CURRICULUM VITAE

Sep 15, 2015

Name, Family name: Forename: Date of birth: Place of birth: Nationality:

Kawashima Takeshi February 27, 1973. Age 42. Osaka Prefecture, Japan Japanese

Affiliation: Position and title: Dept./Laboratory: Institution: Address: Phone: E-mail:

Assistant Professor, Dr. Sci. Faculty of Life and Environmental Sciences University of Tsukuba 1-1-1, Tenoh-dai, Tsukuba, Ibaraki 305-8572, Japan +81-29-853-4671. [email protected]

Home Address: 302-401, 4-9-6, Azuma, Tsukuba, Ibaraki, 305-0031, Japan Education: School of Engineering, Osaka Pref. Univ. (Bachelor’s degree), Graduated in Mar. 1996. Grad. School of Science, Kyoto University (Master’s degree), Graduated in Mar. 1998. Grad. School of Science, Kyoto University (Doctor’s degree), Graduated in Mar. 2001. Received a Dr. Sci. in Mar. 2001 from Kyoto University for a thesis entitled “EST database construction and analysis on maternal mRNAs in the egg of the ascidian, Halocynthia roretzi “. Professional Experience / Research Experience: Served as a JSPS, Postdoctoral Fellowship, Institute of Chemical Research, Kyoto University (2001.4 to 2003.11) Served as an Assistant Professor, Department of Zoology, Faculty of Science, Kyoto University (2003.12 to 2006.3) Served as a JSPS, Postdoctoral Fellowship for Research Abroad, Department of Energy, Joint Genome Institute, USA - external assignment to University of California, Berkeley, USA (2006.4 to 2008.3) Served as a Researcher, Okinawa Institute of Science and Technology (OIST) (2008.4 to 2010.3) Served as a Group Leader, OIST (2011.11 to 2014.3) Served as a Research Scientist III Group Leader, OIST (2011.11 to 2015.3) Visiting Scholar, National Institute of Basic Biology, Okazaki, Japan (2013.4 to 2015.3) Served as an Assistant Professor, University of Tsukuba (2015.4 to date) Other Academic Appointment Researcher Representative, OIST, Board Member Member of Safety and Health Committee, OIST

(2010.5 to 2014.3) (2011.4 to 2015.3)

Recent Research Interest: Comparative Genomics / Evolutionary Biology / Bioinformatics Membership: Zoological Society of Japan Society for Evolutionary Studies, Japan Japanese Society for Bioinformatics, Japan

(Board Member, 2012.1 to 2013.12) (Board Member, 2012 to date)

2. Publication List English

(Three most important papers (1, 4, 5) are marked as “O”).

Lead Author Papers ( includes papers with authorship as "This author contributed equally to this work") 1. Shoguchi E., Shinzato C., Kawashima T., Gyoja F., Mungpakdee S., Koyanagi R., Takeuchi T., Hisata K., Tanaka M., Fujiwara M., Hamada M., Seidi A., Fujie M., Usami T., Goto H., Yamasaki S., Arakaki N., Suzuki Y., Sugano S., Toyoda A., Kuroki Y., Fujiyama A., Medina M., Coffroth MA., Bhattacharya D., Satoh N. Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure. Current Biol. 23: 1-10 (2013) 2. Kawashima T., Takeuchi T., Koyanagi R., Kinoshita S., Endo H. and Endo K. Initiating the mollusk genomics annotation community : Toward creating the complete curated gene-set of the Japanese pearl oyster, Pinctada fucata. Zoological Sci. 30: 794-796 (2013) 3. Takeuchi T., Kawashima T., Koyanagi R., et al. Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology . DNA Res. 19: 117 - 130 (2012) 4. Shinzato C., Shoguchi E., Kawashima T., Hamada M., et al. Using the Acropora digitifera genome to understand coral responses to environmental change. Nature, 476: 320 - 323 (2011) 5. Kawashima T., Kawashima S., Tanaka C., Murai M., Yoneda M., Putnam NH., Rokhsar DS., Kanehisa M., Satoh N., Wada H. Domain shuffling and the evolution of vertebrates. Genome Res., 19:1393– 1403 (2009) 6. Kawashima T., Satou Y., Murakami SD., Satoh N. Dynamic changes in developmental gene expression in the basal chordate Ciona intestinalis. Dev. Growth. Differ., 47: 187-199 (2005) 7. Satou Y., Kawashima T., Shoguchi E., Nakayama A., Satoh N. An Integrated Database of the Ascidian, Ciona intestinalis: Towards Functional Genomics. Zoological Sci., 22: 837-843. (2005) 8. Kawashima T., Kawashima S., Kohara Y., Kanehisa M., Makabe KW. Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags. Nucl. Acid. Res, 30: 119-120. (2002) 9. Kawashima T., Tokuoka M., Awazu S., Satoh N., Satou Y. A genomewide survey of developmentally relevant genes in Ciona intestinalis VIII. Genes for PI3K signaling and cell cycle. Dev. Genes and Evol., 213: 284-290. (2003) 10. Kawashima T., Kawashima S., Kahenisa M., Nishida H., Makabe KW. MAGEST: MAboya Gene Expression patterns and Sequence Tags. Nucl. Acid. Res., 28: 133-135. (2000) 11. Kawashima T., Murakami AR., Ogasawara M., Tanaka KJ., Isoda R., Sasakura Y., Nishikata T., Okano H., Makabe KW. Expression patterns of musashi homologs of the ascidians, Halocynthia roretzi and Ciona intestinalis. Dev. Genes and Evol., 210: 162 - 165. (2000)

Corresponding Author Papers 12. Koyanagi R., Takeuchi T., Hisata K., Gyoja F., Shoguchi E., Satoh N., Kawashima T. MarinegenomicsDB: An integrated genome viewer for community-based annotation of genomes. Zoological Sci. 30:797-800 (2013) 13. Matsumae H., Hamada M., Fujie M., Niimura Y., Tanaka H., Kawashima T. A Methodical Microarray Design Enables Surveying of Expression of a Broader Range of Genes in Ciona intestinalis Gene 519: 82-90 (2013) Other Joint Papers 14. Gusev O., Suetsugu Y., Cornette R., Kawashima T., Logacheva MD., Kondrashov AS., Penin AA., Hatanaka R., Kikuta S., Shimura S., Kanamori H., Katayose Y., Matsumoto M., Shagimardanova E., Alexeev D., Govorun V., Wisecaver J., Mikheyev A., Koyanagi R., Fujie M., Nishiyama T., Shigenobu S., Shibata TF., Golygina V., Hasebe M., Okuda T., Satoh N. & Kikawada T., Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. Nature Communications. 5: 4784 (2014) 15. Satoh N., Tagawa K., Lowe CJ., Yu JK., Kawashima T., Takahashi H., Ogasawara M., Kirschner M., Hisata K., Su YH., Gerhart J. On a Possible Evolutionary Link of the Stomochord of Hemichordates to Pharyngeal Organs of Chordates. Genesis 52:925–934 (2014) 16. Mungpakdee S., Shinzato C., Takeuchi T., Kawashima T., Koyanagi R., Hisata K., Tanaka M., Goto H., Fujie M., Lin S.,Satoh N. & Shoguchi E., Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome. Genome Biology and Evolution 6: 1408-1422 (2014) 17. Tagawa K., Arimito A., Sasaki A., Izumi M., Fujita S., Humphreys T., Fujiyama A., Kagoshima H., Shin-I T., Kohara Y., Satoh N. & Kawashima T., A cDNA resource for gene expression studies of a hemichordate, Ptychodera flava. Zoological Sci. 31: 414-420 (2014) 18. Hamada M., Shoguchi E., Shinzato C., Kawashima T., Miller DJ., Satoh N. The complex NOD-like receptor repertoire of the coral Acropora digitifera includes novel domain combinations. Mol. Biol. Evol. Mol. Biol. Evol. 30: 167-176 (2013) 19. Freeman R., Ikuta T., Wu M., Koyanagi R., Kawashima T., Tagawa K., Humphreys T., Fang GC., Fujiyama A., Saiga H., Lowe C., Worley J., Jenkins J., Schumutz J., Kirschner M., Rokhsar D., Satoh N., and Gerhart J. Identical Genomic Organization of Two Hemichordate Hox Clusters. Current Biology. 22: 2053 - 2058 (2012) 20. Shinzato C., Hamada M., Shoguchi E., Kawashima T., Satoh N. The Repertoire of Chemical Defense Genes in the Coral Acropora digitifera Genome Zoological Sci. 29: 510 - 517. (2012) 21. Gyoja F., Kawashima T., Satoh N. A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot. Dev. Genes. Evol., 222: 63 - 76. (2012)

22. Katayama T., et al. (4th of 57 authors) The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J. Biomed. Semantics. 2011, 2:4. (2011) 23. Hellsten U., et al. (21st of 42 authors) The genome of the western clawed frog Xenopus tropicalis. Science, 328: 633 - 636. (2010) 24. Chapman JA. et al. (19th of 74 authors) The dynamic genome of Hydra. Nature, 464: 592 - 596. (2010) 25. Putnam NH. et al. (6th of 37 authors) The amphioxus genome and the evolution of the chordate karyotype. Nature, 453: 1064 - 1071. (2008) 26. Holland LZ. et al. (23rd of 64 authors64) The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res., 18: 1100 - 1111. (2008) 27. Christiaen L., Davidson B., Kawashima T., Powell W., Nolla H., Vranizan K., Levine M. The Transcription/Migration Interface in Heart Precursors of Ciona intestinalis. Science, 320: 1349 - 1352. (2008) 28. Srivastava M. et al. (6th of 21st aurhors) The Trichoplax genome and the nature of placozoans. Nature, 454: 955 - 960. (2008) 29. Azumi K. et al. (6th of 13 authors) Gene expression profile during the life cycle of the urochordate Ciona intestinalis Developmental Biology, 308: 572-582 (2007) 30. Kawashima S. et al. (2nd of 7 authors) Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genome Genome Inform., 19: 50-60 (2007) 31. Sekiguchi T., Kawashima T., Satou Y. and Satoh N. Further EST analysis of endocrine genes that are preferentially expressed in the neural complex of Ciona intestinalis: R with endocrine system in the neural complex General and Comparative Endocrinology., 150: 233-245 (2007) 32. Shoguchi E., Kawashima T., Satou Y., Hamaguchi M., Sin-I T., Kohara Y., Putnam NH., Rokhsar DS., Satoh N. Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis., Genome Res., 16: 297-303 (2006) 33. Shoguchi E., Kawashima T., Nishida-Umehara C., Matsuda Y., and Satoh N. Molecular Cytogenetic Characterization of Ciona intestinalis Chromosomes Zoological Sci., 22: 511-516 (2005) 34. Satou Y. Kawashima T. Kohara Y. and Satoh N. Large scale EST analyses in Ciona intestinalis - Its application as Northern blot analyses. Dev Genes Evol., 213: 314 - 318. (2003) 35. Satou Y. et al (5th of 14 authors) A cDNA resource from the basal chordate Ciona intestinalis Genesis, 33: 153 - 154. (2002) 36. Dehal P. et al. (16th of 85 authors) The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins Science, 298: 2157 - 2167. (2002)

37. Makabe KW. et al (2nd of 25 authors) Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development Development, 128: 2555 - 2567. (2001) 38. OIST Winter Course "Evolution of Complex Systems". Staff ( 2008, 2009, 2010, 2011, 2012 ) 39. Biohackathon2009 (2009, March 15th to March 21st) 40. Kawashima T., et al., Whole Genome Shotgun Assembly of Acornworm, Ptychodera flava. Okinawa, Dec. 15 - 18 (2009) 41. Kawashima T., et al. Analysis of polymorphism in the genome of the chordate, Ciona intestinalis. The Biology of Genomes, USA, May. 10 - 14 (2006) 42. Kawashima T., An EST clustering approach to the Ciona intestinalis gene content. International Urochordate Meeting, France, Oct. 11 - 15 (2003) 43. Kawashima T., t al., The maternal mRNAs encoding DNA-binding motifs in ascidian egg. Kyoto, Jul. 8 - 12 (2001)