Day 1: Jan 15, 2018.
09:15 - 09:50

Registration Open

09:50 - 10:00

Opening Remarks (Main Hall)

10:00 - 11:00

Keynote Speech (Main Hall)
Modeling cancer evolution from genomic data
Dr. Niko Beerenwinkel
Session Chair: Dr. Yasubumi Sakakibara

11:00 - 11:15

Coffee BreakParallel Session

Comparative Genomics (Main Hall)
Session Chair: Dr. Laxmi Parida

Chemoinformatics (Room 1)
Session Chair: Dr. Shuqin Zhang

11:15 - 11:40[O1] Matching Algorithms for Assigning Orthologs after Genome
Duplication Events
Guillaume Fertin, Falk Hüffner, Christian Komusiewicz and Manuel Sorge[O4] Resource Cut, a New Bounding Procedure to Algorithms forEnumerating Tree-like Chemical Graphs
Yuhei Nishiyama, Aleksandar Shurbevski, Hiroshi Nagamochi and Tatsuya
Akutsu11:40 - 12:05[O2] Phylogenetic signal from rearrangements in 18 Anopheles species by
joint scaffolding extant and ancestral genomes
Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cedric Chauve andSeverine Berard[O5] Optimization of memory use of fragment extension-based proteinligand docking with an original fast minimum cost flow algorithm
Keisuke Yanagisawa, Shunta Komine, Rikuto Kubota, Masahito Ohue andYutaka Akiyama

12:05 - 12:30[O3] Resolution effects in reconstructing ancestral genomes
Chunfang Zheng, Yuji Jeong, Madisyn Gabrielle Turcotte and David Sankoff[O6] Predicting and Understanding Comprehensive Drug-Drug Interactions
via Semi- Nonnegative Matrix Factorization
Hui Yu , Kui‐Tao Mao, Jian‐Yu Shi, Hua Huang, Zhi Chen, Kai Dong and Siu‐Ming Yiu

Lunch

12:30 - 14:00
Parallel Session

Sequence Alignment Algorithms (Main Hall)
Session Chair: Dr. Guillaume FertinMicrobiome Analysis and Mass Spectrometry Analysis (Room 1)
Session Chair: Dr. Naoaki Ono

14:00 - 14:25[O7] Parallel Computation of the Burrows-Wheeler Transform of Short
Reads Using Prefix Parallelism
Kouichi Kimura and Asako Koike[O11] Adjacent Y-ion Ratio Distributions and Its Application in Peptide
Sequencing
Tiancong Wang and Bin Ma

14:25 - 14:50[O8] Hardness of Covering Alignment: Phase Transition in Post-Sequence
Genomics
Romeo Rizzi, Massimo Cairo, Veli Mäkinen, Alexandru I. Tomescu and DanielValenzuela[O12] An Approach for N-linked Glycan Identification from MS/MS Spectraby Target-Decoy Strategy
Weiping Sun, Yi Liu and Kaizhong Zhang

14:50 - 15:15[O9] GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using
Processing-in-Memory Technologies
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose,
Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan and Onur Mutlu[O13] KDiamend: a package for detecting key drivers in a molecular
ecological network of disease
Mengxuan Lyu, Jiaxing Chen, Yiqi Jiang, Wei Dong, Zhou Fang andShuaicheng Li15:15 - 15:40[O10] Hardware Acceleration of BWA-MEM Genomic Short Read Mappingfor Longer Read Lengths
Ernst Houtgast, Vlad‐Mihai Sima, Koen Bertels and Zaid Al‐Ars[O14] Dynamics of the human gut phageome during the antibiotics
treatment
Anna Górska, Silke Peter, Matthias Willmann, Ingo Autenrieth, Robert Schlaberg
and Daniel Huson

Coffee Break

15:40 - 16:00
Parallel Session

Sequence Analysis (Main Hall)
Session Chair: Dr. Y.-H. Taguchi

Protein Structure Analysis (Room 1)
Session Chair: Dr. Mukul Bansal

16:00 - 16:25[O15] SpliceVec: distributed feature representations for splice junction
prediction
Aparajita Dutta, Tushar Dubey, Kusum Kumari Singh and Ashish Anand[O19] RaptorX-Angle: real-value and confidence prediction of protein
backbone dihedral angles through a hybrid method of clustering and deeplearning
Yujuan Gao, Sheng Wang, Minghua Deng and Jinbo Xu

16:25 - 16:50[O16] Towards Pan-Genome Read Alignment to Improve Variation Calling
Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen and Veli Mäkinen[O20] MEGADOCK-Web: an integrated database of high-throughput
structure-based protein- protein interaction predictions
Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue andYutaka Akiyama

16:50 - 17:15[O17] Efficient Algorithms for Polyploid Haplotype Phasing
Dan He, Subrata Saha, Richard Finkers and Laxmi Parida[O21] Computational analysis of the receptor binding specificity of novel
influenza A/H7N9 viruses
Xinrui Zhou, Jie Zheng, Fransiskus Xaverius Ivan, Rui Yin, Shoba
Ranganathan, Vincent T. K. Chow and Chee Keong Kwoh

17:15 - 17:40[O18] NGS‐based likelihood ratio for identifying contributors in two‐ andthree‐person DNA mixtures
Joshua Mun Wei Chan, Zicheng Zhao, Shuai Cheng Li and Yen Kaow Ng[O22] CNNH_PSS: Protein 8-class Secondary Structure Prediction byConvolutional Neural Network with Highway
Jiyun Zhou, Hongpeng Wang, Zhishan Zhao, Ruifeng Xu and Qin Lu

17:40 - 18:40

Poster Session for odd numbers (Room 2 & 3)

Day 2: Jan 16, 2018.
09:00 - 09:30

Registration Open

09:30 - 10:30

Keynote Speech (Main Hall)
AI-supported clinical sequencing in blood cancers
Dr. Arinobu Tojo
Session Chair: Dr. Yasubumi Sakakibara

10:30 - 10:45

Coffee BreakParallel Session

Gene Expression Analysis (1) (Main Hall)
Session Chair: Dr. Yutaro Kumagai

Molecular Interaction Analysis (Room 1)
Session Chair: Dr. Jose Nacher

10:45 - 11:10[O23] The Aquatic Animals’ Transcriptome Resource for Comparative
Functional Analysis
Chih‐Hung Chou, Hsi-Yuan Huang, Wei-Chih Huang, Sheng‐Da Hsu, ChungDer Hsiao, Chia‐Yu Liu, Yu‐Hung Chen, Yu‐Chen Liu, Wei‐Yun Huang, MengLin Lee, Yi-Chang Chen, and Hsien‐Da Huang[O26] Probing the functions of long non-coding RNAs by exploiting thetopology of global association and interaction network
Lei Deng, Hongjie Wu and Jinpu Zhang

11:10 - 11:35[O24] Identification of Usual Interstitial Pneumonia Pattern Using RNA-Seq
and Machine Learning: Challenges and Solutions
Yoonha Choi, Tiffany Ting Liu, Daniel Pankratz, ThomasColby, Neil Barth, David Lynch, Sean Walsh, Ganesh Raghu, Giulia Kennedy
and Jing Huang[O27] Annotating activation/inhibition relationships to protein-protein
interactions using Gene Ontology relations
Soorin Yim, Hasun Yu, Dongjin Jang and Doheon Lee11:35 - 12:00[O25] A Gene Profiling Deconvolution Approach to Estimating Immune Cell
Composition from Complex Tissues
Shu‐Hwa Chen, Wen‐Yu Kuo, Sheng‐Yao Su, Wei‐Chun Chung, Jen‐Ming Ho,
Henry Horng‐Shing Lu and Chung‐Yen Lin[O28] Protein complex prediction by date hub removal
Iana Pyrogova and Limsoon WongLunch

12:00 - 13:30
Parallel Session

Phylogenetics (Main Hall)
Session Chair: Dr. Daniel Valenzuela

microRNA analysis (Room 1)
Session Chair: Dr. Minghua Deng

13:30 - 13:55[O29] GATC: A Genetic Algorithm for gene Tree Construction under theDuplication-Transfer- Loss model of evolution
Emmanuel Noutahi and Nadia El‐Mabrouk[O33] Hierarchical Structural Component Modeling of microRNA-mRNA
Integration Analysis
Yongkang Kim, Sungyoung Lee, Sungkyoung Choi and Taesung Park

13:55 - 14:20[O30] Computing the Diameter of the Space of Maximum Parsimony
Reconciliations in the Duplication-Transfer-Loss Model
Jordan Haack, Eli Zupke, Andrew Ramirez, Yi‐Chieh Wu and Ran Libeskind‐Hadas[O34] Genome-wide identification and comprehensive analysis ofmicroRNAs and phased small interfering RNAs in watermelon
Li Liu, Shuchao Ren, Junqiang Guo, Qingyi Wang, Xiaotuo
Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar and Yun Zheng

14:20 - 14:45[O31] An Integrated Reconciliation Framework for Domain, Gene, andSpecies Level Evolution
Lei Li and Mukul S. Bansal[O35] Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in
circular RNAs revealed through transcriptome sequencing dataset analysis
Yu‐Chen Liu, Hsiao‐Chin Hong, Chi‐Dung Yang, Wei‐Hsiang Lee, Hsin‐Tzu
Huang and Hsien‐Da Huang

14:45 - 15:10[O32] An Exact Algorithm for Sorting by Weighted Preserving GenomeRearrangements
Tom Hartmann, Matthias Bernt and Martin Middendorf[O36] Integrated microRNA and mRNA Expression Profile Analysis ofTumor-Associated Macrophages after Exposure to Single-Dose Irradiation
Wei‐Hsiang Kung, Chi‐Lung Lee, Chi‐Dung Yang, Ching‐
Fang Yu, Men‐Yee Chiew, Fang‐Hsin Chen and Hsien‐Da Huang

15:10 - 15:30

Coffee Break

15:30 - 16:30

Keynote Speech (Main Hall)
Whole-body and whole-organ clearing and imaging with single-cell resolution
toward organism-level systems biology in mammals
Dr. Hiroki R. Ueda
Session Chair: Dr. Yoshihiro Yamanishi
Coffee Break

16:30 - 16:45
Parallel Session

Gene Expression Analysis (2) (Main Hall)
Session Chair: Dr. Alexis Vandenbon

Network Analysis (Room 1)
Session Chair: Dr. Jean-Marc Schwartz

16:45 - 17:10[O37] Identification of Condition Specific Cis- and Trans-acting Elements in
Plant promoters under Various Endo- and Exogenous Stimuli
Chi-Nga Chow, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Han-Qin Zheng, TzongYi Lee, Nai-Yun Wu, Kuan-Chieh Tseng, Ping-Fu Hou, and Wen-Chi Chang[O40] Taming Asynchrony for Attractor Detection in Large Boolean
Networks
Andrzej Mizera, Jun Pang, Hongyang Qu and Qixia Yuan

17:10 - 17:35[O38] Comparisons of gene coexpression network modules in breastcancer and ovarian cancer
Shuqin Zhang[O41] Discovery of Boolean Metabolic Networks: Integer Linear
Programming Based Approach
Yushan Qiu, Hao Jiang, Xiaoqing Cheng and Wai‐Ki Ching

17:35 - 18:00[O39] Automated Transition Analysis of Activated Gene Regulation during
Diauxic Nutrient Shift in Escherichia Coli and Adipocyte Differentiation inMouse Cells
Yoichi Takenaka, Kazuma Mikami, Shigeto Seno and Hideo Matsuda[O42] Counting motifs in dynamic networks
Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher and Tamer
Kahveci

18:00 - 19:00

Poster Session for even numbers (Room 2 & 3)

19:00 - 21:00

Banquet (Event Hall)

Day 3: Jan 17, 2018.
09:00 - 09:30

Registration Open

09:30 - 10:30

Keynote Speech (Main Hall)
In vitro reconstitution of oogenesis in the mouse; how to establish the culture, system, mostly empirical
Dr. Katsuhiko Hayashi
Session Chair: Dr. Yoshihiro Yamanishi
Coffee Break

10:30 - 10:45
Parallel Session

Systems Biology (Main Hall)
Session Chair: Dr. Emmanuel Barillot

Gene Expression Analysis (3) (Room 1)
Session Chair: Dr. Limsoon Wong

10:45 - 11:10[O43] Composite mathematical modeling of calcium signaling behindneuronal cell death in Alzheimer's disease
Bobby Ranjan, Ket Hing Chong and Jie Zheng[O46] ncRNA-disease association prediction based on sequence
information and tripartite network
Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu and JoseNacher

11:10 - 11:35[O44] Regulation of dual specificity phosphatases in breast cancer duringinitial treatment with Herceptin: A Boolean model analysis
Petronela Buiga, Ari Elson, Lydia Tabernero and Jean‐Marc Schwartz[O47] Tensor decomposition/principal component analysis based
unsupervised feature extraction applied to brain gene expression andmethylation profiles of social insects with multiple castes
Y‐H. Taguchi

11:35 - 12:00[O45] Pathway-based approach using hierarchical components of rarevariants to analyze multiple phenotypes
Sungyoung Lee, Yongkang Kim, Sungkyoung Choi, Heungsun Hwang andTaesung Park

[O48] Comprehensive analysis of coding-lncRNA gene co-expression
network uncovers conserved functional lncRNAs in zebrafish
Wen Chen, Xuan Zhang, Jing Li, Shulan Huang, Shuanglin Xiang, Xiang Hu andChangning Liu

Lunch

12:00 - 13:30
Parallel Session

Novel Analytic Methods (Main Hall)
Session Chair: Dr. Jun Pang

Disease Analysis (Room 1)
Session Chair: Dr. Mitsunori Kayano

13:30 - 13:55[O49] Prediction of enhancer-promoter interactions via natural language
processing
Wanwen Zeng, Mengmeng Wu, Rui Jiang[O51] A new method to measure the semantic similarity from queryphenotypic abnormalities to diseases based on the Human Phenotype
Ontology
Xiaofeng Gong, Jianping Jiang, Zhongqu Duan and Hui Lu

13:55 - 14:20[O50] Estimation of Diffusion Constants from Single Molecular
Measurement without Explicit Tracking
Shunsuke Teraguchi and Yutaro Kumagai[O52] VAReporter: Variant reporter for cancer research of massive parallel
sequencing
Po‐Jung Huang, Chi‐Ching Lee, Ling‐Ya Chiu, Kuo‐Yang Huang, Yuan‐Ming
Yeh, Chia‐Yu Yang, Cheng‐Hsun Chiu and Petrus Tang

14:20 - 14:45[O53] cmFSM: A Scalable CPU-MIC Coordinated Drug-Finding Tool byFrequent Subgraph Mining
Shunyun Yang, Quan Zou, Shaoliang Peng and Runxin Guo

14:45 - 15:00

Closing Remarks / Award Ceremony (Main Hall)