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Wednesday, September 9

Workshop Schedule
331 233 235 323 324 328 330
8-9 CompPath (8 am–1 pm) pSALSA(8am-6pm) BigLS (8:25 am–12 pm)
(1:30 pm–5 pm)
CNB‐MAC (8:45 am–11:30 am)
(1 pm–6 pm)
(8:30 am–1 pm)
9-10 GMDM
(9 am–12 pm)
(9 am–1:15 pm)
13-14 MMBD (1:30 pm–5 pm)

Name Organizers
CompPath The Computational Pathology Workshop: Linking Tissue Phenotypes with Genomics and Clinical Outcomes Lee Cooper and David Gutman
GMDM Genomics and Metagenomics Data Mining Workshop Quoc‐Nam Tran and Hairong Wei
MMBD Novel enabling technologies in mining massive biomedical data Zhaohui S Qin and Tianwei Yu
CNB‐MAC Computational Network Biology: Modeling, Analysis, and Control Byung‐Jun Yoon, Xiaoning Qian, and Tamer Kahveci
BigLS Big Data in Life Sciences Ananth Kalyanaraman and Jaroslaw Zola
CHS Computational Health Science Sherry Emery and Christophe Giraud‐Carrier
ParBio Parallel and Cloud‐based Bioinformatics and Biomedicine Mario Cannataro and John A. Springer
pSALSA Parallel Software Libraries for Sequence Analysis Srinivas Aluru and Yongchao Liu

T1 Analysis methods for 3D nucleome data: from processing basics to three‐dimensional modeling Ferhat Ay (; Geet Duggal (; Ming Hu (; Emre Sefer (
T2 Computational Construction of Intra‐Cellular Networks Tolga Can (
T3 Functional Module Identification in Biological Networks Xiaoning Qian (
T4 When imaging informatics meets bioinformatics: How multiple modality image‐omics can integrate with genomics data analysis for personalized medicine Lin Yang (
T5 Computational methods for analyzing intra‐tumor heterogeneity using next‐generation sequencing Iman Hajirasouliha (
Thursday, September 10

7-8:15 Continental breakfast

8:15-8:30 Opening remarksRoom 236

8:30-9:30 Keynote: From Meaningful use to Precision Medicine: Lessons LearnedRoom 236
Douglas B. Fridsma, President and Chief Executive Officer of American Medical Informatics Association

9:30-10:00 Break

10:00-12:00 Session 1A: Genome and Sequence Analysis IRoom 222
Chair: Carl Kingsford, Carnegie Mellon University

10:00-10:24 Alexej Gossmann, Shaolong Cao and Yu-Ping Wang. Identification of significant genetic variants via SLOPE, and its extension to Group SLOPE

10:24-10:48 Aika Terada, Hanyoung Kim and Jun Sese. High-speed Westfall-Young permutation procedure for genome-wide association studies

10:48-11:12 Veronika Strnadova-Neeley, Aydin Buluc, Jarrod Chapman, John Gilbert, Joseph Gonzalez and Leonid Oliker. Efficient Data Reduction for Large-Scale Genetic Mapping

11:12-11:36 Segun Jung, Hongjian Jin and Ramana Davuluri. Identification of Candidate Regulatory SNPs by Integrative Analysis for Prostate Cancer Genome Data

11:36-12:00 Shaolong Cao, Huaizhen Qin, Alexej Gossmann, Hong-Wen Deng and Yu-Ping Wang. Unified tests for fine scale mapping and identifying sparse high-dimensional sequence associations

10:00-12:00 Session 1B: Data Privacy and Epidemiological ModelingRoom 233
Chair: Pierangelo Veltri, University Magna Graecia of Catanzaro

10:00-10:24 Dingcheng Li, Majid Rastegar, Ravikumar Komandur Elayavilli, Yanshan Wang, Yue Yu, Saeed Mehrabi, Naveed Afzal, Sunghwan Sohn, Yanpeng Li and Hongfang Liu. A Frequency-filtering Strategy of Obtaining PHI-free Sentences from Clinical Data Repository

10:24-10:48 Feng Chen, Noman Mohammed, Shuang Wang, Wenbo He, Samuel Cheng and Xiaoqian Jiang. Cloud-Assisted Distributed Private Data Sharing

10:48-11:12 Carl Gunter, Muhammad Naveed, Jean-Pierre Hubaux, Erman Ayday, Ellen Clayton, Xiaofeng Wang, Brad Malin and Jacques Fellay. Privacy in the Genomic Era (H)

11:12-11:36 Suruchi Deodhar, Jiangzhuo Chen, Mandy Wilson, Keith Bisset, Bryan Lewis, Chris Barrett and Madhav Marathe. EpiCaster: An Integrated Web Application For Forecasting of Global Epidemics

11:36-12:00 Sherif Abdelhamid, Chris Kuhlman, Gizem Korkmaz, Madhav Marathe and S. S. Ravi. EDISON: A Web Application for Computational Health Informatics At Scale

10:00-12:20 NIH trainee sessionRoom 334-335
More Information    NIH-NIGMS Session Handbook

12:00-13:15 Lunch

13:15-14:15 Editors-In-Chief PlenaryRoom 236
More Information

14:15-15:30 Session 2A: Genome and Sequence Analysis IIRoom 222
Chair: Ananth Kalyanaraman, Washington State University

14:15-14:40 Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma and Jinbo Xu. Bermuda: Bidirectional de novo assembly of transcripts with new insights for handling uneven coverage

14:40-15:05 Darya Filippova and Carl Kingsford. Rapid Separable Compression Enables Fast Analyses of Sequence Alignments

15:05-15:30 Dan Deblasio and John Kececiogu. Ensemble Multiple Sequence Alignment via Advising

14:15-15:30 Session 2B: Machine Learning and ApplicationsRoom 233
Chair: Umit Catalyurek, Ohio State University

14:15-14:40 Asish Ghoshal, Ananth Grama, Saurabh Bagchi and Somali Chaterji. An Ensemble SVM Model for the Accurate Prediction of Non-Canonical MicroRNA Targets

14:40-15:05 Chanchala Kaddi and May D. Wang. Developing Robust Predictive Models for Head and Neck Cancer across Microarray and RNA-seq Data

15:05-15:30 Dong Nie. A Deep Framework for Bacteria Image Segmentation and Classification

15:30-16:00 Break

16:00-18:00 SIGBio General MeetingRoom 236

18:00-20:00 Poster Reception
Friday, September 11

7-8:30 Breakfast

8:30-9:30 Keynote: Computational biology in the 21st century: Algorithms that scaleRoom 236
Bonnie Berger, Professor of Applied Math and Computer Science at MIT, and head of the Computation and Biology group at MIT's Computer Science and AI Lab

9:30-10:00 Break

10:00-12:00 Session 3A: Networks and OntologiesRoom 222
Chair: Predrag Radivojac, Indiana University

10:00-10:24 Shi Qiao, Mehmet Koyutürk and Z. Meral Özsoyoğlu. Integrated Querying of Disparate Association and Interaction Data in Biomedical Applications

10:24-10:48 Haitham Gabr, Alin Dobra and Tamer Kahveci. Estimating Reachability in Dense Biological Networks

10:48-11:12 Cen Wan and Alex A. Freitas. Two Methods for Constructing a Gene Ontology-based Feature Network for a Bayesian Network Classifier and Applications to Datasets of Aging-related Genes

11:12-11:36 Shufan Ji, Xing Tian and Jin Chen. Improving Biological Signicance of Gene Expression Biclusters with Key Missing Genes

11:36-12:00 Gaurav Pandey, Sonali Arora, Sahil Manocha and Sean Whalen. Enhancing the Functional Content of Eukaryotic Protein Interaction Networks (H)

10:00-12:00 Session 3B: Clinical and Health Decision Support SystemsRoom 233
Chair: Saeid Belkasim, Georgia State University

10:00-10:24 Nikhil Yadav, Christian Poellabauer, Louis Daudet, Tomas Collins, Shane McQuillan, Patrick Flynn and Sandra Schneider. Portable Neurological Disease Assessment Using Temporal Analysis of Speech

10:24-10:48 Michael Uelschen and Heinz-Josef Eikerling. A Mobile Sensor System for Gait Analysis supporting the Assessment of Rehabilitation Measures

10:48-11:12 Xun Lu, Aston Zhang, Carl A. Gunter, Daniel Fabbri, David Liebovitz and Brad Malin. Discovering De Facto Diagnosis Specialties

11:12-11:36 Daniel Riofrio, Shuang Luan, Jun Zhou and Lijun Ma. Particle Swarm Optimization for Radiation Therapy Planning

10:00-12:00 Industry Track: Big Data Analytic Technology for Bioinformatics and Health InformaticsRoom 225
Track Chairs: Xin Deng, Ph.D., Microsoft,
Donghui Wu, Ph.D., Knowledgent,
More information

10:00 - 10:20 Building and Implementing Data Science Products to Change Healthcare IT
Vincent A. Emanuele II, Ph.D, Wellcentive,
David Lloyd, Wellcentive,

10:20 - 10:40 Senior Health Management through Internet of Things and Real-Time Big Data Analytics
Xin Deng, Ph.D., Microsoft,
Donghui Wu, Ph.D., Knowledgent,

10:40 - 11:00 A Bayesian Nonparametric Approach for Latent Class Regression Analysis
Nong Shang, Ph.D., Division of Bacterial Diseases, NCIRD,

11:00 - 11:20 Learning Causal Structures with Background Knowledge in Health Data
Yiheng Liang, Ph.D., University of North Texas,
Armin R. Mikler, Ph.D., University of North Texas,

11:20 - 11:40 Development of a mobile app to address a healthcare gap about laboratory testing
Julie Taylor, Ph.D., CDC,

11:40 - 12:00 Big Data and Predictive Modeling Topics in Healthcare
Panel Chairs: Xin Deng, Ph.D., Microsoft,
Donghui Wu, Ph.D., Knowledgent,

12:00-13:30 Lunch; Women in Bioinformatics panelRoom 158

13:30-15:30 Session 4A: Genome and Sequence Analysis IIIRoom 222
Chair: Vasant Honavar, Pennsylvania State University

13:30-13:54 Dan He and Laxmi Parida. SAME: A Sampling-based Multi-locus Epistasis Algorithm for Quantitative Genetic Trait Prediction

13:54-14:18 Marzieh Ayati and Mehmet Koyuturk. Assessing The Collective Disease Association of Multiple Genomic Loci

14:18-14:42 Aseel Awdeh, Hilary Phenix, Mads Kaern and Theodore Perkins. The Potential Power of Dynamics in Epistasis Analysis

14:42-15:06 Darya Filippova, Rob Patro, Geet Duggal and Carl Kingsford. Identification of alternative topological domains in chromatin (H)

15:06-15:30 David Ream, Asma Riyaz and Iddo Friedberg. An event-driven approach for studying gene block evolution in bacteria (H)

13:30-15:30 Session 4B: Proteins, Structures, and ModelsRoom 233
Mehmet Koyuturk, Case Western Reserve University

13:30-13:54 Chao Ji, Yong Li, Earl Bellinger, Sujun Li, Randy Arnold, Predrag Radivojac and Haixu Tang. A maximum-likelihood approach to absolute protein quantification in mass spectrometry

13:54-14:18 Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li and Xin Gao. Compare Local Pocket and Global Protein Structure Models by Small Structure Patterns

14:18-14:42 Deukhyun Cha, Qin Zhang, Alexander Rand, Jesmin Jahan Tithi, Rezaul Chowdhury and Chandrajit Bajaj. Accelerated Molecular Mechanical and Solvation Energetics on Multicore CPUs and Manycore GPUs

14:42-15:06 Minghan Chen, Fei Li, Kartik Subramanian, John Tyson and Yang Cao. Two-dimensional Model of PopZ Bipolarization in Caulobacter crescentus

15:06-15:30 Jin Chen and Lei Xu. Plant photosynthesis phenomics data quality control (H)

13:30-15:30 National Surveys of Population Health: A CDC PanelRoom 225
More Information

16:00-18:00 NSF travel awardee sessionRoom 225
NSF Forum Handbook

18:30-20:30 Banquet
Saturday, September 12

7-8:30 Breakfast

8:30-9:30 Keynote: What is a gene? How and why computer science helps in answering this Question?Room 236
Paola Bonizzoni, Professor of Computer Science at the Università di Milano-Bicocca

9:30-10:00 Break

10:00-12:00 Session 5A: Genome and Sequence Analysis IVRoom 222
Chair: John Kececioglu, University of Arizona

10:00-10:24 Christopher Hoobin, Trey Kind, Christina Boucher and Simon Puglisi. Fast and Efficient Compression of High-Throughput Sequencing Reads

10:24-10:48 Kun Wang, Kan Cao and Sridhar Hannenhalli. Chromatin and Genomic determinants of alternative splicing

10:48-11:12 Cheng Yang, Po-Yen Wu, Li Tong, John Phan and May Wang. The impact of RNA-seq aligners on gene expression estimation

11:12-11:36 Zihe Chen, Danyang Chen, Xiangyu Wang, Andrew Fritz, Nitasha Sehgal, Ronald Berezney, Jinhui Xu and Hu Ding. Mining k-Median Chromosome Association Graphs from a Population of Heterogeneous Cells

11:36-12:00 Sharma V. Thankachan, Sriram Chockalingam, Yongchao Liu, Alberto Apostolico and Srinivas Aluru. The k-Mismatch Maximal Common Substring Problem: Efficient Algorithms and Applications (H)

10:00-12:00 Session 5B: Predictive Modeling and Text MiningRoom 233
Chair: May Wang, Georgia Tech

10:00-10:24 Hui Li, Xiaoyi Li, Xiaowei Jia, Murali Ramanathan and Aidong Zhang. Bone Disease Prediction and Phenotype Discovery using Feature Representation over Electronic Health Records

10:24-10:48 Nhathai Phan, Dejing Dou, Hao Wang, David Kil and Brigitte Piniewski. Ontology-based Deep Learning for Human Behavior Prediction in Health Social Networks

10:48-11:12 Chih-Wen Cheng and May Wang. Improving Personalized Clinical Risk Prediction Based on Causality-Based Association Rules

11:12-11:36 Sanghoon Lee, Yanjun Zhao, Mohamed Eid Mahmoud Masoud, Maria Valero and Saeid Belkasim. Domain Specific Information Retrieval and Text Mining in Medical Document

11:36-12:00 Anthony Rios and Ramakanth Kavuluru. Convolutional Neural Networks for Biomedical Text Classification: Application in Indexing Biomedical Articles

10:00-12:00 Student Educational SessionRoom 225

10:00-12:00 How to write paper (by communication director at Georgia Tech)

10:00-12:00 How to prepare for career in industry (by Industrial Track chair)

10:00-12:00 How to prepare for career in academic

12:00-13:30 Lunch

13:30-15:30 Session 6A: Genome and Sequence Analysis VRoom 222
Chair: Filip Jagodzinski, Western Washington University

13:30-13:54 Dan Gusfield. Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach

13:54-14:18 Elisabetta Bergamini, Romina D'Aurizio, Mauro Leoncini and Marco Pellegrini. CNVScan: detecting borderline copy number variations in NGS data via scan statistics

14:18-14:42 Chen Peihua, Weiheng Huang and Hongmin Cai. Discrimination of recurrent CNVs from individual ones from multisample aCGH by jointly constrained minimization

14:42-15:06 Subrata Saha and Sanguthevar Rajasekaran. HECTOR: A Novel Paradigm for Correcting Short Reads

15:06-15:30 Hamid Mirebrahim, Timothy Close and Stefano Lonardi. De novo meta-assembly of ultra-deep and single-cell sequencing data (H)

13:30-15:30 Session 6B: Networks and ModulesRoom 233
Chair: Christina Boucher, Colorado State University

13:30-13:54 Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My Thai and Tamer Kahveci. Multiple Reference Networks Improve Accuracy of Signaling Network Construction

13:54-14:18 Andrei Todor, Alin Dobra and Tamer Kahveci. Counting Motifs in Probabilistic Biological Networks

14:18-14:42 Ayat Hatem, Kamer Kaya, Jeffrey Parvin, Kun Huang and Umit Catalyurek. MICA: MicroRNA Integration for Active Module Discovery

14:42-15:06 Guopeng Wei, Connor Walsh, Irina Cazan and Radu Marculescu. Molecular Tweeting: Unveiling the Social Network behind Heterogeneous Bacteria Populations

15:06-15:30 Adib Shafi, Michele Donato and Sorin Draghici. A systems biology approach for the identification of significantly perturbed genes