About me

(日本語はこちら)

A bioinformatician (or computational biologist).

Research Theme

Genome sequence assembly is an inverse problem of reconstructing an original string (of the order of gigabyte in length) from a set of its very short substrings (of kilobyte) that contain observation errors. The difficulty of a genome assembly task depends on the content of the original string, and the main theme in my doctoral research was assembly of repetitive sequences in centromeres and metagenomes. More recently, I have been working both on development of fundamental computational methods/programs for more accurate and efficient genome assembly and on practical assembly projects of several (model/non-model) organisms.

Employment

Jan 2023 –

  • Project Research Associate @ Morishita lab, The University of Tokyo

Apr 2022 – Dec 2022

  • Postdoc @ Morishita lab, The University of Tokyo

Jul 2020 – Mar 2022

  • Postdoc @ Myers Unit, Okinawa Institute of Science and Technology Graduate University

Apr 2020 – Jun 2020

  • Postdoc @ Morishita lab, The University of Tokyo

Education & Thesis

Apr 2017 – Mar 2020

  • Ph.D. (Science) @ Department of Computational Biology and Medical Sciences, The University of Tokyo
  • Thesis title: “Toward complete reconstruction of repetitive sequences in metagenome and centromere”
  • Supervisor: Prof. Shinichi Morishita

Sep 2017 – Mar 2018

  • Visiting Ph.D. student @ Max Planck Institute of Molecular Cell Biology and Genetics
  • Research theme: Sequence assembly of centromeres in Drosophila
  • Advisor: Prof. Gene Myers

Apr 2015 – Mar 2017

  • M.S. @ Department of Computational Biology and Medical Sciences, The University of Tokyo
  • Thesis title: ”De novo metagenome assembly and methylation-guided host-matching of mobile elements using SMRT sequencing”
  • Supervisor: Prof. Shinichi Morishita

Apr 2011 – Mar 2015

  • B.S. @ Department of Bioinformatics and Systems Biology, The University of Tokyo
  • Thesis title: “Metagenome assembly using PacBio long read”
  • Supervisor: Prof. Shinichi Morishita

Fellowships & Experiences

Apr 2018 – Mar 2020

  • JSPS Research Fellowship for Young Scientists DC2

Jul 2016 – Jun 2017

  • Intern (Software development & Data analysis) @ National Graduate Institute for Policy Studies

Dec 2015 – Jan 2016 & Dec 2016 – Jan 2017

  • Teaching Assistant (“Basic Laboratory Work in Information Science”) to Prof. Shinichi Morishita @ The University of Tokyo

Apr 2015 – Mar 2018

  • JSPS Program for Leading Graduate Schools Scholarship (“Global Leader Program for Social Design and Management”, GSDM)

Awards

  • Dean’s Prize for the Ph.D. thesis @ Graduate School of Frontier Sciences, The University of Tokyo. (2020).
  • Excellent Research Award (Best award) for the Ph.D. thesis @ Department of Computational Biology and Medical Sciences, The University of Tokyo. (2020).
  • Excellent Research Award (Best award) for the Master’s thesis @ Department of Computational Biology and Medical Sciences, The University of Tokyo. (2017).

Peer-Reviewed Publications

Journals

  • Takeuchi, T., Suzuki, Y. (joint-first), Watabe, S., Nagai, K., Masaoka, T., Fujie, M., Kawamitsu, M., Satoh, N., & Myers, E. W. A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. DNA Research 29(6), 1-13 (2022). doi:10.1093/dnares/dsac035
  • Suzuki, Y., Nishijima, S., Furuta, Y., Yoshimura, J., Suda, W., Oshima, K., Hattori, M., & Morishita, S. Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. Microbiome 7, 119 (2019). doi:10.1186/s40168-019-0737-z

Conference Proceedings

  • Suzuki, Y. & Myers, G. Accurate k-mer classification using read profiles. In C. Boucher & S. Rahmann (Eds.), 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Leibniz International Proceedings in Informatics, 242, 10:1–20. (2022). doi:10.4230/LIPIcs.WABI.2022.10

Other Publications

Magazine Articles

  • Suzuki, Y. & Morishita, S. The success in completing a human genome and its significance. Experimental Medicine 40(13) (Yodosha, 2022). doi:10.18958/7061-00002-0000208-00
  • Suzuki, Y., Nishijima, S., & Morishita, S. Long-read metagenomcis. Human Microbiome Vol. 2 (ed. Hattori, M.) (NTS, 2020).
  • Suzuki, Y. & Morishita, S. Metagenome analysis using PacBio long reads. Experimental Medicine Separate Volume (ed. Hattori, M.), 149–155 (Yodosha, 2016).

Oral Presentations (presenter in bold style)

International Conferences

  • Suzuki, Y. & Myers, E. W. Accurate k-mer classification using read profiles. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Potsdam, Germany. (Sep 2022).
  • Suzuki, Y. & Myers, E. W. Accurate k-mer classification using read profiles. Biodiversity Genomics 2021, Online Conference. (Sep 2021).
  • Suzuki, Y., Nishijima, S., Furuta, Y., Suda, W., Oshima, K., Hattori, M., & Morishita, S. Highly diversified metamethylome and metamobilome in human gut metagenomes. SMRTLeiden, Leiden, Netherland. (May 2017).
  • Suzuki, Y., Nishijima, S., Furuta, Y., Suda, W., Oshima, K., Hattori, M., & Morishita, S. Metagenome, metamobilome and meta-methylome of human gut flora uncovered by SMRT sequencing. Advances in Genome Biology and Technology (AGBT) General Meeting, Hollywood, Florida. (Feb 2017).

Domestic Conferences

  • Ikeuchi, K., Suzuki, Y., & Hara, Y. Measuring the value of innovations using press releases of companies. The Japanese Economic Association, Kyoto, Japan. (Jun 2017).

Workshops, seminars, and symposiums

  • Suzuki, Y & Myers, E. W. Accurate k-mer classification using read profiles. OIST-UT Genomics Research Seminar, Okinawa, Japan. (Mar 2022).
  • Suzuki, Y. Genome assembly technologies and gut microbiome analysis using long reads. The 164th Committee on Genome Technology, Tokyo, Japan. (Apr 2018).

Poster Presentations (presenter in bold style)

International Conferences

  • Takeuchi, T., Suzuki, Y., Watabe, S., Nagai, K., Masaoka, T., Fujie, M., Kawamitsu, M., Satoh, N., & Myers, E. W. A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. International Genome Graph Symposium (IGGSy), Ascona, Switzerland. (Jul 2022).
  • Suzuki, Y., Nishijima, S., Furuta, Y., Suda, W., Oshima, K., Hattori, M., & Morishita, S. De novo metagenome assembly and methylome of the human gut microbiome using SMRT sequencing. The Biology of Genomes, Cold Spring Harbor Laboratory (CSHL) Meeting, New York. (May 2017).
  • Suzuki, Y., Nishijima, S., Furuta, Y., Suda, W., Oshima, K., Taniguchi, J., Yoshimura, J., Hattori, M., & Morishita, S. Meta-methylome analysis with SMRT sequencing revealed a diversity of DNA methylation motifs in uncultured human gut microbiomes. The Biology of Genomes, Cold Spring Harbor Laboratory (CSHL) Meeting, New York. (May 2016).
  • Suzuki, Y., Nishijima, S., Furuta, Y., Suda, W., Oshima, K., Taniguchi, J., Yoshimura, J., Hattori, M., & Morishita, S. Meta-methylome of human gut microbiome using SMRT sequencing. Advances in Genome Biology and Technology (AGBT) General Meeting, Orlando, Florida. (Feb 2016).
  • Suzuki, Y., Taniguchi, J., Yoshimura, J., Oshima, K., Hattori, M., & Morishita, S. De novo metagenome assembly using PacBio long reads. The Biology of Genomes, Cold Spring Harbor Laboratory (CSHL) Meeting, New York. (May 2015).