Laboratory for Integrated Bioinformatics

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.

Research Fields

Molecular Biology & Genetics / Environment & Ecology

Research Subjects

• Metagenomics
• Bioinformatics
• Data integration

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).