Shujiro Okuda

Shujiro Okuda

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Open Agile text mining for bioinformatics: the PubAnnotation ecosystem.

Bioinformatics 2019 Nov;35(21):4372-4380

Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821251PMC
November 2019

The Human Gut Microbiome is Structured to Optimize Molecular Interaction Networks.

Comput Struct Biotechnol J 2019 29;17:1040-1046. Epub 2019 Jul 29.

Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan.

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http://dx.doi.org/10.1016/j.csbj.2019.07.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700418PMC
July 2019

SMAD4 alteration associates with invasive-front pathological markers and poor prognosis in colorectal cancer.

Histopathology 2019 May 1;74(6):873-882. Epub 2019 Apr 1.

Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://doi.wiley.com/10.1111/his.13805
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http://dx.doi.org/10.1111/his.13805DOI Listing
May 2019

Evolutionary analysis of proline-directed phosphorylation sites in the mammalian growth cone identified using phosphoproteomics.

Mol Brain 2019 May 31;12(1):53. Epub 2019 May 31.

Laboratory of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1186/s13041-019-0476-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545026PMC
May 2019

Knowledge base toward understanding actionable alterations and realizing precision oncology.

Int J Clin Oncol 2019 Feb 12;24(2):123-130. Epub 2018 Dec 12.

Division of Cancer Genome Informatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.

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http://dx.doi.org/10.1007/s10147-018-1378-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373253PMC
February 2019

Next generation sequencing-based gene panel tests for the management of solid tumors.

Cancer Sci 2019 Jan 27;110(1):6-15. Epub 2018 Nov 27.

Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.

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http://doi.wiley.com/10.1111/cas.13837
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http://dx.doi.org/10.1111/cas.13837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317963PMC
January 2019

Identification of TRA-1-60-positive cells as a potent refractory population in follicular lymphomas.

Cancer Sci 2019 Jan 8;110(1):443-457. Epub 2018 Dec 8.

Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1111/cas.13870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317956PMC
January 2019

Novel gene fusions found in cervical cancer.

EBioMedicine 2018 12 13;38:13-14. Epub 2018 Nov 13.

Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S23523964183050
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http://dx.doi.org/10.1016/j.ebiom.2018.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6306337PMC
December 2018

Clinical Significance of BRAF Non-V600E Mutations in Colorectal Cancer: A Retrospective Study of Two Institutions.

J Surg Res 2018 12 3;232:72-81. Epub 2018 Jul 3.

Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata City, Niigata, Japan.

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http://dx.doi.org/10.1016/j.jss.2018.06.020DOI Listing
December 2018

Novel MXD4-NUTM1 fusion transcript identified in primary ovarian undifferentiated small round cell sarcoma.

Genes Chromosomes Cancer 2018 11;57(11):557-563

Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1002/gcc.22668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6221051PMC
November 2018

Common driver mutations and smoking history affect tumor mutation burden in lung adenocarcinoma.

J Surg Res 2018 10 30;230:181-185. Epub 2018 Jul 30.

Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1016/j.jss.2018.07.007DOI Listing
October 2018

Analysis of polyamine biosynthetic- and transport ability of human indigenous Bifidobacterium.

Biosci Biotechnol Biochem 2018 Sep 30;82(9):1606-1614. Epub 2018 May 30.

a Faculty of Bioresources and Environmental Sciences , Ishikawa Prefectural University , Nonoichi , Ishikawa , Japan.

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http://dx.doi.org/10.1080/09168451.2018.1475211DOI Listing
September 2018

Growth Cone Phosphoproteomics Reveals that GAP-43 Phosphorylated by JNK Is a Marker of Axon Growth and Regeneration.

iScience 2018 Jun 31;4:190-203. Epub 2018 May 31.

Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan; Center for Trans-disciplinary Research, Institute for Research Promotion, Niigata University, Chuo-ku, Niigata 951-8510, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2018.05.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6147025PMC
June 2018

AldB controls persister formation in Escherichia coli depending on environmental stress.

Microbiol Immunol 2018 May 24;62(5):299-309. Epub 2018 Apr 24.

Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1111/1348-0421.12587DOI Listing
May 2018

Unique transcriptional profile of native persisters in Escherichia coli.

J Biosci Bioeng 2018 Jan 15;125(1):15-22. Epub 2017 Aug 15.

Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jbiosc.2017.07.015DOI Listing
January 2018

Comprehensive analysis of polyamine transport and biosynthesis in the dominant human gut bacteria: Potential presence of novel polyamine metabolism and transport genes.

Int J Biochem Cell Biol 2017 12 2;93:52-61. Epub 2017 Nov 2.

Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.biocel.2017.10.015DOI Listing
December 2017

Rare PDCD11 variations are not associated with risk of schizophrenia in Japan.

Psychiatry Clin Neurosci 2017 Nov 31;71(11):780-788. Epub 2017 Jul 31.

Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1111/pcn.12549DOI Listing
November 2017

Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex.

Front Neurosci 2017 31;11:307. Epub 2017 May 31.

Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan.

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http://dx.doi.org/10.3389/fnins.2017.00307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5450002PMC
May 2017

Poly(ADP-ribose) polymerase inhibitors activate the p53 signaling pathway in neural stem/progenitor cells.

BMC Neurosci 2017 01 17;18(1):14. Epub 2017 Jan 17.

Laboratory of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan.

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http://dx.doi.org/10.1186/s12868-016-0333-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240207PMC
January 2017

Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome.

Gigascience 2015 6;4:21. Epub 2015 May 6.

Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510 Japan.

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http://dx.doi.org/10.1186/s13742-015-0057-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422407PMC
December 2016

[New Classification for Advanced Colorectal Cancer Using CancerPlex®Genomic Tests].

Gan To Kagaku Ryoho 2016 Nov;43(11):1361-1365

1Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences.

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November 2016

Rare UNC13B variations and risk of schizophrenia: Whole-exome sequencing in a multiplex family and follow-up resequencing and a case-control study.

Am J Med Genet B Neuropsychiatr Genet 2016 09 14;171(6):797-805. Epub 2016 Mar 14.

Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1002/ajmg.b.32444DOI Listing
September 2016

RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi.

PLoS One 2015 11;10(11):e0142731. Epub 2015 Nov 11.

National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142731PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641656PMC
June 2016

Species-function relationships shape ecological properties of the human gut microbiome.

Nat Microbiol 2016 06 13;1(8):16088. Epub 2016 Jun 13.

Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.

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http://dx.doi.org/10.1038/nmicrobiol.2016.88DOI Listing
June 2016

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

J Chem Inf Model 2016 Mar 17;56(3):510-6. Epub 2016 Feb 17.

Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1021/acs.jcim.5b00216DOI Listing
March 2016

Enhanced translocation and growth of Rhodococcus erythropolis PR4 in the alkane phase of aqueous-alkane two phase cultures were mediated by GroEL2 overexpression.

Microbes Environ 2014 11;29(4):346-52. Epub 2014 Oct 11.

Laboratory of Molecular Microbiology, Department of Applied Biological Science, College of Bioresource Sciences, Nihon University.

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http://dx.doi.org/10.1264/jsme2.ME13158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262357PMC
December 2015

Novel kinase fusion transcripts found in endometrial cancer.

Sci Rep 2015 Dec 22;5:18657. Epub 2015 Dec 22.

Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1038/srep18657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687039PMC
December 2015

Cytotoxic Glycosylated Fatty Acid Amides from a Stelletta sp. Marine Sponge.

J Nat Prod 2015 Nov 11;78(11):2808-13. Epub 2015 Nov 11.

Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

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http://dx.doi.org/10.1021/acs.jnatprod.5b00795DOI Listing
November 2015

Human T-cell leukemia virus type 1 Tax oncoprotein represses the expression of the BCL11B tumor suppressor in T-cells.

Cancer Sci 2015 Apr 16;106(4):461-5. Epub 2015 Mar 16.

Division of Virology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; Division of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1111/cas.12618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409891PMC
April 2015

GlycoRDF: an ontology to standardize glycomics data in RDF.

Bioinformatics 2015 Mar 11;31(6):919-25. Epub 2014 Nov 11.

Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btu732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380026PMC
March 2015

Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis.

BMC Genomics 2014 Jul 1;15:546. Epub 2014 Jul 1.

Department of Pathology I, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa 920-0293, Japan.

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http://dx.doi.org/10.1186/1471-2164-15-546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117960PMC
July 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

Introducing glycomics data into the Semantic Web.

J Biomed Semantics 2013 Nov 26;4(1):39. Epub 2013 Nov 26.

Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba Central-2, Umezono 1-1-1, Tsukuba 305-8568, Japan.

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http://dx.doi.org/10.1186/2041-1480-4-39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177142PMC
November 2013

Virtual metagenome reconstruction from 16S rRNA gene sequences.

Nat Commun 2012 ;3:1203

Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan.

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http://dx.doi.org/10.1038/ncomms2203DOI Listing
March 2013

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters.

Nucleic Acids Res 2013 Jan 27;41(Database issue):D353-7. Epub 2012 Nov 27.

Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8585, Japan.

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http://dx.doi.org/10.1093/nar/gks1239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531156PMC
January 2013

In silico study on the substrate binding manner in human myo-inositol monophosphatase 2.

J Mol Model 2011 Oct 7;17(10):2559-67. Epub 2011 Jan 7.

Department of Bioinformatics, College of Information Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.

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http://dx.doi.org/10.1007/s00894-010-0937-8DOI Listing
October 2011

iPath2.0: interactive pathway explorer.

Nucleic Acids Res 2011 Jul 5;39(Web Server issue):W412-5. Epub 2011 May 5.

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkr313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125749PMC
July 2011

ODB: a database for operon organizations, 2011 update.

Nucleic Acids Res 2011 Jan 4;39(Database issue):D552-5. Epub 2010 Nov 4.

College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkq1090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013687PMC
January 2011

Direct observation and analysis of bacterial growth on an antimicrobial surface.

Appl Environ Microbiol 2010 Aug 18;76(16):5409-14. Epub 2010 Jun 18.

Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan.

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http://aem.asm.org/cgi/doi/10.1128/AEM.00576-10
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http://dx.doi.org/10.1128/AEM.00576-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918969PMC
August 2010

Network analysis of adverse drug interactions.

Genome Inform 2008 ;20:252-9

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

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July 2009

Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans.

Carbohydr Res 2009 May 9;344(7):881-7. Epub 2009 Mar 9.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1016/j.carres.2009.03.001DOI Listing
May 2009

Extraction and analysis of chemical modification patterns in drug development.

J Chem Inf Model 2009 Apr;49(4):1122-9

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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http://pubs.acs.org/doi/abs/10.1021/ci8003804
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http://dx.doi.org/10.1021/ci8003804DOI Listing
April 2009

KEGG Atlas mapping for global analysis of metabolic pathways.

Nucleic Acids Res 2008 Jul 13;36(Web Server issue):W423-6. Epub 2008 May 13.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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https://nar.oxfordjournals.org/content/36/suppl_2/W423.full-
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkn282
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http://dx.doi.org/10.1093/nar/gkn282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447737PMC
July 2008

The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes.

J Lipid Res 2008 Jan 7;49(1):183-91. Epub 2007 Oct 7.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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http://www.jlr.org/lookup/doi/10.1194/jlr.M700377-JLR200
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http://dx.doi.org/10.1194/jlr.M700377-JLR200DOI Listing
January 2008

KEGG for linking genomes to life and the environment.

Nucleic Acids Res 2008 Jan 12;36(Database issue):D480-4. Epub 2007 Dec 12.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

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http://dx.doi.org/10.1093/nar/gkm882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238879PMC
January 2008

[Integrated drug information resource].

Tanpakushitsu Kakusan Koso 2007 Oct;52(12):1486-91

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October 2007

Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes.

Genome Inform 2006 ;17(1):230-9

Bioinformatics center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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July 2007

KAAS: an automatic genome annotation and pathway reconstruction server.

Nucleic Acids Res 2007 Jul 25;35(Web Server issue):W182-5. Epub 2007 May 25.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1093/nar/gkm321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933193PMC
July 2007

Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli.

BMC Genomics 2007 Feb 13;8:48. Epub 2007 Feb 13.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1186/1471-2164-8-48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1808063PMC
February 2007

Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic.

Traffic 2006 Aug;7(8):1104-18

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1111/j.1600-0854.2006.00451.xDOI Listing
August 2006

Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli.

Genome Inform 2005 ;16(1):116-24

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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January 2006

ODB: a database of operons accumulating known operons across multiple genomes.

Nucleic Acids Res 2006 Jan;34(Database issue):D358-62

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkj037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347400PMC
January 2006

Electrophoretic mobility of Bacillus subtilis knockout mutants with and without flagella.

J Bacteriol 2003 Jul;185(13):3711-7

Faculty of Science and Engineering, Ritsumeikan University, Kusatsu 525-8577, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC161562PMC
http://dx.doi.org/10.1128/jb.185.13.3711-3717.2003DOI Listing
July 2003