Workshop Schedule (Up-To-Date)

Sept. 9th,2015

All workshops will take place at the Georgia Tech Global Learning Center. The venue opens at 7AM with breakfast service for all attendees.

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

Organizers:Lee Cooper and David Gutman

Format:½ day (8am-1pm morning)




8:00-9:00am: Keynote: Computational pathology for systematic studies of carcinogenesis, Andrew Beck, Harvard Medical School

9:10-9:45am: Biomedical Imaging Big Data Analytics for Precision Medicine, May Wang, Georgia Tech/Emory University

9:45-10:20am: Building an Informatics Platform for Computational Pathology, David Gutman, Emory University

10:20-10:55am: Tissue Pattern Quantification and Classification in Cancer and Age-Related Macular Degeneration, Yi Jiang, Georgia State University

10:55-11:30am: Towards Robust 2D/3D Characterization of the Microenvironment in Brain Tumors, Jun Kong, Emory University

11:30-12:05pm: Integrating Imaging and Omics Features for Cancer Patient Stratification, Kun Huang, Ohio State University

12:05-12:40pm: An Interactive Learning Framework for Scalable Classification of Pathology Images, Michael Nalisnik, Emory University

12:40-1:00pm: Discussion

Genomics and Metagenomics Data Mining Workshop

Organizers:Quoc-Nam Tran and Hairong Wei

Format:½ day (9am-noon morning)


Room: 323


9:00-9:40 AM: Keynote: Comprehensive prediction of drug-protein interactions and side effects for the human proteome, Jeff Skolnick, Georgia Tech, GA.

9:40-10:00 AM: Transcription factor network, Hairong Wei, Michigan Technological University, MI.

10:00-10:20 AM: Multi-core Dynamic Parallelism for Multiple Sequence Alignment and Counting Metrics, Mike Wallinga, Northwestern College, Iowa.

10:20-11:00 AM: Keynote: Gene Finding for NGS Genomes, Mark Borodovsky, Georgia Tech, Centers for Disease Control.

11:00-11:20 AM: Selection of Genes Using Long-term Influence and Sensitivity Analysis, Quoc-Nam Tran, The University of South Dakota, SD.

11:20-11:40 AM: A Generalized Lattice Model for Clustering of Metagenomic Sequences, Manjari Mukhopadhyay, Raunaq Malhotra and Raj Acharya, Pennsylvanian State University, PA.

11:40-12:00 PM: K-algorithms for variant calling and pathogen identification, Fredrik O., Georgia Tech Genome Center, Georgia Tech, GA.

Novel enabling technologies in mining massive biomedical data (MMBD)

Organizers:Zhaohui S Qin and Tianwei Yu

Format:½ day (1:30pm-5:00pm afternoon)


Room: 323


1:30 – 2:00pm MeTDiff: a novel graphical model for differential mRNA methylation analysis for MeRIP-Seq data, Yufei Huang, University of Texas at San Antonio

2:00 - 2:30pm Visualization for Integrative Genomic Applications, Kun Huang, The Ohio State University

2:30 - 3:00pm Privacy-Preserving Horizontal and vertical distributed data analysis, Xiaoqian Jiang, UC San Diego

3:00 - 3:30pm An Interactive Learning Framework for Scalable Classification of Pathology Images, Lee Cooper, Emory University

3:30 - 4:00pm A hidden Markov random field based Bayesian method for the detection of long-range chromosomal interactions in Hi-C Data, Ming Hu, NYU School of Medicine

4:00 - 5:00pm Keynote: Identifying cancer driver mutations and genes from cancer big data, Zhongming Zhao, Vanderbilt University School of Medicine

Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

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

Format:Full day


Room: 324


8:45-9:00am: Opening remarks

9:00-10:00am: Keynote: Multi-omics modeling for systems medicine, Dr. Shuzhao Li Emory University, School of Medicine

10:00-11:30am: Highlight Session I

Network-based isoform quantification with RNA-Seq data for cancer transcriptome analysis, Wei Zhang, Jae-Woong Chang, Lilong Lin, Kay Minn, Baolin Wu, Jeremy Chien, Jeongsik Yong, Hui Zheng and Rui Kuang.

Zodiac: A comprehensive depiction of genetic interactions in cancer by integrating TCGA data, Yitan Zhu and Yuan Ji.

On optimal Bayesian classification and risk estimation under multiple classes, Lori Dalton and Mohammadmahdi Rezaei Yousefi.

11:30-1:00pm: Lunch

1:00-2:00pm: Research Papers

Computing interaction probabilities in signaling networks, Haitham Gabr, Juan Carlos Rivera-Mulia, David Gilbert and Tamer Kahveci.

Inference of protein-protein interaction networks from multiple heterogeneous data, Lei Huang, Li Liao and Cathy H. Wu.

2:00-3:00pm: Highlight Session II

Learning scale-free networks by dynamic node-specific degree prior, Qingming Tang, Siqi Sun and Jinbo Xu.

Analytic representation of Bayes labeling and Bayes clustering operators for random labeled point processes, Lori Dalton, Marco E. Benalcázar, Marcel Brun and Edward Dougherty.

3:00-3:15pm: Break

3:15-3:45pm: Five-Minute Lightning Talks for Posters

An experimental design to reduce dynamics uncertainty in genomic networks, Daniel N. Mohsenizadeh, Roozbeh Dehghannasiri and Edward R. Dougherty.

Identifying molecular complexes in biological networks through context sensitive network querying, Hyundoo Jeong and Byung-Jun Yoon.

Optimal Bayesian feature filtering, Ali Foroughi Pour and Lori Dalton.

A computational framework for finding functional modules across multiple biological networks, Yijie Wang and Xiaoning Qian.

Computational identification of key functional genes associated with Fusarium verticillioides pathogenicity, Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim and Byung-Jun Yoon.

A computationally efficient solution strategy for optimal gene knockouts for targeted overproduction, Meltem Apaydin, Bo Zeng, Shaogang Ren and Xiaoning Qian.

3:45-4:30pm Poster Session

4:30-4:45pm Closing Remarks

4:45-5:00pm Break

5:00-6:00pm Tutorial: Functional Module Identification in Biological Networks, Xiaoning Qian, Texas A&M University

Workshop on: Big Data in Life Sciences (BigLS)

Organizers:Ananth Kalyanaraman and Jaroslaw Zola

Format:Full day




8:25-8:30am: Opening remarks, Ananth Kalyanaraman and Jaroslaw Zola

8:30-9:15am: Building Scalable Health Analytic Platform: Computational Phenotyping and Cloud-based Predictive Modeling, Jimeng Sun, Georgia Tech

9:15-10:00am: Big Data Phylogenetics, Suzanne J. Matthews, US Military Academy

10:00-10:30am: Break

10:30-12:00pm: Keynote: Machine Learning Framework for Classification in Medicine and Biology, Eva K. Lee, Director of the Center for Operations Research in Medicine and HealthCare

12:00-1:30pm: Lunch

1:30-2:15pm: GHOST of Viral Molecular Surveillance, Yury Khudyakov, Chief of Molecular Epidemiology and Bioinformatics Lab, Center for Disease Control and Prevention

2:15-2:45pm: Scalable Multipartite Subgraph Enumeration for Integrative Analysis of Heterogeneous Experimental Functional Genomics Data, C. Phillips, K. Wang, J. Bubier, E. Baker, E. Chesler, M. Langston, University of Tennessee, Jackson Laboratories

2:45-3:15pm: A Multi-Agent System with Reinforcement Learning Agents for Biomedical Text Mining, M. Camara, O. Bonham-Carter, J. Jumadinova, University of Nebraska at Omaha, Allegheny College

3:15-4:00pm: Student poster presentations

4:00pm-5:00pm: Student Mentoring

Workshop on Computational Health Science

Organizers:Sherry Emery and Christophe Giraud-Carrier

Format:Full day


Room: 328


8:30am: Welcome

8:45am: Invited Talk: Using User Generated Content to Learn about Health, Shawndra Hill

Paper session

9:30-10:00am: A Method for Analyzing Health Behavior in Online Forums, Rose Yesha and Aryya Gangopadhyay

10:00-10:30am: How TV Advertising and Social Network Help Tobacco Control Campaigns Influence More, Qianyi Zhan, Sherry Emery and Philip S. Yu

10:30-11:00am: A demographic and sentiment analysis of e-cigarette messages on Twitter, Elaine Cristina Resende and Aron Culotta

10:30-11:00am: Break

11:00-11:45am: Invited Talk: Understanding Sociotechnical Behaviors in Social Media: The Good, Bad, and Ugly, Nitin Agarwal

11:45-12:45pm: Panel Discussion: Donald Adjeroh, Sudha Ram, Shawndra Hill

12:45-13:00pm: Wrap-up

13:00pm Lunch

Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio)

Organizers:Mario Cannataro and John A. Springer

Format:Full day


Room: 330


9:00-9:30am: A Fast and Accurate Parallel Algorithm for Genome Mapping Assembly Aimed at Massively Parallel Sequencers, Wilfredo Lugo and Jaime Seguel.

9:30-10:00am: An Alignment-free Approach to Cluster Proteins Using Frequency of Conserved k-mers, Armen Abnoussi, Shira L. Broschat, Ananth Kalyanaraman

10:00-10:30am: Towards the Assessment of GRN Algorithms based on (Disease) Ontology, Pietro Hiram Guzzi, Marianna Milano and Swarup Roy.

10:30-10:45am: Concluding remarks

10:45-11:30am: Break

11:30-12:00pm: Toward an Analytical Framework for Proteomics Software, Urmi Bhayani and John Springer.

12:00-12:30pm: Efficient Learning of Association Rules from Human Phenotype Ontology, Giuseppe Agapito, Mario Cannataro, Pietro Hiram Guzzi and Marianna Milano.

12:30-1:00pm: Voice signal features analysis and classification: looking for new diseases related parameters, Giuseppe F Tradigo, Barbara Calabrese, Manuela Macri, Nicola Lombardo and Pierangelo Veltri.

1:00-1:15pm: Concluding remarks

Workshop on Parallel Software Libraries for Sequence Analysis (pSALSA)

Organizers: Srinivas Aluru and Yongchao Liu

Format:Full day


Room: 233


8:15-8:30: Opening Remarks
Special guest: Sylvia Spengler, National Science Foundation

8:30–9:30: Keynote: Grand challenges in plant sciences: roles for NGS bioinformatics, Patrick Schnable, Iowa State University


10:00–12:00: Section A

10:00–10:30: The Genome Assembly & Analysis Tool Box (GATB), a low-memory and efficient data structure for de Bruijn Graph applications, Guillaume Rizk, Institute for Research in IT and Random Systems (IRISA), France

10:30–11:00: Skyport - a multi-cloud scientific workflow system with Linux container orchestration to efficiently execute complex data-parallel bioinformatics pipelines, Wolfgang Gerlach, Argonne National Laboratory

11:00–11:30: Similarity detection in large sequence collections, Jaroslaw Zola, University at Buffalo

11:30–12: 00: Spaler: Spark and GraphX based de novo genome assembler, Umit Catalyurek, Ohio State University

12:00–13:30: Lunch

13:30–15:30: Section B

13:30–14:00: Scalable parallel algorithms for de novo assembly of complex genomes, Evangelos Georganas, University of California, Berkeley

14:00–14:30: Functional phylogenomics analysis of microbial genomics and metagenomics using high-performance computing, Chongle Pan, Oak Ridge National Laboratories

14:30–15:00: Exploring tens of thousands of RNA-seq samples with Rail-RNA, Ben Langmead, Johns Hopkins University

15:00–15:30: Parallel software libraries for high-throughput sequencing, Srinivas Aluru, Tony Pan and Patrick Flick, Georgia Institute of Technology

15:30–16:00: Break

16:00–17:30: Open Discussion