Program
Schedule
| Jan.9 | ||
| 10:00 | Opening Remark | |
| Session I Genome of Multicellular organism (Chair: Asao Fujiyama, Nat. Insti. Genetics) | ||
| 10:05 | Mouse genomic variation and its effect on phenotypes and gene regulation | "Thomas Keane (Sanger Insti.)" |
| 10:45 | What we can do with over 300 billion bases of RNA-seq data: The case of Xenopus laevis genome project | "Taejoon Kwon (Univ. Texas Austin)" |
| 11:25 | Coelacanth genomes reveal a variety of signatures for pre-adaptation from water to land | "Norihiro Okada (Tokyo Insti. Tech.)" |
| 12:05 | Lunch | |
| 13:00 | Poster Session | |
| Session II Medical Genomics (Chair: Ituro Inoue. Nat. Insti. Genetics) | ||
| 14:00 | Exome / Genome sequencing as a tool for disease gene discovery | "Michael J. Bamshad (Univ. Washington)" |
| 14:40 | Exploring molecular basis of neurodegenerative diseases based on personal genome analysis. | "Shoji Tsuji (Univ. Tokyo)" |
| 15:20 | What rare coding variation reveals about the genetics of psychiatric illness. | "Benjamin M. Neale (Massachusetts Gen. Hospital)" |
| 16:00 | Break |
|
| Session III Database & ELSI (Chair: Kazuto Kato, Osaka Univ.) | ||
| 16:30 | The dbGaP database of genotypes and phenotypes: an NCBI resource for GWAS and medical resequencing | Stephen Sherry (NCBI) |
| 17:10 | TBA | Paul Flicek (EBI) |
| 17:50 | Human Variation Database in Japanese Integrated Database Project | Katsushi Tokunaga (Univ. of Tokyo) |
| 18:10 | Panel Discussion | |
| 18:30 | End of Session III | |
| 18:45 | Reception | |
| 20:45 | End of the 1st day | |
| Jan.10 | ||
| Session IV Microbial Genomics & Metagenomics (Chair:Tetsuya Hayashi, Miyazaki Univ.) | ||
| 10:00 | Time series metagenomic analysis of soil microbial community | Masataka Tsuda （Tohoku Univ.) |
| 10:40 | The Earth Microbiome Project: Planetary-scale systems ecology. | Sean M. Gibbons (Univ. Chicago) |
| 11:20 | Phylogenomics: tracing the global spread of Shigella sonnei. | Nicholas R. Thomson (Sanger Institute) |
| 12:00 | Lunch |
|
| Session V New Technology (Chair: Sumio Sugano, Univ. Tokyo) | ||
| 13:00 | Life is a game of evolution | Jun Wang (BGI) |
| 13:40 | TBA | Jonas Korlach (Pacific Bioscience) |
| 14:20 | "Integrated Gating Nanopores for Single Molecule DNA and RNA Electrical Sequencing" |
Tomoji Kawai (Osaka Univ.) |
| 15:00 | Break | |
| Session VI Bioinformatics & Computational Biology (Cair: Shinichi Morishita, Univ. Tokyo) | ||
| 15:30 | Reconstructing the evolutionary history of cancer genomes | "Daniel R. Zerbino (UC Santa Cruz)" |
| 16:10 | Sequencing Alchemy: Single-molecule Hybrid Error Correction and Assembly | "Sergey Koren (NBACC)" |
| 16:50 | DNA METHYLATION PATTERNS AND GENOME EVOLUTION | "Wei Qu (Univ. Tokyo)" |
| 17:10 | Chd2 incorporates H3.3 to mark myogenic genes | "Yasuyuki Ohkawa (Kyushu Univ.)" |
| 17:30 | Closing Remark | |
| 17:35 | End of the Symposium | |
Poster Presentation
| Neo-sex chromosome formation can promote genomic divergence between incipient stickleback species |
| Kohta Yoshida1, Takashi Makino２, Katsushi Yamaguchi3, Shuji Shigenobu3, Mitsuyasu Hasebe4, Masakado Kawata2, Seiichi Mori5, Atsushi Toyoda6, Asao Fujiyama6, and Jun Kitano1, 8 1Ecological Genetics Laboratory, National Institute of Genetics, Japan. 2Graduate School of Life Sciences, Tohoku University, Japan. 3NIBB Core Research Facilities, National Institute for Basic Biology, Japan. 4Division of Evolutionary Biology, National Institute for Basic Biology, Japan. 5Gifu-keizai-University, Japan. 6Comparative Genomics Laboratory, National Institute of Genetics, Japan. 8PRESTO, JST, Japan. |
| The Papilio genome project to understand various types of protective mimicry |
| 1Fujiwara, Haruhiko, 1Yamaguchi, Junichi, 1Ando, Toshiya, 1Ijima, Takuro, 2Hori, Hiroshi 3Toyoda, Atsushi 4Ito, Takehiko, 5Hirakawa, Hideki, 5Kosugi, Shunichi, 3Fujiyama, Asao, 1Suzuki, Yutaka, 1Sugano, Sumio, 1Nishikawa, Hideki, 1Futahashi, Ryo and 1Shirataki, Hiroko 1Grad. Sch. Front. Sci., U. of Tokyo, 2Nagoya U., 3Nat. Inst. Genetics, 4Tokyo Inst. Tech., 5 Kazusa DNA Res. Inst. JAPAN |
| Starfish genome project |
| Kazunori Tachibana1, Rei Kajitani1, Eiichi Shoguchi2, Nori Satoh2, Takehiko Ito1, Takeo Kishimoto1
1Tokyo Institute of Technology, Japan, 2Okinawa Institute of Science and Technology Graduate University, Japan |
| Whole-genome sequencing-based identification of GC-rich gamete fusion gene GCS1 in Gonium pectorale |
| Hiroko Kawai-Toyooka1, Toshiyuki Mori2, Takashi Hamaji3, Masahiro Suzuki1, Bradley J.S.C. Olson4, Atsushi Toyoda5, Asao Fujiyama5, and Hisayoshi Nozaki1
1 Department of Biological Sciences, Graduate School of Science, Univ. of Tokyo, Tokyo 113-0033, Japan: 2 Waseda Institute for Advanced Study, Waseda Univ., Tokyo 169-8050, Japan: 3 Donald Danforth Plant Science Center, St. Louis, MO 63132, USA: 4 Ecological Genomics Institute, The Division of Biology, Kansas State Univ., Manhattan, KS 66506, USA: 5 Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan |
| Analysis of the Xenopus laevis J-strain genome by BAC end sequencing, FISH, and RNA-sequence |
| Shuji Takahashi1, Atsushi Toyoda2, Yoko Kuroki3, Yoshinobu Uno4, Hideki Noguchi2, Yumi Izutsu5, Atsushi Suzuki6, Tatsuo Michiue1, Hajime Ogino7, Hirofumi Ochi7, Toshiaki Tanaka8, Akimasa Fukui9, Yuzuru Ito10 Naoto Ueno11, M. Asashima10, Yoichi Matsuda3, Masanori Taira1 and A. Fujiyama2
1The Univ. of Tokyo, 2NIG, 3RIKEN Yokohama Inst., 4Nagoya Univ. 5Nigata Univ., 6Hiroshima Univ., 7NAIST, 8Tokyo Inst. Tech., 9Hokkaido Univ., 10AIST and 11NIBB |
| Whole genome analyses of charophycean alga, Closterium peracerosum-strigosum-littorale complex |
| Hiroyuki Sekimoto1, Jun Abe1, Yuki Tsuchikane1, Atsushi Toyoda2, Yoko Kuroki3, Yutaka Suzuki4, Asao Fujiyama2, Tomoaki Nishiyama5 1Japan Women’s University, Japan; 2National Institute of Genetics, Japan; 3RIKEN, Japan; 4University of Tokyo, Japan; 35Kanazawa University, Japan |
| Evolution of complex traits: detecting the genes responsible for host-plant adaptation in insects |
| Issei Ohshima (Kyoto Prefectural University, Japan), Tomoaki Nishiyama (Kanazawa University, Japan), Mitsuyasu Hasebe (National Institute for Basic Biology, Japan) |
| Exploring key genes responsible for seawater adaptation in teleost fish by transcriptome analyses |
| Yoshio Takei1, Marty Wong1 and Wataru Iwasaki2
1Department of Bioscience and 2Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba 277-8564, Japan |
| Experimental mouse evolution model can produce variable novel phenotypes: the birth of singing mice |
| Arikuni Uchimura, Mayumi Higuchi and Takeshi Yagi
Osaka University, Japan |
| Genome-wide identification of intra- and inter-chromosomal interactions by iChIP-Seq |
| Toshitsugu Fujita, Hodaka Fujii Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan, 565-0871 |
| Identification and analysis of RNA decay factors by directly determining the stabilities of target mRNAs. |
| Naoto Imamachi1, Katsutoshi Imamura1, Yutaka Suzuki2, and Tetsushi Yada3, Nobuyoshi Akimitsu1,
1Radioisotope Center, the University of Tokyo, Japan 2Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Japan 3Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Japan |
| Whole-genome profiling of cytosine methylation in mouse primordial germ cells |
| Hisato Kobayashi1, Takayuki Sakurai1, Fumihito Miura2, Misaki Imai3, Kentaro Mochiduki4, Eikichi Yanagisawa1, Akihiko Sakashita1, Takuya Wakai1, Yutaka Suzuki5, Takashi Ito2, Yasuhisa Matsui4, Tomohiro Kono1, 3
1Department of BioScience, Tokyo University of Agriculture, Tokyo, Japan 2Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan 3Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan 4Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan 5Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan |
| Otx2 and TLE/Groucho occupancy marks tissue-specific cis-regulatory modules for head specification |
| Yuuri Yasuoka1, Yutaka Suzuki2, Shuji Takahashi3, Norihiro Sudou1, Yoshikazu Haramoto4, Ken W. Cho5, Makoto Asashima4, Sumio Sugano2, and Masanori Taira1
1Grad. Sch. of Sci., Univ. of Tokyo, Japan; 2Grad. Sch. of Fro. Sci., Univ. of Tokyo, Japan; 3KOMEX, Univ. of Tokyo, Japan; 4SCRC, AIST, Japan; 5DBC, UC Irvine, USA. |
| Antagonistic Relationship between H3K27me3 and DNA Methylation in Long-term Regulation of Developmental Genes |
| Ryohei Nakamura 1), Taro L Saito 2), Wei Qu 2), Jun Yoshimura 2), Shinichi Morishita 2), Yutaka Suzuki 2), Shinichi Hashimoto 2), Tatsuya Tsukahara 1), Hiroyuki Takeda 1)
1) Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan 2) Department of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, Japan |
| Species-specific insertions generate cis-acting RNA for promoter demethylation in macaques |
| Masahiro Uesaka and Takuya Imamura
Graduate school of Science, Kyoto University, Japan |
| Epigenetic regulation of helper T cells by Polycomb and Trithorax complexes |
| Atsushi Onodera1, Shu Horiuchi2, Tetsya Sasaki1, Hiroyuki Hosokawa1, Yukiko Watanabe1, Yutaka Suzuki3, and Toshinori Nakayama1.
1Department of Immunology, Graduate School of Medicine, Chiba University, Japan; 2Department of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Japan; 3Laboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Japan. |
| GWAS analysis of circadian rhythm sleep disorders |
| Hiroshi Kadotani1, Kazuo Mishima2, Takashi Ebisawa3, Ken Yamamoto4, Hitoshi Okamura5
1. Center for Genomic Medicine, Graduate School of Medicine, Kyoto University. 2. Department of Psychophysiology, National Institute of Mental Health, National Center of Neurology and Psychiatry. 3. Division of Psychiatry, Tokyo Metropolitan Police Hospital. 4. Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu-University. 5. Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University. |
| Genome-wide association study of gout |
| Hirotaka Matsuo1), Ken Yamamoto2), Hirofumi Nakaoka3), Akiyoshi Nakayama1), Kimiyoshi Ichida4,5), Toru Shimizu6), Masayuki Sakiyama1), Toshinori Chiba1), Seiko Shimizu1), Yuzo Takada7), Takahiro Nakamura8), Hiroshi Nakashima9), Yutaka Sakurai9), Ituro Inoue3), Nariyoshi Shinomiya1)
1) Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Japan 2) Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Japan 3) Department of Integrated Genetics, National Institute of Genetics, Japan 4) Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Japan 5) Department of Internal Medicine, Jikei University School of Medicine, Japan 6) Midorigaoka Hospital, Japan 7) Laboratory for Biofunctions, Central Research Institute, National Defense Medical College, Japan 8) Laboratory for Mathematics, Premedical Course, National Defense Medical College, Japan 9) Department of Preventive Medicine and Public Health, National Defense Medical College, Japan |
| Candidate genetic variations in an autosomal-dominant selective immunodeficiency syndrome |
| Akiko Kitamura, Koji Yasutomo
Department of Immunology, Institute of Health Biosciences, University of Tokushima, Japan |
| Molecular mechanisms regulating the expression of imprinted genes on human chromosome 14 |
| Masayo Kagami1, Tomoki Kosho2, Kazuhiko Nakabayashi3, Kentaro Matsuoka4, Tomoko Fuke1, Keiko Matsubara1, Maki Fukami1, Tsutomu Ogata5.
1. Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan 2. Department of Medical Genetics, Shinshu University School of Medicine, Matsu moto, Japan 3. Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan. 4. Departments of Pathology, National Center for Child Health and Development, Tokyo, Japan 5. Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu , Japan |
| Epigenomic difference associated with neurodevelopmental discordance of the twins with Rett syndrome |
| Kunio. Miyake1, Takae Hirasawa1, Yohei. Minakuchi2, Atsushi. Toyoda2, Takeo Kubota1
1) Department of Epigenetic Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan 2) Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics, Japan |
| A common RNA targets of TDP-43 and FUS: an investigation into the disease mechanism of ALS |
| Munetaka Yamamoto1,*, Quan Li1,*, Sigeto Seno2, Hideo Matsuda2, Yutaka Suzuki3, Yukio Kawahara1
1Laboraroty of RNA Function, Graduate School of Medicine, Osaka University 2Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University 3Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo (*equally contributed) |
| Identification of ATP1A3 mutations by exome sequencing as the cause of alternating hemiplegia of childhood in Japanese patients |
| Atsushi Ishii, MD1,2, Yoshiaki Saito, MD, PhD3, Jun Mitsui, MD, PhD 4, Hiroyuki Ishiura, MD, PhD 4, Jun Yoshimura, PhD 5, Hidee Arai, MD, PhD 6, Sumimasa Yamashita, MD, PhD 7, Sadami Kimura, MD 8, Hirokazu Oguni, MD, PhD9, Shinichi Morishita, PhD 5, Shoji Tsuji, MD, PhD 4, Masayuki Sasaki, MD, PhD3, Shinichi Hirose, MD, PhD 1, 2
1Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan; 2Central Research Institute for the Molecular Pathomechanisms of Epilepsy, Fukuoka University, Fukuoka, Japan; 3Department of Child Neurology, National Center of Neurology and Psychiatry, Kodaira, Japan; 4Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; 5Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan; 6Department of Neurology, Chiba Children's Hospital, Chiba, Japan; 7Division of Child Neurology, Kanagawa Children's Medical Center, Yokohama, Japan; 8Division of Child Neurology, Osaka Medical Center and Research Institute for Maternal and Child Health, Izumi, Japan; 9Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan |
| Genetic analysis of Benign Neonatal Epilepsy in Japan |
| Shinichi Hirose, MD, PhD, Atsushi Ishii, MD, and Yukiko Ihara, MD
Departments of aPediatrics, Fukuoka University, Fukuoka, JAPAN |
| Toward the creating marine microbial cell factory for biofuel production |
| Tomoo Sawabe1, Satoshi Nakagawa1, Fumito Maruyama2, Yoshitoshi Ogura3, Tetsuya Hayashi3, Ken Kurokawa4, and Toko Sawabe5 |
| Genome Analysis of Vibrio harveyi Strain S20: Detection and genome feature of the 3rd replicon |
| A.K.M. Rohul Amin1, Satoshi Nakagawa1, Fumito Maruyama2, Yoshitoshi Ogura3, Tetsuya Hayashi3, Ken Kurokawa4, Toko Sawabe5 and Tomoo Sawabe |
| Characterization and mechanistic analysis of novel antibiotics Kaikosin, produced by Lysobacter sp. |
| Hiroshi Hamamoto, Su Jie, Paudel Atomika, Makoto Urai, Kazuhisa Sekimizu
Grad. Sch. of Pharm. Sci., The Univ. of Tokyo |
| Genome-wide response to CO2 deficiency in Chlamydomonas reinhardtii revealed by RNA-seq analysis |
| Takashi Yamano1, Takeaki Taniguchi2, Takeaki Kubo1, Mari Yanase1, Yutaka Suzuki3, Sumio Sugano3, Takehiko Itoh4, Asao Fujiyama5, Yuji Kohara5, Atsushi Toyoda5, Tadasu Shin-i5, Hideya Fukuzawa1
1Kyoto Univ., JAPAN, 2Mitsubishi Res. Inst., JAPAN, 3Univ. of Tokyo, JAPAN, 4Tokyo Tech., JAPAN, 5Nat. Inst. of Genetics, JAPAN |
| Genomic and metagenomic analyses of filamentous nitrate-storing sulfur oxidizer |
| Hisaya Kojima and Manabu Fukui
The Institute of Low Temperature Science, Hokkaido University, Nishi 8, Kita 19, Kita-ku, Sapporo 060-0819, Jappan |
| Genome and transcriptome analysis of Strongyloides venezuelensis, an animal parasitic nematode |
| Eiji Nagayasu1, Yoshitoshi Ogura2, Mitsuru Yabana3, Takehiko Ito3, Tetsuya Hayashi2, Haruhiko Maruyama1
1) Department of Infectious Diseases, Division of Parasitology, Faculty of Medicine, University of Miyazaki, Japan 2) Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Japan 3) Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan |
| Epigenome evolution: Two mechanisms in alteration of DNA sequence recognition domains in restriction-modification systems |
| Yoshikazu Furutaa,b, Mikihiko Kawaic, Ikuo Uchiyamac, Ichizo Kobayashia,b,d
aDepartment of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Japan bInstitute of Medical Science, University of Tokyo, Japan cNational Institute for Basic Biology, Japan dDepartment of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Japan |
| Roles of DNA polymerases η in chronic low dose ultraviolet-induced mutagenesis |
| Nami Haruta1, Yoshino Kubota1 and Takashi Hishida1,2
1Research Institute for Microbial Diseases, Osaka University, Osaka, Japan. 2Department of Molecular Genetics, Graduate School of Life Sciences, Gakushuin University, Tokyo, Japan. |
| Highly efficient NGS methods to explore methylome and transcriptome at single-base resolution |
| Fumihito Miura1, Keiko Nakata2, and Takashi Ito1,2
Department of Biophysics and Biochemistry, Graduate School of Science, and Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo |
| DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition |
| Kengo Sato1), Yuki Kato2), Tatsuya Akutsu3), Kiyoshi Asai4), Yasubumi Sakakibara1)
1) Department of Biosciences and Informatics, Keio University, Japan. 2) Graduate School of Information Science, Nara Institute of Science and Technology, Japan. 3) Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan. 4) Graduate School of Frontier Sciences, University of Tokyo, Japan |
| Detection of Splice Junctions from Mid-to-Long RNA-seq Reads |
| Chao Zeng1 Hiroaki Iwata2 Natsuhiro Ichinose1 Tetsushi Yada1 Osamu Gotoh3
1 Laboratory of Computational Biology, Kyoto University, Japan 2 Medical Institute of Bioregulation, Kyushu University, Japan 3 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan |
| Variant calls with Illumina sequencers |
| Kensuke Nakamura Department of Life Scienec and Informatics, Maebashi Institute of Technology, Gunma, Japan |
| PBSIM: PacBio reads simulator |
| Yukiteru Ono (1), Kiyoshi Asai (2,3) and Michiaki Hamada (2,3)
1. Information and Mathematical Science and Bioinformatics Co., Ltd., Japan 2. Graduate School of Frontier Sciences, University of Tokyo, Japan. 3. Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Japan. |
| Assembling PacBio Continuous Long Reads without Using Other Types of Reads |
| Takamasa Imai1, Hideaki Yurino2, Kenshiro Oshima1, Masahira Hattori1, Shinichi Morishita1, Masahiro Kasahara1
1. The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8583, Japan 2. The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan |
| Platanus : A denovo short-read assembler for highly heterozygous genomes |
| Rei Kajitani1, Takehiko Itoh1
1 Tokyo Institute of Technology, Japan |
| Microbial Genome Annotation Pipeline (MiGAP) fills in the gap between sequencing and annotation |
| Hideaki Sugawara1, Akira Ohyama2, Hiroshi Mori3 , Ken Kurokawa3
1National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan 2In silico biology, Inc., SOHO Station 706, 24-8 Yamashita-cho, Naka-ku, Yokohama, Kanagawa 231-0023, Japan 3Department of Biological Information, Tokyo Institute of Technology, 4259 Nagatsuda, Midori-ku, Yokohama, Kanagawa 226-8501, Japan |
| CLAST: CUDA implemented Large-scale Alignment Search Tool |
| Masahiro Yano, Hiroshi Mori, Ken Kurokawa
Department of Biological Information, Tokyo Institute of Technology, 4259 Nagatsuda, Midori-ku, Yokohama, Kanagawa 226-8501, Japan |