ACM-BCB 2015 Program



Wednesday (9/9)   7:30 am–5:00 pm / Thursday (9/10)   8:00 am–11:00 am / Friday (9/11)   8:00 am–11:00 am


Wednesday, September 9, 2015




Auditorium 235

Classroom 323

Classroom 324

Classroom 233

Classroom 328

Classroom 330



(8 am–1 pm)


(8:25 am–12 pm)

(1:30 pm–5 pm)



(8:45 am–11:30 am)

(1 pm–6 pm)



(8:30 am–1 pm)




(9 am–12 pm)


(9 am–1:15 pm)








(1:30 pm–5 pm)
























CompPath:               The Computational Pathology Workshop: Linking Tissue Phenotypes with Genomics and Clinical Outcomes

                                    Organizer:  Lee Cooper and David Gutman

GMDM:                     Genomics and Metagenomics Data Mining Workshop

                                    Organizer:  Quoc-Nam Tran and Hairong Wei

MMBD:                      Novel enabling technologies in mining massive biomedical data

                                    Organizer:  Zhaohui S Qin and Tianwei Yu

CNB-MAC:                2nd Workshop on Computational Network Biology: Modeling, Analysis, and Control        

                                    Organizer:  Byung-Jun Yoon, Xiaoning Qian, and Tamer Kahveci

BigLS:                          3rd Workshop on: Big Data in Life Sciences

                                    Organizer:  Ananth Kalyanaraman and Jaroslaw Zola

CHS:                            1st workshop on Computational Health Science

                                    Organizer:  Sherry Emery and Christophe Giraud-Carrier

ParBio:                       4th workshop on Parallel and Cloud-based Bioinformatics and Biomedicine

                                    Organizer:  Mario Cannataro and John A. Springer




T1:             Analysis methods for 3D nucleome data: from processing basics to three-dimensional modeling

Contact:   Ferhat Ay (; Geet Duggal (; Ming Hu (;
Emre Sefer (

T2:             Computational Construction of Intra-Cellular Networks

                  Contact:  Tolga Can (

T3:             Functional Module Identification in Biological Networks

                  Contact:  Xiaoning Qian (

T4:             When imaging informatics meets bioinformatics: How multiple modality image-omics can integrate with genomics data
analysis for personalized medicine

                  Contact:  Lin Yang (

T5:             Computational methods for analyzing intra-tumor heterogeneity using next-generation sequencing

                  Contact:  Iman Hajirasouliha (


Thursday, September 10, 2015


Continental Breakfast


Opening Remarks                  (Location:  Room 236)

General Chairs:  Srinivas Aluru, Georgia Institute of Technology & May D. Wang, Georgia Institute of Technology and Emory University 


Keynote Talk 1  (Location:  Room 236)

From Meaningful use to Precision Medicine: Lessons Learned

Douglas B. Fridsma, President and Chief Executive Officer of American Medical Informatics Association

 Session Chairs:  Mark Braunstein and May D. Wang, Georgia Institute of Technology


Morning Break


Session 1A

Location:  Room 222

Genome and Sequence Analysis I

Session Chair:  Carl Kingsford, Carnegie Mellon University

Featured Sessions

Location:  Rooms 334–335

Session Chairs: 
 Greg Gibson & May D. Wang, Georgia Tech

Session 1B

Location:  Room 233

Data Privacy and Epidemiological Modeling

Session Chair:  Pierangelo Veltri, Univ. of Magna Graecia of Catanzaro


L:  10:00–10:24 am

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

L:  10:24–10:48 am

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

L:  10:48–11:12 am

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

L:  11:12–11:36 am

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

L:  11:36–12:00 am

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

NIH/NIGMS Trainee Forum:

 Computational Biology and Medical Informatics at Georgia Tech


Professor Greg Gibson

Director of Integrative Genomics, Georgia Tech

and Four NIH Trainees


L:  10:00–10:24 am

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.

L:  10:24–10:48 am

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

L:  10:48–11:12 am

Carl Gunter, Muhammad Naveed, Jean-Pierre Hubaux, Erman Ayday, Ellen Clayton, Xiaofeng Wang, Brad Malin and Jacques Fellay. Privacy in the Genomic Era.

L:  11:12–11:36 am

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. (H)

L:  11:36–12:00 am

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




Opportunity in Computational Sciences

 Dr. Veerasamy "Ravi" Ravichandran





Editors-In-Chief Plenary  (Location:  Room 236)

Dr. Ying Xu (TCBB EiC) and Briefing from J-BHI EiC


Session 2A

Location:  Room 222

Genome and Sequence Analysis II

Session Chair:  Ananth Kalyanaraman, Washington State University

Featured Sessions




Session 2B

Location:  Room 233

Machine Learning and Applications

Session Chair:  Umit Catayurek, Ohio State University


L:  2:152:40 pm

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.

L:  2:403:05 pm

Darya Filippova and Carl Kingsford. Rapid Separable Compression Enables Fast Analyses of Sequence Alignments.

L:  3:053:30 pm

Dan Deblasio and John Kececiogu. Ensemble Multiple Sequence Alignment via Advising.


L:  2:152:40 pm

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

L:  2:403:05 pm

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

L:  3:053:30 pm

Dong Nie. A Deep Framework for Bacteria Image Segmentation and Classification.


Afternoon Break


ACM SIGBio General Meeting

Location:  Room 236


Poster Reception




Friday, September 11, 2015


Continental Breakfast


Keynote Talk 2  (Location:  Room 236)

Computational biology in the 21st century: Algorithms that scale

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

Session Chairs: T. M. Murali, Virginia Tech & Christopher C. Yang, Drexel University


Morning Break


Session 3A

Location:  Room 222

Networks and Ontologies

Session Chair:  Predrag Radivojac, Indiana University

Featured Sessions

Location:  Room 225

Industry Track: Big Data Analytic Technology for Bioinformatics and Health Informatics

Session Chairs: Xin Deng, Microsoft &

Donghui Wu, Knowledgent

Session 3B

Location:  Room 233

Clinical and Health Decision Support Systems

Session Chair:  Saeid Belkasim, Georgia State University


L:  10:00–10:24 am

Shi Qiao, Mehmet Koyuturk and Z. Meral Özsoyo_lu. Integrated Querying of Disparate Association and Interaction Data in Biomedical Applications.

L:  10:24–10:48 am

Haitham Gabr, Alin Dobra and Tamer Kahveci. Estimating Reachability in Dense Biological Networks.

L:  10:48–11:12 am

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.

L:  11:12–11:36 am

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

L:  11:36–12:00 am

Gaurav Pandey, Sonali Arora, Sahil Manocha and Sean Whalen. Enhancing the Functional Content of Eukaryotic Protein Interaction Networks. (H)

10:00–10:20 am

Building and Implementing Data Science Products to Change Healthcare IT. Vincent A. Emanuele II, Ph.D, Wellcentive & David Lloyd, Wellcentive.

10:20–10:40 am

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 am

A Bayesian Nonparametric Approach for Latent Class Regression Analysis. Nong Shang, Ph.D., Division of Bacterial Diseases, NCIRD.

11:00–11:20 am

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 am

Development of a mobile app to address a healthcare gap about laboratory testing. Julie Taylor, Ph.D., CDC.

11:40–12:00 pm: PANEL DISCUSSION

Big Data and Predictive Modeling Topics in Healthcare.  Chairs: Xin Deng, Ph.D., Donghui Wu, Ph.D.,

L:  10:00–10:24 am

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

L:  10:24–10:48 am

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

L:  10:48–11:12 am

Xun Lu, Aston Zhang, Carl A. Gunter, Daniel Fabbri, David Liebovitz and Brad Malin. Discovering De Facto Diagnosis Specialties.

L:  11:12–11:36 am

Daniel Riofrio, Shuang Luan, Jun Zhou and Lijun Ma. Particle Swarm Optimization for Radiation Therapy Planning.



Women in Bioinformatics Panel

Location:  Room 158

Chair: Wei Wang,  

Univ. of California Los Angeles



Session 4A

Location:  Room 222

Genome and Sequence Analysis III

Session Chair:  Vasant Honavar, Pennsylvania State University

Featured Sessions

Location:  Room 225

Special Panel: National Surveys of Population Health: A CDC Panel

Session Chair: Bruce Schatz, PhD University of Illinois at Urbana-Champaign

Session 4B

Location:  Room 233

Proteins, Structures, and Models

Session Chair:  Mehmet Koyuturk, Case Western Reserve University


L:  1:30–1:54 pm

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

L:  1:54–2:18 pm

Marzieh Ayati and Mehmet Koyuturk. Assessing The Collective Disease Association of Multiple Genomic Loci.

L:  2:18–2:42 pm

Aseel Awdeh, Hilary Phenix, Mads Kaern and Theodore Perkins. The Potential Power of Dynamics in Epistasis Analysis.

L:  2:42–3:06 pm

Darya Filippova, Rob Patro, Geet Duggal and Carl Kingsford. Identification of alternative topological domains in chromatin. (H)

L:  3:06–3:30 pm

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



Machell Town, PhD, Branch Chief, Division of Population Health, National Center for Chronic Disease Prevention and Health Promotion, CDC

Paula Yoon, ScD, Director, Division of Health Informatics and Surveillance, Center for Surveillance, Epidemiology, and Laboratory Services, CDC

Leslie Lenert, MD, Chief Research Information Officer, Medical University of South Carolina; Chief Medical Information Officer, Health Sciences South Carolina; keynote speaker for Health Informatics BCB 2014; former Director of National Center for Public Health Informatics, CDC

Bruce Schatz, PhD, Head, Department of Medical Information Science, University of Illinois at Urbana-Champaign; program chair for Health Informatics at BCB 2014, and panel organizer

L:  1:30–1:54 pm

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.

L:  1:54–2:18 pm

Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li and Xin Gao. Compare Local Pocket and Global Protein Structure Models by Small Structure Patterns.

L:  2:18–2:42 pm

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.

L:  2:42–3:06 pm

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

L:  3:06–3:30 pm

Jin Chen and Lei Xu. Plant photosynthesis phenomics data quality control. (H)


Afternoon Break


NSF Sponsored Student Research Forum

Location:  Room 225











Saturday, September 12, 2015


Continental Breakfast


Keynote Talk 3  (Location:  Room 236)

What is a gene? How and why computer science helps in answering this Question?

Paola Bonizzoni, Professor of Computer Science at the Universitą di Milano-Bicocca

Session Chair: Helene Touzet, CNRS France and Srinivas Aluru, Georgia Tech


Morning Break


Session 5A

Location:  Room 222

Genome and Sequence Analysis IV

Session Chair:  John Kececioglu, University of Arizona

Featured Sessions

Location:  Room 225

Student Education Session Chair: Marzieh Ayati Case Western Reserve Univ.

Co-Chairs: Hang Wu, Li Tong, Georgia Tech

Session 5B

Location:  Room 233

Predictive Modeling and Text Mining

Session Chair:  May D Wang, Georgia Tech and Emory U.


L: 10:00-10:24

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

L: 10:24-10:48        

Kun Wang, Kan Cao and Sridhar Hannenhalli. Chromatin and Genomic determinants of alternative splicing.

L: 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.

L: 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.

L: 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)

How to write a technical paper (by communication director at Georgia Tech)?


How to prepare for a career in academia?

Prof. Meral Ozsoyoglu, Case Western Reserve Univ.

Prof. Aidong Zhang, NSF/CISE/IIS and SUNY at Buffalo


How to land your first job in industry?

Dr. Xin Deng, Microsoft

Dr. Donghui Wu, Knowledgent


L:  10:00–10:24 am

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

L:  10:24–10:48 am

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

L:  10:48–11:12 am

Chih-Wen Cheng and_May Wang. Improving Personalized Clinical Risk Prediction Based on Causality-Based Association Rules.

L:  11:12–11:36 am

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

L: 11:36-12:00

Anthony Rios and Ramakanth Kavuluru. Convolutional Neural Networks for Biomedical Text Classification: Application in Indexing Biomedical Articles.









Session 6A

Location:  Room 222

Genome and Sequence Analysis V

Session Chair:  Filip Jagodzinski, Western Washington University

Session 6B

Location:  Room 233

Networks and Modules

Session Chair:  Christina Boucher, Colorado State University


L:  1:301:54 pm

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

L:  1:542:18 pm

Elisabetta Bergamini, Romina D'Aurizio, Mauro Leoncini and_Marco Pellegrini. CNVScan: detecting borderline copy number variations in NGS data via scan statistics.

L:  2:182:42 pm

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

L:  2:423:06 pm

Subrata Saha and_Sanguthevar Rajasekaran. HECTOR: A Novel Paradigm for Correcting Short Reads.

L:  3:063:30 pm

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

L:  1:301:54 pm

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

L:  1:542:18 pm

Andrei Todor, Alin Dobra and Tamer Kahveci. Counting Motifs in Probabilistic Biological Networks.

L:  2:182:42 pm

Ayat Hatem,_Kamer Kaya,_Jeffrey Parvin, Kun Huang and_Umit Catalyurek. MICA: MicroRNA Integration for Active Module Discovery.

L:  2:423:06 pm

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

L:  3:063:30 pm

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