Secondary structure evolution of Alu sequences in the human genome

• Project/Area Number: 21700330
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: The University of Tokyo
• Principal Investigator: KIRYU Hisanori 東京大学, 大学院・新領域創成科学研究科, 准教授 (80415778)
• Project Period (FY): 2009 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000); Fiscal Year 2010: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2009: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: 進化系統樹 / Alu配列 / RNA二次構造

Research Abstract

We have developed technologies to extract various structural information in RNA sequences by using the algorithms of RNA secondary structure prediction. We have also developed algorithms for computing novel kinds of evolutionary conservation measures by applying the theory of phylogeny.

Research Products

• [Journal Article] Rchange : Algorithms for computing the energy changes of RNA secondary structures in response to base mutations (2012)
  • Author(s): Hisanori Kiryu and Kiyoshi Asai
  • Journal Title: Bioinformatics Volume: 28(8) Issue: 8 Pages: 1093-1101
  • DOI: 10.1093/bioinformatics/bts097
  • Peer Reviewed
• [Journal Article] Sufficient statistics and expectation maximization algorithms in phylogenetic tree models (2011)
  • Author(s): Hisanori Kiryu
  • Journal Title: Bioinformatics Volume: 27(17) Pages: 2346-2353
  • Peer Reviewed
• [Journal Article] A detailed investigation of accessibilities around target sites of siRNAs and miRNAs (2011)
  • Author(s): Hisanori Kiryu、Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai
  • Journal Title: Bioinformatics Volume: 27(13) Pages: 1788-1797
  • Peer Reviewed
• [Journal Article] Generalized Centroid Estimators in Bioinformatics (2011)
  • Author(s): Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai
  • Journal Title: PLoS ONE Volume: 6(2) Issue: 2 Pages: e16450-e16450
  • DOI: 10.1371/journal.pone.0016450
  • Peer Reviewed
• [Journal Article] A detailed investigation of accessibilities around target sites of siRNAs and miRNAs (2011)
  • Author(s): Hisanori Kiryu; Goro Terai; Osamu Imamura; Hiroyuki Yoneyama; Kenji Suzuki; Kiyoshi Asai
  • Journal Title: Bioinformatics Volume: 27 Pages: 1788-1797
  • Peer Reviewed
• [Journal Article] CentroidAlign : Fast and Accurate Aligner for Structured RNAs by Maximizing Expected Sum-of-pairs Score (2009)
  • Author(s): Hamada M, Sato K, Kiryu H, Mituyama T, Asai K.
  • Journal Title: Bioinformatics Volume: 25(24) Issue: 24 Pages: 3236-3243
  • DOI: 10.1093/bioinformatics/btp580
  • Peer Reviewed
• [Presentation] On algorithms for computing thermodynamic entropy of RNA secondary structureｓ (2011)
  • Author(s): Hisanori Kiryu and Kiyoshi Asai
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2011-12-14
• [Presentation] On algorithms for computing thermodynamic entropy of RNA secondary structures (2011)
  • Author(s): Kiyoshi Asai
  • Organizer: CBI/JSBI2011合同大会
  • Place of Presentation: 兵庫県神戸市神戸国際会議場(poster presentation)
  • Year and Date: 2011-11-09
• [Presentation] SEQUENCE ANALYSIS AROUND TARGET SITES OF siRNAs AND miRNAs(ポスター) (2010)
  • Author(s): 木立尚孝
  • Organizer: CBRC2010
  • Place of Presentation: 産総研・生命情報工学研究センター
  • Year and Date: 2010-07-28
• [Presentation] siRNAとmiRNAのターゲット領域の配列解析(ポスター発表) (2010)
  • Author(s): 木立尚孝
  • Organizer: 第12回日本RNA学会年会
  • Place of Presentation: 国立情報学研究所 学術総合センター
  • Year and Date: 2010-07-27
• [Remarks] Rchange 塩基置換にともなうRNA の二次構造的なエネルギー変化を計算するプログラム(2011)
  • URL: http://www.ncrna.org/software/rchange/
• [Remarks] Rentropy RNA の二次構造的なエントロピーを計算するプログラム(2011)
  • URL: http://www.ncrna.org/software/rentropy/
• [Remarks] Fdur 系統樹の十分統計量を計算するプログラム(2011)
  • URL: http://www.ncrna.org/software/fdur/
• [Remarks] Raccess RNA の二次構造的アクセシビリティを計算するプログラム(2010)
  • URL: http://www.ncrna.org/software/Raccess/
• [Remarks]
  • URL: http://www.ncrna.org/software/Raccess/
• [Remarks]
  • URL: http://www.ncrna.org/software/fdur/
• [Remarks]
  • URL: http://www.ncrna.org/software/rentropy/
• [Remarks]
  • URL: http://www.ncrna.org/software/rchange/