Ogura Lab

眼の進化と生物多様性を研究しています。
The eye is one of the most elaborate organs in animals and the study of its evolution is of particular interest. It has been difficult to understand how this complex organ arose. Molluscs provide a good example of the application of evolutionary genomics, as all eye types have evolved in one lineage.
Tag: #Evolution #Eye #Molluscs #Research #Bioinfo #Papers #Photo #Movie #Link

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お茶の水女子大学

Catching Elephant by Andy Taylor

 

Publications & Presentations

  • Publications
  1. Ogura A., Lin M., Shigenobu Y., Ikeo K., Nagai S. “Effective Gene Collection from the Metatranscriptome of Marine Microorganisms” 2011, BMC Genomics, 2011,12:S15doi:10.1186/1471-2164-12-S3-S15
  2. Yoshida M and Ogura A. “Functional novelty for cephalopod camera eye evolution revealed by transcriptomic and developmental studies” 2011, BMC Evolutionary Biology 2011, 11:180.doi:10.1186/1471-2148-11-180
  3. Yoshida M., Ishikura Y., Moritaki T., Shoguchi E., Shimizu K., Sese J., Ogura A. “Genome structure analysis of mollusks revealed whole genome duplication and lineage specific repeat variation” 2011, Gene, 483, 63–7110.1016/j.gene.2011.05.027
  4. Ogura A., Yoshida M., Fukuzaki M., Sese J., “In vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-genome sequenced species” BMC Genomics 2010 11(Suppl 4):S9doi:10.1186/1471-2164-11-S4-S9
  5. Ogura A. “Evolutionary genomics for eye diversification& rdquo; Evol. Biol, 2010, pp 179-186doi:10.1186/1471-2148-11-354
  6. Chapman JA., Kirkness EF., Simakov O, Hampson SE., Mitros T., Weinmaier T., Rattei T., Balasubramanian PG., Borman J., Busam D., Disbennett K., Pfannkoch C., Sumin N., Sutton GG., Viswanathan LD., Walenz B., Goodstein DM., Hellsten U., Kawashima T., Prochnik SE., Putnam NH., Shu S., Blumberg B., Dana CE., Gee L., Kibler DF., Law L., Lindgens D., Martinez DE., Peng J., Wigge PA., Bertulat B., Guder C., Nakamura Y., Ozbek S., Watanabe H., Khalturin K., Hemmrich G., Franke A., Augustin R., Fraune S., Hayakawa E., Hayakawa S., Hirose M., Hwang JS., Ikeo K., Nishimiya-Fujisawa C., Ogura A., Takahashi T., Steinmetz PRH., Zhang X., Aufschnaiter R., Eder MK., Gorny A., Salvenmoser W., Heimberg AM., Wheeler BM., Peterson KJ., Böttger A., Tischler P, Wolf A., Gojobori T., Remington KA., Strausberg RL., Venter JG., Technau U., Hobmayer B., Bosch TCG., Holstein TW., Fujisawa T., Bode  HR., David CN., RokhsarDS., Steele RE. “The Dynamic Genome of Hydra& rdquo; Nature 2010 6729-doi:10.1038/nature08830
  7. Yoshida S., Ogura A., Ishikawa K., Yoshida A., Kohno R., Yamaji Y., Ikeo K., Gojobori T., Kono T., Ishibashi T. “Gene Expression Profile of Fibrovascular Membranes from Patients with Proliferative Diabetic Retinopathy” Br J Ophthalmol 2009 5869-
  8. Landry CR. Castillo-Davis CI. Ogura A. Liu JS. and Hartl DL. & ldquo;Natural Variation and Evolution of Gene Expression in the Drosophila Phototransduction Cascade” PNAS 2007 104,9, 3283-3288
  9. Choy KW. Wang CC. Ogura A. Lau TK. Rogers MS. Ikeo K. Gojobori T. Tang LY. Lam DS. Chun TK. Pang CP. “Molecular characterization of developmental gene in eyes: Through data-mining on integrated transcriptome databases” Clin Biochem 2006 39:224-23010.1016/j.clinbiochem.2005.12.005
  10. Choy KW. Wang CC. Ogura A. Lau TK. Rogers MS. Ikeo K. Gojobori T. Lam DS. Pang CP. “Genomic annotation of 1.809 ESTs identified from pooled early gestation human eyes” Physiological Genomics 2005 2005 25:9-15doi: 10.1152/physiolgenomics.00121.2005
  11. Ogura A. Ikeo K. and Gojobori T. (2005) “Estimation of ancestral gene set of bilaterian animals and its implication to dynamic change of gene content in bilaterian evolution” Gene 2005 345:65- 7110.1016/j.gene.2004.11.036
  12. Ogura A. Ikeo K. and Gojobori T. “Comparative Analysis of Gene Expression for Convergent Evolution of Camera Eye between Octopus and Human” Genome Resarch. 2004 Au.14(8):1555-61doi:10.1101/gr.2268104
  13. Ogura A. Translation of “Section B, Data acquisition (pp.9~ 27)” in “Instant Notes in Bioinformatics”, 2003, Springer Verlag
  14. Nishida H. Ogura A. Yokota A. Yamaguchi I, and Sugiyama J. “ Group I intron located in PR protein homologue gene in Youngia japonica& rdquo; Biosci. Biotechnol. Biochem. 2000, 64(3):606-609doi:10.1271/bbb.64.606
  15. Zimmer T. Ogura A. Takewaka . Zimmer RM. Ohta A. and Takagi M. & ldquo;Gene regulation in response to over expression of cytochrome P450 and proliferation of the endoplasmic reticulum in Saccharomyces cerevisiae” Biosci. Biotechnol. Biochem. 2000, 64(9):1930-1936Zimmer T. Ogura A. Ohta A. and Takagi M. “Misfolded membrane -bound cytochrome P450 activates KAR2 induction through two distinct mechanisms.” J. Biochem. 1999, 126(6): 1080-1089
  • Patent
  1. 小倉淳 吉田真明 福崎睦美 瀬々潤 “新規遺伝子検出用マイクロアレイとその設計手法及びその応用” 2010年 特願2010-265734
  • Presentations @International Conferences
  1. Ogura A., Lin M., Komiyama T. “Comparative Genomics of Cultural Domesticated Chickens” Society for Molecular Biology and Evolution 2011, Japan (Kyoto), July/2011
  2. Kamijo A., Yura K, Ogura A. “Evolution of eye field transcription factors in a variety of animal phylum” Society for Molecular Biology and Evolution 2011, Japan (Kyoto), July/2011
  3. Yoshida M., Ogura A. “Genome Structure Analysis Of Molluscs Revealed Large-Scale Genome Duplication And Lineage Specific Repeat Variation” Society for Molecular Biology and Evolution 2011, Japan (Kyoto), July/2011
  4. Yoshida M., Ogura A. “Identification of a cyclops mutant found in the pygmy squid and its application to developmental study of the cephalopod camera eye” 2nd International Congress on Invertebrate Morphology, USA (Boston), June/2011
  5. Yoshida M., Ogura A. “Identification of novel Pax-6 splicing variants in squids and its relevance to camera eye development of the cephalopods” the 8th International Congress on Comparative Physiology and Biochemistry, Japan (Nagoya), May/2011
  6. Fukuzaki M., Yoshida M., Ogura A., Sese J. “Design of comparative transcriptome microarray with experimentally determined sequence distance” Joint Symposium 2010, Korea (Seoul), December/2010
  7. Konaka Y., Fukuzaki M., Yoshida M., Shimizu K., Ogura A., Sese J. “Gene duplication detection with frequent pattern analysis” Joint Symposium 2010, Korea (Seoul), December/2010
  8. Ogura A., Yoshida M, Fukuzaki M, Sese J. “in vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-genome sequenced species” InCoB2010, Tokyo (Japan), September/2010
  9. Yoshida M., Sato C., Ogura A.  “Genetic mechanisms contributed to the diversification of cephalopod camera eye“ International Symposium on Biodiversity Sciences, Nagoya (Japan), July/2010
  10. Ogura A. “Morphological diversity of molluscan eyes caused by genetic diversity” Society for Molecular Biology and Evolution Conference, France (Lyon), July/2010
  11.  Ogura A., Komiyama T. “Genomic diversity in chickens underlying cultural domestication as revealed by aCGH” Evolution2010, USA (Portland), June/2010
  12. Yoshida M., Sato C., Ogura A. “Diversification mechanisms of squid camera eye” Gordon Research Conference, Visual system development, Italy (Lucca), May/2010
  13. Wang CC., Ogura A, Choy KW., Pang CP., Ikeo K., Gojobori T. “Molecular Evolution of Vertebrate Camera Eye” Marine Genomics, Japan (Okinawa), December/2009
  14. Yoshida M., Satoh C., *Ogura A. “Transcriptomic Analysis of Molluscan Eye and Developmental Expression Studies in Pygmy Squid” OIST Retinal workshop, Japan (Okinawa), November/2009
  15. Ogura A. “Evolutionary Genomics And Transcriptomics For Eye Diversification In Molluscs” Genome Informatics at Cold Spring Harbor Laboratory, USA (New York), October/2009
  16. Ogura A. “Comparative Genomics and Transcriptomics Analyses for the Evolution and Diversification of the Molluscan Eye” 13th Evolutionary Biology Meeting, France (Marseille), September/2009
  17. Ogura A. “Contribution of miRNA-mediated gene regulation to the evolution of animal eye” Albany 2009 16th conversations, USA (Albany), June/2009
  18. Ogura A. “Comparative Genomics Analyses for Evolution of Camera Eye” International Congress of Genetics, Germany (Berlin), July/2008
  19. Ogura A. “Evolution of gene regulation from the viewpoint of vertebrates eye formation” Society for Molecular Biology and Evolution Conference, Spain (Barcelona), June/2008
  20. Ogura A. “Evolutionary mechanism of vertebrates camera eye” Gordon Research Conference, Molecular Evolution 2008, US (Ventura), February/2008
  21. Ogura A. Ikeo K. Tateno Y. Gojobori T. “A method of functional analysis for lineage specific duplicated genes using gene expression data” Microarray and Gene Expression Data Society meeting (MGED10), Australia (Brisbane), September/2007
  22. Ogura A. Choy KW. Wang CC. Ikeo K. Tateno Y. Pang CP. Gojobori T. “Evolution of miRNA target genes in camera eye of vertebrates” Society for Molecular Biology and Evolution Conference, Canada (Halifax), June/2007
  23. Ogura A. Choy KW. Wang CC. Ikeo K. Pang CP. Gojobori T “Evolution of gene regulatory system for camera eye” Marine Genomics 2006, Italy (Sorrento), October/2006
  24. Ogura A. and Daniel L. Hartl “Targets of sex-ratio suppressors in Drosophila revealed by microarray and genome analyses” Society for Molecular Biology and Evolution Conference, USA (Phoenix), May/2006
  25. Ogura A. and Daniel L. Hartl “Genomic Diversity and Speciation of Drosophila Species” Society for Molecular Biology and Evolution Conference, New Zealand (Auckland), June/2005
  26. Gojobori T. Ogura A. and Ikeo K. “Examination of convergent evolution of camera eye structures in octopus and human by gene expression profiling” Comparative and Functional Genomics Workshop, United Kingdom (Hinxton Cambridgeshire), November/2003
  27. Ogura A. Ikeo K. and Gojobori T. “Genomic Diversification of Bilaterian Animals” XIX International Congress of Genetics, Australia (Melbourne), July/2003
  28. Ogura A. Ikeo K. and Gojobori T. “Molecular Examination of Convergent Evolution of Camera Eye Structures in Octopus and Human” Society for Molecular Biology and Evolution Conference, USA (Newport Beach), June/2003
  29. Ogura A. Ikeo K. and Gojobori T. “Evolution by gene loss may play an important role in morphological diversification since the Pre-Cambrian period” Gordon Research Conference on Genomics & Structural/Evolutionary Bioinformatics, USA (SouthHadley), August/2002
  30. Ogura A. Ikeo K. and Gojobori T. “Evolutionary significance of gene loss in morphological diversification since the Pre-Cambrian period - Evolution of camera eye of Octopus and Human” Molecular Evolution Meeting on Evolution, Genomics and Bioinformatics, Italy (Sorrento), June/2002
  31. Ogura A. Imanish T. Ikeo K. and Gojobori T. “Comparative genomics of mouse ESTs with particular reference to evolution of mammalian genomes”  International Mouse Genome Conference, Japan (Narita), November/2000