Program - Keynote Lectures
FRIDAY, NOVEMBER 1
Keynote Lecture 1 / OIST Presidential Lecture Time: 10:50-12:10 / Venue: Auditorium
Chair: Tadashi Yamamoto（OIST/JST, Japan）
KL-01

Deep Learning for Medical Imaging
Lily Peng（Google AI Healthcare, USA）

Dale Webster（Google AI Healthcare, USA）

TUESDAY, NOVEMBER 5
Keynote Lecture 02

Time: 9:40-11:00 / Venue: Auditorium

Chair: Shinya Kuroda（The University of Tokyo, Japan）
KL-02

Nobel Turing Challenge: Creating the Engine for Scientific
Discovery
Hiroaki Kitano（OIST/SBI, Japan）

14

Program - Plenary Lectures
FRIDAY, NOVEMBER 1
Plenary Lecture 01

Time: 12:10-12:50 / Venue: Auditorium

Chair: Uwe Sauer（ETH Zurich, Switzerland）
PL-01

Trans-omic Analysis of Insulin Action
Shinya Kuroda（The University of Tokyo, Japan）

Plenary Lecture 02

Time: 17:40-18:20 / Venue: Auditorium

Chair: Mariko Okada（Osaka University, Japan）
PL-02

Mining non-oncogene addiction for cancer therapy
Hsueh-Fen Juan（Department of Life Science, Graduate Institute of Biomedical
Electronics and Bioinformatics, National Taiwan University, Taiwan）

SATURDAY, NOVEMBER 2Plenary Lecture 03

Time: 9:00-9:40 / Venue: Auditorium

Chair: Miki Ebisuya（EMBL Barcelona, Spain）
PL-03

The mechanism of the somite segmentation clock
Ryoichiro Kageyama（Kyoto University, Japan）

15

Program - Plenary Lectures
Plenary Lecture 04

Time: 9:40-10:20 / Venue: Auditorium

Chair: Silvia Santos（Francis Crick Institute, UK）
PL-04

Deciphering mechanisms regulating erythropoiesis – From thesingle cell to the patient level
Ursula Klingmüller（German Cancer Research Center, Germany）

Plenary Lecture 05

Time: 17:40-18:20 / Venue: Auditorium

Chair: Yuichi Taniguchi（RIKEN BDR, Japan）
PL-05

Deciphering developmental patterning with deep neural network
Chao Tang（Center for Quantitative Biology and School of Physics, Peking University, China）

SUNDAY, NOVEMBER 3
Plenary Lecture 06

Time: 9:00-9:40 / Venue: Auditorium

Chair: Katsuyuki Yugi（RIKEN IMS, Japan）
PL-06

Global redox proteome and phosphoproteome analysis reveals
novel insights into the Insulin Signaling Network
David E James（Charles Perkins Centre, School of Life & Environmental Science,
School of Medicine, University of Sydney, Australia）

16

Plenary Lecture 07

Time: 9:40-10:20 / Venue: Auditorium

Chair: Michael Tyers（University of Montreal, Canada）
PL-07

From phenotypes to pathways: global exploration of cellular
systems using yeast functional genomics
Brenda J Andrews（The Donnelly Centre, University of Toronto, Canada）

MONDAY, NOVEMBER 4Plenary Lecture 08

Time: 9:00-9:40 / Venue: Auditorium

Chair: Kim Avrama Blackwell（George Mason University, USA）
PL-08

Systems Biology of Reinforcement Learning
Kenji Doya（OIST, Japan）

Plenary Lecture 09

Time: 9:40-10:20 / Venue: Auditorium

Chair: Tadashi Yamamoto（OIST/JST, Japan）
PL-09

Impact of PD-1 deficiency on microbiome and brain
Sidonia Fagarasan（Laboratory for Mucosal Immunity, RIKEN IMS, Japan）

17

Program - Plenary Lectures
Plenary Lecture 10

Time: 17:40-18:20 / Venue: Auditorium

Chair: Brenda Andrews（University of Toronto, Canada）
PL-10

Charting the chemical-genetic interaction landscape of humancells through genome-wide CRISPR screensMichael Tyers（Institute for Research in Immunology and Cancer, University of Montreal, Canada）

TUESDAY, NOVEMBER 5
Plenary Lecture 11

Time: 9:00-9:40 / Venue: Auditorium

Chair: Mariko Okada（Osaka University, Japan）
PL-11

18

Our first choices: decoding signals during developmental
transitions
Silvia Santos（Francis Crick Institute, UK）

Program - Luncheon Seminars
FRIDAY, NOVEMBER 1
Luncheon Seminar 01

Time: 13:00-14:00 / Venue: Auditorium

Chair: Shuichi Onami（RIKEN, Japan）
LS-01

Networked biophotonics for image analysis beyond imaging
Sadao Ota（Research Center for Advanced Science and Technology, The University of Tokyo, Japan）

SATURDAY, NOVEMBER 2Luncheon Seminar 02

Time: 13:00-14:00 / Venue: Auditorium

Chair: Matthias Heinemann（University of Groningen, Netherland）
LS-02

Uncovering DNA grammar using deep learning
Aleksej Zelezniak（Chalmers University of Technology, Sweden）

19

Program - Luncheon Seminars
SUNDAY, NOVEMBER 3
Luncheon Seminar 03

Time: 13:00-14:00 / Venue: Auditorium

Chair: Samson Fong（UC San Diego, USA）
LS-03

Accelerating life sciences by AI and robotic biology
Koichi Takahashi（RIKEN BDR, Japan）

MONDAY, NOVEMBER 4
Luncheon Seminar 04

Time: 13:00-14:00 / Venue: Auditorium

Chair: Koichi Takahashi（RIKEN QBiC, Japan）
LS-04

Towards Visible Artificial Intelligence for Cancer Precision
Medicine
Samson Fong 1,2（ 1 Department of Medicine, University of California San Diego, USA）
（ 2 Department of Bioengineering, University of California San Diego, USA）

Luncheon Seminar 05

Time: 13:00-14:00 / Venue: B250

Chair: Hiroaki Kitano（SBI, Japan）
LS-05

Quantitative, population-level microbiome monitoring - the Flemish Gut Flora project
Jeroen Raes 1,2（ 1 Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-University of Leuven, Belgium）（ 2 VIB Center for Microbiology , Leuven , Belgium）

Sponsored: TSUMURA

20

Program - Parallel Sessions
FRIDAY, NOVEMBER 1
Multiscale Systems Biology

Time: 15:30-17:30 / Venue: Auditorium

Chair: Uwe Sauer（ETH Zurich, Switzerland）
Ayako Yachie-Kinoshita（SBI, Japan）
1PS1-01 Boolean signaling inputs control predictable cell fate transitions in mousepluripotency

15:30

Ayako Yachie-Kinoshita（SBI, Japan）
1PS1-02 From cells to tissue: continuum mechanics for tissue and cell population Shuji
Ishihara, Philippe Marcq, Kaoru Sugimura

15:50

Shuji Ishihara（The University of Tokyo, Japan）
1PS1-03 A hybrid mathematical model of the interplay between keratinocyte differentiationand skin barrier function to understand epidermal homeostasis
Elisa Domínguez-Hüttinger（Centre for Mathematical Scienices, National Autonomous University of Mexico, Mexico）

16:10

1PS1-04 Deep Decoding of Network Rewiring Mutations in Cancer
16:30
Rune Linding（Humboldt University of Berlin, Germany）
1PS1-05 Noise==Function: Is Single-cell Expression Variability Functionally Important?
James Cai（Texas A&M University, United States）

16:50

1PS1-06 Towards high-resolution whole-body cell lineage tracing of mammalian developmentusing an evolving DNA barcode technology
Nanami Masuyama（Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo., Japan）

17:10

Methodological Developments for Systems Biology Time: 15:30-17:30 / Venue: B250
Chair: Yong Wang（CAS-AMSS, China）
Atsushi Mochizuki（Kyoto University, Japan）
1PS2-01 Intepretating genetic variants by gene regulatory network
15:30

Yong Wang（Academy of Mathematics and Systems Science, China）

1PS2-02 Statistical test of structured continuous trees based on discordance matrix
15:50
Xiangqi Bai（Academy of Mathematics and System Science, Chinese Academy of Sciences, China）
1PS2-03 Information-theoretic causality predicts proteomic control of clinical parameters
16:10

and reveals cancer network biomarkers
Ian Overton（Queen's University Belfast, University of Edinburgh, United Kingdom）

21

Program - Parallel Sessions
1PS2-04 Understanding the System Dynamics of Mitochondrial Retrograde Signaling from
16:30
a Differential Equation-based Framework
Shao-Ting Chiu（National Taiwan University, Taiwan）
1PS2-05 Model-based identification of ErbB network principles among cell types
16:50
Hiroaki Imoto（Laboratory of Cell Systems, Institute for Protein Research, Osaka University, Japan）
1PS2-06 Origin of adaptation and modularity in chemical reaction networks
17:10
Atsushi Mochizuki（Kyoto University, Japan）

SATURDAY, NOVEMBER 2
Big Data, AI & Laboratory Automation

Time: 10:50-12:50 / Venue: Auditorium

Chair: Ross D. King（The University of Manchester and Alan Turing Institute, UK）
Jun Seita（RIKEN, Japan and Stanford University, USA, Japan）
2PS1-01 Towards the Automation of Systems Biology
10:50
Ross D. King（The University of Manchester and Alan Turing Institute, UK）
2PS1-02 Mechanistic Models of Ligand-induced Programmed Cell Death Fates
11:20
Carlos Lopez（Vanderbilt University, United States）
2PS1-03 Machine learning diagnosis of multiple liver-related diseases by exhaled breath gas
11:38
components
Shingo Shirone（Nara Institute of Science and Technology, Japan）
2PS1-04 Combining interpretable machine learning with high dimensional multi-omics data
11:56

from laboratory evolution
Junichiro Iwasawa（Department of Physics, The University of Tokyo, Japan）

2PS1-05 A human reference interactome map reveals cellular context-specific biological
12:14

mechanisms.
Dae-Kyum Kim（University of Toronto, Canada）

2PS1-06 Deep Learning approaches for reliable quantification of multi-omics cell imaging
12:32
datasets to interrogate RNA and protein spatial and temporal subcellular interactions
Emmanuel Bouilhol（University of Bordeaux - Bordeaux Bioinformatics Center; University of Bordeaux - CNRS, LaBRI, France）

22

Modeling Networks and Circuits

Time: 10:50-12:50 / Venue: B250

Chair: Luonan Chen（Shanghai Institutes for Biological Sciences, CAS, China）
Matteo Barberis（University of Surrey, UK）
2PS2-01 A Novel and Robust Molecular Design Synchronizing Transcriptional with Cell Cycle
10:50
Oscillators
Matteo Barberis（University of Surrey, United Kingdom）
2PS2-02 Success of oscillations in negative feedback gene regulatory networks is determined
11:10
by degradation rate uniformity
Ruben Perez-Carrasco（University College London, United Kingdom）
2PS2-03 Synchronization condition for hydrodynamically coupled Stokes spheres under
11:30
external flow
Yuki Izumida（The University of Tokyo, Japan）
2PS2-04 Model-driven Design of Mycoplasma pneumoniae for vaccine production
11:50
Erika Gaspari（Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands, Netherlands）
2PS2-05 Modelling cell type-specific signalling networks by mass cytometry in colorectal
12:10
cancer organoids
Thomas Sell（Charité Berlin, Germany）
2PS2-06 Dynamic network biomarkers detect tipping points of diseases by quantifying
12:30
their early-warning signals as general dynamic biomarkers
Luonan Chen（Shanghai Institutes for Biological Sciences, CAS, China）

Quantitative Systems Biology

Time: 15:30-17:30 / Venue: Auditorium

Chair: Matthias Heinemann（University of Groningen, Netherland）
Kwang-Hyun Cho（KAIST, Korea）
2PS3-01 A system of coupled oscillators driving the cell cycle
15:30

Matthias Heinemann（Molecular Systems Biology, University of Groningen, Netherland）

2PS3-02 A parallel cell-cycle entry pathway with inverted G1 signaling and alternate point
15:50

of no return
Tobias Meyer（Stanford University, United States）

2PS3-03 Mechanism of Jet lag: Mathematical and Experimental Study
16:10
Hiroshi Kori（The University of Tokyo, Japan）
2PS3-04 Optical control of cell signaling with red/far-red light in human cells, fission yeast,
16:30
and worms
Kazuhiro Aoki（National Institutes of Natural Sciences, National Institute for Basic Biology, Japan）

23

Program - Parallel Sessions
2PS3-05 Bistability in ferroptosis leads to an irreversible switch
16:50
Pedro Mendes（University of Connecticut, United States）
2PS3-06 Tradeoffs between growth and adaptability shape microbial phenotypes
17:10
Markus Basan（Harvard University, United States）

Synthetic Biology

Time: 15:30-17:30 / Venue: B250

Chair: Matthew Wook Chang（National University of Singapore, Singapore）
Miki Ebisuya（EMBL Barcelona, Spain）
2PS4-01 Engineering microbes to rewire host-microbiome interactions
15:30
Matthew Wook Chang（National University of Singapore, Singapore）
2PS4-02 A CRISPR–barcode technology to isolate a target clone from a heterogeneous cell
15:55
population
Soh Ishiguro（Research Center for Advanced Science and Technology, The University of Tokyo., Japan）
2PS4-03 Comparing burden on a single cell with cell consortia using two-stage substrate
16:10
conversion
Zoltan Tuza（Imperial College London, United Kingdom）
2PS4-04 Perfusable synthetic self-organized vascular network - experiment and modeling
16:25
Takashi Miura（Kyushu University, Japan）
2PS4-05 The development of the intestinal circadian clock and its roles in intestinal organoids
16:50
Christian Hong（University of Cincinnati, United States）
2PS4-06 Human Time vs. Mouse Time with Recapitulated Systems
17:05
Miki Ebisuya（EMBL Barcelona, Spain）

SUNDAY, NOVEMBER 3
Systems Medicine and Healthcare

Time: 10:50-12:50 / Venue: Auditorium

Chair: Nathan Price（Institute for Systems Biology, USA）
Reiko Tanaka（Imperial College London, UK）
3PS1-01 Longitudinal Deep Phenotyping of Thousands of People: Insights for Precision
10:50

Medicine
Nathan Price（Institute for Systems Biology, USA）

3PS1-02 Mechanistic modelling towards designing personalised treatment strategies for
11:14
eczemaReiko Tanaka（Department of Bioengineering, Imperial College London, UK）
24

3PS1-03 Data-driven study of cancer evolution and implications in precision oncology
11:38
Jiguang Wang（The Hong Kong University of Science and Technology, Hong Kong）
3PS1-04 eBrain: a Three Dimensional Simulation Tool to Study Drug Delivery in the Brain.
12:02
Yaki Setty（Gateway Institute for Brain Research, Israel）
3PS1-05 Discovering the genes mediating the interactions between chronic respiratory
12:26
diseases in the human interactome
Enrico Maiorino（Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, United States）

Developmental Systems Biology

Time: 10:50-12:50 / Venue: B250

Chair: Mary N. Teruel（Stanford University, USA）
Kaoru Sugimura（Kyoto University, Japan）
3PS2-01 A gradual increase in the duration of an extended G1 period enables stochastic
10:50
competition between the decision to terminally differentiate or enter the next cell
cycle
Mary N. Teruel（Dept. of Chemical and Systems Biology, Stanford University, USA）
3PS2-02 Comprehensive determination of logic functions for genes that initiate expression in
11:14
early ascidian embryos
Yutaka Satou（Kyoto University, Japan）
3PS2-03 Precision of Tissue Patterning is Controlled by Dynamical Properties of Gene
11:38
Regulatory Networks
Edgar Herrera Delgado（The Francis Crick Institute & King's College London, United Kingdom）
3PS2-04 Computational modeling and experiments of cell wrapping: dissecting the
12:02
mechanisms of endothelial cell coverage by pericytes.
Kei Sugihara（Kyushu University Graduate School of Medical Sciences, Japan）
3PS2-05 Planar polarization of the multi-ciliated planarian epidermis by body plan landmarks
12:26

Lutz Brusch（Technische Universität Dresden, Center for Information Services and High Performance Computing, Dresden, Germany）

Systems Biology for Neurosciences and Neural Circuits Time: 10:50-12:50 / Venue: C210
Chair: Kim Avrama Blackwell（George Mason University, USA）
Erik De Schutter（OIST, Japan）
3PS3-01 AMPA-type glutamate receptor subunits in the synapse turnover by monomer
10:50

diffusion; unraveling by single-molecule tracking
Jyoji Morise（Division of Human Health Sciences, Graduate School of Medicine, Kyoto University, Japan）

3PS3-02 Nanoscale analysis of neuronal spine synapses
11:10
Shigeo Okabe（The Unversity of Tokyo, Japan）

25

Program - Parallel Sessions
3PS3-03 The role of dopamine and post-synaptic signaling molecules in synaptic plasticity
11:30
and relapse to alcohol use
Kim Avrama Blackwell（George Mason University, Department of Bioengineering, USA）
3PS3-04 Chronometabolism in diurnal primates and nocturnal rodents
11:50
Hitoshi Okamura（Kyoto University, Japan）
3PS3-05 Modeling Purkinje neuron activity in 3D morphologies at the nanoscale
12:10
Alexey Martyushev（Okinawa Institute of Science and Technology Graduate University OIST, Japan）
3PS3-06 Individuality in the neural network dynamics in C. elegans
12:30
Yuichi Iino（The University of Tokyo, Japan）

MONDAY, NOVEMBER 4
Systems Biophysics

Time: 10:50-12:50 / Venue: Auditorium

Chair: Yuichi Taniguchi（RIKEN BDR, Japan）
Chao Tang（Peking University, China）
4PS1-01 Cooperative reliable response from sloppy gene expression dynamics
Masayo Inoue（Meiji University, Japan）

10:50

4PS1-02 Kinetic uncertainty relations for the control of stochastic reaction networks
Jiawei Yan（Harvard University, United States）

11:14

4PS1-03 A Theoretical Approach to Understand the Role of the Retention Mechanism in
11:38

the Rejuvenation Process
Barbara Schnitzer（University of Gothenburg, Sweden）

4PS1-04 Controlling cell fate specification system by key genes determined from network
12:02
structure
Kenji Kobayashi（Department of Zoology, Graduate School of Science, Kyoto University, Japan）
4PS1-05 Computational analysis of nuclear division dynamics in early C. elegans embryos
Koji Kyoda（RIKEN Center for Biosystems Dynamics Research, Japan）

12:26

EcoSystems Biology

Time: 10:50-12:50 / Venue: B250

Chair: Edda Klipp（Humboldt-Universität zu Berlin, Germany）
Evan P. Economo（OIST, Japan）
4PS2-01 Modeling of yeast growth, division and stress response with focus on differencein the behavior of a single cell and the population
Edda Klipp（Humboldt-Universität zu Berlin, Theoretical Biophysics, Germany）

10:50

26

4PS2-02 Mathematical interaction model of nasal pathogen interaction
11:15
Reihaneh Mostolizadeh（University of Tübingen, Germany）
4PS2-03 Analysis of phenotypic constraints by high-throughput laboratory evolution of
11:40
Escherichia coli
Chikara Furusawa（Center for Biosystems Dynamics Research, RIKEN, Japan）
4PS2-04 The traditional Japanese medicine（Kampo）Bofutsushosan as an anti-obesity
12:05
medication: possible involvement of gut microbiota
Mitsue Nishiyama（Tsumura Kampo Research Laboratories, Tsumura and Co., Japan）
4PS2-05 The methyl cycle is a conserved regulator of biological clocks
12:20
Jean-Michel Fustin（Kyoto University, Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Japan）
4PS2-06 A data-based mathematical model predicts dynamic trajectories of a protected
12:35
plant community under different conservation regimes
Jaime Acosta（Science Faculty, National Autonomous University of Mexico, Mexico）

Single-cell Systems Biology

Time: 15:30-17:30 / Venue: Auditorium

Chair: Roy Wollman（UCLA, USA）
Wataru Fujibuchi（Kyoto University, Japan）
4PS3-01 Decipering Cell States: the relationship between single-cell gene expression and
15:30
phenotypic heterogeneity in calcium signaling
Roy Wollman（University of California, USA）
4PS3-02 Exploring universal aging dynamics using Escherichia coli as a model
15:50

Yifan Yang（Weizmann Institute of Science, Israel）

4PS3-03 Combining single cell and cell population based analysis identifies mechanisms
16:10
leading to Acetaminophen-induced inhibition of cell cycle progression in hepatocytes
Artyom Vlasov（German Cancer Research Center（DKFZ）, Germany）
4PS3-04 Inferring activity and targets of enhancers in single cells through single-cell enhancer
16:30

RNA analysis
Haruka Ozaki（Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Japan）

4PS3-05 Single-cell trajectories reconstruction, exploration and mapping of omics data with
16:50

STREAM
Andrei Zinovyev（Institut Curie, France）

4PS3-06 Multiscale clonal model of Germinal Center B cell differentiation
17:10

Maria Rodriguez Martinez（IBM, Zurich Research Laboratory, Switzerland）

27

Program - Parallel Sessions
Multi-omics

Time: 15:30-17:30 / Venue: B250

Chair: Jason W Locasale（Duke University, USA）
Katsuyuki Yugi（RIKEN IMS, Japan）
4PS4-01 Trans-omic analysis of the central metabolism of Saccharomyces cerevisiae by
15:30
integration of metabolome, metabolic flux, and proteome data
Fumio Matsuda（Osaka University, Japan）
4PS4-02 From protein translation to fluxes – quantitative systems biology of yeast stress
15:50
responses
Petri-Jaan Lahtvee（University of Tartu, Estonia）
4PS4-03 Unraveling the impact of compensatory evolution on metabolic divergence
16:10
Dorottya Kalapis（HAS, Biological Research Centre, Hungary）
4PS4-04 Unraveling acetogen gas fermentation using quantitative systems biology
16:30
Kaspar Valgepea（ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Estonia）
4PS4-05 Systems Biology of Herbal Medicine: Elucidating the complex interactions between
16:50
traditional herbal medicine and endogenous biological systems
Akinori Nishi（Tsumura Kampo Research Laboratories, Tsumura and Co., Japan）
4PS4-06 Quantitative approaches to understanding metabolism in cancer
17:10
Jason W Locasale（Department of Pharmacology and Cancer Biology, Duke University School of Medicine, USA）

28

Program - Poster Sessions
FRIDAY, NOVEMBER 1
Time: 14:10-15:30 / Venue: Tunnel Gallery

Big Data, AI & Laboratory Automation
1P-001

Deep Learning-based quantitative evaluation of early embryo in infertility treatments
Yuta Tokuoka（Keio University, Japan）

1P-002

Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs
Dirk Fey（Systems Biology Ireland, Ireland）

1P-003Cell Image Segmentation Using Attention Module at Each Layer
Daisuke Matsuzuki（Meijo University, Japan）

1P-004

Image Translation for Cell Image Segmentation Using Deep Learning
Sota Kato（Meijo University, Japan）

1P-005Subcellular mitochondria structure prediction in label-free microscope images using
convolutional neural networks
Chan-Min Hsu（National Taiwan University, Taiwan）

Developmental Systems Biology
1P-006

Theoretical tool bridging cell polarities with development of robust morphologies
Silas Boye Nissen（Niels Bohr Institute, University of Copenhagen, Denmark）

1P-007

Vascular intraluminal pressure inhibits angiogenic branch elongation
Koichi Nishiyama（Kumamoto University, Japan）

1P-008Force-sensitivity of alpha-catenin and epithelial morphogenesis
Shigenobu Yonemura（Tokushima University Graduate School of Medical Science, Japan）

1P-009Perivascular pericytes facilitate endothelial branch elongation in angiogenesis:
possible involvement of biomechanical mechanisms
Yasuyuki Hanada（Nagoya University, Kumamoto University, Japan）

1P-010

Vascularization of a tumor spheroid in a microfluidic device to investigate floweffects on growth and drug delivery
Yuji Nashimoto（Tohoku University, Japan）

Methodological Developments for Systems Biology
1P-011

Towards a physiological scale of vocal fold agent-based biological models:sensitivity analysis, calibration and validation
Nicole Y. K. Li-Jessen（McGill University, Canada）

29

Program - Poster Sessions
1P-012

Regulating Pseudomonas aeruginosa Biofilm using Spatio-Temporal Cellular
Automata
Kumar Selvarajoo（Agency for Science, Technology & Research（A*STAR）, Singapore）

1P-013

The rubber band method of ranking network mechanisms rather than claiming
the single best: E. coli's active ammonium transport is 130 times better than thepassive transport network
Kazuhiro Maeda（Kyushu Institute of Technology, Japan）

1P-014A distributed computing framework to reconstruct lineage trees of millions ofsequences
Naoki Konno（The University of Tokyo, Japan）

1P-015

Quantification of the methylation-based cellular memory in Escherichia coli
chemotaxis
Jürgen Pahle（Heidelberg University, Germany）

1P-016

A Semigroup Formalism for Biochemical Reaction Networks
Dimitri Loutchko（The University of Tokyo, Japan）

1P-017

Vesicle modeling extension to reaction-diffusion simulator STEPS
Iain Hepburn（Okinawa Institute of Science and Technology Graduate University, Japan）

Modeling Networks and Circuits
1P-018High Throughput Genome-Scale Metabolic Model Reconstruction and Reconciliation
with Tn-seq Data
Jose Faria（Data Science and Learning, Argonne National Laboratory, Argonne, IL, United States）

1P-019Withdrawn

1P-020Genetic interactions derived from high-throughput phenotyping of 7,350 yeast cell
cycle mutants
Jenna Gallegos（Colorado State University, United States）

1P-021

Detecting the early-warning signal of the critical transition for complex diseases
Pei Chen（South China University of Technology, China）

1P-022In silico lymphangiogenesis: Development of an intracellular network model ofreceptor trafficking and signaling pathway in lymphatic endothelial cells
Sophie Bekisz（University of Liege, Belgium）

1P-023

A whole cell modeling of bacteria from genomic sequence
Kazunari Kaizu（RIKEN Center for Biosystems Dynamics Research, Japan）

30

1P-024

Ensemble boolean modeling sheds light on the molecular mechanisms of tumor
invasion
Vincent Noel（Institut Curie, PSL Research University, Mines Paris Tech, Inserm, France）

1P-025

Scalable Simulation of Biochemical Models with PySB
Alexander Lubbock（Vanderbilt University, United States）

1P-026

Modeling signal transduction networks in heterogeneous colon cancer using single
cell modelling
Nils Blüthgen（Charite, Germany）

1P-027

Withdrawn

1P-028Mathematical modeling for endothelial cell migration during sprouting angiogenesis
Tatsuya Hayashi（Faculty of Information Science and Technology, Hokkaido University, Japan）

1P-029Hematopoiesis modeling and applications
Nathaniel Mon Pere（Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium）

1P-030Modeling of infection in a growing plaque to quantify role of amino acid mutations
in GP of filovirus
Kwangsu Kim（Department of Biology, Faculty of Sciences, Kyushu University, Japan）

1P-031

In silico and in vivo experiments reveal mechanism of centrosome positioning duringmitosis
Yoshitaka Yamazaki（Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Japan）

1P-032

Post-transcriptional regulation, noise and spatial transcript localization of small
RNA-controlled genes in an Escherichia coli stress response network
Rinat Goren（Weizmann Institute of Science, Israel）

1P-033Development of an in silico chondrocyte via mechanistic and data-driven modelingfor the study Osteoarthritis progression and the identification of potential intervention
targets.
Raphaëlle Lesage（Katholieke Universiteit Leuven, Belgium）

1P-034

Synthetic genetic networks based on neural models in living cells
Ramez Daniel（Technion- Israel Institute of Technology, Israel）

1P-035

Viruses are modulators in the human molecular system
Vandana Ravindran（MRC-Centre for Virus Research University of Glasgow, United Kingdom）

1P-036

Investigating Pulsed Neural Network Structures in a Framework of Dynamical
Bayesian Network by a Greedy Searching
Chaoyi Dong（Inner Mongolia University of Technology, China）

1P-037

Sensitivity analysis for elementary circuits in signal transduction model
Kentaro Inoue（University of Miyazaki, Japan）
31

Program - Poster Sessions
Multi-omics
1P-038

DEIso: a database for differentially expressed isoforms/genes in human cancers
Wei-Sheng Wu（National Cheng Kung University, Taiwan）

1P-039Workflow for TF knockout simulations on transcriptome primed whole genome
metabolic model reconstructions for 10 antibiotic resistant E. coli strains
Daria Gaidar（Saarland University, Germany）

1P-040Time Series Transomics: Integrated analysis through multiple molecular layers
Fumiko Matsuzaki（Kyushu University, Japan）

1P-041

Prediction of pioneer transcription factors from DNA methylation profiles
Harukazu Suzuki（RIKEN IMS, Japan）

1P-042

Exploring the landscape of regulatory elements on promoter regions of cassava
AGPase genes via TFBS scan and phylogenetic footprinting approach
Saowalak Kalapanulak（King Mongkut's University of Technology Thonburi, Thailand）

1P-043

Effect of Synechocystis-Hik28 deletion on photosynthetic activity and fatty acidprofile under nitrogen and temperature stresses
Pavinee Rakruangdet（National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand）

1P-044

Proteomic and phosphoproteomic profiling of lineage transition in mice from lung
ADC to SCC represent molecular mechanism for drug resistance
Chen Li（Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China）

1P-045Interconnection of carbon- and nitrogen metabolism and its possible role intemperature stress response in Arthrospira（Spirulina）platensis C1
Apiradee Hongsthong（National Science and Technology Development Agency, Thailand）

1P-046

A trans omic analysis of insulin action in Drosophila S2R+ cells acrossphosphoproteome, protein-protein interactions, transcriptome, and metabolome
Akira Terakawa（The University of Tokyo, Japan）

Multiscale Systems Biology
1P-047

Time-series analysis of the concentration changes of human blood metabolites
and hormones after oral glucose ingestion
Suguru Fujita（The University of Tokyo, Japan）

1P-048

Deciphering Yeast Physiology by a Multi-scale Framework Integrating Cell Cycle
and Metabolism
Matteo Barberis（University of Surrey, United Kingdom）

32

1P-049

Trans-omic analysis reveals different responses to glucose in the muscle duringobesity
Miki Eto（The University of Tokyo, Japan）

1P-050Metabolome analysis of glucose dose-dependent metabolism in mice liver
Yifei Pan（The University of Tokyo, Japan）

1P-051Modeling the coupled within- to between-host dynamics of a viral infectious disease
Alexis Erich Almocera（Division of Physical Sciences and Mathematics, University of the Philippines Visayas, Miag-ao, Philippines）

Quantitative Systems Biology
1P-052

Nitrogen limitation reveals large reserves in the metabolic and translational capacities
of yeast
Rosemary Yu（Chalmers University of Technology, Sweden）

1P-053

Role of temporal waveform of biological rhythms and its quantification
Shingo Gibo（Interdisciplinary Theoretical and Mathematical Sciences Program, RIKEN, Japan）

1P-054

Metabolic flux changes over time and the regulatory mechanisms in insulinstimulated adipocytes
Satoshi Ohno（Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, Japan）

1P-055CRISPR-PCA screens highlight the contribution of protein context to the regulationof SRC Homology 3（SH3）domains protein-protein interactions
Ugo Dionne（Laval University, Canada）

1P-056

Systematic Identification of Genes Whose Overexpression Works Adaptively Using
the ADOPT System
Nozomu Saeki（Okayama University, Japan）

1P-057Creating consortia metabolic models for Next Generation Probiotics
Isma Belouah（Tartu University Institute of Technology, Estonia）

1P-058Large-scale morphological feature extraction by spherization and sphericalharmonics decomposition from in vivo 3D migrating immune cells
Saori Uematsu（The University of Tokyo, Japan）

1P-059Quantitative insights into the cyanobacterial cell economy
Marjan Faizi（Humboldt University Berlin, Germany）

1P-060Withdrawn

1P-061

Environment-dependent binary protein interactome of a cell
Dayag Sheykhkarimli（Department of Molecular Genetics, University of Toronto; Donnelly Centre; Lunenfeld-Tanenbaum Research Institute., Canada）

1P-062

GB-X Map: Causal Pathways and Motifs common in IBD and Schizophrenia
Saptarshi Bej（University of Rostock, Institute of Computer Science, Department of Systems Biology and Bioinformatics, Germany）
33

Program - Poster Sessions
Systems Biophysics
1P-063

Allosteric regulation of Glutamate dehydrogenase deamination activity
Soumen Bera（Central University of Rajasthan, India, India）

1P-064

Essential role of cytoskeleton polarity for alignment and orientation of basal bodies
in multi-ciliated cellToshinori Namba（The University of Tokyo, Japan）

1P-065

TPPP3 promotes microtubule networking adaptive to the external stress changes
Kazuhiro Oiwa（National Institute of Information and Communications Technology, Japan）

1P-066

Quantitative analysis of cellular dynamics in C. elegans embryos
Yusuke Azuma（RIKEN Center for Biosystems Dynamics Research, Japan）

1P-067

Evaluation of the time-delay effect of molecular surface diffusion due to positive
Gaussian curvature of dendritic spine head
Kenji Kimura（Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Japan）

1P-068Signal transduction systems run by metastable molecular complexes: discoveries
by single-molecule tracking
Akihiro Kusumi（Okinawa Institute of Science and Technology Graduate University, Japan）

Systems Medicine and Healthcare
1P-069Functional analysis of the MAPK scaffold KSR1 in malignant melanoma
Zhi Liu（Systems Biology Ireland, University College Dublin, Ireland）

1P-070An in silico approach to identify potential interactors of toxic huntingtin proteins
Do Young Hyeon（Seoul National University, South Korea）

1P-071

The innate immune response to respiratory fungal infections: a systems medicine
approach
Reinhard Laubenbacher（University of Connecticut School of Medicine, United States）

1P-072

Personalized Microbiota Dynamics for Disease Classification
Xiangtian Yu（Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China）

1P-073

Trans-omic analysis reveals allosteric and gene regulation-axes for alteredglucose-responsive liver metabolism associated with obesity
Toshiya Kokaji（Department of Biological Sciences, Graduate School of Science, University of Tokyo., Japan）

1P-074

Pan-Cancer Analyses Reveal Signaling Entropy Features associated with Tumor
Stemness, Metastasis and Prognosis
Rong Zeng（Shanghai Institute of Biochemistry and Cell Biology, CAS, China）

34

1P-075

Comprehensive metabolite profiling of traditional herbal medicine in human plasma:from metabolites to phenotypes
Katsuya Ohbuchi（Tsumura & Co., Japan）

1P-076Predicting the responsiveness of targeted anti-cancer drugs based on signal flow
distribution by mapping genomic data onto the topological signaling network
Yunseong Kim（Laboratory for Systems Biology and Bio-Inspired Engineering, KAIST, South Korea）

1P-077On the prediction of protein abundance from RNA
Rasmus Magnusson（Linköping University, Sweden）

1P-078The methodological trends of traditional herbal medicine employing network
pharmacology methods
Won-Yung Lee（College of Korean Medicine, Gachon University, South Korea）

Methodological Developments for Systems Biology
1P-079Design and construction of novel one-carbon assimilation pathways
Hongwu Ma（Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China）

1P-080GlycoMaple for global mapping of glycosylation pathways in human-derived cells
Morihisa Fujita（Jiangnan University, China）

1P-081

OpenCOR: a modelling environment for reproducible science
Alan Garny（The University of Auckland, New Zealand）

Modeling Networks and Circuits
1P-082

Hepatocyte growth factor increases glycolytic flux in HepG2 cells by inducing gene
expression of multiple isoforms of hexokinase and glucose transporter type 1
Irina Titkova（German Cancer Research Center（DKFZ）, Germany）

1P-083A landscape view on the interplay between EMT and cancer metastasis
Chunhe Li（Fudan University, China）

1P-084

Error-speed correlations in biopolymer synthesis
Davide Chiuchiù（Okinawa Institute for Science and Technology, Japan）

Quantitative Systems Biology
1P-085

The role of sigma factors in circadian transcriptional output networks of unicellularcyanobacteria
Koji Kawasaki（Department of Electrical Engineering and Bioscience, Waseda University, Japan, Japan）

35

Program - Poster Sessions
SATURDAY, NOVEMBER 2
Time: 14:10-15:30 / Venue: Tunnel Gallery

Big Data, AI & Laboratory Automation
2P-001FAIR data exchange in the life sciences by standardization of heterogenous data
and models
Martin Golebiewski（HITS gGmbH, Germany）

2P-002The JSBML Project: A Fully Featured Java API for Working with Systems BiologicalModelsAndreas Dräger（Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, University of Tübingen, Germany）

2P-003

SSBD: an open public database of microscopy images and quantitative data of
biological dynamics facilitating the reuse and reanalyze of biological data
Kenneth Ho（RIKEN Center for Biosystems Dynamics Research（BDR）, Japan）

2P-004

ProtFunAI - An artificial intelligence for prediction of protein function from protein
sequence alone
Torbjörn E. M. Nordling（Department of Mechanical Engineering, National Cheng Kung University, Taiwan）

2P-005

Estimation of intracellular key enzymes by applying machine learning algorithm
Kakeru Kosaka（Nara Institute of Science and Technology, Japan）

Developmental Systems Biology
2P-006

Maternal factors involved in developmental buffering
Atsuko Sato（Ochanomizu University, Japan）

2P-007

Reconstruction and understanding of long-term microvascular remodeling in a
microfluidic platform
Takanori Sano（Kyushu University, Japan）

2P-008

A microfluidic chip to evaluate the role of pericytes and fluid flow in vasculardevelopment
Scott Erickson（Kyoto University, Japan）

2P-009Inferring gene regulatory network and differentiation dynamics of human embryonicstem cell
Yukitaka Isaka（RIKEN and The University of Tokyo, Japan）

2P-010On-chip 3D biomimetic model to reconstitute vital phenomena with vascular andinterstitial flow
Sanshiro Hanada（Kumamoto University, Japan）

36

EcoSystems Biology
2P-011

A Theory on the Survival of Species in a Microbial Aquatic Food Web with Chytrids
Alexis Erich Almocera（Division of Physical Sciences and Mathematics, University of the Philippines Visayas, Miag-ao, Philippines）

2P-012

Identification of microbial community functioning for sulfide removal and electricity
generation in microbial fuel cell: Application for wastewater treatment of canned
pineapple factory in Thailand
Nattawet Sriwichai（King Mongkut's Uinversity of Technology Thonburi, Thailand）

2P-013

Identification of mutations conferring resistance to anti-tuberculosis drugs bylaboratory evolution of non-pathogenic Mycobacterium on agar plate
Tomoya Maeda（RIKEN Center for Biosystems Dynamics Research, Japan）

Methodological Developments for Systems Biology
2P-014Tools for scalable simulation and parameter estimation of ordinary differential
equation models
Daniel Weindl（Helmholtz Zentrum München, Germany）

2P-015

BioModels Parameters: A resource to search and retrieve parameters from publishedsystems models
Rahuman Sheriff（European Bioinformatics Institute - European Molecular Biology Laboratory（EMBL-EBI）, United Kingdom）

2P-016

Efficient parameter estimation methods for integration of qualitative data inquantitative models
Leonard Schmiester（Helmholtz Zentrum München, Germany）

2P-017

SABIO-RK: a comprehensive reaction kinetics information system
Andreas Weidemann（HITS gGMBH, Germany）

2P-018Automated search of a minimal set of adjustable parameters optimizing constrained
kinetic model of metabolism
Egils Stalidzans（University of Latvia, Latvia）

2P-019Deciphering animal decision making by inverse reinforcement learning
Honda Naoki（Kyoto University, Japan）

2P-020E-Cell System version 4: An integrated platform for cell simulations
Kozo Nishida（RIKEN Center for Biosystems Dynamics Research, Japan）

Modeling Networks and Circuits
2P-021

Establishment and Maintenance of two opposing transcriptional states during
random X-chromosome inactivation
Verena Mutzel（Max Planck Institute for Molecular Genetics, Germany）

37

Program - Poster Sessions
2P-022

Withdrawn

2P-023Discrete empirical interpolation for model reduction in biological systems
Neveen Ali Salem Eshtewy（Freie Universität Berlin, Germany）

2P-024Model-driven Safety-by-design in Synthetic Biology
Erika Gaspari（Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands, Netherlands）

2P-025

Automatic Adaptive Refinement of Bayesian Networks for Biomarker Discovery from
Heterogeneous Healthcare Data
Ann-Kristin Becker（University Medicine Greifswald, Germany）

2P-026

Deciphering the differential NF-κB activity regulation due to different posttranslational modifications of NF-κB complex subunits
Ahmed Mobeen（CSIR - Institute of Genomics and Integrative Biology; Academy of Scientific & Innovative Research（AcSIR）, India）

2P-027

Exploring glioblastoma cell state dynamics using single cell lineage tracing
Ida Larsson（Uppsala University, Sweden）

2P-028The polarising world of Cdc42: the importance of geometry in cell division
Johannes Borgqvist（University of Gothenburg, Sweden）

2P-029Withdrawn

2P-030Cost-speed trade-off and optimal strategies for biochemical regulation
Ken-Ichi Hironaka（The University of Tokyo, Japan）

2P-031Mathematical modelling of the interplay between early viral replication and immune
signalling
Darius Schweinoch（University Medicine Greifswald, Institute of Bioinformatics, Germany）

2P-032Growth-coupled overproduction is theoretically possible for most metabolites in
Saccharomyces cerevisiae under anaerobic condition
Takeyuki Tamura（Kyoto University, Japan）

2P-033

Non-sinusoidal waveform in biological rhythms and a method to predict a black box
using its waveform
Gen Kurosawa（RIKEN iTHEMS, Japan）

2P-034

Alteration in MicroRNA dynamics fine-tunes Nanog expression heterogeneity
Tagari Samanta（INDIAN INSTITUTE OF TECHNOLOGY BOMBAY, India）

38

2P-035

Withdrawn

2P-036

Atlas of Cancer Signaling Network: a resource of multi-scale biological maps tostudy disease mechanisms
Inna Kuperstein（Institut Curie, France）

2P-037

A Realistic Spatial Model of the Complete Synaptic Vesicle Cycle
Andrew Gallimore（Okinawa Institute of Science and Technology Graduate University, Japan）

2P-038

Withdrawn

2P-039A hybrid mathematical model for design and optimization of tamoxifen treatment in
MCF-7 breast cancer cells
Elisa Domínguez-Hüttinger（Centre for Mathematical Sciences, National Autonomous University of Mexico, Mexico）

2P-040Withdrawn

Multi-omics
2P-041

Differential trans-omic networks in the liver and muscles between healthy andobese mice
Riku Egami（Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo., Japan）

2P-042

Withdrawn

2P-043

Sequential pattern fusion analysis for brain evolution analysis by cross-species andcross-tissues omics data
Tao Zeng（Key Laboratory of Systems Biology, SIBS, CAS, China）

2P-044

Genome-wide CRISPR screen identifies TMEM41B as a gene required for
autophagosome formation
Keigo Morita（Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Japan）

2P-045

Bioinformatic pipeline aided proteome-wide analysis for deciphering bioactive
peptides from the Spirulina proteins
Jittisak Senachak（National Center for Genetic Engineering and Biotechnology, Thailand）

2P-046Comprehensive characterization of chromatome by SWATH-MS
Atsushi Hatano（RIKEN Center for Integrative Medical Sciences, Japan）

2P-047Comparative genomics of two tardigrades with different cryptobiotic capacities
Yuki Yoshida（Keio University, Japan）

Quantitative Systems Biology
2P-048Multi-dimensional analysis of NF-κB nuclear dynamics
Johannes Nicolaus Wibisana（Osaka University, Japan）

2P-049A NF-κB - p38 MAPK crosstalk shapes oscillatory gene expression
Hiroki Michida（Osaka University, Japan）

2P-050

Hsp90-dependent strain-specific differential gene expression is common in yeast
populations
Po-Hsiang Hung（Institute of Molecular Biology, Academia Sinica, Taiwan）
39

Program - Poster Sessions
2P-051

Systems-level modelling of meiosis regulatory network
Prakrati Dangarh（International Institute of Information and Technology, Hyderabad, India）

2P-052Controlling biological networks using Boolean algebra
Chun-Kyung Lee（Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology（KAIST）., Korea）

2P-053

Predicting cell-line specific drug response profiles from analysis of the pan-cancer
genetic regulatory network
Yun-Won Kang（Korea Advanced Institute of Science and Technology, South Korea）

2P-054

Carbon Flux Partition Underlying Storage Root Growth of Cassava Variety KU50
Inferred by Transcriptome-Integrated Metabolic Model
Ratchaprapa Kamsen（King Mongkut's University of Technology Thonburi, Thailand）

2P-055High-resolution live-cell imaging analysis in the formative process of coordinatedairway ciliary beating
Satoshi Konishi（Osaka Univesity, Kyoto University, Japan）

2P-056

A Multi-layer Analysis of Signal-dependent Cell Cycle Progression
Kyoichi Ebata（Laboratory of Cell Systems, Institute for Protein Research, Osaka University, Japan）

2P-057

Absolute Quantification of the Mitochondrial Proteome Reveals the Dual Role inDiauxic growth of Saccharomyces cerevisiae
Carl Malina（Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden）

2P-058

Proteome Re-Allocation Towards Amplified Translational Machinery as the Limiting
Factor for Increased Growth Rate of Amino Acid Supplemented Saccharomyces
cerevisiae.
Johan Björkeroth（Chalmers University of Technology, Sweden）

Single-cell Systems Biology
2P-059A multi-omic approach to predict gene expression and specific metabolic function
from label-free spectral imaging of living cells.
Arno Germond（RIKEN, Japan）

2P-060Modelling of single-cell mass cytometry data to unravel breast cancer heterogeneity
Maria Rodriguez Martinez（IBM, Zurich Research Laboratory, Switzerland）

2P-061

Multi-step structure of cell fate decisions in murine neural crestPeter Kharchenko（Harvard University, United States）

2P-062Single-cell information analysis reveals small intracellular and large intercellularvariations increase cellular information capacity
Takumi Wada（The University of Tokyo, Japan）

40

Synthetic Biology
2P-063Engineering 16-repeats PUF proteins to sequence-specifically manipulate RNAfunctions
Miki Imanishi（Kyoto University, Japan）

2P-064

A single base editor for simultaneous C:G to T:A and A:T to G:C mutations
Rina Sakata（The University of Tokyo, Japan）

2P-065Pooled matrix screen of protein interactomes using Barcode Fusion GeneticsProtein-fragment Complementation Assay（BFG-PCA）
Daniel Evans-Yamamoto（Research Center for Advanced Science and Technology, The University of Tokyo, Japan）

2P-066

Systematic perturbation of yeast essential genes using base editing
Philippe Després（IBIS, Université Laval, Canada）

2P-067

Barcode Split Genetics（BSG）Public-key Cryptography
Sean Leo Kito Okawa（Research Center for Advanced Science and Technology, The University of Tokyo, Japan）

2P-068A genome-wide CRISPR screen reveals novel genetic vulnerabilities to telomerase
inhibition and telomere erosion
Lea Harrington（University of Montreal, Canada）

Systems Biophysics
2P-069Transient dimerization of a postsynaptic cell adhesion molecule neuroligin and its
implications in the regulation of trans-synaptic adhesion
Saahil Acharya（Okinawa Institute of Science and Technology（OIST）, Japan）

2P-070Transient hetero-dimerization of opioid receptors（GPCRs）and their formation
mechanisms revealed by single-molecule tracking
Peng Zhou（Membrane Cooperativity Unit, Okinawa institute of Science and Technology Graduate University（OIST）., Japan）

2P-071

Feedback design for desynchronization based on the analysis of the SakaguchiKuramoto model
Ayumi Ozawa（Ochanomizu University, Japan）

2P-072

N-terminal reagion of Drosophila Argonaute2 can form amyloid fibrils
Haruka Narita（The University of Tokyo, Japan）

2P-073Single-molecule tracking of the RNA cleavage and the dissociation driven bysilkworm PIWI-clade Argonaute Siwi and RNA helicase Vasa
Sotaro Uemura（The University of Tokyo, Japan）

41

Program - Poster Sessions
Systems Medicine and Healthcare
2P-074Computational modeling identifies optimal use of EGFR tyrosine kinase inhibitors
for lung cancer patients with EGFR mutations
Hiroshi Haeno（The University of Tokyo, Japan）

2P-075

Variant effect mapping of coding mutations in the human low density lipoprotein
receptor（LDLR）gene
Atina Cote（University of Toronto, Canada）

2P-076

Metabolic Network Modelling of Neuro-Psychatric Disorders
Sai Teja Reddy Moolamalla（International Institute of Information Technology, India）

2P-077A missense variant effect map for the human MTHFR gene in two common genetic
backgrounds
Jochen Weile（The Donnelly Centre & Lunenfeld-Tanenbaum Research Institute; University of Toronto, Canada）

2P-078Metabolic Fingerprint of Hepatic Tumor Cells
Gerda Schicht（Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital Leipzig, Germany）

2P-079Dynamic modelling of cancer signalling for improved patient stratification
Dirk Fey（Systems Biology Ireland, Ireland）

2P-080Quantification of heterogeneity of gastric cancer tumors based on Matrix-Assisted
Laser Desorption Ionization or MALDI data using Machine Learning
Majid Abedi（Helmholtz Centre for Infection Research（HZI）, Braunschweig Integrated Centre of Systems Biology（BRICS）, Germany）

2P-081

Immuno-metabolic target discovery using integrated metabolic maps（imMAPS）
Keng Soh（Rheos Medicines, Inc, United States）

EcoSystems Biology
2P-082

A novel keystone species in the rhizosphere microbiome of tomato that contributes
to bacterial wilt resistanceJihyun F. Kim（Yonsei University, South Korea）

Methodological Developments for Systems Biology
2P-083

The Center for Reproducible Biomedical ModelingDavid Nickerson（The University of Auckland, New Zealand）

2P-084

Pathway-specific model estimation for improved pathway annotation by network
crosstalkMiguel Castresana Aguirre（Stockholm university, Sweden）

42

2P-085

CodonAdjust: a software to design codon nucleotide compositions for generating
mutagenesis libraries
Thuy Duong Nguyen（National Institute of Advanced Industrial Science and Technology, AI Research Center, Japan）

Systems Biophysics
2P-086

Optimal information processing of time-varying signals through metastable states atcriticality
Akhilesh P. Nandan（Max Planck Institute of Molecular Physiology, Germany）

Systems Medicine and Healthcare
2P-087

What do we really mean by Health?: On the way towards Precision HealthGokhan Ertaylan（Flemish Institute for Technological Research（VITO）, Netherlands）

43

Program - Poster Sessions
MONDAY, NOVEMBER 4
Time: 14:10-15:30 / Venue: Tunnel Gallery

Big Data, AI & Laboratory Automation
4P-001

Automatic tumor identification from ultrasonic liver images using deep learning
Kenji Karako（Department of Human and Engineered Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Japan）

4P-002

Medical image segmentation by CNN using the relationship between features ofdifferent layers
Yuki Hiramatsu（Meijo University, Japan）

4P-003

Classification of Pluripotent genes using Machine Learning Techniques
Saurabh Kumar（IIIT Bhubaneswar, India）

Developmental Systems Biology
4P-004

Planar cell polarity-dependent distribution of apical microtubules in tracheal
multiciliated cells
Shogo Nakayama（Dept. of Bio Sci., Grad. Sch. of Medicine, Osaka University, Japan）

4P-005

Analysis of shear stress for angiogenic sprouting using on-chip microvascular model
Ryuji Yokokawa（Kyoto University, Japan）

4P-006

Thymocytes reprogram in the face of progenitor shortage
Adrien Jolly（DKFZ, Germany）

EcoSystems Biology
4P-007Development of Novel Immunoassay using a recombinant scFv Antibody Specificto Potato Leafroll Virus
Mi-Gi Lee（Biocenter, Gyeonggido Business & Science Accelerator, South Korea）

4P-008Chromosome-scale comparative sequence analysis among Oikopleura dioica
individuals sampled from globally distributed locations
Aleksandra Bliznina（Okinawa Institute of Science and Technology Graduate University, Japan）

44

4P-009SPADE for exploring periodic sequence repeats as potential genome editing
modules
Hideto Mori（Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Japan）

4P-010The zooplankton Oikopleura dioica from the point of view of systems biology
Charles Plessy（Okinawa Institute of Science and Technology Graduate University（OIST）, Japan）

Methodological Developments for Systems Biology
4P-011Visualizing Metabolic Network Dynamics through Time-Series Metabolomics Data
Andreas Dräger（Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, University of Tübingen, Germany）

4P-012Mining of cell-intrinsic core-regulatory circuits driving tumor-related phenotypes with
the I3-OncoNet cycle
Mohamed Elati（Université de Lille, France）

4P-013

Diverse metabolic modeling capabilities and its use of scientific applications in
KBase
Janaka Edirisinghe（Argonne National Laboratory, United States）

4P-014

Benchmarking Time-Series Data Discretization on Reverse Engineering Methods
Paola Vera-Licona（Center for Quantitative Medicine, University of Connecticut School of Medicine, United States）

4P-015Integrative workflow of modelling and parameter estimation for quantitative
multicellular systems biology
Jörn Starruß（TU Dresden, Germany）

4P-016GlycoSim : a web tool for modeling and simulation of glycan biosynthesis pathways
Sachiko Akase（Bioinformatics Department, Graduate School of Engineering, SOKA University, Japan）

4P-017

Withdrawn

4P-018Computing all possible cell differentiation pathways from time-series data
Zoltan Tuza（Imperial College London, United Kingdom）

Modeling Networks and Circuits
4P-019Validity of quasi-steady-state approximation for a Michaelis-Menten-type reaction
in regulatory reaction networks
Takashi Naka（Kyushu Sangyo University, Japan）

4P-020Effects of 1-Methyltryptophan on the kynurenine pathway in pigs
Dana Kleimeier（Institute of Bioinformatics, University Medicine Greifswald, Germany）

4P-021

Disease-gene prioritization by link prediction identifies candidate genes for complex
disease.
Ilyes Abdelhamid（Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, United States）

4P-022

A novel approach for the generation of disease specific genetic interaction datausing gene-based statistical epistasis
Sathish Periyasamy（Queensland Brain Institute; Queensland Centre for Mental Health Research, Australia）

4P-023

Withdrawn

45

Program - Poster Sessions
4P-024

Local-community network automata modelling based on length three-paths forprediction of complex network structures in protein interactomes, food webs andmore
Ilyes Abdelhamid（Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, United States）

4P-025

A stochastic spatial model of the vesicular trafficking of AMPA-receptors
Sarah Nagasawa（Okinawa Institute of Science and Technology, Japan）

4P-026The Systems Biology Graphical Notation: a standardised representation of biologicalmaps
Andreas Dräger（Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, University of Tübingen, Germany）

4P-027

Reconstruction of Boolean gene regulatory network model based on pseudotime
analysis of single-cell RNA-Seq data
Hoon-Min Kim（Korea Advanced Institute of Science and Technology, South Korea）

4P-028Development of simultaneous measurement system for transcription and RNA
degradation rates using modified nucleic acid
Kentaro Kawata（The University of Tokyo, Japan）

4P-029Integrating statistical methods and modeling approaches reveals the synergistictranscriptional control mechanism of the primary B cell
Sufeng Chiang（Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taiwan）

4P-030

Probabilistic critical controllability analysis on protein interaction network integrating
normal brain aging gene expression profiles
Eimi Yamaguchi（Toho University, Japan）

4P-031An Integer Linear Programming-based Approach for Identifying Driven Nodes inComplex Networks
Yuma Shinzawa（Toho University, Japan）

4P-032

A computational method to infer consensus formation processes during celldifferentiation
Shinji Nakaoka（Hokkaido University, Japan）

4P-033

Random responses to specific stimuli, modelling the σB mediated stress response
in B. Subtilis
Torkel Loman（University of Cambridge, United Kingdom）

4P-034

MODELING THE IMPACT OF DOUBLE X-DOSAGE ON SIGNALING PATHWAYSIMPLICATED IN PLURIPOTENCY
Zeba Sultana（Max Planck Institute for Molecular Genetics, Berlin, Germany）

4P-03546

Regulatory networks driving circRNA expression in breast cancer
Wanwan Feng（CAS-MPG Partner Institute for Computational Biology（PICB）, Chinese Academy of Sciences（CAS）, China）

4P-036

Computational model to predict O-linked glycosylation of glycoprotein PSGL-1 in
CHO cells
Thukaa Kuoka（Graduate School of Engineering, SOKA University, Japan）

4P-037

Analyzing whole-brain dynamics of C. elegans with statistical approach
Yuko Murakami（Kyushu University, Japan）

4P-038A Framework for Building Models for Biomolecular Systems from Experimental Data
AutomaticallyZoltan Tuza（Imperial College London, United Kingdom）

4P-039

Molecular Interpolation of multi dimensional space to predict Monomeric high scaled
Enzymatic protein from NEAT Neural Networks
Lokesh Thangamani（Bharathiar University, India）

Multi-omics
4P-040Comprehensive detection of group II intron sequences from genome data and their
phylogenetic profiles in bacteria
Masahiro C. Miura（Keio University, Japan）

4P-041

Identifying Potential Candidate Genes by Combining Gene Regulatory and ProteinProtein Interaction Networks Using a Multiplex PageRank Algorithm
Annika Röhl（Harvard University, United States）

4P-042

Generating hypothesis from microRNA - mRNA expression data using the smirk R
package.
Krutik Patel（Newcastle University, United Kingdom）

4P-043

pirScan: a webserver to predict piRNA targeting sites and to avoid transgene
silencing in C. elegans
Wei-Sheng Wu（Dept. of Electrical Engineering, Nat'l Cheng Kung University, Taiwan）

4P-044

Transcriptomic and metabolic integrative study inferring the dynamics of cyanogenic
glucoside biosynthesis in developing storage roots of cassava
Wanatsanan Siriwat（King Mongkut's University of Technology Thonburi, Thailand）

4P-045Using multi-omics approaches to identify pathogenic pathways associated withsystematic vasculitis
Tai-Ming Ko（National Chiao Tung University, Taiwan）

4P-046

Automated Reconstruction, Evaluation and Comparison of Diverse Genome-Scale
Fungal Metabolic Models
Janaka Edirisinghe（Argonne National Laboratory, United States）

47

Program - Poster Sessions
Quantitative Systems Biology
4P-047

Feedback control of evolutionary trajectory of bacterial cells on fitness landscapeAtsushi Shibai（RIKEN, Japan）

4P-048Sporadic gene expression dynamics : a clever strategy for virus persistence
Shingo Iwami（Kyushu University, Japan）

4P-049

Apical cytoskeleton mediates coordinated beating of cilia in tracheal multiciliatedcells for apical functioning of epithelia
Sachiko Tsukita（Teikyo University, Osaka University, Japan）

4P-050Withdrawn

4P-051

Reversion of Chemoresistance in a Triple Negative Breast Cancer Subtype
Paola Vera-Licona（Center for Quantitative Medicine, UConn Health, United States）

4P-052

Withdrawn

4P-053Signaling network of apoptosis/necroptosis in bortezomib and oncolytic virus
therapy and miR-451-LKB1-AMPK-Oct1 signaling in glioblastoma
Yangjin Kim（Konkuk University Ohio State University, South Korea）

4P-054

Revealing the functional role of FABP5 in stratification of lung cancer patients
Pouyan Ghaffari（Technical University of Denmark, Denmark）

4P-055Comparative transcriptome analysis of idiopathic pulmonary fibrosis and lungcancerYosui Nojima（National institutes of biomedical innovation, health and nutrition, Japan）

4P-056

A Computational Model for Programmed Necrosis in Cancer
Iman Tavassoly（Icahn School of Medicine at Mount Sinai, United States）

4P-057

Wnt/beta-catenin modulates lung adeno-to-squamous transdifferentiation
Zhaoyuan Fang（Shanghai Institute of Biochemistry and Cell Biology, China）

Single-cell Systems Biology
4P-058Single-cell frequency response of intracellular signal transduction based on livecell active sensing and nonlinear system identification
Katsuyuki Kunida（Graduate School of Science and Technology, and Data Science Center, Nara Institute of Science and Technology, Japan）

4P-059Bioinformatic processing of single-cell RNA-seq data for genome-wide parameter
estimation upon eukaryotic gene expressions
Keita Iida（Osaka University, Japan）

4P-06048

rCASC, Reproducible Classification Analysis of Single Cell sequencing data
Luca Alessandrì（Department of Molecular Biotechnology and Health Sciences, University of Torino, Italy）

4P-061

Thermodynamically motivated cell segmentation for single-cell modeling of GAL1 in
yeast
Cheng-Hui Chen（National Cheng Kung University, Taiwan）

4P-062

A Systems Biology Study on Parkinson s Disease Based on Single Cell RNA
Sequencing in Drosophila Model
Zhirong Sun（School of Life Sciences, Tsinghua University, China）

Systems Biology for Neurosciences and Neural Circuits
4P-063Astrocyte Neuron Simulation Environment Platform: ANSEP
Andres Pinzón Velasco（Universidad Nacional de Colombia, Colombia）

4P-064Circuit-level analysis of deviance detection and adaptation by in vivo calcium imaging
of mouse auditory cortex
Shunsuke Mizutani（Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Japan）

4P-065Computational geometry analysis of spine morphology in living neurons
Yutaro Kashiwagi（The University of Tokyo, Japan）

4P-066

Circadian characteristics of behavioral and physiological rhythms in diurnal primate
common marmosets（Callithrix jacchus）.
Iori Murai（Graduate School of Pharmaceutical Sciences, Kyoto University, Japan）

4P-067Whole-brain imaging reveals dynamical structure of neural signaling in C. elegans
Taichi Isaka（Ibaraki University, Japan）

4P-068Does maternal rhythm affect the development of circadian rhythm of the offspring?
Keiko Tominaga（Osaka University, Japan）

Systems Biophysics
4P-069RNA helicase DDX43 drives Ago3-dependent piRNA biogenesis in ping-pong cycle
Ryo Murakami（The University of Tokyo, Japan）

4P-070A pipeline of bio-image informatics for whole-brain imaging of C. elegans andanalysis of the neural activity
Yu Toyoshima（The University of Tokyo, Japan）

4P-071

Numerical simulation of multiciliated cells cilia translational and rotational selforganization by the interaction with the apical cytoskeleton and asymmetric timedependent boundary conditions
Fermin Franco Medrano（Osaka University, Japan）

4P-072

Simulation of live-cell imaging system reveals hidden uncertainties in cooperative
binding measurements
Masaki Watabe（RIKEN Center for Biosystems Dynamics Research, Japan）
49

Program - Poster Sessions
4P-073Phase-field modeling for 3D dynamics in macropinocytosis
Nen Saito（The University of Tokyo, Japan）

Systems Medicine and Healthcare
4P-074

Individual gene expression profiles identify responders and non-responders to
Imatinib in severe asthmatics.
Seung Han Baek（Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, United States）

4P-075Novel relationship between osteoporosis and genes: potential role of Vit. D
metabolism and sex hormone
Sang Wook Kang（Dankook University, South Korea）

4P-076

DrugComb: an integrative cancer drug combination data portal.
Bulat Zagidullin（University of Helsinki, Finland）

4P-077

Integrative analysis of multi-Omics data reveals that the dysregulation of
splicingrelated proteins in prostate cancer is controlled by FOXA1
Marco Del Giudice（Italian Institute for Genomic Medicine, Italy）

4P-078

Evaluation of enhanced intracellular delivery of doxorubicin in metastatic cancer cellsby systems Biology approach
Dongqing Wei（Shanghai Jiao Tong University, China）

4P-079Translational Informatics and Systems Healthcare in the Era of 5G Networks
Bairong Shen（West China Hospital, Sichuan University, China）

4P-080

Ambient MS-based tissue profiling for assistance on neurosurgery operations ofbrain cancer
Anatoly Sorokin（Moscow Institute of Physics and Technology, Russia）

4P-081

Towards discovery of human disease mechanisms by graph-based contextual
integration of omics signatures.
Artem Lysenko（RIKEN, Japan）

Big Data, AI & Laboratory Automation
4P-082

The generalized relationship between gene intrinsic properties and phenotypicfeatures revealed by multi-omic big data mining
Dong Yang（Institute of Lifeomics, AMMS, China, China）

4P-08350

Detection and quantification of necrosis in glioma using deep learning on whole slide
imagesHanli Huang（The Hong Kong University of Science and Technology, Hong Kong）

Methodological Developments for Systems Biology
4P-084

Improved gene regulatory network inference with consensus methods
Thomas Hillerton（Stockholm University, Sweden）

4P-085

A Benchmark Study Highlighting the Importance of Perturbation Design for Accurate
Gene Regulatory Network Inference
Deniz Seçilmis,（Stockholm Bioinformatics Center, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden）

4P-086Integrated networks in Salmonella research
Márton Ölbei（Earlham Institute, Norwich and Quadram Institute Biosciences, Norwich, UK）

Systems Biology for Neurosciences and Neural Circuits
4P-087

Neural synchrony as a coupling mechanism of multi-agent systems
Ana Lucia Valencia（UNAM, Mexico）

4P-088Self-optimization in biologically-inspired topologies: the case of the C. elegans
connectome
Alejandro Ehecátl Morales Huitrón（Universidad Nacional Autónoma de México, Mexico）

51

Program - Tutorials & Satellite Workshops
Workshop 01

Precision Network Medicine in the era of big data!
Date: October 31, 2019, 9:00-18:00
Venue: Auditorium
Organizer: Amitabh Sharma（Harvard Medical School）

Workshop 02 BioNetVisA: from biological network reconstruction to data visualization andanalysis in molecular biology and medicine
Date: October 31, 2019, 9:00-18:00
Organizer: Inna Kuperstein（Institut Curie）

Venue: B250

Workshop 03 Singularity Biology: small elements change the function of the whole systems
Date: October 31, 2019, 9:00-14:00
Venue: Meeting room 1
Organizer: Shuichi Onami（RIKEN BDR）
Workshop 04 Trans-Omics workshop – The 3rd International Symposium for Trans-Omics –Date: October 31, 2019, 14:00-18:00
Venue: Meeting room 1
Organizer: Shinya Kuroda（The University of Tokyo）
Workshop 05 Qualitative computational modeling for biological networks
Date: October 31, 2019, 9:00-18:00
Venue: Meeting room 3
Organizer: Adrien Faure/Denis Thieffry（Yamaguchi University/Univ Paris-Saclay）
Workshop 06 KBase: free, open platform for genomics analysis of microbes, plants, and theircommunities
Date: October 31, 2019, 9:00-12:00
Venue: Meeting room 4
Organizer: Jose P. Faria（Argonne National Laboratory）
Workshop 07 Putting metabolomic data into context: An introduction to the Virtual Metabolic
Human database（www.vmh.life）and metabolic modeling
Date: October 31, 2019, 14:00-18:00
Venue: Meeting room 4
Organizer: Cyrille C. Thinnes（Universte du Luxembourg）
Tutorial 01

Advanced Modelling with COPASI
Date: October 31, 2019, 9:00-13:00
Venue: C209
Organizer: Sven Sahle（Universitat Heidelberg）

Tutorial 02

COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology
Date: October 31, 2019, 9:00-18:00
Venue: C210
Organizer: Martin Golebiewski（HITS gGmbH）

52