5th Annual Meeting

Latest information

go to Japanese page

• New!!Downloading the program and poster abstracts is now available. Details have been sent to participants by e-mail(121119).
• Payment of the registration fee has been started through the paypal system. Details have been sent to participants by e-mail. Deadline is Nov. 16th(121110).
• The submission of abstracts starts for poster presentations. Details have been sent to participants by e-mail. Deadline is at noon on Oct. 31st(121018).
• Registration closes for the annual meeting(121002).
• Registration opens(120925).
• Home page of the 5th Annual Meeting opens(120803).

Registration

The registration is closed for the annual meeting.

Please register from the following link for the tutorials ( the page is in japanese).

Registration page

Important Notices

The official language of the meeting is Japanese.

Due to the capacity of the venue, the numbers of participants are limited to approximately 120 for the annual meeting, and 200 for the tutorials. It is highly recommended to register as soon as possible after the registration begins. In recent years, the registrations closed in a few days.

It is also reminded that all general participants should give poster presentations.

Outline of the 5th Annual Meeting

Objective

The Japanese Society for Quantitative Biology (Q-BioJP) is a non-profit organization founded in 2008 that is dedicated to the advancement of the field of quantitative biology.

Sessions

In the 5th Annual Meeting, we organize four oral sessions: "Life and constructive approach", "Life dynamics through statistical time-series analysis", "New field in quantitative biology", and "Robustness in life". We will also have a short talk session. In the poster sessions, all general participants give poster presentations.

Tutorials

This year, we organize, for the first time, a tutorial by an expert in the field of image analysis, aiming toward integrative collaborations between the fields of image analysis and quantitative biology. We also organize tutorials on numerical analysis of modeling quantitative dynamics of life, Next Generation Sequencer and quantitative biology.

Date

• Tutorials : November 23rd (Fri), 2012.
• Annual meeting : November 24th (Sat), 25th (Sun), 2012.

Venue

Convention hall, An Block, Institute of Industrial Science,
Komaba Ⅱ Research Campus, The University of Tokyo.
Access to Komaba Ⅱ Research Campus
Campus map

Registration Fee

• Annual meeting : 1200 yen ( costs for snacks in the poster sessions and the banquet.)
• Alcoholic beverages in the banquet ( if you wish ) : 700 yen
• Lunch boxes on Nov. 24th and 25th ( if you wish ) : 830 yen for each day.
• Tutorials : Free

Seating capacity

• Tutorials : Approximately 200.
• Annual meeting : Approximately 120, excluding speakers ( approx. 20 people ).

Remarks

• Poster sessions
  • The size of a poster panel is 1130 mm width and 1630 mm height. Up to a standard B0 size will be possible to post.
• Payment of the registration fee
  • You will be requested to pay the registration fee through the paypal system. Instructions will be announced soon by e-mail. There will NOT be the on-site payment.
• Receipt
  • You will be receiving a receipt of the payment through the paypal system. A printable pdf file will be created with a registered mailing address and details of the fee. If you have any special request, please ask at a reception desk.
• Internet
  • Wireless internet access will be available. Limited numbers of electric outlets and wired LAN cables are also available.

Scientific Program

Tutorials ( Nov. 23rd )

All tutorials are admission free. Please register from the registration page[1].

Tutorial 1

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Time: 10:00 - 12:00

Numerical Calculation and Quantitative Biology
by Akira Funahashi( Dept. of Biosciences and Informatics, Keio University )

References:
1. UNIXワークステーションによる科学技術計算ハンドブック: 基礎篇C言語版, 戸川隼人 (サイエンス社, 1998) [2]

2. 数値計算の常識, 伊理正夫, 藤野和建 (共立出版, 1985) [3]

Tutorial 2

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Time: 13:00 - 14:30
Chair: TBA

What are researchers on image informatics doing?
by Seiichi Uchida( Kyushu University )

References:
A publication list of the speaker is available [4]
A homepage of bioimageinformatics is also available.[5]

Tutorial 3

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Time: 15:00 - 16:30
Chair: TBA

Introduction to Bayesian analysis: concept and usage
by Kazuyuki Nakamura( Grad. Sch. of Advanced Mathematical Sciences, Meiji University )

References:
K. Nakamura, R. Yoshida, M. Nagasaki, S. Miyano and T. Higuchi, "Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing," The Proceedings of 14th Pacific Symposium on Biocomputing, pp. 227-238, 2009.

H. Koyama, T. Umeda, K Nakamura, T. Higuchi and A. Kimura, “A high-resolution shape fitting and simulation demonstrated equatorial cell surface softening during cytokinesis and its promotive role in cytokinesis,” PLoS ONE 7(2), e31607, 2012.

樋口知之編著「データ同化入門―次世代のシミュレーション技術―」

Tutorial 4

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Time: 17:00 - 18:00

Crosslinking Q-bio and Omics
by Itoshi Nikaido( RIKEN CDB )

References:
ENCODE Project Consortium, An integrated encyclopedia of DNA elements in the human genome, Nature. 2012 Sep 6;489(7414):57-74.[6].

Sessions ( Nov. 24th, 25th )

Session: Life and constructive approaches

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Date and Time: Nov. 24th 10:30-12:30
Chair: TBA
Speakers:
Hirohide Saito (Kyoto University, The Hakubi Center, CiRA )
Yutaka Sumino ( Aichi Univ. of Edu. )
Mitsuhiro Matsuda ( Dept. of Cell and Dev. Biol., Grad. Sch. of Biostudies, Kyoto Univ. )
Yusuke T. Maeda ( The Hakubi Center, Kyoto University; PRESTO )


Synthetic RNA-based approaches towards autonomous control of mammalian cell fate
by Hirohide Saito (Kyoto University, The Hakubi Center, CiRA )

References:
1.Saito H, Kobayashi T, Hara T, Fujita Y, Hayashi K, Furushima R, Inoue T., Synthetic translational regulation by an L7Ae-kink-turn RNP switch., Nat Chem Biol. 2010 Jan;6(1):71-8.[7]
2.Ohno H, Kobayashi T, Kabata R, Endo K, Iwasa T, Yoshimura SH, Takeyasu K, Inoue T, Saito H., Synthetic RNA-protein complex shaped like an equilateral triangle., Nat Nanotechnol. 2011 Feb;6(2):116-20.[8]
3.Saito H, Fujita Y, Kashida S, Hayashi K, Inoue T., Synthetic human cell fate regulation by protein-driven RNA switches., Nat Commun. 2011 Jan 18;2:160.[9]
4.Kashida S, Inoue T, Saito H., Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation., Nucleic Acids Res. 2012 Jul 18.[10]

Large scale vortex formation of self-propelled microtubules
by Yutaka Sumino ( Aichi Univ. of Edu. )

References:
[1] S. Ramaswamy, "The mechanics and statistics of active matter," Ann. Rev. Cond. Matt. Phys. 1, 323-345 (2010).
[2] Y. Sumino, K. H. Nagai, Y. Shtaka, D. Tanaka, K. Yoshiakwa, H. Chaté, and K. Oiwa, ."Large-scale vortex lattice emerging from collectively moving microtubules, " Nature 483, 448-452 (2012). [11]
[3] T. Vicsek, A. Czirók, E. Ben-Jacob, I. Cohen, and O. Schochet, "Novel type of phase transition in a system of self-driven particles," Phys. Rev. Lett. 75, 1226-1229 (1995). [12]
[4] G. Grégoire and H. Chaté "Onset of Collective and Cohesive Motion" Phys. Rev. Lett. 92, 025702 (2004). [13]


Multicellular patterns generated by intercellular feedback circuits
by Mitsuhiro Matsuda ( Dept. of Cell and Dev. Biol., Grad. Sch. of Biostudies, Kyoto Univ. )

References:
Matsuda M, Koga M, Nishida E, Ebisuya M. Synthetic signal propagation through direct cell-cell interaction. [14]

DNA and RNA in temperature gradients: Molecular transport from the origin of life to cell manipulation
by Yusuke T. Maeda ( The Hakubi Center for Advanced Research, Kyoto University; PRESTO, Japan Science and Technology Agency )

References:
[1] YT Maeda, A Buguin, A Libchaber (2011) Phys. Rev. Lett. 107: 038301.
[2] YT Maeda, T Tlusty, A Libchaber, PNAS in press.

Session: Life dynamics through statistical time-series analysis

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Date and Time: Nov. 24th 15:45-17:15
Chair: TBA
Speakers:
Michio Hiroshima ( RIKEN QBiC/ASI )
Toshiaki Omori ( Graduate School of Engineering, Kobe University )
Yohei Kondo ( Department of Basic Science, The University of Tokyo )


Single-molecule analysis of ErbB signaling in living cells
by Michio Hiroshima ( RIKEN QBiC/ASI )

References:
[1] Low-Nam S., Lidke K., Cutler P., Roovers R., van Bergen en Henegouwen P., Wilson B., Lidke D. ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand binding. Nature Str. Mol. Biol. 2011;18(11):1244-1250.
[2] Hiroshima M., Saeki Y., Okada-Hatakeyama M., Sako Y. Dynamically varying interactions between heregulin and ErbB proteins detected by single-molecule analysis in living cells. Proc. Natl. Acad. Sci. USA. 2012;109(35):13984-13989.


Estimating Spatiotemporal Dynamics of Dendritic Membrane Potential
– Information Extraction Using Bayesian Statistics -
by Toshiaki Omori ( Graduate School of Engineering, Kobe University )

References:
[1]N. Spruston. Pyramidal Neurons: Dendritic Structure and Synaptic Integration Nature Rev. Neurosci. (2008) 9, 206.
[2] T. Omori, T. Aonishi, H. Miyakawa, M. Inoue, and M. Okada. Estimated Distribution of Specific Membrane Resistance in Hippocampal CA1 Pyramidal NeuronBrain Res. (2006) 1125, 199
[3] T. Omori, T. Aonishi, H. Miyakawa, M. Inoue, and M. Okada. Steep Decrease in the Specific Membrane Resistance in the Apical Dendrites of Hippocampal CA1 Pyramidal NeuronsNeurosci. Res. (2009) 64, 83


Reconstructing core mechanisms from single-cell time series
by Yohei Kondo ( Department of Basic Science, The University of Tokyo )>

References:
Y. Kondo, K. Kaneko, S. Ishihara, Identifying dynamical systems with bifurcations from noisy partial observation [15]

Session: New fields in quantitative biology

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Date and Time: Nov. 25th 10:00-11:30
Chair: TBA
Speakers:
Yutaro Kumagai ( IFReC, Osaka University )
Masaya Oki ( Department of Applied Chemistry & Biotechnology, Graduate school of engineering, University of Fukui )
Yoshimi Haga ( Glycometabolome Team, RIKEN Advanced Science Institute )


Control of innate immune response via RNA degradation
by Yutaro Kumagai ( IFReC, Osaka University )

References:
[1] Takeuchi O and Akira S. "Pattern recognition receptors and inflammation" Cell. 2010 Mar 19;140(6):805-20.
[2] Hornung G and Barkai N. "Noise propagation and signaling sensitivity in biological networks: a role for positive feedback" PLoS Comput Biol. 2008 Jan;4(1):e8.


Analysis of the epigenetic gene expression mechanism by using the single cell chase system
by Masaya Oki ( Department of Applied Chemistry & Biotechnology, Graduate school of engineering, University of Fukui )

References:
1.Hatanaka A, Chen B, Sun JQ, Mano Y, Funakoshi M, Kobayashi H, Ju Y, Mizutani T, Shinmyozu K, Nakayama J, Miyamoto K, Uchida H, Oki M., Fub1p, a novel protein isolated by boundary screening, binds the proteasome complex., Genes Genet Syst. 2011;86(5):305-14.[16]
2.Sun JQ, Hatanaka A, Oki M., Boundaries of transcriptionally silent chromatin in Saccharomyces cerevisiae., Genes Genet Syst. 2011;86(2):73-81.[17]
3.Dhillon N, Oki M, Szyjka SJ, Aparicio OM, Kamakaka RT., H2A.Z functions to regulate progression through the cell cycle., Mol Cell Biol. 2006 Jan;26(2):489-501.[18]
4.Oki M, Kamakaka RT., Barrier function at HMR., Mol Cell. 2005 Sep 2;19(5):707-16.[19]
5.Oki M, Valenzuela L, Chiba T, Ito T, Kamakaka RT., Barrier proteins remodel and modify chromatin to restrict silenced domains., Mol Cell Biol. 2004 Mar;24(5):1956-67.[20]
6.Oki M, Kamakaka RT., Blockers and barriers to transcription: competing activities?, Curr Opin Cell Biol. 2002 Jun;14(3):299-304.[21]


Imaging of glycoforms: a sweet tool to visualize the dynamics of specific glycoproteins
by Yoshimi Haga ( Glycometabolome Team, RIKEN Advanced Science Institute )

References:
1.Haga Y, Ishii K, Hibino K, Sako Y, Ito Y, Taniguchi N, Suzuki T., Visualizing specific protein glycoforms by transmembrane fluorescence resonance energy transfer., Nat Commun. 2012 Jun 19;3:907.[22]
2. Haga Y, Ishii K, Suzuki T., N-glycosylation is critical for the stability and intracellular trafficking of glucose transporter GLUT4., J Biol Chem. 2011, 286(36):31320-7. [23]

Session: Robustness in life

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Date and Time: Nov. 25th 14:00-16:00
Chair: TBA
Speakers:
Hidehiko Inomata ( RIKEN CDB )
Daisuke Kiga ( Dept. of Computational Intelligence and Systems Science, Tokyo Institute of Technology )
Tetsuhiro S. Hatakeyama ( Department of Basic Science, The University of Tokyo )
Tomoya Kitajima ( RIKEN CDB )


Embryo Size-dependent Self-regulation of Spemann's Organizer Signal by Dynamic Degradation Control
by Hidehiko Inomata ( RIKEN CDB )

References:
Inomata H, Haraguchi T, Sasai Y., Robust stability of the embryonic axial pattern requires a secreted scaffold for chordin degradation., Cell. 2008 Sep 5;134(5):854-65. [24]

PDCA cycle of artificial genetic circuit based on modeling and quantitative results
by Daisuke Kiga ( Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology )

References:
Sekine R, Yamamura M, Ayukawa S, Ishimatsu K, Akama S, Takinoue M, Hagiya M, Kiga D. Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling., Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):17969-73.

Temperature compensation of biochemical oscillators by “enzyme-limited competition”
by Tetsuhiro S. Hatakeyama ( Department of Basic Science, The University of Tokyo )

References:
Hatakeyama TS, Kaneko K., Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration., Proc Natl Acad Sci U S A. 2012 May 22;109(21):8109-14. [25]

Quantitative live imaging of chromosome dynamics in mammalian oocytes
by Tomoya Kitajima ( RIKEN CDB )

References:
Kitajima TS, Ohsugi M, Ellenberg J., Complete kinetochore tracking reveals error-prone homologous chromosome biorientation in mammalian oocytes., Cell. 2011 Aug 19;146(4):568-81. [26]

Poster sessions ( Nov. 24th, 25th )

• Session 1 (11/24 13:30-15:30)
  • 13:30-14:30 Presentations for posters of odd number
  • 14:30-15:30 Presentations for posters of even number
• Session 2 (11/24 18:00-20:00)
  • 18:00-20:00 Free
• Session 3 (11/25 11:45-14:00; including lunch time)
  • 12:00-12:30 Presentations for posters of odd number
  • 12:30-13:00 Presentations for posters of even number
  • 13:00-14:00 Free
• Poster presentations
  • A list of poster presentations
• Remarks
  • The poster room will be available to present your poster from Nov. 24th. Please remove your poster by Nov. 25th 14:00.

Other events ( Nov. 24th )

• Poster guide( instructions of poster presentations )
• Banquet

Presentation style

• Oral presentations
  • Oral presentations are only for invited speakers and selected short talks.
• General participants
  • All participants should give poster presentations.

Schedule

Nov. 23rd, 2012 (Tutorials)

10:00-12:00		(Tutorial 1) Numerical Calculation and Quantitative Biology
		by Akira Funahashi( Keio University )
12:00-13:00		Lunch
13:00-14:30		(Tutorial2) What are researchers on image informatics doing?
		by Seiichi Uchida( Kyushu University )
15:00-16:30		(Tutorial3) Introduction to Bayesian analysis: concept and usage
		by Kazuyuki Nakamura( Meiji University )
17:00-18:00		(Tutorial4) Crosslinking Q-bio and Omics
		by Itoshi Nikaido( RIKEN CDB )

Nov. 24th, 2012(1st day)

10:00-10:30		Opening
10:30-12:30		Session 1: Life and constructive approaches
		Hirohide Saito
		Yutaka Sumino
		Mitsuhiro Matsuda
		Yusuke T. Maeda
12:30-12:35		Poster guidance
12:35-13:30		Lunch
13:30-15:30		Poster session１
15:45-17:15		Session 2: Life dynamics through statistical time-series analysis
		Michio Hiroshima
		Toshiaki Omori
		Yohei Kondo
17:20-17:45		Short talk session 1
18:00-20:00		Poster session 2 and banquet

Nov. 25th, 2012 (2nd day)

10:00-11:30		Session 3: New fields in quantitative biology
		Yutaro Kumagai
		Masaya Oki
		Yoshimi Haga
11:30-11:45		Short talk session 2
11:45-14:00		Lunch and Poster session 3
14:00-16:00		Session 4: Robustness in life
		Hidehiko Inomata
		Daisuke Kiga
		Tetsuhiro S. Hatakeyama
		Tomoya Kitajima
16:15-17:15		Discussions

The Organizing Committee

• Akatsuki Kimura ( Cell Architecture Laboratory, National Institute of Genetics )
• Tetsuya J. Kobayashi ( Institute of Industrial Science, The University of Tokyo )
• Noriko Hiroi ( Department of Biosciences and Informatics, Keio University )
• Akira Funahashi ( Department of Biosciences and Informatics, Keio University )
• Atsushi Kamimura ( Department of Basic Science, The University of Tokyo )

Sponsors

This meeting is co-organzied by Research Group on Engineering in Medicine and Biology, Institute of Industrial Science, The University of Tokyo. This meeting is also supported by KAKENHI research group "the physicochemical field for genetic activities", "哺乳類初期発生の細胞コミュニティー", and "Cross-talk between moving cells and microenvironment as a basis of emerging order in multicellular system" MEXT, Japan.

Contact

E-mail: q.bio2012 at gmail.com ( please replace `at' with `@' )