Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences

Lab Introduction

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.

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Team Members

Recent Highlights

  • "Lactobacillus fermentum FTDC 8312 combats hypercholesterolemia via alteration of gut microbiota DOI 10.1016/j.jbiotec.2017.09.007." Lye HS, Kato T, Low W-Y, Taylor TD, Prakash T, Lew LC, Ohno H, Liong MT. Journal of Biotechnology TBD:TBD. (September 19, 2017)
  • "Whole exome sequencing in eight Thai patients with Leber Congenital Amaurosis reveals mutations in the CTNNA1 and CYP4V2 genes." Jinda W, Taylor TD, Suzuki Y, Thongnoppakhun W, Limwongse C, Lertrit P, Trinavarat A, Atchaneeyasakul LO. Invest Ophthalmol Vis Sci 58(4):2413-2420. (April 1, 2017) PMID 28453600
  • "Draft genome sequence of Magnetovibrio blakemorei strain MV-1, a marine vibrioid magnetotactic bacterium." Trubitsyn D, Abreu F, Ward FB, Taylor T, Hattori M, Kondo S, Trivedi U, Staniland S, Lins U, Bazylinski DA. Genome Announcements 4(6):e01330-16. (November 23, 2016) PMID 27881550
  • "Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium." Zafra G, Taylor TD, Absalón AE, Cortés-Espinosa DV. Journal of Hazardous Materials 318:702-710. (July 26, 2016) PMID 27484946
  • "The rubber tree genome shows expansion of gene family associated with rubber biosynthesis [1]." Lau N-S, Makita Y, Kawashima M, Taylor TD, Kondo S, Othman AS, Shu-Chien AC, Matsui M. Scientific Reports 6:28594. (June 24, 2016) PMID 27339202
  • "MetaTreeMap: an alternative visualization method for displaying metagenomic phylogenic trees [2]." Hebrard M, Taylor TD. PLOS One 11(6):e0158261. (June 23, 2016) PMID 27336370
  • "Improving the connectivity, searchability and discoverability of scientific media through annotations with iCLiKVAL." Todd Taylor. Faculty of Medicine Siriraj Hospital Special Lecture. Mahidol University, Bangkok, Thailand. June 20, 2016. (Invited Talk & Workshop)
  • "A novel start codon mutation of the MERTK gene in a patient with retinitis pigmentosa." Jinda W, Poungvarin N, Taylor TD, Suzuki Y, Thongnoppakhun W, Limwongse C, Lertrit P, Suriyaphol P, Atchaneeyasakul L. Molecular Vision 22:342-351. (April 21, 2016) PMID 27122965
  • "The gut microbiome of healthy Japanese and its microbial and functional uniqueness." Nishijima S, Suda W, Oshima K, Kim SW, Hirose Y, Morita H, Hattori M. DNA Res 23(2):125-33. (April, 2016) PMID 26951067
  • "Improved discoverability and connectivity of all scientific media through iCLiKVALannotations." Todd Taylor. Ninth International Biocuration Conference. Campus Biotech Geneva, Geneva, Switzerland. April 12, 2016. (Poster)


Tools, Resources, Projects

  • MetaTreeMap - an online tool for visualizing taxonomic assignments of metagenomic sequences
  • GRD - a manually-curated 16S rRNA database
  • iCLiKVAL - a crowdsourcing tool for connecting and curating all types of scientific media
  • MetaBin - a program for accurate, fast and highly sensitive taxonomic assignments of metagenomic sequences
  • ConjoinG - a database of human conjoined genes
  • MetaBioME - a database to explore commercially useful enzymes in metagenomic datasets
  • Past Projects

Other Information