Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences


Lab Introduction

Unfortunately, the Laboratory for Integrated Bioinformatics was closed at the end of March, 2018. However, we still maintain most of our databases and tools.

We developed computational tools and databases for the analysis of various large-scale datasets. Our goal was 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 provided some centralized bioinformatics support for other research laboratories in the center.

Follow us on Twitter: #ToddTaylorRIKEN

Team Members

Recent Highlights

  • "A novel and wide substrate specificity polyhydroxyalkanoate (PHA) synthase from unculturable bacteria found in mangrove soil". Foong CP, Lakshmanan M, Abe H, Taylor TD, Foong SY, Sudesh K. Journal of Polymer Research 25(23):DOI:10.1007/s10965-017-1403-4. (December 18, 2017)
  • "An integrative study on biologically recovered polyhydroxyalkanoates (PHAs) and simultaneous assessment of gut microbiome in yellow mealworm." Ong SY, Kho H-P, Riedel SL, Kim S-W, Gan C-Y, Taylor TD, Sudesh K. Journal of Biotechnology 265:31-39. (October 31, 2017) PMID 29101024
  • "Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm." Chin KCJ, Taylor TD, Hebrard M, Anbalagan K, Dashti MG, Phua KK. BMC Genomics 18(1):836-844. (October 31, 2017) PMID 29089020
  • "Lactobacillus fermentum FTDC 8312 combats hypercholesterolemia via alteration of gut microbiota." Lye HS, Kato T, Low W-Y, Taylor TD, Prakash T, Lew LC, Ohno H, Liong MT. Journal of Biotechnology 262:75-83. (September 19, 2017) PMID 28935567
  • "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

Publications

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