International Conference on Intelligent Biology and Medicine (ICIBM 2014)

December 4-6 , 2014, San Antonio, TX, USA



      Dec4, 2014


      10:00– 12:00pm:                   Registration



      12:00-1:00pm:  Session Chair: YidongChen

      MagnoliaRoom                   Keynote: Single-Cell Analysis of Tumor Heterogeneity

      Dr. Tim Huang, Professor and Chair,
      Department of Molecular Medicine, The University of      Texas Health Science Center at San Antonio


      1:00– 1:15pm:   Break


Magnolia Room

1:15-3:45pm       Tutorial 1: Proteomics and Metabolomics

                                Susan E Weintraub, Chair

Steve Patrie

Bill Alley and

Michelle Zhang


3:45 – 4:00pm Break


4:00 – 5:30pm Tutorial 2: Next-generation sequencing and data analysis

Yunlong Liu, Chair

Kun Huang,


Baker Room

1:15-3:45pm       Tutorial 3: Single-cell

Chun-Liang Chen, Chair

Chenghang Zong

Zhao Lai

Yidong Chen


3:45-4:00pm     Break


4:00-5:30pm     Tutorial 4: Metagenomics

Babu Guda, Chair

Qunfeng Dong



Dec5, 2014


8:00-8:30am                      Breakfast

8:30-9:30am                      SessionChair: Zhongming Zhao

MagnoliaRoom             Keynote: Identifying all of cancer’s manifestations through integrated Pan-Canceranalysis

Dr.Josh Stuart, Professor, Biomolecular EngineeringDepartment Baskin Engineering Endowed Chair
Associate Director, Center for Biomolecular Scienceand Engineering, University of California Santa Cruz



9:30– 9:40 am Break

Magnolia Room

9:40 -12:00am:  Gene Regulation and Protein Interaction Networks, I

Session Chair: Dr. Feixiong Cheng

9:40 – 10:00am: A Translational Bioinformatic Approach In Identifying And Validating An Interaction Between Vitamin A And Cyp19a1, Santosh Philips, Guanglong Jiang, Lei Wang, Todd Skaar and Lang Li

10:00 – 10:20am: Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao, Jing Chen, Xue-Ting Wu, Yi-Qin Xu, Yang Zhong, Yi-Xue Li, Jia-Kuan Chen, Xuan Li and Peng Nan

10:20 – 10:40am: BMRF-MI: integrative identification of protein interaction network by modeling the gene dependency, Xu Shi, Xiao Wang, Ayesha Shajahan, Leena Hilakivi-Clarke, Robert Clarke and Jianhua Xuan.

10:40 – 11:00am: Network-based stratification analysis of 13 major cancer types using mutations in panels of cancer genes, Xue Zhong, Hushan Yang, Shuyang Zhao, Yu Shyr and Bingshan Li.

11:00 – 11:20am: Network-based Gene Prediction for Plasmodium falciparum Malaria Towards Genetics-based Drug Discovery, Yang Chen and Rong Xu.

11:20 – 11:40am: Ishwor Thapa, Howard Fox and Dhundy Bastola. Co-expression network analysis of miRNA-142 over-expression in neuronal cells

11:40 – 12:00pm: Studying Tumorigenesis through Network Evolution and Somatic Mutational Perturbations in the Cancer Interactome, Feixiong Cheng and Zhongming Zhao (highlight talk)


Baker Room

9:45-12:00am:  Algorithms in NGS Data Analysis

Session Chair: Dr. Eric Chuang

9:40 – 10:00am: Hung-I Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang and Yidong Chen. Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads

10:00 – 10:20am: Adam Cornish and Chittibabu Guda. A comparison of variant calling pipelines using Genome in a Bottle as a reference

10:20 – 10:40am: Yang Xiang and Sarath Janga. Building integrated ontological knowledge structures with efficient approximation algorithms

10:40 – 11:00am: Qi Liu, Xue Zhong and Yu Shyr. Assessing Computational Steps for CLIP-Seq Data Analysis

11:00 – 11:20am: Yu-Ching Hsu, Yu-Chiao Chiu, Yidong Chen, Eric Y. Chuang and Tzu-Hung Hsiao. A gene set approach to analyze copy number alterations profiles of breast cancer

11:20 – 11:40am: Kashish Chetal and Sarath Chandra Janga. OperomeDB: a database of condition-specific transcription units in prokaryotic genomes

11:40 – 12:00pm: Amplification of Distant Estrogen Response Elements Deregulates Target Genes Associated with Tamoxifen Resistance in Breast Cancer, Pei-Yin Hsu (highlight talk)


Noon-1:30 pm:  Lunch break



1:30-2:30pm:     Session Chair: Victor Jin

MagnoliaRoom          Keynote: GenomicMedicine:  Transforming Cancer Researchand Care

Dr.Lynda Chin, Professor and Chair,
Department of Genomic Medicine, Division of Cancer Medicine, TheUniversity of Texas MD Anderson Cancer Center


2:30– 2:40 pm                 Break

Magnolia Room

2:40-6:00pm:  Gene Regulation and Protein Interaction Networks, II

Session Chair: Drs. Yufang Jin, Yongsheng Bai

2:40 – 3:00pm MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures, Yizhe Zhang, Yupeng He, Guangyong Zheng and Chaochun Wei.

3:00 – 3:20pm Kevin Zhu, Qi Liu, Yubo Zhou, Cui Tao, Hua Xu and Jingchun Sun. Oncogenes and tumor suppressor genes: comparative genomics and network perspectives

3:20 – 3:40pm Liang-Chin Huang, Ergin Soysal, W. Jim Zheng, Hua Xu and Jingchun Sun. A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case

3:40 – 4:00pm Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network, Tingting Qin, Nabil Matmati, Lam Tsoi, Bidyut Mohanty, Nan Gao, Jijun Tang, Andrew Lawson, Yusuf Hannun and W. Jim Zheng (highlight talk)

4:00 – 4:10pm Coffee Break

4:10 – 4:30pm Nguyen T. Nguyen, Merry L. Lindsey and Yu-Fang Jin. Systems analysis of gene ontology and biological pathways post-myocardial infarction

4:30 – 4:50pm Yu-Chiao Chiu, Chin-Ting Wu, Tzu-Hung Hsiao, Yi-Pin Lai, Chuhsing K. Hsiao, Yidong Chen and Eric Y. Chuang. Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes

4:50 – 5:10pm Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation, Junbai Wang, Agnieszka Malecka, Gunhild Trøen and Jan Delabie

5:10 – 5:30pm Lei Wang, Chiangwei Chang, Hong Liang, Heng-Yi Wu, Weixing Feng, Sara Quinney, Jin Li and Lang Li. How to Choose In Vitro Systems to Predict In Vivo Drug Clearance: A System Pharmacology Prospective

5:30 – 5:50: Emad Ramadan, Moataz Ahmed and Ahmed Naef. Bio-inspired Algorithm for Identifying Overlapping Clusters in Protein-Protein Interaction Networks

5:50 – 6:10pm Novel Bioinformatics Method for Identification of Genome-Wide Non-Canonical Spliced Regions Using RNA-Seq Data, Yongsheng Bai (highlight talk)


Baker Room

2:40-6:00pm  Metagenomics and Bioinformatics methods

Session Chair: Drs. Chittibabu Guda, Patrick Zhao

2:40 – 3:00pm Akram Mohammed and Chittibabu Guda. Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism

3:00 – 3:20pm Rong Xu, Quanqiu Wang and Li Li. A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat

3:20 – 3:40pm Yukun Chen, Jingchun Sun, Liang-Chin Huang, Hua Xu and Zhongming Zhao. Classification Of Cancer Primary Sites Using Machine Learning And Somatic Mutations

3:40 – 4:00pm MeT-DB: A database of transcriptome methylation in mammalian cells, Lui Hui, Mario Flores, Jia Meng, Lin Zhang, Xinyu Zhao, Manjeet Rao, Yidong Chen and Yufei Huang (highlight talk)


4:00 – 4:10pm Coffee Break


4:10 – 4:30pm Yanhui Liang, Fusheng Wang, Darren Treanor, Derek Magee, George Teodoro, Yangyang Zhu and Jun Kong. A Framework for 3D Vessel Analysis with Whole Slide Images of Serial Liver Sections

4:30 – 4:50pm Pei-Fang Su, Yan Guo, Chung-I Li, Qi Liu, John Boice and Yu Shyr. Paired mitochondrial DNA data analysis using bivariate Poisson regression model

4:50 – 5:10pm Jun Li and Patrick Xuechun Zhao. Mining functional modules in heterogeneous biological networks using Multiplex PageRank method

5:10 – 5:30pm Shilin Zhao, Yan Guo, Quanhu Sheng, Mingsheng Guo, Brian Lehmann, Jennifer Pietenpol, David Samuels and Yu Shyr. RNAseq by Total RNA Library Identifies Additional lncRNA Compared to Poly(A) RNA library

5:30 – 5:50pm Weirong Cui, Yulan Qian, Xiaoke Zhou, Yuxin Lin, Junfeng Jiang, Jiajia Chen, Zhongming Zhao and Bairong Shen. Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data

5:50 – 6:10pm Detecting evolutionary strata on the human x chromosome in the absence of gametologous y-linked sequences, Ravi Shanker Pandey, Melissa Wilson Sayres and Rajeev Azad (highlight talk)

6:30-8:30pm      Banquet

Dec6, 2014

8:00-8:30am                      Breakfast

8:30-9:30am                       SessionChair: Victor Jin

MagnoliaRoom          Keynote:MakeBig Data Useful: Horizontal and Vertical Data Integration to Study Genes,Networks and Diseases

Dr. Jasmine Zhou, Professor,

Departments of Biological Sciences andComputer Science, University of Southern California


9:30– 9:45am   Break

Magnolia Room

9:45 – 1:15pm: Epigenetics & Systems Biology

   Session Chair: Drs. Steve Qin and Jason Ernst


  9:45 – 10:15am:  Systematic epigenome imputation of over 4000 datasets, Jason Ernst

10:15 – 10:45am:  Base-resolution methylation patterns accurately predict transcription factor bindings in vivo, Steve Qin

10:45 – 11:15am:  Synthetic long read next generation sequencing, Jeremy Edwards

11:15 – 11:35am:  Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors, Zhenqing Ye, Zhong Chen, Xun Lan, Stephen Hara, Benjamin Sunkel, Tim Huang, Laura Elnitski, Qianben Wang and Victor Jin (highlight talk)


11:35 – 11:50 am                Coffee Break


11:50 – 12:20pm: Toward personalized cancer medicine: A cancer hallmark network framework, Edwin Wang

12:20 – 12:50pm: A comparative analysis of the cis-regulatory landscape between human and mouse, Feng Yue, Yin Shen, Samantha Kuan, Zhen Ye, Weisheng Wu, Ross Hardison, Mike Beer, Bing Ren & The mouse ENCODE consortium

12:50 – 1:10pm Prediction of promoters and enhancers using multiple DNA methylation-associated features, Woochang Hwang, Verity Oliver, Shannath Merbs, Heng Zhu and Jiang Qian.

1:10 – 1:30pm: Hong Cai, Timothy Lilburn, Changjin Hong, Jianying Gu, Rui Kuang and Yufeng Wang. Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments

Baker Room

9:45 – 1:15pm: Biomarker Identification Methods
   Session Chair: Drs. Jianhua Ruan, Fuhai Li

9:45 – 10:05am Ghim Siong Ow and Vladimir Kuznetsov. Multiple signatures of a disease in potential biomarker space: Getting the signatures consensus and identification of novel biomarkers

10:05 – 10:25am Lin Wang, Fuhai Li, Jianting Sheng and Stephen T.C. Wong. A Computational Method for Clinically Relevant Cancer Stratification and Driver Mutation Module Discovery Using Personal Genomics Profiles

10:25 – 10:45am Jing Wang, Qi Liu and Yu Shyr. Dysregulated transcription across diverse cancer types reveals the importance of RNA-binding protein in carcinogenesis

10:45 – 11:05am: A Personalized Committee Classification Approach to Improving Prediction of Breast Cancer Metastasis, Md Jamiul Jahid, Tim Huang and Jianhua Ruan (highlight talk)

11:05 – 11:25am Coffee Break


11: 25 – 11:50am Jian-Yu Shi, Zun Liu, Hui Yu and Yong-Jun Li. Drug Repositioning Via Drug-Target Pair Space Built by Within-Score and Between-Score Features

11:50 – 12:15pm William Budd, Greg Meyers, Jeri Dilts, Katherine O'Hanlon, John Woody, David Bostwick, John Drury and Thomas Reynolds. Next Generation Sequencing Reveals Disparate Population Frequencies Among Cytochrome P450 Genes: Clinical Pharmacogenomics of the CYP2 Family

12:15 – 12:40pm Fan Zhang, Mu Wang and Renee Drabier. Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq

12:40 – 1:05pm Jasjit Banwait, Kaitlin Goettsch and Dhundy Bastola. Proteins localized to human mitochondria show structural element enrichment in their corresponding mRNA

1:05 – 1:25pm: Improve the prognostic estimation of cancer patients by incorporating the molecular data of tumor samples, Han Liang (Highlight talk)