Ryo Nakaki

Personal Profile

A computational biologist specializing in computational and statistical analysis of high-dimensional biological data, with many experiences in researches based on next generation sequencing data. Current focus is to elucidate the switching mechanisms of the combinational associations among transcriptional regulators in different contexts. Develops new algorithms based on the three following interests;

  1. Transcriptional co-factors: Co-localization analysis though comparing multiple epi-genome data (e.g., ChIP-seq data for transcriptional regulators and histone modifications, open chromatin regions)
  2. Recognition sequences and chromatin structures: Footprint analysis integrating recognition motifs and DNase I cleavages obtained by DNase-seq and ATAC-seq
  3. Genome-wide interactions: Mapping analysis integrating the binding sites of transcriptional regulators and genome-wide interactions obtained by ChIA-PET and HiC

Email: nakaki@genome.rcast.u-tokyo.ac.jp

Skills and competence

Data processing for next generation sequencing:

  • Mapping (Bowtie, BWA, BatMis, TopHat)
  • Peak calling (MACS, PeakSeq, SICER, PeakRanger)
  • De novo motif identification (MODIC, MDscan, Weeder, DME, Bioprospector, MEME)

Programming language:

  • Software development (Java, Python, Java, C)
  • Web development (PHP, Javascript, HTML)
  • Analysis (R, Python)
  • Others (Perl)

Expertise of cellular Biology:

  • Hematopoietic differentiation
  • Myocardial differentiation
  • Endothelial differentiation
  • Adipocyte differentiation

Work experience

  • 2015-present Chief Executive Officer at Rhelixa Inc., Tokyo, Japan (See: Rhelixa’s Homepage)
  • 2015-present Special research Fellowship for Young Scientists (for Ph.D), Japan’s Society for the Promoter of Science (JSPS), Tokyo, Japan
  • 2014-present Chief Analytics Officer at SYMAX Inc., Tokyo, Japan


  • 2015 Best Poster Award, the 11th International Workshop on Advanced Genomics, Tokyo, Japan
  • 2015 Runner-up, Japan Business Model Competition 2015, Tokyo, Japan
  • 2014 Championship, Business Model competition, University of Tokyo, Tokyo, Japan
  • 2013 Most Valuable Presenter Award, Tokyo, the 87th Annual Meeting of the Japanese Biochemical Society, Japan
  • 2012 National Certificate of Radiation Protection Supervision (Category 1), Tokyo, Japan, 2012


  • 2015 Y. Abe, R. Rozqie, Y. Matsumura, T. Kawamura, Nakaki, Y. Tsurutani, K. Tanimura-Inagaki, A. Shiono, K. Magoori, K. Nakamura, S. Kajimura, H. Kimura, T. Tanaka, K. Fukami, TF. Osborne, T. Kodama, H. Aburatani, T. Inagaki, J. Sakai “PKA phospho-switch on JMJD1A Regulates Long-range Chromatin Association with SWI/SNF and PPARγ for BAT Function.” Nature communications
  • 2015 T. Inagaki, S. Iwasaki, Y. Matsumura, T. Kawamura, T. Tanaka, Y. Abe, A. Yamasaki, Y. Tsurutani, A. Yoshida, Y. Chikaoka, K. Nakamura, K. Magoori, Nakaki, TF. Osborne, K. Fukami, H. Aburatani, T. Kodama, J. Sakai. “The FBXL10/KDM2B scaffolding protein associates with novel polycomb repressive complex-1 to regulate adipogenesis.” J Biol Chem. Feb 13;290(7):4163-77
  • 2012 Nakaki, J. Kang, M. Tateno, “A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions.” Nucleic Acids Res. Oct;40(18):8835-48


  • 2014-2015 Special research Fellowship for Young Scientists, JSPS, Tokyo, Japan
  • 2013-2014 Special Research Fellowship for Engineering, University of Tokyo, Tokyo, Japan
  • 2012-2013 Special Research Fellowship for Engineering, Global CEO Program of Japan, Tokyo, Japan


  • Designing and creating Lego robots
  • Stained glass art
  • Modern Japanese history
  • Changing the notion on hair loss
  • Creating new Japanese dishes (4-year experience cooking at a traditional Japanese restaurant)
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