ICIBM 2019

  • Jeremy Edwards, PhD Dr. Jeremy Edwards, PhD , Professor, Department of Chemistry & Chemical Biology, Albuquerque, NM, USA
  • Peter Karp, PhD Dr. Peter Karp , Director, Bioinformatics Research Group, Artificial Intelligence Center, SRI
  • Elaine R. Mardis, PhD Dr. Elaine Mardis Co-executive Director of the Institute for Genomic Medicine at Nationwide Children’s Hospital and the Nationwide Foundation Endowed Chair of Genomic Medicine, Professor of Pediatrics at The Ohio State University College of Medicine.
  • T. M. Murali, PhD Dr. T. M. Murali Department of Computer Science, Virginia Tech, Blacksburg VA

For ICIBM 2019, registration will start early, at 9 am , with our Keynote Lecture from Dr. Mardis at 10:15 am
*The program is not yet finalized so check frequently for updates.*


Schedule

 

SUNDAY, JUNE 9th

9:00 am

Registration opens

CONCURRENT WORKSHOPS

Room A

Room B

10:15 am - 11:00 am

Keynote Lecture – Dr. Elaine Mardis
Co-executive Director of the Institute for Genomic Medicine at Nationwide Children’s Hospital
Nationwide Foundation Endowed Chair of Genomic Medicine
Professor of Pediatrics at The Ohio State University College of Medicine.
Title: A System for Pediatric Precision Cancer Medicine

11:00 am - 11:20 am

Break

11:20 am - 1:30 pm

Dr. Wenjin Zheng
UTH
Science for Cancer Research

11:20 am - 1:30 pm

Dr. Yan Guo
Advanced Machine Learning

1:30 pm - 1:45 pm

Lunch break

1:45 pm - 3:45 pm

Dr. Yufei Huang
UTSA
Deep learning for computational genomics and drug response

1:45 pm - 3:45 pm

Dr. Jianrong Wang
Michigan State University
Epigenetics data analysis

3:45 pm - 4:00 pm

Break

4:00 pm - 6:00 pm

Poster Session (Room: TBD)


MONDAY, JUNE 10th

7:30 am - 8:30 am

Registration Open and Buffet Breakfast

8:30 am - 8:40 am

Opening Remarks

8:40 am - 9:30 am

Keynote Lecture (Room: TBD) Dr. Peter Karp, PhD  
Director, Bioinformatics Research Group
Artificial Intelligence Center
SRI International
Title:BioCyc Tools for Metabolic Modeling and Omics Data Analysis

9:30 am - 9:40 am

Break

9:40 am - 10:00 am

Eminent Scholar Talk (Room: TBD) Jeff Parvin, MD, PhD 
Professor, Department of Biomedical Informatics
Associate Dean of Graduate Studies
Co-Director, Biomedical Sciences Gradate Program
The Ohio State University
Title:The impact of sequence variants on protein function

10:00 am - 10:10 am

Break for parallel sessions

CONCURRENT SESSIONS

Room: TBD
NGS & Tools
Session Chair: 1
 

Room: TBD
General Genomics
Session Chair: 2
 

Room: TBD
Bioinformatics
Session Chair:3
 

10:10 am - 10:30 am

An ancestral informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data
Li-Ju Wang, Catherine Zhang, Sophia Su, Hung-I Chen, Yu-Chiao Chiu, Zhao Lai, Hakim Bouamar, Francisco Cigarroa, Lu-Zhe Sun and Yidong Chen

10:10 am - 10:30 am

Association Analysis of Common and Rare SNVs using Adaptive Fisher Method to Detect Dense and Sparse Signals
Xiaoyu Cai, Lo-Bin Chang and Chi Song

10:10 am - 10:30 am

The Comparisons of Prognostic Power and Expression Level of Tumor Infiltrating Leukocytes in Hepatitis B- and Hepatitis C-related Hepatocellular Carcinomas
Yi-Wen Hsiao, Lu-Ting Chiu, Ching-Hsuan Chen, Wei-Liang Shih and Tzu-Pin Lu

10:30 am - 10:50 am

normGAM: An R package to remove systematic biases in genome architecture mapping data
Tong Liu and Zheng Wang

10:30 am - 10:50 am

An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate
Fangfang Yan, Yulin Dai, Junichi Iwata, Zhongming Zhao and Peilin Jia

10:30 am - 10:50 am

SigUNet: signal peptide recognition based on semantic segmentation
Jhe-Ming Wu, Yu-Chen Liu and Tien-Hao Chang

10:50 am - 11:10 am 

Sparse Convolutional Denoising Autoencoders for Genotype Imputation
Junjie Chen and Xinghua Shi

10:50 am - 11:10 am 

Association between ALS and retroviruses: Evidence from bioinformatics analysis
Jon Klein, Zhifu Sun and Nathan Staff

10:50 am - 11:10 am 

Integrated metabolomics and transcriptomics study of traditional herb AstragalusmembranaceusBge.var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients
Xueting Wu, Xuetong Li, Wei Wang, Yuanhong Shan, Cuiting Wang, Mulan Zhu, Qiong La, Yang Zhong, Ye Xu, Peng Nan and Xuan Li

11:10 am - 11:20 am

Coffee/Tea Break

11:20 am - 11:40 am 

High dimensional model representation of log likelihood ratio: Binary classification with SNP data
Ali Foroughi Pour, Maciej Pietrzak, Lara E. Sucheston-Campbell, Ezgi Karaesmen, Lori A. Dalton and Grzegorz A. Rempala

11:20 am - 11:40 am 

ManiNetCluster: A novel manifold learning approach to reveal the functional links between gene networks
Nam Nguyen, Ian Blaby and Daifeng Wang

11:20 am - 11:40 am 

BayesMetab: Treatment of Missing Values in Metabolomic Studies using a Bayesian Modeling Approach
Jasmit Shah, Guy Brock and Jeremy Gaskins

11:40 am - 12:00 pm 

Decoding regulatory structures and features from epigenomics profiles: a Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model
Ruifeng Hu, Guangsheng Pei, Peilin Jia and Zhongming Zhao

11:40 am - 12:00 pm 

Human protein-RNA interaction network is highly stable across vertebrates
Aarthi Ramakrishnan and Sarath Chandra Janga

11:40 am - 12:00 pm 

Dense module searching for gene networks associated with multiple sclerosis
Astrid Manuel, Yulin Dai, Leorah Freeman, Peilin Jia and Zhongming Zhao

12:00 pm - 12:20 pm 

A unified STR profiling system across multiple species with whole genome sequencing data
Liu Yilin, Xu Jiao and Li Shuaicheng

12:00 pm - 12:20 pm 

Differential co-expression analysis reveals early stage gene dis-coordination in Alzheimer's disease
Yurika Upadhyaya, Linhui Xie, Paul Salama, Sha Cao, Kwagnsik Nho, Andrew Saykin and Jingwen Yan

12:00 pm - 12:20 pm 

Expression correlation attenuates within and between key signaling pathways in CKD progression
Hui Yu, Danqian Chen, Olufunmilola Oyebamiji, Yan Guo and Ying-Yong Zhao

12:20 pm - 1:30 pm

Lunch Break-Buffet Lunches  

1:30 pm - 1:50 pm

Eminent Scholar Talk (Room: TBD) Alla Karnovsky, PhD 
Research Associate Professor of Computational Medicine & Bioinformatics
Assistant Director, Masters Program
University of Michigan
Title:Identifying biologically relevant modules in metabolomics and lipidomics data with Differential Network-based Enrichment Analysis (DNEA)

1:50 pm - 2:00 pm

Short Break

2:00 pm - 2:45 pm

Keynote Lecture (Room: TBD) T.M. Murali, Ph.D. 
Professor, Department of Computer Science
Co-director, ICTAS Center for Systems Biology of Engineered Tissues
Virginia Tech
Title:Pathways on Demand: Automated Reconstruction of Human Signaling Networks

2:45 pm - 3:00 pm

Coffee/Tea Break for parallel sessions

CONCURRENT SESSIONS

Room: TBD NGS & Tools Session Chair: 4

Room: TBD Bioinformatics Session Chairs: 5

Room: TBD Cancer Genomics Session Chairs: 6

3:00 pm - 3:20 pm 

DeepShape: Estimating Isoform-Level Ribosome Abundance and Distribution with Ribo-seq data
Hongfei Cui, Hailin Hu, Jianyang Zeng and Ting Chen

3:00 pm - 3:20 pm 

M3S: A comprehensive model selection for multi-modal single-cell RNA sequencing data
Yu Zhang, Changlin Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao and Chi Zhang

3:00 pm - 3:20 pm 

Comparative evaluation of network features for the prediction of breast cancer metastasis
Nahim Adnan, Zhijie Liu, Tim Huang and Jianhua Ruan

3:20 pm - 3:40 pm 

Prediction of circRNA-disease associations based on inductive matrix completion
Menglu Li, Mengya Liu, Yannan Bin and Junfeng Xia

3:20 pm - 3:40 pm 

Multi-objective optimized fuzzy clustering for detecting cell clusters from single cell expression profiles
Saurav Mallik and Zhongming Zhao

3:20 pm - 3:40 pm 

Highly robust model of transcription regulator activity predicts breast cancer overall survival
Chuanpeng Dong, Jiannan Liu, Steven X. Chen, Tianhan Dong, Guanglong Jiang, Yue Wang, Huanmei Wu, Jill L. Reiter and Yunlong Liu

3:40 pm - 4:00 pm 

CNV detection from circulating tumor DNA in late stage non-small cell lung cancer patients
Hao Peng, Qiangsheng Dai, Zisong Zhou, Xiaochen Zhao, Dadong Zhang, Kejun Nan, Zhu-An Ou, Fugen Li, Hua Dong, Lei Tian and Yu Yao

3:40 pm - 4:00 pm 

Network-based single-cell RNA-seq data imputation enhances cell type identification
Maryam Zand and Jianhua Ruan

3:40 pm - 4:00 pm 

Pseudogene-gene functional networks are prognostic of patient survival in breast cancer
Sasha Smerekanych, Travis Johnson, Kun Huang and Yan Zhang

4:00 pm - 4:10 pm

Coffee/Tea Break

4:10 pm - 4:30 pm 

A Protocol to Evaluate RNA Sequencing Normalization Methods
Zachary Abrams, Travis Johnson, Kun Huang, Philip Payne and Kevin Coombes

4:10 pm - 4:30 pm 

The landscape of alternative splicing in HIV-1 infected CD4 T-cells
Seyoun Byun, Seonggyun Han, Yue Zheng, Vicente Planelles and Younghee Lee

4:10 pm - 4:30 pm 

Deep Learning-based Cancer Survival Prognosis from RNA-seq Data: Approaches and Evaluations
Zhi Huang, Travis Johnson, Zhi Han, Bryan Helm, Sha Cao, Chi Zhang, Paul Salama, Maher Rizkalla, Christina Yu, Jun Cheng, Shunian Xiang, Xiaohui Zhan, Jie Zhang and Kun Huang

4:30 pm – 4:50 pm 

Fully Moderated T-statistic in Linear Modeling of Mixed Effects for Differential Expression Analysis
Lianbo Yu, Jianying Zhang, Guy Brock and Soledad Fernandez

4:30 pm – 4:50 pm 

Biological Representation of Chemicals Using Latent Target Interaction Profile
Mohamed Ayed, Hansaim Lim and Lei Xie

4:30 pm – 4:50 pm 

DNA methylation markers for pan-cancer prediction by deep learning
Biao Liu, Yulu Liu, Mengyao Li, Shuang Yang, Shuai Cheng Li and Xingxin Pan

4:50 pm – 5:00 pm 

SMaSH: Sample Matching using SNPs in Humans
Maximillian Westphal, David Frankhouser, Carmine Sonzone, Peter G. Shields, Pearlly Yan and Ralf Bundschuh

4:50 pm – 5:00 pm 

Long non-coding RNA expression levels modulate cell-type specific splicing patterns by altering their interaction landscape with RNA-binding proteins
Felipe Wendt Porto, Swapna Vidhur Daulatabad and Sarath Chandra Janga

4:50 pm – 5:00 pm 

A pan-cancer study of class-3 semaphorins as therapeutic targets in cancer
Xiaoli Zhang, Brett Klamer, Jin Li, Soledad Fernandez and Lang Li

5:00 pm – 5:10 pm 

BISR-RNAseq: An efficient and scalable RNAseq analysis workflow with interactive report generation
Venkat Sundar Gadepalli, Hatice Gulcin Ozer, Ayse Selen Yilmaz, Maciej Pietrzak and Amy Webb

5:00 pm – 5:10 pm 

Super Clustering Approach for Fully Automated Single Particle Picking in Cryo-EM
Adil Al-Azzawi, Anes Ouadou and Jianlin Cheng

5:00 pm – 5:10 pm 

Transcription factor expression as a predictor of colon cancer prognosis: A machine learning practice
Jiannan Liu, Chuanpeng Dong, Guanglong Jiang, Xiaoyu Lu, Yunlong Liu and Huanmei Wu

5:10 pm – 5:20 pm 

Clonal reconstruction from time course genomic sequencing data
Wazim Mohammed Ismail and Haixu Tang

5:10 pm – 5:20 pm 

Investigating Skewness to Understand Gene Expression Heterogeneity in Large Patient Cohorts
Benjamin Church, Henry Williams and Jessica Mar

5:00 pm – 5:20 pm 

Predicting Re-admission to Hospital for Diabetes Treatment: A Machine Learning based Solution
Satish Mahadevan Srinivasan, Yok-Fong Paat, Philmore Halls, Ruth Kalule and Thomas E. Harvey.

6:30 pm

BANQUET (bus provided to Park of Roses)

TUESDAY, JUNE 11th

7:30 am - 8:40 am

Registration Open and Buffet Breakfast

8:40 am - 9:30 am

Keynote Lecture (Room: TBD) Dr. Jeremy Edwards Ph.D 

Professor, Department of Chemistry & Chemical Biology
The University of New Mexico
Title:TBD

9:30 am - 9:40 am

Break

9:40 am - 10:00 am

Eminent Scholar Talk (Room: TBD) Bruce Aronow, Ph.D. 
Professor, UC Department of Pediatrics
Co-director, Computational Medicine Center
Cincinnati Children's Hospital Medical Center
Title: ToppCell: A Workbench for the Analysis, Modeling and Prediction of the Molecular Basis of Development and Function of Cells and Tissues based on Single Cell Atlas Datasets

10:00 am - 10:10 am

Break for parallel sessions

CONCURRENT SESSIONS

Room: TBD Cancer Genomics Session Chair: 7

Room: TBD Scientific Databases Session Chair: 8

Room: TBD Computational drug discovery Session Chair: 9

10:10 am - 10:30 am 

Identify rewired pathways between primary breast cancer and liver metastatic cancer using transcriptome data
Limei Wang, Jin Li, Enze Liu, Garrett Kinnebrew, Yang Huo, Zhi Zeng, Wanli Jiang, Lijun Cheng, Hongchao Lv, Weixing Feng and Lang Li

10:10 am - 10:30 am 

MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals
Xikang Feng, Zishuai Wang, Hechen Li and Shuaicheng Li

10:10 am - 10:30 am 

A deep learning-based method for drug-target interaction prediction based on long short-term memory neural network
Yanbin Wang, Zhuhong You, Shan Yang, Haicheng Yi, Zhanheng Chen and Kai Zheng

10:30 am -10:50 am  

Kinetic modeling of DUSP regulation in Herceptin-resistant HER2-positive breast cancer
Petronela Buiga, Ari Elson, Lydia Tabernero and Jean-Marc Schwartz

10:30 am - 10:50 am 

dbMTS: a comprehensive database of putative human microRNA target site SNVs and their functional predictions
Chang Li, Michael Swartz, Bing Yu and Xiaoming Liu

10:30 am - 10:50 am 

Mining and visualizing high-order directional drug interaction effects using the FAERS database
Xiaohui Yao, Tiffany Tsang, Sara Quinney, Pengyue Zhang, Xia Ning, Lang Li and Li Shen

10:50 am - 11:10 am 

Gene co-expression networks restructured by gene fusion in rhabdomyosarcoma cancers
Bryan Helm, Xiaohui Zhan, Zhi Han, Dong Ni, Jie Zhang and Kun Huang

10:50 am - 11:10 am 

A harmonized neurodegenerative transcriptome database to nominate mouse models for functional follow-up and validation of Alzheimer’s gene networks
Rami Al-Ouran, Ying-Wooi Wan and Zhandong Liu

10:50 am - 11:10 am 

SCNrank: Spectral Clustering for Network-based target Ranking to reveal potential drug targets and its application in pancreatic ductal adenocarcinoma
Enze Liu, Xiaoqi Liu, Zhuangzhuang Zhang, Xiaolin Cheng, Murray Korc and Lijun Cheng

11:10 am - 11:20 am

Coffee/Tea Break

11:20 am - 11:40 am 

Synonymous mutations in regulatory elements contribute to the genetic aetiology of melanoma
Di Zhang and Jufeng Xia

11:20 am - 11:40 am 

Forming Big Datasets through Latent Class Concatenation of Imperfectly Matched Databases Features
Christopher Bartlett, Brett Klamer, Steven Buyske, Stephen Petrill and William Ray

11:20 am - 11:40 am 

iGMDR: an integrative resource for investigating genetic model of drug response in cancer
Xiang Chen

11:40 am - 12:00 pm am 

Integrative Network Analysis Identifies Potential Targets and Drugs for Ovarian Cancer
Tianyu Zhang, Liwei Zhang and Fuhai Li

11:40 am - 12:00 pm 

Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM Proteogenomics Sub-Challenge
Tara Eicher, Andrew Patt, Esko Kautto, Raghu Machiraju, Ewy Mathe and Yan Zhang

11:40 am - 12:00 pm 

Computational Drug Repositioning for Precision Cancer Medicine Based on Cancer Cells Screening
Abhishek Majumdar, Shaofeng Wu and Yaoqin Lu

12:00 pm - 12:20 pm 

Convolutional neural network models for cancer type prediction based on gene expression
Milad Mostavi, Yu-Chiao Chiu, Yufei Huang and Yidong Chen

12:00 pm - 12:20 pm 

TBA

12:00 pm - 12:20 pm 

Network as a biomarker: A novel network-based sparse Bayesian machine for pathway-driven drug response prediction
Lei Frank Huang, Hongting Liu, Yi Zheng and Richard Lu

12:20 pm - 1:35 pm

Lunch Break - Buffet Lunches  

1:35 pm - 1:55 pm

Eminent Scholar Talk (Room: TBD) – Dr. Haixu Tang 
Professor of Informatics and Computing
Director, Data Science Academic Programs
Adjunct Professor of Biology
Indiana University

Title: Prediction, Searching and Clustering of Tandem Mass Spectra of Peptides

1:55 pm - 2:10 pm

Award presentations

2:10 pm - 2:20 pm

Coffee/Tea Break

CONCURRENT SESSIONS

Room: TBD International PI Talk Session Chair: 10

Room: TBD Systems Immunology Session Chair: 11

Room: TBD Cancer Genomics Session Chair: 12

2:20 pm - 2:40 pm 

ProGeo-neo: a Customized Proteogenomic Workflow for Neoantigen Prediction and Selection
Yuyu Li, Guangzhi Wang, Xiaoxiu Tan, Jian Ouyang, Menghuan Zhang, Xiaofeng Song, Qi Liu, Qibin Leng, Lanming Chen and Lu Xie

2:20 pm - 2:40 pm 

On the analysis of the human immunome via an information theoretical approach
Maciej Pietrzak, Gerard Lozanski, Michael Grever, Jeffrey Jones, Leslie Andritsos, James Blachly, Kerry Rogers and Michal Seweryn.

2:20 pm - 2:40 pm 

TBA
TBA

2:40 pm - 3:00 pm 

Regional changes in microbial community diversity in oil reservoir
Jingjing Liu, Jing Wu, Jiawei Lin, Jian Zhao, Tianyi Xu, Qichang Yang, Jing Zhao, Zhongming Zhao and Xiaofeng Song

TBA

2:40 pm - 3:00 pm 

TBA 

3:00 pm - 3:20 pm 

TBA 

TBA

3:00 pm - 3:20 pm 

TBA 

3:20 pm - 3:40 pm 

TBA 

TBA

3:20 pm - 3:40 pm 

TBA 

3:40

Adjourn