Program

Program as of Thursday, 19 Sept. 2013

9:30-18:30

Registration ( First floor Foyer )

Program as of Friday, 20 Sept. 2013

8:00	Registration (First floor Foyer)
Venue	Ballrooms A & B
8:30	Welcome to InCoB2013 Conference Chair: Bairong Shen APBioNet President: Shoba Ranganathan
8:50	Photos
9:00	Keynote 1: Yunping Zhu - Efficient labeled and label-free algorithms lay a solid foundation for quantitative proteomics. Chair: Bairong Shen
9:45	Keynote 2: Wen-Hsiung Li - Assembling a genome using short sequencing reads Chair: Shoba Ranganathan
10:30	Coffee Break
11:00	Status and Future of InCoB2013 - Christian Schönbach
11:30- 12:30	Poster Session 1 (The Second Floor Foyer): odd number posters
12:30	Lunch Break
Venue	Guoda Ballroom A		Guoda Ballroom B
13:30 15:35	1. Systems Biology Chair: Bairong Shen	13:30 15:25	2. Disease Informatics Chair: Christian Schönbach
13:30	Plenary lecture 1: Keith Dunker - An IDP-based Swiss-army-knife-like toolkit for signaling diversification.	13:30	Plenary lecture 2: Jürgen Brosius - New parts of existing genes: a double-edged sword.
13:50	1. Y López, A Patil and K Nakai. Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.	13:50	1. R Zhang, L Hao, L Wang, M Chen, W Li, M Esteban, J Yu, J Xiao and J Wu. Gene expression analysis of induced pluripotent stem cells from aneuploid chromosomal syndromes.
14:05	2. Haijun Gong. Analysis of intercellular signal transduction in the tumor microenvironment.	14:05	2. Y Xiang, J Zhang and K Huang. Mining Tissue-Tissue Gene Co-expression network for tumor microenvironment study and biomarker prediction.
14:20	3. K Yoshida, K Maeda, H Kusuhara and A Konagaya.Estimation of feasible solution space using Cluster Newton method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models.	14:20	3. Z Xiang, T Qin, Z Qin and Y He. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks.
14:35	4. P Chumnanpuen, I Nookaew and J Nielsen. Integratedanalysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast.	14:35	4. Z Li, Y He, Q Liu, L Wong, CK Kwoh, H Nguyen and J Li. Structural analysis on mutation residues and interfacial water molecules for understanding genetic disease.
14:50	5. A Batagov, A Yarmishyn, P Jenjaroenpun, Y Nishida, I Kurochkin and JZ Tan. Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells.	14:50	5. Y Tang, J Chen, C Luo, A Kaipia and B Shen. Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer.
15:05	A. I Tawornsamretkit, S Cheevadhanarak, D Waraho and A Meechai. Rational design for efficient linalool production in synthetic Escherichia coli.(10 min)	15:05	A. V Phav and A Konagaya. Comparison of computational approaches to estimate long-range chromatin interaction between human breast cancer candidate genes and estrogen receptor alpha proteins.(10 min)
15:15	B. Y-S Lo, S-H Huang, C-Y Lin, T-L Lee and J-M Yang. Infer human and zebrafish interactomes through structure protein protein interaction families. (10 min)	15:15	B. MP Grover, S Ballouz, KA Mohanasundaram, RA George, C Sherman, TM Crowley and M Wouters. Identification of novel therapeutics for complex diseases from genome-wide association data. (10 min)
15:25	C. S Sriganesh. Evolution and controllability of cancer networks: a Boolean perspective. (10 min)
15:35	Break
16:00 17:55	3. Imaging and Emerging Bioinformatics Applications Chair: Tin Wee Tan	16:00 17:55	4. Immunoinformatics Chair: Vladimir Brusic
16:00	Plenary lecture 3: Kun Huang - Beyond co-expression: integrating nonlinear correlation with Boolean relationships for biological network inference	16:00	Plenary lecture 4: Luonan Chen - Early diagnosis on complex diseases by dynamical network biomarkers
16:20	1. D Laksameethanasan, R Zhen Tan, GW-L Toh and L-H Loo. cellXpress: a fast and user-friendly software platform for profiling cellular phenotypes.	16:20	1. I-H Liu, Y-S Lo and J-M Yang. Genome-wide structural modelling of TCR-pMHC interactions.
16:35	2. Y Wang, W Goh, L Wong and G Montana. Random forests on Hadoop for genome-wide studies of multivariate neuroimaging phenotypes.	16:35	2. L Guo, C Luo and S Zhu. MHC2SKpan: A novel kernel based approach for pan specific MHC class II peptide binding prediction.
16:50	3. P Charoenkwan, E Hwang, RW Cutler, H-C Lee, L-W Ko, H-L Huang and S-Y Ho. HCS-Neurons: Identifying phenotypic changes in multi-neuron images upon drug treatments of high-content screening.	16:50	3. K-C Huang, K-C Yang, H Lin, TT-H Tsao, W-K Lee, S-A Lee and C-Y Kao. Analysis of schizophrenia and hepatocellular carcinoma genetic network with corresponding modularity and pathways: Novel insights to the immune system.
17:05	4. R Uttamatanin, P Yuvapoositanon, A Intarapanich, S Kaewkamnerd, R Phuksaritanon, A Assawamakin and S Tongsima. METASEL: A Metaphase selection tool using Gaussian-based classification technique.	17:05	4. M Pennisi, A-M Rajput, L Toldo and F Pappalardo. Agent based modeling of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis.
17:20	5.TW Tan, C Xie, M De Silva, K Siong Lim, CPK Patro, SJ Lim, KR Govindarajan, JC Tong, KH Choo, S Ranganathan and AM Khan. Simple re-instantiation of small databases using cloud computing.	17:20	5. CTT Su, X Ouyang, J Zheng and C-K Kwoh. Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with the current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K.
17:35	A. Y-H Tseng, C-L Tsai, C-C Lin and J-Y Peng. 3D morphological analysis reveals mitochondrial biogenesis and quality control in cell cycle. (10 min)	17:35	6. LR Olsen, UJ Kudahl, O Winther and V Brusic. Literature classification for semi-automated updating of biological knowledgebases.
17:45	B. C Yan and Y Zhu. Chemical compounds classification using graph methods. (10 min)
18:00- 18:30	Reception Party

Program as of Saturday, 21 Sept. 2013

8:00	Registration (First floor Foyer)
Venue	Guoda Ballrooms A & B
9:00	Keynote 3: Philip Payne - Translational Informatics: enabling knowledge-driven healthcare Chair: Bairong Shen
9:45	Keynote 4: Manyuan Long - New genes as drivers of phenotypic evolution: The implication and challenge to translational medical studies Chair: Tin Wee Tan
10:30	Coffee Break
11:00	APBioNet 2013 Report & AGM - Shoba Ranganathan, Kenta Nakai, Christian Schönbach, Asif M Khan, Tin Wee Tan
11:30	Poster Session 2 (The Second Floor Foyer): even number posters
12:30	Lunch Break
Venue	Guoda Ballroom A		Guoda Ballroom B
13:30- 15:30	5. Pathways & Networks Chair: Kenta Nakai	13:30- 15:30	6. Non-coding RNAs Chair: Christian Schönbach
13:30	Plenary lecture 5: Paul Horton - Advances in predicting protein sub-cellular localization signals.	13:30	Plenary lecture 2: Xu Dong - Role of DNA methylation in cancers.
13:50	1. D L-K Wong, X-L Li, M Wu, J Zheng and S-K Ng. PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks.	13:50	1. Xing Tang, Mei Hou, Yang Ding, Zhaohui Li, Lichen Ren and Ge Gao. Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell.
14:05	2. J Li and Z Lu. Pathway-based drug repositioning using causal inference.	14:05	2. Y Kremenska, V Nair, P Jenjaroenpun, M Kremenskoy, I Kurochkin and B Joseph. Distinct features of RNA in exosomes produced by human breast cancer cell lines revealed by next-generation sequencing based approach.
14:20	3. C Wu, J-MSchwartz and G Nenadic. PathNER: a tool for systematic identification of biological pathway mentions in the literature	14:20	3. D Kim, HH Shin, J-G Joung, SY Lee and JH Kim. Intra-relation reconstruction from inter relation: miRNA to gene expression.
14:35	4. M Lee, K Park and D Kim. Interaction network among functional drug groups.	14:35	4. K-W Tsai, W-S Chen, T-W Chen, T-H Yang, L-Y Hu, H-W Pan, S-C Li, M-R Ho, S-Y Yu, Y-T Tu, W-C Lin, TT Wu, C-W Shu and PF Liu. Co-modulated behavior and effects of differentially expressed miRNA in colorectal cancer.
14:50	5. AW-Ti Chiang and M-J Hwang. A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits.	14:50	5. Y-J Na and JH Kim. Understanding cooperativity of microRNAs via microRNA association networks.
15:05	6. PB. Madhamshettiwar, SR Maetschke, MJ. Davis and Mark A. Ragan. RMaNI: Regulatory Module Network Inference Framework.	15:05	6. J-K Rhee, S-Y Shin and B-T Zhang. Construction of microRNA functional families by a mixture model of position weight matrices.
15:20	A. W Yan, M un, G Hu, J Zhou, J Chen, B Chen and B Shen. Characterization of protein structure and evolution with amino acid network. (10 min)	15:20	A. I Kurochkin and A Batagov. Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3'-untranslated regions. (10 min)
15:30	Coffee Break
16:00- 17:30	7. Proteins, motifs, ligands Chair: Shoba Ranganathan	16:00- 17:30	8. Sequencing, Sequences, Evolution Chair: Asif Khan
16:00	1. B Shashni, K Sharma, R Singh, K Sakharkar, S Dhillon, Y Nagasaki and M Sakharkar. Coffee component Hydroxyl Hydroquinone (HHQ) as a putative ligand for PPAR gamma and implications in breast cancer.	16:00	1.Chin Lui Goi, Peter Little and Chao Xie. Cell-type and Transcription factorspecific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seqdata.
16:15	2. M-G Su and TY Lee. Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures.	16:15	2. S Mitra, K Foerster-Fromme, A Damms-Machado, T Scheurenbrand, S Biskup, DH. Huson and SC. Bischoff. Analysis of the intestinal microbiota using SOLiD 16SrRNA gene sequencing and SOLiD shotgun sequencing.
16:30	3. PV Nguyen, S Srihari and HW Leong. Identifying conserved protein complexes between species by constructing interolog networks.	16:30	3. D Strbenac, N Armstrong and J Yang. Detection and classification of peaks in 5' Cap RNA sequencing data.
16:45	4.K-Y Huang, C-T Lu, NA Bretaña, TY Lee and T-H Chang. ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins.	16:45	4.D Biswal, S Ghatani, J Shylla, R Sahu, N Mullapudi, A Bhattacharya and V Tandon. An integrated pipeline for next-generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899 (Digenea: Fasciolidae).
17:00	5. Liang Jiang, Hua-Zhang Zhu, Yin-Zhen Xu, Yan Zhang, Jia-Zuan Ni and Qiong Liu. Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes.	17:00	5. D Biswal, J Valrie and P Tandon. Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) with a Bayesian relaxed clock implying phylogeographic inference in continuous space.
17:15	6.Afiahayati, K Sato and Y Sakakibara. An extended genovo metagenomic assembler by incorporating paired-end information.	17:15	6. J Choi, K-T Kim, JJeon and Y-H Lee. Fungal plant cell wall-degrading enzyme database: a platform for comparative and evolutionary genomics in fungi and oomycetes.
18:00 20:30	Conference Dinner

Program as of Sunday, 22 Sept. 2013

8:00	Registration (First floor Foyer)
Venue	Guoda Ballrooms A & B
9:00	Keynote 5: Kazuyuki Aihara - Mathematical modeling and its application to personalized medicine for prostate cancer Chair: Jinn-Moon Yang
9:45	Plenary lecture 7: Zhao Zhongming - A personalized mutation network approachfor detecting putative cancer genes from next-generation sequencing data Chair: Chen Luonan
10:10	Bioinformatics education session Chair: Shoba Ranganathan
10:45	Coffee break
11:15	Plenary lecture 8: Ruiqiang Li - Bioinformatics development for next-generation sequencing data analysis
11:40	Closing session - Bairong Shen, Shoba Ranganathan, Kenta Nakai, Christian Schönbach - Best paper awards and Poster prizes - APBioNet awards - Announcement of InCoB2014
12:30	End of InCoB2013 and lunch