Accuracy improvement of allele and gene expression analyses by next generation sequencer

• Project/Area Number: 22680023
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Osaka University
• Principal Investigator: TAKENAKA Yoichi 大阪大学, 大学院・情報科学研究科, 准教授 (00324830)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000); Fiscal Year 2012: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2011: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2010: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
• Keywords: 生体生命情報学 / ゲノム / 生物情報学 / バイオインフォマティクス / 次世代シーケンサー / 対立染色体 / 対立染色体配列

Research Abstract

I studied the method to determine the allele sequences of diploids from DNA fragments generated from next generation DNA sequencer and where the proposed algorithm used directed acyclic graph to express DNA subsequences. The study includes gene expression profile analyses such as a crosstalk model of cell differentiation, a stochastic method to reduce the time complexity of Bayes Network estimation, iterative genome mapping for accurate expression profile of each isoform and perfect hamming code.

Research Products

• [Journal Article] n estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles (2013)
  • Author(s): Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: Gene Volume: Volume 518, Isusue 1 Pages: 17-25
  • Peer Reviewed
• [Journal Article] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles (2013)
  • Author(s): Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: Gene Volume: Vol.518 Issue: 1 Pages: 17-25
  • DOI: 10.1016/j.gene.2012.11.090
  • Peer Reviewed
• [Journal Article] A method for isoform prediction from RNA-Seq data by iterative mapping (2012)
  • Author(s): Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: IPSJ Transactions on Bioinformatics Volume: Vol.5 Pages: 27-33
  • NAID: 130002124175
  • Peer Reviewed
• [Journal Article] An Estimation Method for Inference of Gene Regulatory Network Using Bayesian Network with Uniting of Partial Problems (2012)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: BMC Genetics Volume: Vol. 13(suppl 1)
  • Peer Reviewed
• [Journal Article] A method for isoform prediction from RNA-Seq data by iterative mapping (2012)
  • Author(s): Tomoshige Ohno
  • Journal Title: IPSJ Transactions on Bioinformatics Volume: 5
  • Peer Reviewed
• [Journal Article] An estimation method for inference of gene regulatory network using Bayesian network with uniting of partial problems (2012)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: BMC Genomics Volume: Vol.13 Issue: Suppl 1 Pages: S12-S12
  • DOI: 10.1186/1471-2164-13-s1-s12
  • Peer Reviewed
• [Journal Article] Inference of S-system Models of Gene Regulatory Networks using Immune Algorithm (2011)
  • Author(s): Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: Journal of Bioinformatics and Computational Biology Volume: Vol. 9(suppl 01)
  • Peer Reviewed
• [Journal Article] Perfect Hamming code with a hash table for faster genome mapping (2011)
  • Author(s): Yoichi Takenaka
  • Journal Title: BMC Genomics Volume: Vol.12 Issue: Suppl 3 Pages: S8-S8
  • DOI: 10.1186/1471-2164-12-s3-s8
  • Peer Reviewed
• [Journal Article] 細胞分化クロストークのモデル化と細胞分化クロストーク遺伝子の推定手法 (2011)
  • Author(s): 吉澤陽志、瀬尾茂人、竹中要一、松田秀雄
  • Journal Title: 情報処理学会論文誌 数理モデル化と応用(TOM) Volume: Vol. 4, No. 4 Pages: 59-68
  • NAID: 40019257169
  • Peer Reviewed
• [Journal Article] 細胞分化クロストークのモデル化と細胞分化クロストーク遺伝子の推定手法 (2011)
  • Author(s): 吉澤陽志、瀬尾茂人、竹中要一、松田秀雄
  • Journal Title: 情報処理学会論文誌数理モデル化と応用(TOM) Volume: 4 Pages: 59-68
  • NAID: 40019257169
  • Peer Reviewed
• [Presentation] Improvement of the Accuracy of Mapping by Composing Alleles (2013)
  • Author(s): 奥田華代,竹中要一,大野朋重,瀬尾茂人,松田秀雄
  • Organizer: 理学会 第75回全国大会
  • Place of Presentation: 東北大学川内キャンパス 宮城
  • Year and Date: 2013-03-06
• [Presentation] 複数時系列遺伝子発現プロファイルを利用した遺伝子制御ネットワーク推定の精度向上手法 (2013)
  • Author(s): 渡邉之人,瀬尾茂人,竹中要一,松田秀雄
  • Organizer: 情報処理学会研究報告 第92回数理モデル化と問題解決
  • Place of Presentation: 佐賀県武雄市 武雄市文化会館
  • Year and Date: 2013-02-27
• [Presentation] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles (2012)
  • Author(s): Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Proceedings of the 2012 International Conference on 図 2 細胞分化系列における発現解析手法図 3 アイソフォームと発現量の同時推定法 Genome Informatics (GIW2012)
  • Place of Presentation: Tainan, TAIWAN
  • Year and Date: 2012-12-13
• [Presentation] All the 1+3n one-mismatch sequences of n-mer DNA are involved in 22.2+0.00879n strings of Perfect Linear Code words on DNA (2012)
  • Author(s): Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
  • Organizer: International Conference on Intelligent Systems for Molecular Biology (ISMB2012)
  • Place of Presentation: Longbeach CA USA
  • Year and Date: 2012-07-17
• [Presentation] An Estimation Method for Inference of Gene Regulatory Network Using Bayesian Network with Uniting of Partial Problems (2012)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: The tenth Asia Pacific Bioinformatics Conference (APBC2012)
  • Place of Presentation: Melbourne, Australia
  • Year and Date: 2012-01-17
• [Presentation] Bayes-based inference of gene regulatory network for multiple time series gene expression profile, Joint Conference on Informatics is Biology (2012)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Medicine and Pharmacology (日本バイオインフォマティクス学会 2012年年会 生命医薬情報学連合大会)
  • Place of Presentation: Tower hall Funabori, Tokyo
• [Presentation] Estimation of Dynamic Gene Regulatory Networks for Cell Differentiation by Splitting Time Course Data, Joint Conference on Informatics is Biology (2012)
  • Author(s): Tomoyoshi Nakayama, Yoshiyuki Kido, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Medicine and Pharmacology (日本バイオインフォマティクス学会 2012年年会 生命医薬情報学連合大会)
  • Place of Presentation: Tower hall Funabori, Tokyo
• [Presentation] Comparison of Gene Expressions measured by RNA-seq and Microarray for Transcriptome Analysis of Adipose Tissues, Joint Conference on Informatics is Biology (2012)
  • Author(s): Masakazu Sugiyama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Medicine and Pharmacology (日本バイオインフォマティクス学会 2012年年会生命医薬情報学連合大会)
  • Place of Presentation: Tower hall Funabori, Tokyo
• [Presentation] Transcript-Type Dependent Normalization of Expression Levels in RNA-Seq Data for Non-Coding RNA Analysis, Joint Conference on Informatics is Biology (2012)
  • Author(s): Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Medicine and Pharmacology (日本バイオインフォマティクス学会 2012年年会 生命医薬情報学連合大会)
  • Place of Presentation: Tower hall Funabori, Tokyo
• [Presentation] Perfect linear code reduces the solution space of genome mapping from 1+3n to 22.2 + 0.00879n to find one-mismatch for n-mer short reads (2012)
  • Author(s): Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
  • Organizer: Special Interest Group Meetings of High-Throughput Sequencing at International Conference on Intelligent Systems for Molecular Biology (ISMB2012)
  • Place of Presentation: Longbeach CA USA
• [Presentation] Bayes-based inference of gene regulatory network for multiple time series gene expression profile (2012)
  • Author(s): Yukito Watanabe
  • Organizer: Joint Conference on Informatics is Biology, Medicine and Pharmacology
  • Place of Presentation: Tokyo
• [Presentation] Two-stage method to infer gene regulatory network utilizing Link Prediction (2012)
  • Author(s): Sho Ohsuga
  • Organizer: Joint Conference on Informatics is Biology, Medicine and Pharmacology
  • Place of Presentation: Tokyo
• [Presentation] Estimation of Dynamic Gene Regulatory Networks for Cell Differentiation by Splitting Time Course Data (2012)
  • Author(s): Tomoyoshi Nakayama
  • Organizer: Joint Conference on Informatics is Biology, Medicine and Pharmacology
  • Place of Presentation: Tokyo
• [Presentation] Comparison of Gene Expressions measured by RNA-seq and Microarray for Transcriptome Analysis of Adipose Tissues (2012)
  • Author(s): Masakazu Sugiyama
  • Organizer: Joint Conference on Informatics is Biology, Medicine and Pharmacology
  • Place of Presentation: Tokyo
• [Presentation] Transcript-Type Dependent Normalization of Expression Levels in RNA-Seq Data for Non-Coding RNA Analysis (2012)
  • Author(s): Tomoshige Ohno
  • Organizer: Joint Conference on Informatics is Biology, Medicine and Pharmacology
  • Place of Presentation: Tokyo
• [Presentation] Perfect linear code reduces the solution space of genome mapping from 1+3n to 22.2 + 0.00879n to find one-mismatch for n-mer short reads (2012)
  • Author(s): Yoichi Takenaka
  • Organizer: Special Interest Group Meetings of High-Throughput Sequencing at International Conference on Intelligent Systems for Molecular Biology
  • Place of Presentation: CA USA
• [Presentation] Inference of S-system Models of Gene Regulatory Networks using Immune Algorithm (2011)
  • Author(s): Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Proceedings of the 2011 International Conference on Genome Informatics (GIW2011)
  • Place of Presentation: Busan, KOREA
  • Year and Date: 2011-12-06
• [Presentation] Perfect Hamming code with Burrow-Wheeler translation for genome mapping (2011)
  • Author(s): Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
  • Organizer: InCoB/ISCB Asia 2011
  • Place of Presentation: Kuala Lumpur MALAYSIA
  • Year and Date: 2011-12-01
• [Presentation] Perfect Hamming code with a hash table for faster genome mapping (2011)
  • Author(s): Yoichi Takenaka, Shigeto Seno and Hideo Matsuda
  • Organizer: Asia Pacific Bioinformatics Network's 10th InCoB - 1st ISCB Asia Joint Conference 2011 (InCoB/ISCB Asia 2011)
  • Place of Presentation: Kuala Lumpur MALAYSIA
  • Year and Date: 2011-11-30
• [Presentation] Sequence determination and expression estimation of alleles from RNA-Seq data (2011)
  • Author(s): Yoichi Takenaka, Tomoshige Ohno, Kayo Okuda, Shigeto Seno, Hideo Matsuda
  • Organizer: InCoB/ISCB Asia 2011
  • Place of Presentation: Kuala Lumpur MALAYSIA
  • Year and Date: 2011-11-30
• [Presentation] Mutation-aware clustering with error correction for short-read genome mapping (2011)
  • Author(s): Daisuke Ueta, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: The 2011 Jointa Conference of CBI&JSBi
  • Place of Presentation: Kobe
  • Year and Date: 2011-11-08
• [Presentation] A Directed Graphical Gaussian Model for Inferring Gene Regulatory Networks (2011)
  • Author(s): Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: Vienna, Austria
  • Year and Date: 2011-07-18
• [Presentation] Perfect Hamming Code as Hash key for Fast Genome Mapping (2011)
  • Author(s): Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: Vienna Australia
  • Year and Date: 2011-07-18
• [Presentation] A method for risk predicition of a serious disease using rule-based analysis (2011)
  • Author(s): Masakazu Sugiyama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: ウィーン オーストリー
  • Year and Date: 2011-07-18
• [Presentation] Feature selection for specifying experimental conditions that activate gene transcriptions (2011)
  • Author(s): Sho Ohsuga, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: ウィーン オーストリー
  • Year and Date: 2011-07-18
• [Presentation] Perfect Hamming Code as Hash key for Fast Genome Mapping (2011)
  • Author(s): Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: ウィーン オーストリー
  • Year and Date: 2011-07-18
• [Presentation] A Directed Graphical Gaussian Model for Inferring Gene Regulatory Networks (2011)
  • Author(s): Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: ウィーン オーストリー
  • Year and Date: 2011-07-18
• [Presentation] A Method for Inference of Gene Regulatory Network based on Bayesian Network with Uniting of Partial Problems (2011)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: Vienna, Austri
  • Year and Date: 2011-07-17
• [Presentation] A Method for Inference of Gene Regulatory Network based on Bayesian Network with Uniting of Partial Problems (2011)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: ウィーン オーストリー
  • Year and Date: 2011-07-17
• [Presentation] An Improved RNA-Seq Analysis Method for Isoform Prediction by Iterative Mapping (2010)
  • Author(s): Tomoshige Ohno, Motokazu Ishikawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Proceedings of the 2010 International Conference on Genome Informatics (GIW2010)
  • Place of Presentation: Hangzhou
  • Year and Date: 2010-12-16
• [Presentation] An Improved RNA-Seq analysis method for Isoform prediction by Iterative Mapping (2010)
  • Author(s): Ohno T, …, Takenaka Y., et.al
  • Organizer: International Conference on Genome Informatics
  • Place of Presentation: 中国・杭州
  • Year and Date: 2010-12-16
• [Presentation] Revealing regulatory relationships of crosstalk with multiple time-series gene expression profiles (2010)
  • Author(s): Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Proceedings of the 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
  • Place of Presentation: Fukuoka
  • Year and Date: 2010-12-13
• [Presentation] A bootstrapping method of S-system model for estimating timeline gene regulatory networks (2010)
  • Author(s): Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Annual Conference of the Japanese Society for Bioinformatics
  • Place of Presentation: 福岡
  • Year and Date: 2010-12-13
• [Presentation] Revealing regulatory relationships of crosstalk with multiple time-series gene expression profiles (2010)
  • Author(s): Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Annual Conference of the Japanese Society for Bioinformatics
  • Place of Presentation: 福岡
  • Year and Date: 2010-12-13
• [Presentation] A Metadata Management System for Composing Bioinformatics Workflows (2010)
  • Author(s): Takuya Ishibashi, Yoshiyuki Kido, Takanori Fukumoto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: 9th International Conference on Bioinformatics
  • Place of Presentation: 東京
  • Year and Date: 2010-09-28
• [Presentation] A method for detecting structural variants from massive paired end genome sequences by mapping signatures (2010)
  • Author(s): Daisuke Ueta, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Proceedings of the 18th Annual International Conference on Intelligent Sysmtes for Molecular Biology (ISMB2010)
  • Place of Presentation: Boston
  • Year and Date: 2010-07-11
• [Presentation] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles
  • Author(s): Ryo Araki
  • Organizer: Conference on Genome Informatics (GIW2012)
  • Place of Presentation: Tainan Taiwan
• [Presentation] Improvement of the Accuracy of Mapping by Composing Alleles
  • Author(s): Kayo Okuda
  • Organizer: 情報処理学会 全国大会
  • Place of Presentation: 仙台
• [Presentation] Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data
  • Author(s): Tomoyoshi Nakayama
  • Organizer: the 2012 International Conference on Genome Informatics (GIW2012)
  • Place of Presentation: Tainan Taiwan
• [Presentation] All the 1+3n one-mismatch sequences of n-mer DNA are involved in 22.2+0.00879n strings of Perfect Linear Code words on DNA
  • Author(s): Yoichi Takenaka
  • Organizer: International Conference on Intelligent Systems for Molecular Biology (ISMB2012)
  • Place of Presentation: CA USA
• [Presentation] ゲノムマッピング: Burrows-Wheeler transformの次のアルゴリズム
  • Author(s): 竹中要一
  • Organizer: NGS現場の会
  • Place of Presentation: 大阪