14. Epub 2006 Nov 30.

Institute for Advanced Biosciences, Keio University, 5322 Endo, Fujisawa 252-8520, Kanagawa, Japan.

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http://dx.doi.org/10.1016/j.febslet.2006.11.053DOI Listing
December 2006

GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness.

In Silico Biol 2006 ;6(1-2):49-60

Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520 Kanagawa, Japan.

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November 2006

KEGG-based pathway visualization tool for complex omics data.

In Silico Biol 2005 ;5(4):419-23

Institute for Advanced Biosciences, Keio University, Endo 5322, Fujisawa, Kanagawa 252-8520, Japan.

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March 2006

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes.

BMC Bioinformatics 2006 Mar 23;7:168. Epub 2006 Mar 23.

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://dx.doi.org/10.1186/1471-2105-7-168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435936PMC
March 2006

A comprehensive software suite for the analysis of cDNAs.

Genomics Proteomics Bioinformatics 2005 Aug;3(3):179-88

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172547PMC
http://dx.doi.org/10.1016/s1672-0229(05)03023-8DOI Listing
August 2005