Centers & Labs

RIKEN Center for Integrative Medical Sciences

Laboratory for Integrated Bioinformatics

Team Leader: Todd Duane Taylor (Ph.D.)
Todd Duane Taylor(Ph.D.)

We develop computational tools and databases for the analysis of various large-scale datasets. Our goal is to create easy-to-use tools capable of efficiently processing, analyzing and visualizing data from a variety of sources, with an emphasis on metagenomics. We also provide some centralized bioinformatics support for other research laboratories in the center, and together we are developing an integrated database and sample-tracking system for the storage, distribution, and analysis of various types of experimental data.

Main Research Field

Complex systems

Related Research Fields

Informatics / Environmental science / Biological Sciences / Biology

Keywords

  • Informatics
  • Genomics
  • Data Analysis
  • Data Visualization
  • Databases

Selected Publications

  1. Jinda, W., Taylor, T.D., Suzuki, Y., Thongnoppakhun, W., Limwongse, C., Lertrit, P., Trinavarat, A., and Atchaneeyasakul, L.O.:
    "Whole exome sequencing in eight Thai patients with Leber Congenital Amaurosis reveals mutations in the CTNNA1 and CYP4V2 genes"
    Investigative Ophthalmology & Visual Science 58, 2413-2420. (2017).
  2. Trubitsyn, D., Abreu, F., Ward, F.B., Taylor, T., Hattori, M., Kondo, S., Trivedi, U., Staniland, S., Lins, U., and Bazylinski, D.A.:
    "Draft genome sequence of Magnetovibrio blakemorei strain MV-1, a marine vibrioid magnetotactic bacterium"
    Genome Announcements 4, e01330-16. (2016).
  3. Zafra, G., Taylor, T.D., Absalón, A.E., and Cortés-Espinosa, D.V.:
    "Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium"
    Journal of Hazardous Materials 318, 702-710. (2016).
  4. Lau, N.-S., Makita, Y., Kawashima, M., Taylor, T.D., Kondo, S., Othman, A.S., Shu-Chien, A.C., and Matsui, M.:
    "The rubber tree genome shows expansion of gene family associated with rubber biosynthesis"
    Scientific Reports 6, 28594. (2016).
  5. Hebrard, M., and Taylor, T.D.:
    "MetaTreeMap: Visual representation for taxonomic assignment"
    PLoS One 11, e0158261. (2016).
  6. Jinda, W., Poungvarin, N., Taylor, T.D., Suzuki, Y., Thongnoppakhun, W., Limwongse, C., Lertrit, P., Suriyaphol, P., and Atchaneeyasakul, L.:
    "A novel start codon mutation of the MERTK gene in a patient with retinitis pigmentosa"
    Molecular Vision 22, 342-351. (2016).
  7. Nishijima, S., Suda, W., Oshima, K., Kim, S.W., Hirose, Y., Morita, H., and Hattori, M.:
    "The gut microbiome of healthy Japanese and its microbial and functional uniqueness"
    DNA Research 23, 125-133. (2016).
  8. Fujimura, R., Kim, S.W., Sato, Y., Oshima, K., Hattori, M., Kamijo, T., and Ohta, H.:
    "Unique pioneer microbial communities exposed to volcanic sulfur dioxide"
    Scientific Reports 6, 1-9. (2016).
  9. Dinesh, B., Lau, N.-S., Furusawa, G., Kim, S.W., Taylor, T.D., Foong, S., and Chong, A.:
    "Comparative genome analyses of novel Mangrovimonas-like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes"
    Marine Genomics 25, 115-121. (2016).
  10. Nanthini, J., Chia, K.-H., Thottathil, G.P., Taylor, T.D., Kondo, S., Najimudin, N., Baybayan, P., Singh, S., and Sudesh, K.:
    "Complete genome sequence of Streptomyces sp. strain CFMR 7, a natural rubber degrading actinomycete isolated from Penang, Malaysia"
    Journal of Biotechnology 214, 47-48. (2015).

Lab Members

Principal Investigator

Todd Duane Taylor
Team Leader

Core Members

Naveen Kumar
Senior Technical Scientist
Seok Won Kim
Postdoctoral Researcher
Maxime Hebrard
Postdoctoral Researcher

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan
Tel: +81-(0)45-503-7034
Fax: +81-(0)45-503-9694

Email: taylor [at] riken.jp

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