Centers & Labs

RIKEN Center for Integrative Medical Sciences

Laboratory for Integrated Bioinformatics

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

The general goal of this laboratory is to provide centralized bioinformatics support for the other research laboratories in this center. We will develop an infrastructure of pipelines and tools for the efficient handling of both small-scale and large-scale data sets and for the analysis of various types of data produced from expression profile analysis, transcription network analysis, biomarker discovery analysis, and so on, with a special emphasis on metagenomic and metatranscriptomic analysis.

Main Research Field

Molecular Biology & Genetics

Related Research Fields

Environment & Ecology

Research Subjects

  • Metagenomics
  • Bioinformatics
  • Data integration

Selected Publications

  1. Hariharan, R., Simon, R., Pillai, M.R., and Taylor T.D.:
    "Comparative analysis of DNA word abundances in four yeast genomes using a novel statistical background model"
    PLoS One 8, e58038. (2013).
  2. Fukuda, S., Toh, H., Taylor, T.D., Ohno, H., and Hattori, M.:
    "Acetate-producing bifidobacteria protect the host from enteropathogenic infection via carbohydrate transporters"
    Gut Microbes 3, 449-454. (2012).
  3. Prakash, T., and Taylor, T.D.:
    "Functional assignment of metagenomic data: challenges and applications"
    Briefings in Bioinformatics 13, 1-17. (2012).
  4. Sharma, V.K., Kumar, N., Prakash, T., and Taylor, T.D.:
    "Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin"
    PLoS ONE 7, e34030. (2012).
  5. Nishida, H., Kondo, S., Matsumoto, T., Suzuki, Y., Yoshikawa, H., Taylor, T.D., and Sugiyama, J.:
    "Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping"
    Open Biology 2, 120043. (2012).
  6. Toh, H., Sharma, V.K., Oshima, K., Kondo, S., Hattori, M., Ward, F.B., Free, A., and Taylor, T.D.:
    "Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp. strain L, both isolated from a microbial fuel cell"
    J Bacteriol 193, 6411-6412. (2011).
  7. Prakash, T., Oshima, K., Morita, H., Fukuda, S., Imaoka, A., Kumar, N., Sharma, V.K., Takahashi, M., Saitou, N., Taylor, T.D., Ohno, H., Umesaki, Y., and Hattori, M.:
    "Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of Th17 cell differentiation"
    Cell Host & Microbe 10, 273-284. (2011).
  8. Avasthi, T.S., Devi, S.H., Taylor, T.D., Kumar, N., Baddam, R., Kondo, S., Suzuki, Y., Lamouliatte, H., Mégraud, F., and Ahmed, N.:
    "Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient"
    J Bacteriol 193, 3385-3386. (2011).
  9. Fukuda, S., Toh, H., Hase, K., Oshima, K., Nakanishi, Y., Yoshimura, K., Tobe, T., Clarke, J.M., Topping, D.L., Suzuki, T., Taylor, T.D., Itoh, K., Kikuchi, J., Morita, H., Hattori, M., and Ohno, H.:
    "Bifidobacteria can protect from enteropathogenic infection through production of acetate"
    Nature 469, 543-547. (2011).
  10. Prakash, T., Sharma, V.K., Adati, N., Ozawa, R., Kumar, N., Nishida, Y., Fujikake, T., Takeda, T., and Taylor, T.D.:
    "Expression of conjoined genes: another mechanism for gene regulation in eukaryotes"
    PLoS ONE 5, 1-9. (2010).

Lab Members

Principal Investigator

Todd Duane Taylor
Team Leader

Core Members

Naveen Kumar
Technical Scientist
SeokWon 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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