ICIBM 2016


Schedule

→ Click to view ICIBM 2016 Program at-a-glance PDF 

Thursday, December 8th
10:00 AM Registration opens 1st floor lobby/Pre-function area
11:00 AM - 12:00 PM Box Lunches Available
(Eat in auditorium, outside or event/exhibition space)
Pre-function area
12:00 PM - 2:00 PM Introduction to Pathway and Network Analysis 
Dr. Amin Momin, MD Anderson Cancer Center
Auditorium
12:00 PM - 3:00 PM High Throughput Data Analysis, DNA, RNA, Microbiome Sequencing and Genotyping
Dr. Yan Guo, Vanderbilt University
Lecture Hall – Room 280
2:00 PM - 2:15 PM BREAK (Auditorium sessions)
2:15 PM - 4:15 PM Statistical Methods for Integrative Clustering Analysis of Multi-omics Data
Dr. Qianxing Mo, Baylor College of Medicine
Auditorium
3:00 PM - 3:15 PM BREAK (Lecture Hall - Room 280 sessions)
3:15 PM - 4:15 PM Interactive Workshop on ENCODE Data Analysis and Visualization
Dr. Feng Yue, Pennsylvania State University
Lecture Hall - Room 280
4:15 PM - 4:30 PM BREAK
4:30 PM - 5:20 PM Keynote Lecture
Siri of the Cell – Intelligent agents for systems medicine constructed using systems data
Trey Ideker, Ph.D., Professor, University of California San Diego
Auditorium
5:20 PM - 5:30 PM BREAK Event/Exhibition Space
5:30 PM - 7:30 PM Poster Session and Reception
Friday, December 9th
7:30 AM - 8:30 AM Registration Open and Breakfast
(Eat in auditorium, outside or Event/exhibition space)
Pre-function area
8:30 AM - 8:40 AM Opening Remarks
8:40 AM - 9:30 AM Keynote Lecture
Evolution and the proteome: Insights into protein function from deeply conserved gene modules

Edward Marcotte, Ph.D., Professor, University of Texas at Austin
Auditorium
9:30 AM - 9:40 AM BREAK
Genome Structure Analysis and Visualization - Concurrent Sessions
Session Chair: Kai Wang
Auditorium
NGS Analysis and Tools I - Concurrent Sessions
Session Chair: Ranadip Pal
Lecture Hall - Room 280
9:40 AM - 10:00 AM SVachra: A tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads
Oliver A. Hampton, Adam C. English, Mark Wang, William J. Salerno, Yue Liu, Donna M. Muzny, Yi Han, David A. Wheeler, Kim C. Worley, James R. Lupski and Richard A. Gibbs
Part of concurrent sessions: Genome Structure Analysis and Visualization
Auditorium
9:40 AM - 10:00 AM 3' -UTR Shortening Represses Tumor Suppressors in trans by Disrupting ceRNA Crosstalk
Wei Li
Part of concurrent sessions: NGS Analysis and Tools I
Lecture Hall - Room 280
10:00 AM - 10:20 AM PennCNV in whole-genome sequencing data
Leandro de Arau´jo Lima and Kai Wang
Part of concurrent sessions: Genome Structure Analysis and Visualization
Auditorium
10:00 AM - 10:20 AM Optimal Choice of Word Length When Comparing Two Markov Sequences Using a chi-square statistic
Xin Bai, Kujin Tang, Jie Ren, Michael Waterman, Fengzhu Sun
Part of concurrent sessions: NGS Analysis and Tools I
Lecture Hall - Room 280
10:20 AM - 10:40 AM A Flexible Approach to Reconstruct Genomic Spatial Structure by Genetic Algorithms
Yan Zhang, William Hoskins, Ruofan Xia, Xiya Xia, W. Jim Zheng and Jijun Tang
Part of concurrent sessions: Genome Structure Analysis and Visualization
Auditorium
10:20 AM - 10:40 AM The Discrepancy among Single Nucleotide Variants Detected by DNA and RNA High Throughput Sequencing Data
Yan Guo, Shilin Zhao, Quanhu Sheng, David C Samuels, Yu Shyr
Part of concurrent sessions: NGS Analysis and Tools I
Lecture Hall - Room 280
10:40 AM - 10:50 AM BREAK
10:50 AM - 11:10 AM Genomic Diversity and Phylogeography of Norovirus in China
Niu Qiao, Lei Liu
Part of concurrent sessions: Genome Structure Analysis and Visualization
Auditorium
10:50 AM - 11:10 AM STRScan: Targeted Profiling of Short Tandem Repeats in Whole-Genome Sequencing Data
Haixu Tangaa, Etienne Nzabarushimanaaa
Part of concurrent sessions: NGS Analysis and Tools I
Lecture Hall - Room 280
11:10 AM - 11:30 AM Visualizing Human Genome in Time and Space
Jieyi Zhao, Lingxi Zhou, Hua Xu, Jijun Tang and W. Jim Zheng
Part of concurrent sessions: Genome Structure Analysis and Visualization
Auditorium
11:10 AM - 11:30 AM XBSeq2: a fast and accurate quantification of differential expression and differential Polyadenylation
Yuanhang Liu, Ping Wu, Jingqi Zhou, Teresa L Johnson-Pais, Zhao Lai, Ronald Rodriguez, Yidong Chen
Part of concurrent sessions: NGS Analysis and Tools I
Lecture Hall - Room 280
11:30 AM - 11:50 AM HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
Chenchen Zou, Yuping Zhang and Zhengqing Ouyang
Part of concurrent sessions: Genome Structure Analysis and Visualization
Auditorium
11:30 AM - 11:50 AM SAIC: An Iterative Clustering Approach for Analysis of Single Cell RNA-seq Data
Lu Yang, Jiancheng Liu, Qiang Lu, Arthur Riggs, Xiwei Wu
Part of concurrent sessions: NGS Analysis and Tools I
Lecture Hall - Room 280
11:50 AM - 12:10 PM Modeling Tumor-stroma crosstalk in tumor microenvironment for drug combinations and biomarker discovery in cancer
Steve Wong
Part of concurrent sessions: Genome Structure Analysis and Visualization
Auditorium
11:50 AM - 12:10 PM Tumor phylogeny inference from single-cell DNA sequencing data
Ken Chen
Part of concurrent sessions: NGS Analysis and Tools I
Lecture Hall - Room 280
12:10 PM - 1:30 PM Lunch Break - Box Lunches Available
(Eat in auditorium, outside or event/exhibition space)
Pre-function area
1:30 PM - 2:20 PM Keynote Lecture
Molecular Profiling of Cancers: The Cancer Genome Atlas Project and Beyond

John N. Weinstein, MD, PhD, MD Anderson Cancer Center
Auditorium
2:20 PM - 2:30 PM BREAK
Computational Drug Discovery - Concurrent Sessions
Session Chairs: Zhandong Liu
Auditorium
Medical Informatics and Big Data - Concurrent Sessions
Session Chairs: Hua Xu, Yang Gong, Cui Tao
Lecture Hall - Room 280
2:30 PM - 2:50 PM Toward repurposing metformin as a precision anti-cancer therapy using structural systems pharmacology
Thomas Hart, Shihab Dider, Weiwei Han, Hua Xu, Zhongming Zhao & Lei Xie
Part of concurrent sessions: Computational Drug Discovery
Auditorium
2:30 PM - 2:45 PM Developing a Self-Learning Module for Patient Safety Event Reporting System Using Semantic Similarity Measures
Hong Kang and Yang Gong
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
2:50 PM - 3:10 PM A systematic analysis of FDA-approved anticancer drugs
Jingchun Sun, Yubo Zhou, Jingqi Wang, Qi Liu, Hua Xu
Part of concurrent sessions: Computational Drug Discovery
Auditorium
2:45 PM - 3:00 PM Evaluation of the informatician perspective: determining types of research papers preferred by clinicians
Hong Kang and Yang Gong
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
3:00 PM - 3:15 PM How the public use social media WeChat to obtain health information in China: a survey study
Xingting Zhang, Dong Wen and Jianbo Lei
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
3:10 PM - 3:30 PM ScaPD: a database for human scaffold proteins
Xiaomei Han, Jenny Wang, Jie Wang, Sheng Liu, Jianfei Hu, Heng Zhu, Jiang Qian
Part of concurrent sessions: Computational Drug Discovery
Auditorium
3:15 PM - 3:30 PM Predictive Models for Pressure Ulcers from Intensive Care Unit Electronic Health Records using Bayesian Networks
Pacharmon Kaewprag, Cheryl Newton, Brenda Vermillion, Sookyung Hyun, Kun Huang and Raghu Machiraju
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
3:30 PM - 3:50 PM MD-Miner: A network-based approach for personalized drug prediction
Haoyang Wu, Elise Miller, Denethi Wijegunawardana Kelly Regan, Philip Payne, Fuhai Li
Part of concurrent sessions: Computational Drug Discovery
Auditorium
3:50 PM - 4:00 PM BREAK
4:00 PM - 4:20 PM Identifying of ligand-receptor interactions via a noval computational method: strategy on drug discovery
Fei Guo
Part of concurrent sessions: Computational Drug Discovery
Auditorium
4:00 PM - 4:15 PM Lightweight Predicate Extraction For Patient-Level Cancer Information and Ontology Development
Muhammad Amith, Hsing-Yi Song, Yaoyun Zhang and Cui Tao
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
4:15 PM - 4:30 PM Leveraging Machine Learning Based Approaches to Assess Human Papillomavirus Vaccination Sentiment Trends with Twitter Data
Jingcheng Du, Jun Xu, Hsing-Yi Song and Cui Tao
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
4:20 PM - 5:00 PM Permutation test for inferring order of somatic mutations in cancer based on binary data
Lief Peterson and Tatiana Kovyrshina
Part of concurrent sessions: Computational Drug Discovery
Auditorium
4:30 PM - 4:45 PM A Signal Detection method for Temporal Variation of Adverse Effect with Vaccine Adverse Event Reporting System data
Yi Cai, Jingcheng Du, Jing Huang, Cui Tao and Yong Chen
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
4:45 PM - 5:00 PM An Active Learning-enabled Annotation System for Clinical Named Entity Recognition
Yukun Chen, Thomas Lasko, Qiaozhu Mei, Qingxia Chen, Sungrim Moon, Jingqi Wang, Ky Nguyen, Tolulola Dawodu, Trevor Cohen, Joshua Denny and Hua Xu
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
5:00 PM - 5:20 PM Heterogeneity in untreated, stressed and drug tolerant cells: insights to evolution of cancer resistance
Bhagya Wijayawardena, Gopinath Sivasankaran, Lang Li
Part of concurrent sessions: Computational Drug Discovery
Auditorium
5:00 PM - 5:15 PM Detecting Clinically Relevant New Information in Clinical Notes Across Specialties and Settings
Rui Zhang, Serguei Pakhomov, Elliot Arsoniadis, Janet Lee, Yan Wang and Genevieve Melton
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
5:15 PM - 5:30 PM Entity Recognition from Clinical Texts via Recurrent Neural Network
Zengjian Liu, Xiaolong Wang, Qingcai Chen and Buzhou Tang
Part of concurrent sessions: Medical Informatics and Big Data
Lecture Hall - Room 280
5:20 PM - 5:40 PM Inhibition of Polyamine biosynthesis for toxicity control in Serratia marcescens strain WW4 by targeting ornithine decarboxylase: A structure-based virtual screening study
Kalyani Dhusia, Pramod Yadav, Rohit Farmer, Pramod Ramteke
Part of concurrent sessions: Computational Drug Discovery
Auditorium
5:40 PM - 6:00 PM BREAK
6:00 PM - 8:00 PM COCKTAILS AND BANQUET Event/Exhibition Space
Saturday, December 10th
7:30 AM - 8:30 AM Registration Open and Breakfast
(Eat in auditorium, outside or Event/exhibition space)
Pre-function area
8:30 AM - 9:20 AM Keynote Lecture
Elucidate Transcriptome Isoform Complexity Using Massive RNA-seq Data

Yi Xing, PhD, Professor, University of California, Los Angeles
Auditorium
9:20 AM - 9:30 AM BREAK
NGS Analysis and Tools II - Concurrent Sessions
Session Chair: Han Leng
Auditorium
Cancer Genomics - Concurrent Sessions
Session Chair: Eric Huang
Lecture Hall - Room 280
9:30 AM - 9:50 AM Logo2PWM: a tool to convert sequence logo to position weight matrix
Zhen Gao and Jianhua Ruan
Part of concurrent sessions: NGS Analysis and Tools II
Auditorium
9:30 AM - 9:50 AM System modeling reveals the molecular mechanisms of HSC cell cycle alteration mediated by Maff and Egr3 under leukemia
Rudong Li, Yin Wang, Hui Cheng, Gang Liu, Tao Cheng, Yunlong Liu, Lei Liu
Part of concurrent sessions: Cancer Genomics
Lecture Hall - Room 280
9:50 AM - 10:10 AM Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly
Yongsheng Bai, Jeff Kinne, Lizhong Ding, Ethan C. Rath, Aaron Cox, Siva, Dharman Naidu, Youping Deng
Part of concurrent sessions: NGS Analysis and Tools II
Auditorium
9:50 AM - 10:10 AM Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma
Xinan (Holly) Yang, Fangming Tang, Jisu Shin, John M Cunningham
Part of concurrent sessions: Cancer Genomics
Lecture Hall - Room 280
10:10 AM - 10:30 AM Evaluation of biological and technical variations in low-input RNA-Seq and single-cell RNA-Seq
Fan Gao, Jae Mun Kim, Jihong Kim, Ming-Yi Lin, Charles Liu, Jonathan Russin, Reymundo Dominguez, Christopher Walker, Adrian Camarena, Joseph Nguyen, Jennifer Herstein, William Mack, Oleg Evgrafov, Robert Chow, James Knowles, Kai Wang
Part of concurrent sessions: NGS Analysis and Tools II
Auditorium
10:10 AM - 10:30 AM Identification of Common Oncogenic and Early Developmental Pathways in the Ovarian Carcinomas Controlling by Distinct Prognostically Significant MicroRNA Subsets
Vladimir A. Kuznetsov, Zhiqun Tang, Anna V. Ivshina
Part of concurrent sessions: Cancer Genomics
Lecture Hall - Room 280
10:30 AM - 10:40 AM BREAK
10:40 AM - 11:00 AM A GPU-CPU Heterogeneous Algorithm for NGS Read Alignment
Ahmad Al Kawam, Sunil Khatri and Aniruddha Datta
Part of concurrent sessions: NGS Analysis and Tools II
Auditorium
10:40 AM - 11:00 AM Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening
Guangchun Han, Wei Zhao, Patrick Kwok-Shing Ng, Jose A. Karam, Eric Jonasch, Gordon B. Mills, Zhiyong Ding, Peilin Jia, Zhongming Zhao
Part of concurrent sessions: Cancer Genomics
Lecture Hall - Room 280
11:00 AM - 11:20 AM Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models
Hari Krishna Yalamanchili, Qiumin Tan, Jeehye Park, Antonia De Maio, Hsiang-Chih Lu, Ying-Wooi Wan, Joshua J. White, Vitaliy V Bondar, Layal S. Sayegh, Xiuyun Liu, Yan Gao, Roy V. Sillitoe, Harry T. Orr, Zhandong Liu and Huda Y. Zoghbi
Part of concurrent sessions: NGS Analysis and Tools II
Auditorium
11:00 AM - 11:20 AM Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer
Yu-Chiao Chiu, Li-Ju Wang, Tzu-Hung Hsiao, Eric Y. Chuang, Yidong Chen
Part of concurrent sessions: Cancer Genomics
Lecture Hall - Room 280
11:20 AM - 11:40 AM Roles of alternative splicing in modulating transcriptional regulation
Jin Li, Yang Wang, Xi Rao, Yue Wang, Weixing Feng, Hong Liang, Yunlong Liu
Part of concurrent sessions: NGS Analysis and Tools II
Auditorium
11:20 AM - 11:40 AM Signal Translational Efficiency between mRNA Expression and Antibody-based Protein Expression for
Aida Yazdanparast, Lang Li, Lijun Cheng
Part of concurrent sessions: Cancer Genomics
Lecture Hall - Room 280
11:40 AM - 1:30 PM Lunch Break
Systems Biology - Concurrent Sessions
Session Chair: Xiaoning Qian
Auditorium
Big Data and Machine Learning - Concurrent Sessions
Session Chair: Genevera Allen
Lecture Hall - Room 280
1:30 PM - 2:00 PM Functional proteomics as a major approach for precision cancer medicine
Han Liang, Invited Speaker, Associate Professor, MDACC
Part of concurrent sessions: Systems Biology
Auditorium
1:30 PM - 2:00 PM Unsupervised Deep Learning Reveals Prognostically Relevant Subtypes of Glioblastoma
Jonathan D. Young, Chunhui Cai, Xinghua Lu
Part of concurrent sessions: Big Data and Machine Learning
Lecture Hall - Room 280
2:00 PM - 2:20 PM Neural signature of event related N200 and P300 modulation in parietal lobe during human response inhibition
Rupesh Kumar Chikara and Li-Wei Ko
Part of concurrent sessions: Systems Biology
Auditorium
2:00 PM - 2:20 PM Using Machine learning algorithms to identify genes essential for cell survival
Santosh Philips, Heng-Yi Wu, Lang Li
Part of concurrent sessions: Big Data and Machine Learning
Lecture Hall - Room 280
2:20 PM - 2:40 PM Hybrid-analysis method for construction of heterogeneous networks from multiomics data
Chia-Yu Huang, Tzu-Pin Lu, Yu-Chiao Chiu, Yu-Ching Hsu, Eric Y. Chuang and Tzu-Hung Hsiao
Part of concurrent sessions: Systems Biology
Auditorium
2:20 PM - 2:40 PM DRREP: Deep Ridge Regressed Epitope Predictor
Gene Sher, Degui Zhi, Shaojie Zhang
Part of concurrent sessions: Big Data and Machine Learning
Lecture Hall - Room 280
2:40 PM - 3:00 PM Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations
Jaejoon Song, Michelle Carey, Hongjian Zhu, Hongyu Miao, Juan Camilo Ramirez and Hulin Wu
Part of concurrent sessions: Systems Biology
Auditorium
2:40 PM - 3:00 PM A New Statistical Method for Estimation of Recombination Fractions in F2 population
Yuan-De Tan, Xiang H. F. Zhang, Qianxing Mo
Part of concurrent sessions: Big Data and Machine Learning
Lecture Hall - Room 280
3:00 PM - 3:10 PM BREAK
3:10 PM - 3:30 PM Pathway-based method to detect association with Alzheimer's disease
Jeffrey Mitchel, Laszlo Prokai, Youping Deng, Fan Zhang and Robert Barber
Part of concurrent sessions: Systems Biology
Auditorium
3:10 PM - 3:30 PM Robust mutant strain design by pessimistic optimization
Meltem Apaydin, Liang Xu, Bo Zeng, Xiaoning Qian
Part of concurrent sessions: Big Data and Machine Learning
Lecture Hall - Room 280
3:30 PM - 3:50 PM Native State of Complement Protein C3d Analyzed via Hydrogen Exchange and Conformational Sampling
Didier Devaurs, Malvina Papanastasiou, Dinler Antunes, Jayvee Abella, Mark Moll, Daniel Ricklin, John Lambris and Lydia Kavraki
Part of concurrent sessions: Systems Biology
Auditorium
3:30 PM - 3:50 PM CNN-based Ranking for Biomedical Entity Normalization
Haodi Li, Qingcai Chen, Buzhou Tang
Part of concurrent sessions: Big Data and Machine Learning
Lecture Hall - Room 280
3:50 PM - 4:10 PM Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis
Biao Li, Juan Jose Deudero, Fatih Semerci, Amanda Sierra, Andrew Laitman, Marek Kimmel, Mirjana Maletic-Savatic
Part of concurrent sessions: Systems Biology
Auditorium
3:50 PM - 4:10 PM A Statistical Biclustering Method for Sequence Count Data
TBD
Part of concurrent sessions: Big Data and Machine Learning
Lecture Hall - Room 280
4:10 PM - 4:30 PM A Link Prediction Approach to Cancer Drug Sensitivity Prediction
Turki Turki and Zhi Wei
Part of concurrent sessions: Systems Biology
Auditorium
4:30 PM Adjourn