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2017 Fiscal Year Annual Research Report

Regulatory DNA conserved between Phyla

Research Project

Project/Area Number 26700030
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

Frith Martin  国立研究開発法人産業技術総合研究所, 情報・人間工学領域, 上級主任研究員 (40462832)

Project Period (FY) 2014-04-01 – 2018-03-31
Keywordsgenome
Outline of Annual Research Achievements

This year, several direct and indirect research outcomes were finalized and published. A survey of sequence rearrangements in human DNA was published in NAR. A simplified "child table" algorithm, for finding similar sequences, was published in IEEE/ACM TCBB. A method for detecting genome variations was published in BMC Medical Genomics. Our method for considering DNA neighbor-base preferences, which improves bacterial strain discrimination, was published in BMC Bioinformatics. Our analysis methods are proving useful for recent "long" DNA-read data.

Research Progress Status

29年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

29年度が最終年度であるため、記入しない。

  • Research Products

    (5 results)

All 2018 2017 Other

All Journal Article (4 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 4 results,  Open Access: 4 results) Remarks (1 results)

  • [Journal Article] EAGLE: Explicit Alternative Genome Likelihood Evaluator2018

    • Author(s)
      Kuo Tony、Frith Martin C.、Sese Jun、Horton Paul
    • Journal Title

      BMC Medical Genomics

      Volume: 11 Pages: 28~28

    • DOI

      10.1186/s12920-018-0342-1

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A Simplified Description of Child Tables for Sequence Similarity Search2018

    • Author(s)
      Frith Martin、Shrestha Anish
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: - Pages: 1~1

    • DOI

      10.1109/TCBB.2018.2796064

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A survey of localized sequence rearrangements in human DNA2017

    • Author(s)
      Frith Martin C、Khan Sofia
    • Journal Title

      Nucleic Acids Research

      Volume: 46 Pages: 1661~1673

    • DOI

      10.1093/nar/gkx1266

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads2017

    • Author(s)
      Poulsen Thomas M.、Frith Martin
    • Journal Title

      BMC Bioinformatics

      Volume: 18 Pages: 299~299

    • DOI

      10.1186/s12859-017-1710-0

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Remarks] local-rearrangements

    • URL

      https://github.com/mcfrith/local-rearrangements

URL: 

Published: 2018-12-17  

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