TAKEUCHI Fumihiko: publications

• publications on life science
  • Association study of common diseases and quantitative traits
  • Association study for warfarin pharmacogenomics
  • Other human genetics papers
  • Infectious disease transmission on human contact networks
  • Genomics of Staphylococci
  • Mutations of Staphylococcus aureus
  • Other Staphylococcus aureus papers
  • Nucleotide sequences and evolution
• publications on triangulations
  • Enumeration of triangulations
  • Minimum weight triangulation
  • Polytopes of triangulations
  • Triangulations and dissections
  • Geometric shellings of 3-polytopes
  • Extendable shellability, vertex decomposability
  • View graphs of triangulations
  • Combinatorics of triangulations
  • Pseudo-triangulations
• softwares on life science
• softwares on triangulations
• patents
• grants
• awards
• miscellaneous

publications on life science (PubMed) (PubMed)

• Association study of common diseases and quantitative traits
  • Takeuchi, F. et al. (2003)
    Empirical evaluation of large-scale SNP and microsatellite analyses for exploring disease susceptibility genes by candidate chromosomal region approaches,
    in Proc. 48th annual meeting of the Japan society of human genetics, Nagasaki, 116. (HTML 3KB, in Japanese)
  • Takeuchi, F. et al. (2003)
    Empirical evaluation of large-scale SNP and haplotype analyses for exploring disease susceptibility mutations by candidate gene approaches,
    in Proc. 48th annual meeting of the Japan society of human genetics, Nagasaki, 116. (HTML 3KB, in Japanese)
  • Takeuchi, F. et al. (2005)
    Linkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs,
    Genetics 170, 291--304. (PubMed)
  • Takeuchi, F. et al. (2007)
    Search of type 2 diabetes susceptibility gene on chromosome 20q,
    Biochem Biophys Res Commun. 357, 1100--1106. (PubMed)
  • Takeuchi, F., McGinnis, R. (2007)
    Quantifying disease genotype enrichment under multiple causative loci,
    in Proc. 16th annual meeting of the International Genetic Epidemiology Society, York, Genetic Epidemiology, 31, 646. (TEXT 4KB)
  • Takeuchi, F. et al. (2008)
    HapMap coverage for SNPs in the Japanese population,
    J Hum Genet. 53, 96--99. (PubMed)
  • Kato, N. et al. (2008)
    High-density association study and nomination of susceptibility genes for hypertension in the Japanese national project,
    Hum Mol Genet. 17, 617--627. (PubMed)
  • Takeuchi, F. et al. (2008)
    Search of type 2 diabetes susceptibility genes on chromosomes 1q, 3q and 12q,
    J. Hum. Genet. 53, 314. (PubMed)
  • Hunt, KA. et al. (2008)
    Newly identified genetic risk variants for celiac disease related to the immune response,
    Nat. Genet. 40, 395. (PubMed)
  • Takeuchi, F., McGinnis, R. (2008)
    Mathematical characterization of complex disease: Analytic expressions for the multi-locus additive model,
    in Proc. 58th annual meeting of the Americal Society of Human Genetics, Philadelphia. (HTML)
  • Takeuchi, F. et al. (2009)
    Genome-wide association study of type 2 diabetes in the Japanese using 550K array and the verification of genetic effects,
    in Proc. 52nd annual meeting of the Japan Diabetes Society, Osaka, Journal of the Japanese Diabetes Society 52, Supplement 1, S-286. (in Japanese, HTML)
  • Takeuchi, F. et al. (2009)
    Confirmation of multiple risk loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population,
    Diabetes 58, 1690--1699. (PubMed) (Tables in Excel format)
  • Takeuchi, F. et al. (2009)
    Evaluation of genetic loci influencing adult height in the Japanese,
    in Proc. 54th annual meeting of the Japan Society of Human Genetics, Tokyo, 216. (in Japanese, PDF)
  • Takeuchi, F. et al. (2009)
    Ethnic diversity in fine mapping of the susceptibility loci G6PC2-ABCB11 for fasting glucose and CDKAL1 for type 2 diabetes,
    in Proc. 59th annual meeting of the American Society of Human Genetics, Honolulu, 1976. (HTML)
  • Takeuchi, F. et al. (2009)
    Confirmation of eight loci associated with measures of obesity in two Asian populations with substantial ethnic heterogeneity,
    in Proc. 27th annual scientific meeting of the Obesity Society, Washington DC; Obesity 17, Supplement 2, S81.
  • Takeuchi, F. et al. (2011)
    Association of genetic variants for susceptibility to obesity with type 2 diabetes in the Japanese,
    Diabetologia, 54, 1350--1359.
  • Takeuchi, F. et al. (2009)
    Evaluation of genetic loci influencing adult height in the Japanese,
    J. Hum. Genet., 54, 749--752. (PubMed)
  • Takeuchi, F. et al. (2009)
    Common variants at the GCK, GCKR, G6PC2-ABCB11, and MTNR1B loci are associated with fasting glucose in two Asian populations,
    Diabetologia, 53, 299--308. (PubMed)
  • Takeuchi, F. et al. (2010)
    Blood pressure and hypertension are associated with seven loci in the Japanese population,
    Circulation, 121, 2302--2309. (PubMed)
  • Takeuchi, F. et al. (2010)
    Blood pressure and hypertension are associated with seven loci in the Japanese population,
    in Proc. 33rd annual scientific meeting of the Japanese Society of Hypertension, Fukuoka, 247 and 319.
  • International HapMap 3 Consortium (2010)
    Integrating common and rare genetic variation in diverse human populations,
    Nature, 467, 52--58. (PubMed)
  • Takeuchi, F., Kato, N. (2010)
    Testing heterogeneity of quantitative trait variance among genotype classes guides fine mapping of association signals (in Japanese),
    in Proc. 55th annual meeting of the Japan Society of Human Genetics, Ohmiya, 205.
  • Takeuchi, F., Kato, N. (2010)
    Testing heterogeneity of quantitative trait variance among genotype classes guides fine mapping of association signals,
    in Proc. 60th annual meeting of the American Society of Human Genetics, Washington DC, Program Number 2829. (ASHG)
  • Takeuchi, F. et al. (2011)
    Detection of common single nucleotide polymorphisms synthesizing quantitative trait association of rarer causal variants,
    Genome Res, published online.
  • Kato, N, Takeuchi, F. et al. (2011)
    Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians,
    Nature Genet, published online.
  • Takeuchi, F. et al. (2010)
    Confirmation of ALDH2 as a major locus of drinking behavior and of its variants regulating multiple metabolic phenotypes in Japanese,
    Circulation J, 75, 911--918.
  • Kooner, JS. et al. (2011)
    Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci,
    Nature Genet, published online.
  • Takeuchi, F. et al. (2011)
    Genome-wide association study of coronary artery disease in the Japanese,
    European Journal of Human Genetics, accepted.
  • Takeuchi, F. (2011)
    Fine-mapping of 13q14 locus associated with susceptibility to leprosy and Crohn's disease,
    in Proc. 61th annual meeting of the American Society of Human Genetics, Montreal, Program Number 467T. (ASHG)
• Association study for warfarin pharmacogenomics
  • McGinnis, R. et al. (2008)
    Genome-wide association scan for genetic determinants of warfarin dose,
    in Proc. 58th annual meeting of the Americal Society of Human Genetics, Philadelphia. (HTML)
  • Press release: GenomeWeb Daily News, November 14, 2008.
  • Takeuchi, F. et al. (2009)
    A genome-wide association study confirms VKORC1, CYP2C9 and CYP4F2 as principal genetic determinants of warfarin dose,
    PLoS Genet. 5, e1000433 (supplementary program)
  • Takeuchi, F. et al. (2010)
    Evaluation of pharmacogenetic algorithm for warfarin dose requirements in Japanese patients,
    Circulation J, 74, 977--982. (PubMed)
• Other human genetics papers
  • Tsuchihashi-Makaya et al. (2009)
    Gene-environmental interaction regarding alcohol metabolizing enzymes in the Japanese general population,
    Hypertension Res. 32, 207--213. (PubMed)
• Infectious disease transmission on human contact networks
  • Takeuchi, F., Yamamoto, K. (2005)
    Effectiveness of vaccination strategies for infectious diseases according to human contact networks,
    in Proc. 54th Japan National Congress for Theoretical and Applied Mechanics, Tokyo, 131--132. (PDF 195KB)
  • Takeuchi, F., Yamamoto, K. (2005)
    Effectiveness of vaccination strategies for infectious diseases according to human contact networks,
    in Proc. 5th International Conference on Computational Science (ICCS 2005), Atlanta, Lecture Notes in Computer Science 3514, Springer-Verlag, 2005, 956--962. (Abstract) (PDF 318KB)
  • Press release: Nikkei Science, June 2005, 74.
  • Takeuchi, F. (2005)
    Effectiveness of vaccination strategies for infectious diseases according to human contact networks (review),
    in Proc. 16th Annual Conference of the Japanese Society for Bio-Defense Research, Tokyo, 52. (HTML 5KB)
  • Press release: Medical Tribune, 38(36), September 8, 2005, 24.
  • Takeuchi, F. (2005)
    Effectiveness of vaccination strategies for infectious diseases according to human contact networks (review),
    Jpn. J. Infect. Dis. 58, S16--S17. (PubMed) (PDF 46KB)
  • Takeuchi, F., Yamamoto, K. (2006)
    Effectiveness of realistic vaccination strategies for contact networks of various degree distributions,
    J. Theor. Biol. 243, 39--47. (PubMed) (Mathematica program for simulation)
• Genomics of Staphylococci
  • Baba T. et al. (2002)
    Genome and virulence determinants of high virulence community-acquired MRSA,
    Lancet 359, 1819--1827. (PubMed)
  • Takeuchi, F., Yamamoto, K. (2002)
    Comparative genomics of MRSA strains,
    in Proc. 10th international symposium on staphylococci and staphylococcal infections, Tsukuba, 135. (PDF 3KB)
  • Katayama Y. et al. (2003)
    Identification in Methicillin-Susceptible Staphylococcus hominis of an Active Primordial Mobile Genetic Element for the Staphylococcal Cassette Chromosome mec of Methicillin-Resistant Staphylococcus aureus,
    J. Bacteriol. 185, 2711--2722. (PubMed) (Abstract)
  • Takeuchi, F., Hiramatsu, K. (2003)
    Comparative genomics among Staphylococcus species and strains for the identification of genomic islands (Gislands) involved in pathogenesis and drug resistance,
    in Proc. 3rd Awaji international forum on infection and immunity, Awaji Island, P-095. (HTML 2KB)
  • Baba, T. et al. (2004)
    The Staphylococcus aureus genome,
    in Ala'aldeen, Dlawer and Hiramatsu, Keiichi editors, Staphylococcus aureus: Molecular and Clinical Aspects, Horwood Publishing Limited, Chichester, ISBN: 1-898563-96-9.
  • Takeuchi, F. et al. (2004)
    Comparative genomics and evolution of Staphylococcus aureus, epidermidis and haemolyticus,
    Japanese Journal of Bacteriology 59, 124. (HTML 2KB, in Japanese)
  • Takeuchi, F. et al. (2004)
    Comparative genomics and evolution of Staphylococcus aureus, epidermidis and haemolyticus,
    in Proc. Genomes 2004, Hinxton, 81--82. (HTML 3KB)
  • Takeuchi, F. et al. (2005)
    Whole genome sequencing of Staphylococcus haemolyticus uncovers extreme plasticity of its genome and dynamism in the evolution of human-colonizing staphylococcal species,
    in Proc. 5th Awaji international forum on infection and immunity, Awaji Island, P-001, 61. (HTML 2KB)
  • Takeuchi, F. et al. (2005)
    Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species,
    J. Bacteriol. 187, 7292--7308. (PubMed) (Abstract) (erratum) (slides focused on oriC environ, PDF 1.4MB)
  • Takeuchi, F. et al. (2005)
    Chromosomal distribution of homologs extracts horizontally transferred genomic regions in Staphylococcus aureus, epidermidis and haemolyticus,
    in Proc. the Tapestry of life: Lateral transfers of heritable elements, Sackler colloquia, Irvine, 48. (HTML 3KB)
  • Takeuchi, F. et al. (2006)
    Speciation of Staphylococci and the oriC environ,
    in Proc. 12th international symposium on staphylococci and staphylococcal infections, Maastricht, 127. (HTML 2KB)
  • Takeuchi, F. et al. (2007)
    Comparative analysis of MRSA,
    in Ji, Yindou editor, Methicillin-Resistant Staphylococcus aureus (MRSA) Protocols, Humana Press, Totowa, ISBN: 1-58829-655-5.
  • Baba, T. et al. (2009)
    Complete Genome Sequence of Macrococcus caseolyticus Strain JSCS5402, Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci,
    J. Bacteriol. 191, 1180--1190. (PubMed) (Abstract)
• Mutations of Staphylococcus aureus
  • Kapi, M. et al. (2002)
    Spontaneous mutation accompanying decreased growth rate confers vancomycin resistance in the subpopulation of hetero-VRSA strain Mu3,
    in Proc. 10th international symposium on staphylococci and staphylococcal infections, Tsukuba, 51. (PDF 6KB)
• Other Staphylococcus aureus papers
  • Kuroda, M. et al. (2003)
    Two-component system VraSR positively modulates the regulation of cell-wall biosynthesis pathway in Staphylococcus aureus,
    Mol Microbiol. 49, 807--21. (PubMed)
  • Ito, T. et al. (2004)
    Novel type V staphylococcal cassette chromosome mec driven by a novel cassette chromosome recombinase, ccrC,
    Antimicrob Agents Chemother. 48, 2637--51. (PubMed)
  • Hiramatsu, K. et al. (2004)
    Genetic characterization of methicillin-resistant Staphylococcus aureus,
    Vaccine 2 Suppl 1, S5--8. (PubMed)
  • Watanabe, S. et al. (2005)
    Structural comparison of ten serotypes of Staphylocoagulases in Staphylococcus aureus,
    J. Bacteriol. 187, 3698--3707. (PubMed)
  • Watanabe, S. et al. (2007)
    Precise excision and self-integration of a composite transposon as a model for spontaneous large-scale chromosome inversion/deletion of the Staphylococcus haemolyticus clinical strain JCSC1435,
    J. Bacteriol. 189, 2921--2925. (PubMed)
  • Neoh, HM. et al. (2007)
    Impact of reduced vancomycin susceptibility on the therapeutic outcome of MRSA bloodstream infections,
    Ann of Clin Microbiol Antimicrob. 6, 13 (PubMed)
  • Neoh, HM. et al. (2008)
    Mutated response regulator graR is responsible for phenotypic Conversion of Staphylococcus aureus from heterogeneous Vancomycin-intermediate resistance to Vancomycin-intermediate resistance,
    Antimicrob Agents Chemother. 52, 45--53. (PubMed)
  • Baba, T. et al. (2008)
    Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands,
    J. Bacteriol. 190, 300--310. (PubMed)
  • Han, X. et al. (2009)
    Identification of a novel variant of staphylococcal cassette chromosome mec, type II.5, and its truncated form by insertion of putative conjugative transposon Tn6012,
    Antimicrob Agents Chemother. 53, 2616-2619. (PubMed)
• Nucleotide sequences and evolution
  • Takeuchi, F., Yamamoto, K., Yoshikura, H. (2000)
    Analysis of DNA coding regions,
    in Proc. 1st international conference on systems biology (ICSB 2000), Tokyo, 233-238. (PDF 169KB)
  • Takeuchi, F., Yamamoto, K., Yoshikura, H. (2001)
    How random are nucleotide sequences in coding regions?,
    in Proc. Human genome meeting 2001, Edinburgh, 85. (HTML 6KB)
  • Takeuchi, F., Yamamoto, K. (2001)
    Randomness of nucleotide sequences for gene finding,
    in Proc. Bioinformatics and genome research, San Francisco. (PDF 100KB)
  • Takeuchi, F., Yamamoto, K. (2001)
    Evolution is increasing randomness of nucleotides in coding sequences,
    in Proc. 24th annual meeting of the molecular biology society of Japan, Yokohama, 859. (HTML 2KB)
  • Takeuchi, F., Futamura, Y., Yoshikura, H., Yamamoto, K. (2002)
    Statistics of trinucleotides in coding sequences and evolution,
    in Proc. Human genome meeting 2002, Shanghai, 89. (HTML 3KB)
  • Takeuchi, F., Futamura, Y., Yoshikura, H., Yamamoto, K. (2003)
    Statistics of trinucleotides in coding sequences and evolution,
    J. Theor. Biol. 222, 139--149. (PubMed) (PDF 373KB)
  • Takeuchi, F., Futamura, Y., Yoshikura, H., Yamamoto, K. (2003)
    Trinucleotide statistics classify viruses and bacteriophages of different nucleotide types,
    in Proc. Human genome meeting 2003, Cancun, 86. (HTML 3KB)

• Enumeration of triangulations
  • Fumihiko Takeuchi, Hiroshi Imai & Keiko Imai:
    Enumerating triangulations for arbitrary configurations of points and for products of two simplices,
    Surikaisekikenkyujo Kokyuroku 992, ``Keisanriron to sono ouyou'', 1997, 98--105. (PDF 241KB)
  • Fumihiko Takeuchi & Hiroshi Imai:
    Enumerating triangulations for products of two simplices and for arbitrary configurations of points,
    in Proc. of Computing and combinatorics: third annual international conference (COCOON'97), Lecture Notes in Computer Science 1276, Springer-Verlag, 1997, 470--481. (PDF 238KB)
  • Fumihiko Takeuchi:
    Enumerating triangulations in general dimension,
    master thesis, Univ. of Tokyo, 1998. (PDF 521KB) and related files in Mathematica
  • Hiroshi Imai, Tomonari Masada, Fumihiko Takeuchi & Keiko Imai:
    Enumerating triangulations in general dimension,
    Int. J. of Comput. Geom. and Appl., 12 (2002), 455--480. (PDF 300KB)
• Minimum weight triangulation
  • Yoshiaki Kyoda, Keiko Imai, Fumihiko Takeuchi & Akira Tajima:
    A branch-and-cut approach for minimum weight triangulation,
    in Proc. of Algorithms and computation---8th international symposium (ISAAC '97), Lecture Notes in Computer Science 1350, Springer-Verlag, 1997, 384--393. (PDF 196KB)
• Polytopes of triangulations
  • Fumihiko Takeuchi, Hiroshi Imai & Keiko Imai:
    Polytopes of linear programming relaxation for triangulations,
    Surikaisekikenkyujo Kokyuroku 1068, ``Surisaitekika no riron to ouyou'', 1998, 121--133. (PDF 179KB)
• Triangulations and dissections
  • Jesus A. De Loera, Francisco Santos & Fumihiko Takeuchi:
    Extremal properties for dissections of convex 3-polytopes,
    SIAM J. Discrete Math. 14 (2001), 143--161. (PDF 344KB)
• Geometric shellings of 3-polytopes
  • Takayuki Ishizeki & Fumihiko Takeuchi:
    Geometric shellings of 3-polytopes,
    in Proc. of 11th Canadian conference on computational geometry, Vancouver, 1999, 132--135. (PDF 209KB)
• Extendable shellability, vertex decomposability
  • Sonoko Moriyama & Fumihiko Takeuchi:
    Incremental construction properties in dimension two---shellability, extendable shellability and vertex decomposability,
    in Proc. of 12th Canadian conference on computational geometry, Fredericton, 2000, 65--72. (PDF 176KB)
  • Sonoko Moriyama & Fumihiko Takeuchi:
    Incremental construction properties in dimension two---shellability, extendable shellability and vertex decomposability,
    Disc. Math. 263 (2003), 295--296. (PDF 103KB)
• View graphs of triangulations
  • Fumihiko Takeuchi:
    Nonregular triangulations, view graphs of triangulations, and linear programming duality,
    Surikaisekikenkyujo Kokyuroku 1175, ``Algebraic combinatorics and convex polytopes'', 2000, 77--85. (PDF 167KB)
  • Fumihiko Takeuchi:
    Nonregular triangulations, view graphs of triangulations, and linear programming duality,
    Discrete and computational geometry: Japanese conference; revised papers (JCDCG 2000), Lecture Notes in Computer Science 2098, Springer-Verlag, 2001, 330--338. (PDF 165KB) Appendix (PDF 43KB)
• Combinatorics of triangulations
  • Fumihiko Takeuchi:
    Combinatorics of triangulations,
    Ph.D thesis, Univ. of Tokyo, 2001. (English, PDF 811KB) (With Japanese, PDF 960KB)
• Pseudo-triangulations
  • Lutz Kettner, David Kirkpatrick, Andrea Mantler, Jack Snoeyink, Bettina Speckmann & Fumihiko Takeuchi:
    Tight degree bounds for pseudo-triangulations of points,
    Computational Geometry: Theory and Applications 25 (2003), 3--12.

• ldgroup: linkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs.
  The program written in R is available here. This is still developmental. Any comments or requests are welcome! README.txt ldgroup.R test.phased test.geno test.dat
• A program for testing if an SNP represents a synthetic association. The program written in R is available here. synthetic.R

• Enumeration of all triangulations (in Mathematica)
• Enumeration of regular triangulations by Tomonari Masada

• 2004.07--2006.09
  'Special Coordination Funds for Promoting Science and Technology' from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.
• 2005.04--2006.09
  'Grant-in-Aid for Young Scientists (B)' from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.
• 2010.04--2011.03
  PI: Teruyo Ito, 'Grant-in-Aid for ???' from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan. For the SCCmec database

• The Japanese Society of Hypertension, Young Investigator's Award 2010

• Statistical genetics for hunting disease susceptibility genes: GWAS and next
  Lecture given at the Univ of Tokyo, 1 July 2011 (lecture slides; in Japanese)
• Statistical genetics for post-GWAS: meta-analysis and fine mapping
  Lecture given at RIKEN, 16 Sept 2011 (lecture slides; in Japanese)