GIW / InCoB 2015 at MIRAIKAN, Odaiba, Tokyo, Japan







Venue National Museum of Emerging Science and Innovation (Miraikan) AIST Annex
Room Miraikan Hall Conference Room 2 Conference Room 1 Innovation Hall 11F
Capacity 300 84 56 103 250






Day 1 Wednesday, September 9, 2015
8:00 – 8:30 Site Preparation
 No Conference Activity at AIST Annex
8:30 – 17:00 Registration Desk Open
8:45 – 9:00 Opening Remarks
9:00 – 10:00 Keynote: Arne Elofsson
What is missing from a complete structural map of the cell?
10:00 – 10:20 Day 1, Morning  ☕ Coffee Break ☕

Spectral Processing / Transcription Factor Pairs
Shoba Ranganathan
 Software Demos
Toutai Mituyama
 High Dimensional Data / Feature Selection
Tsuda Koji
10:20 – 10:40 J73 Xuetao Wang  Preprocess and condensation of Raman spectrum for single-cell phenotype analysis D121 Tyler Weirick  C-It-Loci: A knowledge database for tissue-enriched loci J23 Tomokazu Konishi  Principal component analysis for designed experiments
10:40 – 11:00 J62 Chalini Wijetunge  A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model D122 David John  RNAeditor: a bioinformatics tool to analyze RNA editing events J02 Y-H. Taguchi  Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin linea
11:00 – 11:20 J16 Wei-Sheng Wu  Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out D128 Eric Bonnet  NaviCell technology and Atlas of Cancer Signaling Network: a systems biology resource for integrative analysis of cancer data J17 Ping Zhang  An Adaptive Genetic Algorithm for Selection of Blood-based Biomarkers for Prediction of Alzheimer's Disease Progression
11:20 – 11:40 J6+19 Wei-Sheng Wu  Computational Identification of Cooperative Transcription Factor Pairs in Yeast: A newly developed algorithm and web tool for performance evaluation D155 Srinath Sridharan  Health on the go: mobile health analytics apps in the modern technological era
11:40 – 12:55 Offsite Lunch (You must fend for yourself; there are many restaurants and indoor food stalls within walking distance)
12:55 – 13:00 Announcements
13:00 – 14:00 Keynote: Mark Baker
The Human Proteome Project’s Efforts to Find the “Missing Proteins” and Develop a Common Informatics Language
14:00 – 14:20 Day 1, Afternoon  ☕ Coffee Break ☕

Chemical Informatics
Paul Horton
 Genomics & NGS
Siu Ming Yiu
 Pathway and Gene Association
Anton Kratz
 Bioconductor
Matt Ritchie
14:20 – 14:50 T2 Kenta Oono Preferred Networks
Recent Development of Deep Learning Technology and its Application to Quantitative Structure-Activity Relationship		 J77 Chee Keong Kwoh  ARG-walker Inference of Individual Specific Strengths of Meiotic Recombination Hotspots by Population Genomics Analysis J60 Ruth Stoney  Disentangling the multigenic and pleiotropic nature of molecular function S1a Martin Morgan  An overview of genomic data analysis in Bioconductor
14:50 – 15:20 J47 Zhanzhan Cheng  Effectively identifying compound-protein interactions by learning from positive and unlabeled examples H105 Martin Frith  Split-alignment of genomes finds orthologies more accurately J93 Adam Handen  LENS: Web-based Lens for Enrichment and Network Studies of Human Proteins S1b Peter Hickey  Analysing DNA methylation data with Bioconductor
15:20 – 15:50 J64 Yung-Hao Wong  Cocktail Multiple Drug Targets Design by Attacking on the Core Network Markers of Four Cancers with Ligand-Based and Structure-Based Virtual Screening Methods J40 Zhen Zhang  Sprites: detection of deletions from low-coverage sequencing data by re-aligning split reads J05 Chia-Chun Chiu  YAGM: a web tool for mining associated genes in yeast based on diverse biological association S1c Charity Law & Matthew Ritchie  RNA-seq analysis in Bioconductor
15:50 – 16:20 J88 Kana Shimizu  Privacy-preserving search for chemical compound databases J46 Kouichi Kimura  Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data
S1d Jianmiao Chen  Cytofkit: a mass cytometry data analysis toolkit for mapping cellular heterogeneity and progression AIST Annex Open for Poster Put-up
16:20 – 16:30 Delegates move from MIRAIKAN to AIST Annex 11F -------------------->
16:30 – 17:30 MIRAIKAN Venue Closed
 Odd Numbered Posters @ AIST Annex 11 Floor
(Odd posters may be taken down at the end)
17:30 AIST Annex Venue Closed












Day 2 Thursday, September 10, 2015
8:00 – 8:30 Site Preparation
 No Conference Activity at AIST Annex
8:30 – 17:00 Registration Desk Open
8:55 – 9:00 Announcements
9:00 – 10:00 Keynote: Edward Marcotte
Evolution, the Proteome & Human Disease
10:00 – 10:20 Day 2, Morning  ☕ Coffee Break ☕

Protein Classification
Kentaro Tomii
 Virus Classification & Metagenomics
Ugur Sezerman
 Assorted Topics
Limsoon Wong
10:20 – 10:40 J63 Qingyao Wu  Markov chain based semi-supervised Multi-instance Multi-labeled method for protein function prediction J09 Tsunglin Liu  Obtaining long 16S rDNA sequences using multiple primers and its application on dioxin-containing samples J38 Takeyuki Tamura  Computing Minimum Reaction Modifications in a Boolean Metabolic Network
10:40 – 11:00 J85 Hiroto Saigo  Improved Classification of Nuclear Receptors with Random Forest J74 Chieh-Hua Lin  Precise Genotyping and Recombination Detection of Enterovirus J22 Che-Wei Chang  Light-RCV: a lightweight read coverage viewer for next generation sequencing data
11:00 – 11:20 J69 Nam-Ninh Nguyen  EnzDP: improved enzyme annotation for metabolic network reconstruction based on domain composition profiles J95 Muhammad Farhan Sjaugi  g-FLUA2H: A web-based application to study the dynamics of animal-to-human mutation transmission for influenza viruses
11:20 – 11:40 J59 Yi-Fan Liou  SCMMTP: Identifying and characterizing membrane transport proteins using propensity scores of dipeptides J27 Saman K. Halgamuge  Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness
11:40 – 12:55 Offsite Lunch (You must fend for yourself; there are many restaurants and indoor food stalls within walking distance)
12:55 – 13:00 Announcements
13:00 – 14:00 ISCB Keynote: Yana Bromberg
Interpreting Genomic Data to Inform Pathogenesis Pathways
14:00 – 14:20 Day 2, Afternoon  ☕ Coffee Break ☕

Cancer I
Christian Schönbach
 Epitope
Asif Khan
 Protein-{Protein,RNA,DNA} Interface
Yasubumi Sakakibara
14:20 – 14:50 J86 Karen Ryall  An integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer J03 Vladimir Brusic  A computational method for identification of viral vaccine targets from protein regions of conserved HLA binding J32 Kengo Sato  A max-margin model for predicting residue-base contacts in protein-RNA interactions
14:50 – 15:20 H142 Inna Kuperstein  Finding metastasis inducers in colon cancer through network analysis: concomitant Notch activation and p53 deletion trigger the process J04 Vladimir Brusic  A systematic analysis of a broadly neutralizing antibody AR3C epitopes on Hepatitis C virus E2 envelope glycoprotein and their cross-reactivity J26 Shoba Ranganathan  Discrete structural features among interface residue-level classes
15:20 – 15:50 J25 Ugur Sezerman  A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology J66 Ming-Ju Tsai  Prediction of linear B-cell epitopes of hepatitis C virus for vaccine development J81 Yi-Fan Liou  Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes
15:50 – 16:20 H132 Emmanuel Barillot  Disentangling bladder cancer progression pathways by pan-cancer deconvolution of tumoral transcriptomes J48 Jing Ren  Positive-unlabeled learning for the prediction of conformational B-cell epitopes J84 Shayoni Dutta  A theoretical investigation of DNA dynamics and desolvation kinetics for zinc finger protein Zif268 AIST Annex Open for Even Number Poster Put-up
16:20 – 16:30 Delegates move from MIRAIKAN to AIST Annex 11F -------------------->
16:30 – 17:30 MIRAIKAN 7th Floor Venue Closed Even Numbered Posters @ AIST Annex 11 Floor
(Please take all posters down at the end)
17:30 – 18:00 <-------------------- Delegates move from AIST Annex back to Miraikan 1F
18:00 – 19:45 Banquet @ Miraikan 1st Floor Under the Globe!
20:00 Venue Closed


















Day 3 Friday, September 11, 2015
8:00 – 8:30 Site Preparation
 No Conference Activity at AIST Annex
8:30 – 17:00 Registration Desk Open
8:55 – 9:00 Annoucements
9:00 – 10:00 Keynote: Gil Ast
Chromatin organization, epigenetics and alternative splicing
10:00 – 10:20 Day 3, Morning  ☕ Coffee Break ☕

miRNA & other topics
Hideo Matsuda
 Protein Sequence analysis
Kenta Nakai
 Image Processing
Akihiko Konagaya
 NGS
Paoyang Chen
10:20 – 10:50 H136 Christophe Lefèvre  The short message in milk; secretory miRNA in marsupial milk T1 Kentaro Tomii AIST
Bioinformatics tools for protein sequence/structure analysis in high-throughput biology
S2a Yu-Jung Chang  CloudDOE: A User-Friendly Tool for Speeding up Hadoop Cloud Deployment and Genomic Data Analysis Using MapReduce
10:50 – 11:20 J80 Chia-Chun Chiu  Investigation of microRNAs in mouse macrophage responses to lipoposaccharide-stimulation by combining gene expression with microRNA-target information J41 Ahmet Sinan Yavuz  Prediction of neddylation sites from protein sequences and sequence-derived properties J53 Osamu Hirose  SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter S2b Shu-Hwa Chen  Multi-Omics Online Analysis System (MOLAS)
11:20 – 11:50 J37 Etienne Birmele  A model for gene deregulation detection using expression data J75 Hui-Ju Kao  A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs J82 Saowaluck Kaewkamnerd  Automatic Genotyping from DNA Gel Electrophoresis Images using Bio-image Processing Technique S2c Pao-Yang Chen  The Investigation of Genome wide DNA Methylation
11:50 – 12:20 H151 Yana Bromberg  Functional basis of microorganism classification T3 Bruno Gaeta ISCB
International Society for Computational Biology (ISCB) － Invest in You, Your Research Field: An Open Forum to Learn More about ISCB and Its Programs		 J28 Lee Kien Leow  Automated identification of copepods using digital image processing and artificial neural network S2d Jui-Hung Hung  Studying RNA processing of small silencing RNAs by NGS
12:20 – 13:00 APBioNet General Meeting with lunchboxes provided

Cancer II
Vladimir Brusic
 DNA methylation, NGS
Martin Frith
 Dynamic Network Inference
Jun Sese
13:00 – 13:30 H141 Steve Rozen  Mutation signatures implicate aristolochic acid in bladder cancer development J65 Yutaka Saito  Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions H150 Kentaro Inoue  Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activation
13:30 – 14:00 H129 Inna Kuperstein  Atlas of Cancer Signaling Network: a systems biology research for integrative analysis of cancer data with Google Maps J55 Jonghun Lee  An Integrative Approach for Efficient Analysis of Whole Genome Bisulfite Sequencing Data J76 Yung-Hao Wong  Identification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data
14:00 – 14:30 H138 Grace Shieh  CSNK1E/CTNNB1 Are Synthetic Lethal to TP53 in Colorectal Cancer and are Markers for Prognosis J70 Ming-Ren Yen  MethGO: a comprehensive tool for analyzing whole genome bisulfite sequencing data J52 Renhua Song  Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets
14:30 – 15:00 J51 Jean-Marc Schwartz  Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events J90 Yu-Jung Chang  Subset Selection of High-Depth Next Generation Sequencing Reads for De Novo Genome Assembly Using MapReduce Framework J13 Yoichi Takenaka  Detecting the shifts of gene regulatory networks during time-course experiments with a single time point temporal resolution
15:00 – 15:20 Day 3, Afternoon  ☕ Coffee Break ☕
15:20 – 16:20 Keynote: Annie De Groot
A Computational Pipeline for Personalized Cancer Vaccines On Demand: Yes we Can!
16:20 – 16:40 Awards, InCoB 2016 & GIW 2016 Announcement, Closing Remarks
16:45 Venue Closed