Script of bioinformatics   Twitter   LinkedIn   Slideshare   GitHub   Goggle+   Qiita

 E-mail: k.t.the-answer[at]hotmail.co.jp    (at -> @)

 Affilation

  Department of Medicinal and Life Science  Faculty of Pharmaceutical Sciences
  Tokyo University of Science
  Miyazaki Laboratory (Bioinformatics)
 Ph.D Student (2nd grade)

 Bioinformatics Research Unit
  Advanced Center for Computing and Communication
  RIKEN
  Junior Research Associate(JRA)

 Background

  Pharmacy, Microbiology, Bioinformatics, Systemsbiology

 Profile

 Publications

 Journal Papers

  1. Koki Tsuyuzaki, Daisuke Tominaga, Kwon Yeondae, Satoru Miyazaki, Two-way AIC: detection of differentially expressed genes from large scale microarray meta-dataset. BMC Genomics, 14(Suppl 2):S9, (2013) Fulltext  PDF
  2. Koki Tsuyuzaki, Gota Morota, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido, MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. BMC Bioinformatics 16;45 (2015) Fulltext  PDF
  3. Gota Morota, Francisco Penagaricano, Jessica L Petersen, Daniel C Ciobanu, Koki Tsuyuzaki, Itoshi Nikaido, An application of MeSH enrichment analysis in livestock. Animal Genetics (Accepted)

 International Conferences

 Oral Presentation
  1. Koki Tsuyuzaki, Daisuke Tominaga, Kwon Yeondae, Satoru Miyazaki, Two-way AIC: Detection of Differentially Expressed Genes from Large Scale Microarray Meta-Dataset. ISCB-ASIA 2012 (2012/12/17-19)

 Domestic Conferences

 Oral Presentation
  1. Haruka Ozaki, Koki Tsuyuzaki, Takao Yokoyama, "Misconversion of Gene Symbol in using Excel", BioHack Competition in JSBi2013, (2013/10/29-31)
    GitHub
  2. Koki Tsuyuzaki, Itoshi Nikaido, Gota Morota, Takeru Nakazato "MeSHR framework", BioHack Competition in JSBi2013, (2013/10/29-31)
    GitHub
  3. Koki Tsuyuzaki, Daisuke Tominaga, Kwon Yeondae, Satoru Miyazaki, Two-way AIC: Detection of Differentially Expressed Genes from Large Scale Microarray Meta-Dataset. 27th SIG-BIO (2011/12/1-2)
 Poster
  1. Koki Tsuyuzaki, Itoshi Nikaido, Satoru Miyazaki, Meta-analysis of multiple RNA-seq Datasets. JSBi2013, Poster No. 7, (2013/10/29-31)
  2. Koki Tsuyuzaki, Akimasa Seno, Tamotsu Sugawara, Tomonori Suzuki, Satoru Miyazaki, Elucidation of dynamics of Quorum Sensing of Pseudomonas aeruginosa. CBI 2010, P9-06, (2010/9/15-17)

 Softwares

 R-packages

  1. metaSeq
    Package to conduct meta-analysis using RNA-seq count datasets (Bioconductor 2.13 - )
    Bioconductor   PDF
  2. MeSH.db
    Package to use general information about MeSH (Bioconductor 2.14 - )
    Bioconductor   PDF
  3. MeSH.AOR.db
    Package to use AOR (Ancestor-Offspring Relationship) of MeSH (Bioconductor 2.14 - )
    Bioconductor   PDF
  4. MeSH.PCR.db
    Package to use PCR (Parent-Child Relationship) of MeSH (Bioconductor 2.14 - )
    Bioconductor   PDF
  5. org.MeSH.XXX.db-type packages (XXX is an abbreviation e.g., Hsa: Homo sapiens)
    Packages to use the correspondense between MeSH ID and NCBI Entrez Gene ID (Bioconductor 2.14 - )
    Bioconductor   PDF
  6. MeSHDbi
    Package to generate user's custom org.MeSH.XXX.db-type package (Bioconductor 2.14 - )
    Bioconductor   PDF
  7. meshr
    Package to conduct enrichment analysis of MeSH (Bioconductor 2.14 - )
    Bioconductor   PDF

 Others

  1. Pubmed_small
    Pipeline for converting .xml to .sqlite of Pubmed (PMC)
    GitHub
  2. Pubmed_large
    Pipeline for converting .xml to .sqlite of Pubmed (NLM licensed)
    GitHub

 Society

 Other Info

 Research Interests

 Cell-cell communication
 Omics analysis
 High performance computing / parallel computing
 Next-generation sequencing
 Non-model organisms
 Single-cell sequencing

 Hobbies

 Motorcycle(SR400 Yamaha), Fishing, Surfing, Cooking, Travel, Smoking(Food), Book

 Contact

  278-8510
 2641, Yamazaki, Noda-shi, Chiba, Japan

 Feel free to contact me

 E-mail: k.t.the-answer[at]hotmail.co.jp    (at -> @)