Publications

Recent Publications

  • "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
  • "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

Past Publications

  • "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
  • "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
  • "Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater." Foong CP, Lau N-S, Deguchi S, Toyofuku T, Taylor T, Sudesh K, Matsui M. BMC Microbiol 17(1):7 [Epub ahead of print]. (December 24, 2014) PMID 25539583
  • "Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis." International Glossina Genome Initiative. Science 344(6182):380-386. (April 25, 2014) PMID 24763584
  • "Whole exome sequencing in Thai patients with retinitis pigmentosa reveals novel mutations in six genes." Jinda W, Taylor TD, Suzuki Y, Thongnoppakhun W, Limwongse C, Lertrit P, Suriyaphol P, Trinavarat A, Atchaneeyasakul LO. Invest Ophthalmol Vis Sci 55(4):2259-2268. (April 7, 2014) PMID 24618324
  • "Comparative analysis of DNA word abundances in four yeast genomes using a novel statistical background model." Hariharan R, Simon R, Pillai MR, Taylor TD. PLoS One 8(3):e58038. (March 5, 2013) PMID 23472131
  • "Acetate-producing bifidobacteria protect the host from enteropathogenic infection via carbohydrate transporters." Fukuda S, Toh H, Taylor TD, Ohno H, Hattori M. Gut Microbes 3(5):449-454. (September 1, 2012) PMID 22825494
  • "Functional assignment of metagenomic data: challenges and applications." Prakash T, Taylor TD [3]. Briefings in Bioinformatics 13(E6):1-17. (July 6, 2012) PMID 22772835
  • "Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin." Sharma VK, Kumar N, Prakash T, Taylor TD. PLoS ONE 7(3):e34030. (April 4, 2012) PMID 22496776
  • "Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping." Nishida H, Kondo S, Matsumoto T, Suzuki Y, Yoshikawa H, Taylor TD, Sugiyama J. Open Biology 2(4):120043. (April, 2012) PMID 22724063
  • "Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp. strain L, both isolated from a microbial fuel cell." Toh H, Sharma VK, Oshima K, Kondo S, Hattori M, Ward FB, Free A, Taylor TD. J Bacteriol 193(22):6411-6412. (November, 2011) PMID 22038970
  • "Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of Th17 cell differentiation." Prakash T, Oshima K, Morita H, Fukuda S, Imaoka A, Kumar N, Sharma VK, Takahashi M, Saitou N, Taylor TD, Ohno H, Umesaki Y, Hattori M. Cell Host & Microbe 10(3):273-284. (September 15, 2011) PMID 21925114
  • "Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient." Avasthi TS, Devi SH, Taylor TD, Kumar N, Baddam R, Kondo S, Suzuki Y, Lamouliatte H, Mégraud F, Ahmed N. J Bacteriol 193(13):3385-3386. (July, 2011) PMID 21515762
  • "Bifidobacteria can protect from enteropathogenic infection through production of acetate." Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, Tobe T, Clarke JM, Topping DL, Suzuki T, Taylor TD, Itoh K, Kikuchi J, Morita H, Hattori M, Ohno H. Nature 469(7331):543-547. (January 26, 2011) PMID 21270894
  • "Expression of conjoined genes: another mechanism for gene regulation in eukaryotes." Prakash T, Sharma VK, Adati N, Ozawa R, Kumar N, Nishida Y, Fujikake T, Takeda T, Taylor TD. PLoS ONE 5(10):1-9 e13284. (October 12, 2010) PMID 20967262
  • "The genome of Helicobacter pylori strain 908." Devi SH, Taylor TD, Avasthi TS, Kondo S, Suzuki Y, Megraud F, Ahmed N. J Bacteriol 192(24):6488-6489. (October 15, 2010) PMID 20952566
  • "Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2." Toh H, Oshima K, Toyoda A, Ogura Y, Ooka T, Sasamoto H, Park SH, Iyoda S, Kurokawa K, Morita H, Itoh K, Taylor TD, Hayashi T, Hattori M. J Bacteriol 192(4):1165-1166. (December 11, 2009) PMID 20008064
  • "MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets." Sharma VK, Kumar N, Prakash T, Taylor TD. Nucleic Acids Research 38(Database):D468-D472. (November 11, 2009) PMID 19906710
  • "Complete genome sequence of the probiotic Lactobacillus rhamnosus ATCC 53103." Morita H, Toh H (co-first author), Oshima K, Murakami M, Taylor TD, Igimi S, Hattori M. J Bacteriol 191(24):7630-7631. (October 9, 2009) PMID 19820099
  • "The human intestinal microbiome: A new frontier of human biology." Hattori M, Taylor TD. DNA Research 16(1):1-12. (January 15, 2009) PMID 19147530
  • "Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut." Hongoh Y*, Sharma VK*, Prakash T, Noda S, Toh H, Taylor TD, Kudo T, Sakaki Y, Toyoda A, Hattori M, Ohkuma M (* These authors contributed equally to this work). Science 322(5904):1108-1109. (November 14, 2008) PMID 19008447
  • "Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult." Oshima K*, Toh H*, Ogura Y, Sasamoto H, Morita H, Park SH, Ooka T, Iyoda S, Taylor TD, Hayashi T, Itoh K, Hattori M. (*Toh H and Oshima K contributed equally to this work). DNA Research 15(6):375-386. (October 17, 2008) PMID 18931093
  • "Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell." Hongoh Y*, Sharma VK*, Prakash T, Noda S, Taylor TD, Kudo T, Sakaki T, Toyoda A, Hattori M, Ohkuma M (* These authors contributed equally to this work). Proc Natl Acad Sci USA 105(14):5555-5560. (April 8, 2008) PMID 18391199
  • "Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes." Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M. DNA Research 14(4):169-181. (August, 2007) PMID 17916580
  • "A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q: Comparison with chromosome 21q." Yamada Y, Shirakawa T, Taylor TD, Okamura K, Soejima H, Uchiyama M, Iwasaka T, Mukai T, Muramoto K-I, Sakaki Y, Ito T. DNA Seq 17(4):300-306. (August, 2006) PMID 17312950
  • "Human chromosome 11 DNA sequence and analysis including novel gene identification." Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim D-W, She X, Barlow KF, Bloom T, Bruford E, Chang JL, Cuomo CA, Eichler E, FitzGerald MG, Jaffe DB, LaButti K, Nicol R, Park H-S, Seaman C, Sougnez C, Yang X, Zimmer AR, Zody MC, Birren BW, Nusbaum C, Fujiyama A, Hattori M, Rogers R, Lander ES, Sakaki Y. Nature 440(7083):497-500. (March 23, 2006) PMID 16554811
  • "Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway." Kuroki Y, Toyoda A, Noguchi H, Taylor TD, Itoh T, Kim D-S, Kim D-W, Choi S-H, Kim I-C, Choi HH, Kim YS, Satta Y, Saitou N, Yamada T, Morishita S, Hattori M, Sakaki Y, Park H-S, Fujiyama A. Nat Genet 38(2):157-167. (February, 2006) PMID 16388311
  • "Identification of large ancient duplications associated with human gene deserts." Itoh T, Toyoda A, Taylor TD, Sakaki Y, Hattori M. Nat Genet 37(10):1041-1043. (October, 2005) PMID 16186813
  • "DNA sequence and analysis of human chromosome 18." Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Yang X, Abouelleil A, Allen NR, Anderson S, Bloom T, Bugalter B, Butler J, Cook A, DeCaprio D, Engels R, Garber M, Gnirke A, Hafez N, Hall JL, Norman CH, Itoh T, Jaffe DB, Kuroki Y, Lehoczky J, Lui A, Macdonald P, Mauceli E, Mikkelsen TS, Naylor JW, Nicol R, Nguyen C, Noguchi H, O'Leary SB, Piqani B, Smith CL, Talamas JA, Topham K, Totoki Y, Toyoda A, Wain HM, Young SK, Zeng Q, Zimmer AR, Fujiyama A, Hattori M, Birren BW, Sakaki Y, Lander ES. Nature 437(7058):551-555. (September, 2005) PMID 16177791
  • "Finishing the euchromatic sequence of the human genome." International Human Genome Sequencing Consortium. Nature 431(7011):931-945. (October, 2004) PMID 15496913
  • "Integrative annotation of 21,037 human genes validated by full-length cDNA clones." Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S. PLoS Biol 2(6):856-875. (June, 2004) PMID 15103394
  • "DNA sequence and comparative analysis of chimpanzee chromosome 22." Watanabe H, Fujiyama A, Hattori M, Taylor TD, Toyoda A, Kuroki Y, Noguchi H, BenKahla A, Lehrach H, Sudbrak R, Kube M, Taenzer S, Galgoczy P, Platzer M, Scharfe M, Nordsiek G, Blocker H, Hellmann I, Khaitovich P, Paabo S, Reinhardt R, Zheng HJ, Zhang XL, Zhu GF, Wang BF, Fu G, Ren SX, Zhao GP, Chen Z, Lee YS, Cheong JE, Choi SH, Wu KM, Liu TT, Hsiao KJ, Tsai SF, Kim CG, Oota S, Kitano T, Kohara Y, Saitou N, Park HS, Wang SY, Yaspo ML, Sakaki Y. Nature 429(6990):382-388. (May, 2004) PMID 15164055
  • "Human versus chimpanzee chromosome-wide sequence comparison and its evolutionary implication." Chimpanzee Chromosome 22 Sequencing Consortium. Sakaki Y, Watanabe H, Taylor T, Hattori M, Fujiyama A, Toyoda A, Kuroki Y, Itoh T, Saitou N, Oota S, Kim CG, Kitano T, Lehrach H, Yaspo ML, Sudbrak R, Kahla A, Reinhardt R, Kube M, Platzer M, Taenzer S, Galgoczy P, Kel A, Blöecker H, Scharfe M, Nordsiek G, Hellmann I, Khaitovich P, Pääbo S, Chen Z, Wang SY, Ren SX, Zhang XL, Zheng HJ, Zhu GF, Wang BF, Zhao GP, Tsai SF, Wu K, Liu TT, Hsiao KJ, Park HS, Lee YS, Cheong JE, Choi SH. Cold Spring Harb Symp Quant Biol 68:455-460. (September 1, 2003) PMID 15338648
  • "Comparative genomic sequence analysis of the human chromosome 21 down syndrome critical region." Toyoda A, Noguchi H, Taylor TD, Ito T, Pletcher MT, Sakaki Y, Reeves RH, Hattori M. Genome Res 12(9):1323-1332. (September, 2002) PMID 12213769
  • "Identification of two novel primate-specific genes in DSCR." Takamatsu K, Maekawa K, Togashi T, Choi D-K, Suzuki Y, Taylor TD, Toyoda A, Sugano S, Fujiyama A, Hattori M, Sakaki Y, Takeda T. DNA Research 9(3):89-97. (June, 2002) PMID 12168953
  • "Construction and analysis of a human-chimpanzee comparative clone map." Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, Tsai S-F, Park H-S, Yaspo M-L, Lehrach H, Chen Z, Fu G, Saitou N, Osoegawa K, de Jong PJ, Suto Y, Hattori M, Sakaki Y. Science 295(5552):131-134. (January, 2002) PMID 11778049
  • "Molecular cloning and characterization of a gene expressed in mouse developing tongue, mDscr5 gene, a homolog of human DSCR5 (Down syndrome Critical Region gene 5)." Choi DK, Suzuki Y, Yoshimura S, Togashi T, Hida M, Taylor TD, Wang Y, Sugano S, Hattori M, Sakaki Y. Mamm Genome 12(5):347-351. (May, 2001) PMID 11331941
  • "Initial sequencing and analysis of the human genome." International Human Genome Sequencing Consortium. Nature 409(6822):860-921. (February, 2001) PMID 11237011
  • "Architecture and anatomy of the genomic locus encoding the human leukemia-associated transcription factor RUNX1/AML1." Levanon D, Glusman G, Bangsow T, Ben-Asher E, Male DA, Avidan N, Bangsow C, Hattori M, Taylor TD, Taudien S, Blechschmidt K, Shimizu N, Rosenthal A, Sakaki Y, Lancet D, Groner Y. Gene 262(1-2):23-33. (January, 2001) PMID 11179664
  • "[Determination of DNA sequence of the whole chromosome 21]." Sakaki Y, Hattori M, Toyoda A, Watanabe H, Yada T, Taylor TD, Park HS, Totoki Y, Fujiyama A. Tanpakushitsu Kakusan Koso 45(15):2520-2527. (November, 2000) PMID 11086412
  • "A novel gene, DSCR5, from the distal Down syndrome critical region on chromosome 21q22.2." Togashi T, Choi DK, Taylor TD, Suzuki Y, Sugano S, Hattori M, Sakaki Y. DNA Res 7(3):207-212. (June, 2000) PMID 10907851
  • "The DNA sequence of human chromosome 21." Hattori M, Fujiyama A, Taylor TD, Watanabe H, Yada T, Park HS, Toyoda A, Ishii K, Totoki Y, Choi DK, Soeda E, Ohki M, Takagi T, Sakaki Y, Taudien S, Blechschmidt K, Polley A, Menzel U, Delabar J, Kumpf K, Lehmann R, Patterson D, Reichwald K, Rump A, Schillhabel M, Schudy A, Zimmermann W, Rosenthal A, Kudoh J, Shibuya K, Kawasaki K, Asakawa S, Shintani A, Sasaki T, Nagamine K, Mitsuyama S, Antonarakis SE, Minoshima S, Shimizu N, Nordsiek G, Hornischer K, Brant P, Scharfe M, Schon O, Desario A, Reichelt J, Kauer G, Blocker H, Ramser J, Beck A, Klages S, Hennig S, Riesselmann L, Dagand E, Haaf T, Wehrmeyer S, Borzym K, Gardiner K, Nizetic D, Francis F, Lehrach H, Reinhardt R, Yaspo ML. Nature 405(6784):311-319. (May, 2000) PMID 10830953