Laboratory for Integrated Bioinformatics

RIKEN Center for Integrative Medical Sciences

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. Learn more »

Recent Highlights
  • "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 iCLiKVAL annotations." Todd Taylor. Ninth International Biocuration Conference. Campus Biotech Geneva, Geneva, Switzerland. April 12, 2016. (Poster)
  • "Increasing discoverability and connectivity of scientific media through annotation with iCLiKVAL." Todd Taylor. Advances in Genome Biology and Technology. JW Marriott, Grande Lakes, Orlando, Florida, USA. February 11-12, 2016. (Software demonstration)
  • "Unique pioneer microbial communities exposed to volcanic sulfur dioxide." Fujimura R, Kim SW, Sato Y, Oshima K, Hattori M, Kamijo T, Ohta H. Scientific Reports 6(19687):. (January 21, 2016) PMID 26791101
  • "Comparative genome analyses of novel Mangrovimonas-like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes." Dinesh B, Lau NS, Furusawa G, Kim SW, Taylor TD, Foong S, Chong A. Marine Genomics 25():115-121. (January 11, 2016) PMID 26795059
  • "Increasing discoverability and connectivity of scientific media through annotation with iCLiKVAL." Todd Taylor. Plant and Animal Genome XXIV Conference. Town and Country Hotel, San Diego, CA, USA. January 9-13, 2016. (Demonstration & Poster)
  • "Increasing discoverability and connectivity of scientific media through crowdsourced annotation with iCLiKVAL." Todd Taylor. Open Data Science Conference (West). San Francisco Airport Marriott Waterfront, Burlingame, CA, USA. November 14, 2015. (Talk)
  • "Scientific Literature Curation Workshop - iCLiKVAL: Bioinformatics resource to increase scientific literature and media discovery through crowdsourcing." 29th Annual Conference of the International Mammalian Genome Society. Yokohama Port Opening Memorial Hall, Yokohama, Japan. November 9, 2015. (Workshop)
  • "iCLiKVAL: an open-access tool for adding value to scientific literature one annotation at a time through the power of crowdsourcing." Todd Taylor. 65th Annual Meeting of the American Society of Human Genetics. Baltimore Convention Center, Baltimore, Maryland, USA. October 10, 2015. (Talk)
  • "Complete genome sequence of Streptomyces sp. strain CFMR 7, a natural rubber degrading actinomycete isolated from Penang, Malaysia." Nanthini J, Chia K-H, Thottathil GP, Taylor TD, Kondo S, Najimudin N, Baybayan P, Singh S, Sudesh K. J Biotechnol 214():47-48. (September 12, 2015) PMID 26376470
  • "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." Miyake S, Kim S, Suda W, Oshima K, Nakamura M, Matsuoka T, Chihara N, Tomita A, Sato W, Kim SW, Morita H, Hattori M, Yamamura T. PLoS One 10(9):e0137429. (September 14, 2015) PMID 26367776

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