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To let you know about our research, this area contains 4 types of information about CLST; “Article”, “Videos”, “Event” and “Study”.
At “Article”, you can read articles on interviews and lectures, and you can enjoy the videos about CLST at “Videos”. If you want to meet and talk directly with the researcher, “Visit” give you some information of such events. You can find more difficult contents to know about our research deeply at “Study”.
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Labs & Technologies

Phyloinformatics Unit

From experiment design to informatics - bringing evolving technologies into biology

 

* Due to the reorganization starting as new centers in April 2018, this laboratory is now belong to the Center for Biosystems Dynamics Research. As for the latest information, please see the following URL below.
> The webpage of Laboratory for Phyloinformatics, Center for Biosystems Dynamics Research

Unit Leader
Shigehiro Kuraku  Ph.D.

2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

3_15_kuraku.png

>>> Lab Site

Research Area

We are the only core facility of RIKEN in western Japan that provides technical support on both next-generation sequencing and mass spectrometry. We host postdoctoral lab experts for sample QC as well as bioinformaticians who process large-scale sequence analysis, and this staff organization has enabled handling of diverse projects in a biologist-oriented manner. Following contributions to international genome consortia for several non-model animals, we aim to conduct original research and technical development by means of molecular evolutionary approaches for sound cross-species comparisons of DNA and protein sequences.

 

Overview of our research support lineup


・next-generation sequencing
・Sanger (capillary) sequencing
・mass spectrometry
・DNA clone distribution
・DNA/protein sequence informatics
・ChIP-seq sample preparation
・various analysis consultations (ChIP、NGS library preparation、NGS informatics、DNA cloning）

 

Research Topics

Main Publications List

1

gVolante for standardizing completeness assessment of genome and transcriptome assemblies

Nishimura O, Hara Y, Kuraku S
Bioinformatics,, in press (2017).
2

CTCF binding landscape in jawless fish with reference to Hox cluster evolution.

Kadota M, Hara Y, Tanaka K, Takagi W, Tanegashima C, Nishimura O, Kuraku S.
Sci Rep, 7(1), 4957 (2017).
3

Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain

Sugahara F, Pascual-Anaya J, Oisi Y, Kuraku S, Aota S, Adachi N, Takagi W, Hirai T, Sato N, Murakami Y, Kuratani S.
Nature, 531(7592), 97-100 (2016).
4

Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene

Sunagawa GA, Sumiyama K, Ukai-Tadenuma M, Perrin D, Fujishima H, Ukai H, Nishimura O, Shi S, Ohno R, Narumi R, Shimizu Y, Tone D, Ode KL, Kuraku S, Ueda HR
Cell Rep, 14(3), 662-77 (2016).
5

Evolution of the fish heart by sub/neofunctionalization of an elastin gene.

Moriyama Y, Ito F, Takeda H, Yano T, Okabe M, Kuraku S, Keeley FW, Koshiba-Takeuchi K.
Nat Commun, 7, 10397 (2016).
6

Incorporating tree-thinking and evolutionary time scale into developmental biology.

Kuraku S, Feiner N, Keeley SD, Hara Y.
Dev Growth Differ., 58(1), 131-42 (2016).
7

Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing

Tatsumi K, Nishimura O, Itomi K, Tanegashima C, and Kuraku S.
Biotechniques, 58(5), 253-257 (2015).
8

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.

Kuraku S, Zmasek CM, Nishimura O, Katoh K.
Nucleic Acids Res, 41, W22-28 (2013).
9

Sequencing of the sea lamprey (Petromyzon marinus) genome provide insights into vertebrate evolution

Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W.
Nat Genet, 45(4), 415-421 (2013).
10

Impact of asymmetric gene repertoire between cyclostomes and gnathostomes.

Kuraku S.
Semin Cell Dev Biol, 24(2), 119-127 (2013).

Member  *concurrent

  • Shigehiro Kuraku

    Unit Leader

    >>>Curriculum vitae
  • Mitsutaka Kadota

    Senior Technical Scientist

  • Osamu Nishimura

    Technical Scientist

  • Reiko Nakagawa

    Technical Scientist

  • Yuichiro Hara

    Special Postdoctoral Researcher

  • Koh Onimaru

    Research Scientist

  • Kazuaki Yamaguchi

    Postdoctoral Researcher

  • Mohamed Rehab

    Technical Staff I

  • Chiharu Tanegashima

    Technical Staff II

  • Kaori Tatsumi

    Technical Staff II

  • Sean Keeley

    Technical Staff II

  • Sayo Saito

    Assistant

CLST was reorganized into three centers according to the RIKEN 4th Medium-Term Plan from April 1, 2018. For the latest information of Phyloinformatics Unit, please visit the following websites.


> The webpage of Laboratory for Phyloinformatics, Center for Biosystems Dynamics Research [http://www.bdr.riken.jp/en/research/labs/kiyosue-y/index.html]


> If you continue to browse this site, click here.