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 WangPreprocess and condensation of Raman spectrum for single-cell phenotype analysis D121 Tyler WeirickC-It-Loci: A knowledge database for tissue-enriched loci J23 Tomokazu KonishiPrincipal component analysis for designed experiments
10:40 – 11:00 J62 Chalini WijetungeA new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model D122 David JohnRNAeditor: a bioinformatics tool to analyze RNA editing events J02 Y-H. TaguchiIdentification 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 WuFunctional 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 BonnetNaviCell technology and Atlas of Cancer Signaling Network: a systems biology resource for integrative analysis of cancer data J17 Ping ZhangAn Adaptive Genetic Algorithm for Selection of Blood-based Biomarkers for Prediction of Alzheimer's Disease Progression
11:20 – 11:40 J6+19 Wei-Sheng WuComputational Identification of Cooperative Transcription Factor Pairs in Yeast: A newly developed algorithm and web tool for performance evaluation D155 Srinath SridharanHealth 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
Matt Ritchie
14:20 – 14:50 T2 Kenta OonoPreferred Networks
Recent Development of Deep Learning Technology and its Application to Quantitative Structure-Activity Relationship
J77 Chee Keong KwohARG-walker Inference of Individual Specific Strengths of Meiotic Recombination Hotspots by Population Genomics Analysis J60 Ruth StoneyDisentangling the multigenic and pleiotropic nature of molecular function S1a Martin MorganAn overview of genomic data analysis in Bioconductor
14:50 – 15:20 J47 Zhanzhan ChengEffectively identifying compound-protein interactions by learning from positive and unlabeled examples H105 Martin FrithSplit-alignment of genomes finds orthologies more accurately J93 Adam HandenLENS: Web-based Lens for Enrichment and Network Studies of Human Proteins S1b Peter HickeyAnalysing DNA methylation data with Bioconductor
15:20 – 15:50 J64 Yung-Hao WongCocktail 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 ZhangSprites: detection of deletions from low-coverage sequencing data by re-aligning split reads J05 Chia-Chun ChiuYAGM: a web tool for mining associated genes in yeast based on diverse biological association S1c Charity Law & Matthew RitchieRNA-seq analysis in Bioconductor
15:50 – 16:20 J88 Kana ShimizuPrivacy-preserving search for chemical compound databases J46 Kouichi KimuraAnalysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data
S1d Jianmiao ChenCytofkit: 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 WuMarkov chain based semi-supervised Multi-instance Multi-labeled method for protein function prediction J09 Tsunglin LiuObtaining long 16S rDNA sequences using multiple primers and its application on dioxin-containing samples J38 Takeyuki TamuraComputing Minimum Reaction Modifications in a Boolean Metabolic Network
10:40 – 11:00 J85 Hiroto SaigoImproved Classification of Nuclear Receptors with Random Forest J74 Chieh-Hua LinPrecise Genotyping and Recombination Detection of Enterovirus J22 Che-Wei ChangLight-RCV: a lightweight read coverage viewer for next generation sequencing data
11:00 – 11:20 J69 Nam-Ninh NguyenEnzDP: improved enzyme annotation for metabolic network reconstruction based on domain composition profiles J95 Muhammad Farhan Sjaugig-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 LiouSCMMTP: Identifying and characterizing membrane transport proteins using propensity scores of dipeptides J27 Saman K. HalgamugeAccurate 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
Asif Khan
Protein-{Protein,RNA,DNA} Interface
Yasubumi Sakakibara

14:20 – 14:50 J86 Karen RyallAn integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer J03 Vladimir BrusicA computational method for identification of viral vaccine targets from protein regions of conserved HLA binding J32 Kengo SatoA max-margin model for predicting residue-base contacts in protein-RNA interactions
14:50 – 15:20 H142 Inna KupersteinFinding metastasis inducers in colon cancer through network analysis: concomitant Notch activation and p53 deletion trigger the process J04 Vladimir BrusicA systematic analysis of a broadly neutralizing antibody AR3C epitopes on Hepatitis C virus E2 envelope glycoprotein and their cross-reactivity J26 Shoba RanganathanDiscrete structural features among interface residue-level classes
15:20 – 15:50 J25 Ugur SezermanA novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology J66 Ming-Ju TsaiPrediction of linear B-cell epitopes of hepatitis C virus for vaccine development J81 Yi-Fan LiouCharacterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes
15:50 – 16:20 H132 Emmanuel BarillotDisentangling bladder cancer progression pathways by pan-cancer deconvolution of tumoral transcriptomes J48 Jing RenPositive-unlabeled learning for the prediction of conformational B-cell epitopes J84 Shayoni DuttaA 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
Paoyang Chen
10:20 – 10:50 H136 Christophe LefèvreThe 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 ChangCloudDOE: A User-Friendly Tool for Speeding up Hadoop Cloud Deployment and Genomic Data Analysis Using MapReduce
10:50 – 11:20 J80 Chia-Chun ChiuInvestigation of microRNAs in mouse macrophage responses to lipoposaccharide-stimulation by combining gene expression with microRNA-target information J41 Ahmet Sinan YavuzPrediction of neddylation sites from protein sequences and sequence-derived properties J53 Osamu HiroseSPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter S2b Shu-Hwa ChenMulti-Omics Online Analysis System (MOLAS)
11:20 – 11:50 J37 Etienne BirmeleA model for gene deregulation detection using expression data J75 Hui-Ju KaoA two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs J82 Saowaluck KaewkamnerdAutomatic Genotyping from DNA Gel Electrophoresis Images using Bio-image Processing Technique S2c Pao-Yang ChenThe Investigation of Genome wide DNA Methylation
11:50 – 12:20 H151 Yana BrombergFunctional basis of microorganism classification T3 Bruno GaetaISCB
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 LeowAutomated identification of copepods using digital image processing and artificial neural network S2d Jui-Hung HungStudying 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 RozenMutation signatures implicate aristolochic acid in bladder cancer development J65 Yutaka SaitoDetection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions H150 Kentaro InouePositive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activation
13:30 – 14:00 H129 Inna KupersteinAtlas of Cancer Signaling Network: a systems biology research for integrative analysis of cancer data with Google Maps J55 Jonghun LeeAn Integrative Approach for Efficient Analysis of Whole Genome Bisulfite Sequencing Data J76 Yung-Hao WongIdentification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data
14:00 – 14:30 H138 Grace ShiehCSNK1E/CTNNB1 Are Synthetic Lethal to TP53 in Colorectal Cancer and are Markers for Prognosis J70 Ming-Ren YenMethGO: a comprehensive tool for analyzing whole genome bisulfite sequencing data J52 Renhua SongInference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets
14:30 – 15:00 J51 Jean-Marc SchwartzConstructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events J90 Yu-Jung ChangSubset Selection of High-Depth Next Generation Sequencing Reads for De Novo Genome Assembly Using MapReduce Framework J13 Yoichi TakenakaDetecting 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