ICIBM 2018


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Sunday, June 10th
12:00 Registration opens
Room: Santa Monica Room: Grand Imperial North
1:00 - 2:30 Dr. Yan Guo
University of New Mexico
Machine Learning
1:00 - 2:30 Dr. Feng Yue
Pennsylvania State University
3D Genome Organization
2:30 - 2:40 Break
2:40 - 4:10 Chi Zhang; Xiao Dong
Indiana University; Albert Einstein College of Medicine
Single-cell sequencing analysis
2:40 - 4:10 Dr. Ting Wang
Washington University
WashU Epigenome Browser
4:10 - 4:30 Coffee/Tea Break
4:30 - 5:20 Keynote Lecture (Room: Grand Imperial North)

Josh Denny, MD, MS
Professor of Biomedical Informatics and Medicine
Vanderbilt University
Member, National Academy of Medicine

Title: Huge cohorts, genomics, and clinical data to personalize medicine
5:20 - 5:30 Break
5:30 - 7:30 Poster Session (Room: Grand Imperial Foyer)

Monday, June 11st
7:30 -8:30 Registration Open and Breakfast
8:30 -8:40 Opening Remarks
8:40 -9:30 Keynote Lecture (Room: Grand Imperial North)

Paul Thomas, Ph.D.
Associate Professor of Preventive Medicine
Director of Division of Bioinformatics
University of Southern California
PI, Gene Ontology Consortium

Title: Reconstructing the large-scale evolution of genomes and gene functions
9:30 -9:40 Break
9:40 -10:00 Eminent Scholar Talk (Room: Grand Imperial North)

Xinghua Lu, MD, PhD
Professor of Biomedical Informatics
University of Pittsburgh

Title: From Big Data to Bedside (BD2B): Precision Oncology in an Era of Artificial Intelligence
10:00 -10:05 Break for parallel session
Room: Grand Imperial North
NGS & Tools
Session Chair: Youping Deng
Room: Santa Monica
Systems Biology
Session Chair: Yin Liu
Room: Hollywood
Session Chair: Li Liu
10:05 -10:25 Development of somatic mutation signatures for risk stratification and prognosis in lung and colorectal adenocarcinomas

Mark Menor, Yong Zhu, Bin Jiang and Youping Deng

10:05 -10:25 A Hidden Markov Model-based approach to reconstructing double minute chromosome amplicons

Ruslan Mardugalliamov, Kamal Al Nasr and Matthew Hayes

10:05 -10:25 A Graph-based Algorithm for Estimating Clonal Haplotypes of Tumor Sample from Sequencing Data

Yixuan Wang, Rong Zhang, Xinyu Sun, Yu Geng, Jianye Liu, Zhongmeng Zhao, Xuanping Zhang, Yi Huang and Jiayin Wang

10:25 -10:45 Genomic copy number variations in large screening for pediatrics sarcomas chemotherapy

Lijun Cheng, Pooja Chandra, Limei Wang, Karen Pollok, Pankita Pandya, Mary Murray, Jacquelyn Carter, Michael Ferguson, Mohammad Reza Saadatzadeh, Mashall Mark, Li Lang and Jamie Renbarger

10:25 -10:45 Classifying Mild Traumatic Brain Injuries with Functional Network Analysis

Francis San Lucas, John Redell, Dash Pramod and Yin Liu

10:25 -10:45 A new insight into underlying disease mechanism through semi-parametric latent differential network model

Yong He, Jiadong Ji, Lei Xie, Xinsheng Zhang and Fuzhong Xue

10:45 -11:05 Computational identification of deleterious synonymous variants in human genomes using a feature-based approach

Fang Shi, Yao Yao and Junfeng Xia

10:45 -11:05 scDNA: a fast and comprehensive tool for single-cell differential network analysis

Yu-Chiao Chiu, Tzu-Hung Hsiao, Li-Ju Wang, Yidong Chen and Yu‐hsuan Shao

10:45 -11:05 Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search

Vladimir Kogan, Joshua Millstein, Stephanie J London, Carole Ober, Steven R White, Edward T Naureckas, W James Gauderman, Daniel J Jackson, Albino Barraza-Villarreal, Isabelle Romieu, Benjamin A Raby and Carrie V Breton

11:05 -11:15 Coffee/Tea Break
11:15 -11:35 High scoring segment selection for pairwise whole genome sequence alignment with the maximum scoring subsequence and GPUs

Abdulrhman Aljouie, Ling Zhong and Usman Roshan

11:15 -11:35 Multiple transcription factors contribute to inter-chromosomal interaction in yeast

Yulin Dai, Chao Li, Guangsheng Pei, Dong Xiao, Guohui Ding, Zhongming Zhao, Yixue Li and Jia Peilin

11:15 -11:35 DLAD4U: deriving and prioritizing disease lists from PubMed literature

Junhui Shen, Suhas Vasaikar and Bing Zhang

11:35 -11:55 Detecting virus integration sites based on mul-tiple related sequencing data by VirTect

Yuchao Xia, Yun Liu, Minghua Deng and Ruibin Xi

11:35 -11:55 Metabolomics of Mammalian Brain Reveals Regional Differences

William Choi, Mehmet Tosun, Cemal Karakas, Fatih Semerci, Zhandong Liu and Mirjana Maletic-Savatic

11:35 -11:55 A multitask bi-directional RNN model for named entity recognition on electronic medical records

Shanta Chowdhury, Xishuang Dong, Lijun Qian, Xiangfang Li, Yi Guan, Jinfeng Yang and Qiubin Yu

11:55 -12:15 Comprehensive assessment of genotype imputation performance

Shuo Shi, Na Yuan, Ming Yang, Zhenglin Du, Jinyue Wang, Sheng Xin, Jiayan Wu and Jingfa Xiao

11:55 -12:15 Boosting Gene Expression Clustering with System-Wide Biological Information: A Robust Autoencoder Approach

Hongzhu Cui, Chong Zhou, Xinyu Dai, Yuting Liang, Randy Paffenroth and Dmitry Korkin

11:55 -12:15 iMEGES: integrated Mental-disorder GEnome score for prioritizing the susceptibility genes for mental disorders in personal genomes

Atlas Khan, Qian Liu and Kai Wang

12:15 - 1:35 Lunch Break - Lunch
1:35 - 1:55 Eminent Scholar Talk (Room: Grand Imperial North)

Ting Wang, PhD
Associate Professor of Genetics
Washington University

Title: Exploring the dark matter in genomics data
1:55 - 2:00 Short Break
2:00 -2:50 Keynote Lecture (Room: Grand Imperial North)

Alex Hoffmann, Ph.D.
Thomas M. Asher Professor of Microbiology
Director of the Institute for Quantitative and Computational Biosciences
University of California Los Angeles

Title: Learning how to predict immune responses in terms of molecular underpinnings
2:50 -3:00 Break for parallel sessions
Room: Grand Imperial North
NGS & Tools
Session Chair: Lei Xie
Room: Santa Monica
Systems Biology
Session Chair: Matthew Hayes
Room: Hollywood
Medical Informatics
Session Chairs: W. Jim Zheng
3:00 - 3:20 Reconstructing the High-resolution Chromosomal 3D structure by Hi-C Complex Network

Tong Liu and Zheng Wang

3:00 - 3:20 Prediction of Protein Self-Interactions using Stacked Long Short-Term Memory from Protein Sequences Information

Yanbin Wang, Zhuhong You, Xiao Li, Tonghai Jiang, Li Cheng and Zhanheng Chen

3:00 - 3:20 Building a high performance computing infrastructure for cancer research

W. Jim Zheng

3:20 - 3:40 CeL-ID: Cell Line Identification using RNA-seq data

Tabrez A Mohammad, Yun S Tsai, Safwa Ameer, Hung-I H Chen, Yu-Chiao Chiu and Yidong Chen

3:20 - 3:40 Circular RNA Expression Profiles during the Differentiation of Mouse Neural Stem Cells

Qichang Yang, Jing Wu, Jian Zhao, Tianyi Xu, Zhongming Zhao, Xiaofeng Song and Ping Han

3:20 - 3:40 Dynamic Prediction of Hospital Admission with Medical Claim Data

Tianzhong Yang, Yang Yang, Yugang Jia and Xiao Li

3:40 - 4:00 Comparison of SureSelect and Nextera exome capture performance in single-cell sequencing

Wendy Huss, Qiang Hu, Sean Glenn, Kalyan Gangavarapu, Jianmin Wang, Jesse Luce, Paul Quinn, Elizabeth Brese, Fenglin Zhan, Jeffrey Conroy, Gyorgy Paragh, Barbara Foster, Carl Morrison, Song Liu and Lei Wei

3:40 - 4:00 Identification of Gene Signatures from RNA-seq Data Using Pareto-optimal Cluster Algorithm

Saurav Mallik and Zhongming Zhao

3:40 - 4:00 Early prediction of acute kidney injury following ICU admission

Lindsay P. Zimmerman, Paul A. Reyfman, Angela D. R. Smith, Zexian Zeng, Abel Kho, L. Nelson SanchezPinto and Yuan Luo

4:00 - 4:10 Coffee/Tea Break
4:10 - 4:30 A PheWAS Study of a Large Observational Epidemiological Cohort of African Americans: the REGARDS Study

Xueyan Zhao, Xin Geng, Vinodh Srinivasasainagendra, Suzanne Judd, Virginia Wadley, Orlando Gutierrez, Henry Wang, Ethan Lange, Leslie Lange, Daniel Woo, Fred Unverzagt, Monika Safford, Mary Cushman, Nita Limdi, Rakale Quarells, Donna Arnett, Marguerite Irvin and Degui Zhi

4:10 - 4:30 An experimental design framework for Markovian gene regulatory networks under stationary control policy

Roozbeh Dehghannasiri, Mohammad Shahrokh Esfahani and Edward Dougherty

4:10 - 4:30 Epileptic foci localization based on mapping the synchronization of dynamic brain network

Mei Tian, Wei Xiaoyan, Chen Ziyi, Tian Xianghua, Dong Nan, Li Dongmei and Zhou Yi

4:30 – 4:50 NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data

Qian Liu, Daniela C. Georgieva, Dietrich M. Egli and Kai Wang

4:30 – 4:50 GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

Hung-I Chen, Yu-Chiao Chiu, Tinghe Zhang, Songyao Zhang, Yufei Huang and Yidong Chen

4:30 – 4:50 Gene Fingerprint model for Literature based detection of the associations among complex diseases: A case study of COPD

Guocai Chen, Yuxi Jia, Lisha Zhu, Ping Li, Lin Zhang, Cui Tao and W. Jim Zheng

4:50 – 5:00 Joint Principal Trend Analysis for Longitudinal High-Dimensional Genomic Data

Yuping Zhang and Zhengqing Ouyang (selected abstract talk)

4:50 – 5:00 Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages

Daifeng Wang, John Haley and Patricia Thompson (selected abstract talk)

4:50 – 5:10 Integrating Sentence Sequence Representation and Shortest Dependency Path into a Deep Learning Framework for Relation Extraction in Clinical Text

Zhiheng Li, Zhihao Yang, Chen Shen, Jun Xu, Yaoyun Zhang and Hua Xu

5:00 – 5:10 Inferring Drug-Target Associations based on perturbational profiles in L1000 Data

Pei-Han Liao, Tzu-Hung Hsiao, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu and Eric Y. Chuang (selected abstract talk)

5:00 – 5:10 Epigenomic Patterns Are Associated with Gene Haploinsufficiency and Predict Risk Genes of Developmental Disorders

Siying Chen, Xinwei Han and Yufeng Shen (selected abstract talk)

5:10 – 5:20 Predict effective drug combination by deep believe network and Ontology Fingerprints

Guocai Chen, Lam Tsoi, Hua Xu and W. Jim Zheng (selected abstract talk)

5:10 – 5:20 Genetic Association of Arterial Stiffness Index with Incident Coronary Artery Disease and Congestive Heart Failure

Seyedeh Zekavat, Mary Haas, Krishna Aragam, Connor Emdin, Amit Khera, Derek Klarin, Hongyu Zhao and Pradeep Natarajan (selected abstract talk)

5:10 – 5:30

Tuesday, June 12nd
7:30 -8:40 Registration Open and Breakfast
8:40 -9:30 Keynote Lecture (Room: Grand Imperial North)

Jason Moore, Ph.D
Edward Rose, M.D. And Elizabeth Kirk Rose, M.D. Professor of Biostatistics, Epidemiology and Informatics
Director, Institute for Biomedical Informatics
University of Pennsylvania

Title: Accessible artificial intelligence for data science
9:30 -9:40 Break
9:40 -10:00 Eminent Scholar Talk (Room: Grand Imperial North)

Grace Xiao, Ph.D.
Professor of Integrative Biology and Physiology

Title: Deciphering the function of single-nucleotide variants in the RNA
10:00 -10:05 Break for parallel sessions
Room: Grand Imperial North
Cancer Genomics
Session Chair: Bin Chen
Room: Santa Monica
Systems Biology
Session Chair: Fan Zhang
Room: Hollywood
Computational drug discovery
Session Chair: Zhifu Sun
10:05 -10:25 Identification of exon skipping events associated with Alzheimer's disease in the human hippocampus

Seonggyun Han, Jason Miller, Seyoun Byun, Dokyoon Kim, Shannon Leigh Risacher, Andrew Saykin, Younghee Lee and Kwangsik Nho

10:05 -10:25 Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics

Guangsheng Pei, Hua Sun, Yulin Dai, Peilin Jia and Zhongming Zhao

10:05 -10:25 Drug-Drug Interaction Prediction based on Co-Medication Patterns and Graph Matching

Wen-Hao Chiang, Li Shen, Lang Li and Xia Ning

10:25 -10:45 Brain-wide structural connectivity alterations under the control of Alzheimer risk genes

Jingwen Yan, Vinesh Raja V, Zhi Huang, Amico Enrico, Kwangsik Nho, Shaifen Fang, Olaf Sporns, Yu-Chien Wu, Andrew Saykin, Joaquin Goni and Li Shen

10:25 -10:45 Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data

Sijia Huang, Fadhl Alakwaa and Lana Garmire

10:25 -10:45 Predicting drug response of tumors from integrated genomic profiles by deep neural networks

Yu-Chiao Chiu, Hung-I Chen, Tinghe Zhang, Songyao Zhang, Li-Ju Wang, Yufei Huang and Yidong Chen

10:45 -11:05 Context-sensitive Network Analysis Identifies Food Metabolites Associated with Alzheimer’s Disease: An Exploratory Study

Yang Chen and Rong Xu

10:45 -11:05 Gene2Vec: Distributed Representation of Genes Based on Co-Expression

Jingcheng Du, Peilin Jia, Yulin Dai, Cui Tao, Zhongming Zhao and Degui Zhi

10:45 -11:05 Predicting Adverse Drug Reactions through Interpretable Deep Learning Framework

Sanjoy Dey, Heng Luo, Achille Fokoue-Nkoutche, Jianying Hu and Ping Zhang

11:05 -11:15 Coffee/Tea Break
11:15 -11:35 Using natural language processing and machine learning to identify breast cancer local recurrence

Zexian Zeng, Sasa Espino, Ankita Roy, Xiaoyu Li, Seema Khan, Susan Clare, Xia Jiang, Richard Neapolitan and Yuan Luo

11:15 -11:35 A robust fuzzy rule based integrative feature selection strategy for gene expression data in TCGA

Shicai Fan

11:15 -11:35 Predicting drug sensitivity of cancer cells with pathway activity inference

Xuewei Wang, Zhifu Sun, Michael Zimmerman, Andrej Bugrim and Jean-Pierre Kocher

11:35 -11:55 Identification of long non-coding RNA-related and –coexpressed mRNA biomarkers for hepatocellular carcinoma

Fan Zhang, Linda Ding, Li Cui, Robert Barber and Bin Deng

11:35 -11:55 Pessimistic optimization for modeling microbial communities with uncertainty

Meltem Apaydin, Liang Xu, Bo Zeng and Xiaoning Qian

11:35 -11:55 Application of Transfer Learning for Cancer Drug Sensitivity Prediction

Saugato Rahman Dhruba, Raziur Rahman, Kevin Matlock, Souparno Ghosh and Ranadip Pal

11:55 -12:15 Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes

Alice Djotsa and Xiaoming Liu

11:55 -12:15 Evaluation of Top-Down Mass Spectral Identification with Homologous Protein Sequences

Ziwei Li, Yunlong Liu, Xiaowen Liu and Weixing Feng

11:55 -12:15 Large-scale mining disease comorbidity relationships from post-market drug adverse events surveillance data

Chunlei Zheng and Rong Xu

12:15 - 1:30 Lunch Break - Lunch
1:30 -1:50 Eminent Scholar Talk (Room: Grand Imperial North)

Charles Wang, MD, PhD, MPH
Professor & Director Center for Genomics
Loma Linda University

Title: Vegetarian diet-modulated epigenetic reprogramming/epigenetic clocks and longevity
1:50 -2:10 Award presentation
2:10 -2:20 Coffee/Tea Break
Room: Grand Imperial North
International PI Talk
Session Chair: Yu Xue, Xiaofeng Song

Room: Santa Monica
Cancer Genomics
Session Chair: Jun Wan
2:20 - 2:40 Bioinformatics research on potential ability of circular RNA encoding protein

Xiaofeng Song

2:20 - 2:40 Selecting precise reference normal tissue samples for cancer research using a deep learning approach

William Zeng, Benjamin Glicksberg, Yangyan Li and Bin Chen

2:40 - 3:00 The impact of genetic admixture and natural selection on driving population differences in East Asia

Shuhua Xu

2:40 - 3:00 Modeling of Hypoxia gene expression for three different cancer cell lines

Babak Soltanalizadeh, Erika Gonzalez Rodriguez, Vahed Maroufy and Hulin Wu

3:00 - 3:20 Identification of functional PTM events in autophagy

Yu Xue

3:00 - 3:20 Inferring gene-disease association by an integrative analysis of eQTL GWAS and Protein-Protein Interaction data

Jun Wang, Jiashun Zheng, Zengmiao Wang, Hao Li and Minghua Deng

3:20 - 3:40 Tumor heterogeneity in hepatocellular carcinoma and intrahepatic cholangiocarcinoma

Ruibin Xi

3:20 - 3:40 Network-based identification of critical regulators as putative drivers of human cleft lip

Aimin Li, Guimin Qin, Akiko Suzuki, Mona Gajera, Junichi Iwata, Peilin Jia and Zhongming Zhao

3:40 Adjourn