International Conference on Intelligent Biology and Medicine (ICIBM)

2015 International Conference on Intelligent Biology and Medicine

Indianapolis, IN, USA

Program at-a-glance (November 13-15, 2015)

Friday, Nov 13	1:00 - 2:00pm			Keynote #1 Jiajie Zhang, Rm 118
	2:15 - 3:45pm			Tutorial #1 NGS data analysis Yan Guo, Rm 118	Tutorial #2 Bioimage informatics Kun Huang and Lee Cooper, Rm 206
	4:00 - 5:30pm				Tutorial #3 Top-down proteomics Xiaowen Liu, Rm 206
	5:30 - 7:30pm			Reception, 2^nd floor auditorium lobby

Saturday, Nov 14	8:30 - 9:30am			Keynote #2 Chris Sander, Rm 118
	9:50 - 12:20pm			Session #1 NGS data analysis Chair: Kun Huang, Rm 206	Session #2 Systems Biology Chair: Yufei Huang, Rm 208
	12:20 - 1:30pm			Lunch, Tower Dining
	1:30 - 2:50pm			Session #3 NGS data analysis II Chair: Yongsheng Bai, Rm 206	Session #4 Integrative Genomics Chair: Ewy Mathe, Rm 208
	3:10 - 4:30pm			Session #5 Genomics and Genetics Chair: Yidong Chen, Rm 206	Session #6 Epigenomics, Proteomics, and Metabolomics Chair: Lei Liu, Rm 208
	4:50 - 6:20pm			Keynote #3 A. Keith Dunker, Rm 118
	7:00 - 9:00pm			Banquet Rathskeller Restaurant (401 E Michigan St, Indianapolis, IN 46204)

Sunday, Nov 15	8:30 - 9:30am			Keynote #4 Sylvia Plevritis
	9:50 - 12:20pm			Session #7 Biomarker Discovery and Precision Medicine Chair: Yan Guo, Rm 206	Session #8 Pharmacogenetics and Systems Medicine Chair: Yidong Chen, Rm 208

Friday, November 13, 2015
10:00 – 5:00pm			Registration (1^st floor lobby)

1:00 – 2:00pm			Keynote lecture (Room 118)
			Dr. Jiajie Zhang, The University of Texas School of Biomedical Informatics Beyond Big Data: New Trends in Biomedical Informatics Research and Education Session chair: Dr. Zhongming Zhao
2:00 – 2:15pm			Coffee Break

2:15 – 5:30pm			Concurrent tutorial sessions

2:15 – 5:30pm			Tutorial #1 (Room 118)
			Next Generation Sequencing Data Analysis Dr. Yan Guo Vanderbilt University

2:15 – 3:45pm			Tutorial #2 (Room 206)
			Bioimage informatics with a focus on histology image analysis Dr. Lee Cooper, Emory University Dr. Kun Huang, The Ohio State University
3:45 – 4:00pm			Break

4:00 – 5:30pm			Tutorial #3 (Room 206)
			Computational Challenges in Top-Down Proteomics Dr. Xiaowen Liu Indiana University Purdue University Indianapolis

5:30 – 7:30pm			Poster and Reception 2^nd floor auditorium lobby
Morning, Saturday, November 14, 2015
8:00 – 4:30pm		Registration (1^st floor lobby)

8:30 – 9:30am		Keynote lecture (Room 118)
		Dr. Chris Sander, Memorial Sloan-Kettering Cancer Center Systems Biology in Action: Prediction of Large Protein 3D Structures and Design of Cancer Combination Therapy Session chair: Dr. Lang Li
9:30 – 9:50am		Coffee break (2^nd floor auditorium lobby)

9: 50 – 12:20pm		Concurrent session #1. NGS data analysis Session chair: Dr. Kun Huang Room 206
9:50 – 10:10am		Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe, Chandirasegaran Massilamany, Akram Mohammed, John Dustin Loy, Tanya Purvis, Bharathi Krishnan, Rakesh Halekote Basavalingappa, Christy M. Kelley, Chittibabu Guda, Raul G. Barletta, Etsuko N Moriyama, Timothy P. L. Smith and Jay Reddy.
10:10 – 10:30am		Statistical Modeling for Sensitive Detection of Low-Frequency Single Nucleotide Variants, Yangyang Hao, Pengyue Zhang, Xiaoling Xuei, Harikrishna Nakshatri, Howard Edenberg, Lang Li and Yunlong Liu.
10:30 – 10:50am		Detection of high variability in gene expression from single-cell RNA-seq profiling, Hung-I Chen, Yufang Jin, Yufei Huang and Yidong Chen.
10:50 – 11:10am		XMRF: An R package to Fit Markov Networks to High-Throughput Genetics Data, Zhandong Liu, Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Young and Pradeep Ravikumar
11:10 – 11:20am		Break
11:20 – 11:40am		Read-Split-Run: An improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data, Yongsheng Bai, Jeff Kinne, Brandon Donham, Justin Hassler and Randal Kaufman.
11:40 – 12:00am		An Overview of Copy Number Variations in the Lung Adenocarcinomas, Mathew Palakal and Meeta Pradhan, presented by Swapna Vidhur Daulatabad
12:00 – 12:20pm		Mitochondria Single Nucleotide Variant Among Six Different Cell Types, Pan Zhang, David Samuels, Yu Shyr and Yan Guo

9: 50 – 12:20pm		Concurrent session #2. Systems Biology Session chair: Dr. Yufei Huang Room 208
9:50 – 10:10am		Towards understanding brain-gut-microbiome connections in Alzheimer's disease, Rong Xu and Quanqiu Wang.
10:10 – 10:30am		Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach, Feixiong Cheng, Chuang Liu, Bairong Shen and Zhongming Zhao, presented by Junfei Zhao
10:30 – 10:50am		A genomics-based systems approach towards drug repositioning for rheumatoid arthritis, Rong Xu and Quanqiu Wang.
10:50 – 11:10am		*Highlight Talk #1: Co-expression analysis in single cells* Dr. Jiang Qian (Johns Hopkins University)
11:10 – 11:20am		Break
11:20 – 11:40am		State Feedback Control Design for Boolean Networks, Rongjie Liu and Yufang Jin.
11:40 – 12:00am		A Matrix Rank Based Concordance Index for Evaluating and Detecting Conditional Specific Co-Expressed Gene Modules, Zhi Han, Jie Zhang, Guoyuan Sun, Gang Liu and Kun Huang.
12:00 – 12:20pm		Comprehensive Comparison of Molecular Portraits between Cell Lines and Tumor in Breast Cancer, Lijun Cheng, Guanglong Jiang, Shijun Zhang, Aida Yazdanparast, Meng Li, Yunlong Liu and Sai Inavolu.
12:20 – 1:30pm		Lunch (Tower Dining Cafeteria)
Afternoon, Saturday, November 14, 2015
1:30 – 2:50pm		Concurrent session #3. NGS data analysis II Session chair: Dr. Yongsheng Bai Room 206
1:30 – 1:50pm		Benchmarking of de novo assembly algorithms for nanopore data reveals optimal performance of OLC approaches, Yesesri Cherukuri and Sarath Chandra Janga.
1:50 – 2:10pm		Lipopolysaccharide treatment induces genome-wide pre-mRNA splicing pattern changes in mouse bone marrow stromal stem cells, Ao Zhou, Meng Li, Bo He, Weixing Feng, Keith Dunker, Yunlong Liu and Yue Wang.
2:10 – 2:30pm		Whole blood transcriptional profiling comparison between different milk yield of Chinese Holstein cows using RNA-seq data, Xue Bai, Bin Liu, Xiaoyang Ji, Wenguang Zhang and Yongsheng Bai.

2:30 – 2:50pm		Improving De Novo Metatranscriptome Assembly via Machine Learning Algorithms, Hussein Mohsen, Haixu Tang and Yuzhen Ye.
1:30 – 2:50pm		Concurrent session #4. Integrative Genomics Session chair: Dr. Ewy Mathe Room 208
1:30 – 1:50pm		An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC), Yuanyuan Wang, Xingyi Guo, Michael Bray and Zhongming Zhao.
1:50 – 2:10pm		Structured Sparse CCA for Brain Imaging Genetics via Graph OSCAR, Lei Du, Heng Huang, Jingwen Yan, Sungeun Kim, Shannon Risacher, Mark Inlow, Jason Moore, Andrew Saykin and Li Shen.
2:10 – 2:30pm		Integrative Analysis of Somatic Mutations and Transcriptomic Data to Functionally Stratify Breast Cancer Patients, Jie Zhang, Zachary Abrams, Jeffrey Parvin and Kun Huang.
2:30 – 2:50pm		Inference of tumor proliferation networks from functional and genomic data, Noah Berlow and Ranadip Pal.
2:50 – 3:10pm		Coffee break (2^nd Floor Auditorium Lobby)

3:10 – 4:30pm		Concurrent session #5. Genomics and Genetics Session chair: Dr. Yidong Chen Room 206
3:10 – 3:30pm		Expression Quantitative Locus Mapping for Identification of Hotspots Using an Empirical Bayes Mixture Model, Guanglong Jiang, Yingqiang Fu, Zhigao Li, Shirin Ardeshirrouhanifard, Pengyue Zhang, Lijun Cheng, Lang Li and Arindom Chakraborty.
3:30 – 3:50pm		Computational Tools for Genome-wide R-loops Identification and Characterization, Rongjie Liu and Yidong Chen.
3:50 – 4:10pm		Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study, Min Zhao and Zhongming Zhao.
4:10 – 4:30pm		*Highlight Talk #2: On understanding molecular mechanisms of disease and genome interpretation* Dr. Predrag Radivojac (Indiana University)
Afternoon, Saturday, November 14, 2015
3:10 – 4:30pm		Concurrent session #6. Epigenomics, Proteomics, and Metabolomics Session chair: Dr. Lei Liu Room 206
3:10 – 3:30pm		An HMM-based Hierarchical Model for Detecting Methylation Sites in MeRIP-Seq Data, Xiaodong Cui, Jia Meng, Manjeet Rao, Yidong Chen and Yufei Huang.
3:30 – 3:50pm		Whole Genome Sequencing reveals Enhancer as major Methylation Target during Human pluripotent stem Cell early neural Induction, Gang Liu, Yang Bai, Lei Liu, Jiaxi Zhou, Pei Su, Jie Wang, Biqing Li, Lisha Lu, Tao Xiong and Fei Wang.
3:50 – 4:10pm		Genomic data mining reveals a rich repertoire of transport proteins in Streptomyces, Zhan Zhou, Ning Sun, Shanshan Wu, Yong-Quan Li and Yufeng Wang.
4:10 – 4:30pm		*Highlight Talk #3: Metabolomics as a powerful tool in biomarkers studies: an example in lung cancer* Dr. Ewy Mathe (the Ohio State University)
4:30 – 4:50pm		Break

4:50 – 6:20pm		Keynote lecture (Room 118)
		Dr. A. Keith Dunker, Indiana University School of Medicine Intrinsically Disordered Protein and the Origins of Complex Multicellular Organisms Session chair: Dr. Yunlong Liu
7:00 – 9:00pm		Banquet
		Rathskeller Restaurant Street address: 401 E Michigan St, Indianapolis, IN 46204
Morning, Sunday, November 15, 2015
8:00 – 12:00pm		Registration (1^st floor lobby)

8:30 – 9:30am		Keynote lecture (Room 118)
		Dr. Sylvia Plevritis, Stanford University Optimizing Combination Cancer Therapy Based on Single Cell Analysis Session chair: Dr. Kun Huang
9:30 – 9:50am		Coffee break (2^nd floor auditorium lobby)

9: 50 – 12:20pm		Concurrent session #7. Biomarker Discovery and Precision Medicine Session chair: Dr. Yan Guo Room 206
9:50 – 10:10am		CrossLink: A Novel Method for Cross-Condition Classification of Cancer Subtypes, Chifeng Ma, Konduru Sastry, Mario Flores, Salah Gehani, Issam Al-Bozom, Yusheng Feng, Erchin Serpedin, Lotfi Chouchane, Yidong Chen and Yufei Huang.
10:10 – 10:30am		Digitalization of a non-irradiated acute myeloid leukemia model, Rudong Li, Hui Cheng, Tao Cheng and Lei Liu.
10:30 – 10:50am		A Method for Identifying Discriminative Isoform-Specific Peptides for Clinical Proteomics Application, Fan Zhang and Jake Chen.
10:50 – 11:10am		Break
11:10 – 11:30am		Classification of breast cancer patients using somatic mutation profiles and machine learning approaches, Suleyman Vural, Xiaosheng Wang and Chittibabu Guda.
11:30 – 11:50am		Towards precision medicine-based therapies for glioblastoma: interrogating human disease genomics and mouse phenotypes, Yang Chen, Zhen Gao, Bingcheng Wang and Rong Xu.
11:50 – 12:10am		A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes, Sujuan Wu, Junyi Li, Mushui Cao, Jing Yang, Yi-Xue Li and Yuan-Yuan Li.
9: 50 – 12:20pm		Concurrent session #8. Pharmacogenetics and Systems Medicine Session chair: Dr. Yidong Chen Room 208
9:50 – 10:10am		A simple gene set-based method accurately predicts the synergy of drug pairs, Yu-Ching Hsu, Yu-Chiao Chiu, Yidong Chen, Tzu-Hung Hsiao and Eric Chuang.
10:10 – 10:30am		Leveraging Syntactic and Semantic Graph Kernels to Extract Pharmacokinetic Drug Drug Interactions from Biomedical Literature, Yaoyun Zhang, Heng-Yi Wu, Jun Xu, Jingqi Wang, Ergin Soysal, Lang Li and Hua Xu.
10:30 – 10:50am		Improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies, Weixing Feng, Dingkai Xue, Fengfei Song, Sen Zhao, Ziwei Li, Duojiao Chen, Yangyang Hao and Yunlong Liu.
10:50 – 11:10am		Break
11:10 – 11:30am		PageRank influence analysis of protein-protein association networks in the malaria parasite Plasmodium falciparum, Xinran Yu, Timothy Lilburn, Hong Cai, Jianying Gu, Turgay Korkmaz and Yufeng Wang.
11:30 – 11:50am		Identification of rifampin-regulated functional modules and related microRNAs in human hepatocytes based on the protein interaction network, Jin Li, Ying Wang, Lei Wang, Xuefeng Dai, Wang Cong, Weixing Feng, Chengzhen Xu, Yulin Deng, Todd C Skaar, Hong Liang and Yunlong Liu.
11:50 – 12:10am		Using a Computational Model of Cancer to Test the Effectiveness of Imatinib Resistant GIST Drug Regimes, Malcolm Callis and David Liebner.