ACM-BCB 2016 The 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics October 2-5, 2016 Organizing Committee General Chairs: Steering Committee: Ümit V. Çatalyürek, Georgia Institute of Technology Aidong Zhang, State University of NeW York at Buffalo, Genevieve Melton-Meaux, University of Minnesota Co-Chair May D. Wang, Georgia Institute of Technology and Program Chairs: Emory University, Co-Chair John Kececioglu, University of Arizona Srinivas Aluru, Georgia Institute of Technology Adam Wilcox, University of Washington Tamer Kahveci, University of Florida Christopher C. Yang, Drexel University Workshop Chair: Ananth Kalyanaraman, Washington State University Tutorial Chair: Mehmet Koyuturk, Case Western Reserve University Demo and Exhibit Chair: Robert (Bob) Cottingham, Oak Ridge National Laboratory Poster Chairs: Lin Yang, University of Florida Dongxiao Zhu, Wayne State University Registration Chair: Preetam Ghosh, Virginia CommonWealth University Publicity Chairs Daniel Capurro, Pontificia Univ. Católica de Chile A. Ercument Cicek, Bilkent University Pierangelo Veltri, U. Magna Graecia of Catanzaro Student Travel Award Chairs May D. Wang, Georgia Institute of Technology and Emory University JaroslaW Zola, University at Buffalo, The State University of NeW York Student Activity Chair Marzieh Ayati, Case Western Reserve University Dan DeBlasio, Carnegie Mellon University Proceedings Chairs: Xinghua Mindy Shi, U of North Carolina at Charlotte Yang Shen, Texas A&M University Web Admins: Anas Abu-Doleh, The Ohio State University Hyun Anderson, The Ohio State University Jonathan Kho, Georgia Institute of Technology 2 ACM-BCB 2016 Program REGISTRATION Sunday 7:30 – 16:00 / Monday-Tuesday 8:00 – 16:00 / Wednesday 8:00 – 11:00 Sunday, October 2, 2016 Continental Breakfast 8 am Location: Fourth Floor Breakstation Seattle 1 Seattle 2 Seattle 3 Belltown Pioneer First Hill Emerald II 8:25 am Tutorial 1 (T1) 10 am BigLS MAHA ParBio Tutorial 2 pSALSA TDA-Bio CNB-MAC (8:25 am – (8:25 am – (10 am – (T2) (8:25 am – (8:50 am – (8:50 am – 12 pm) 11:40 am) 12 pm) 12 pm) 12:05 pm) 12 pm 12 pm) (1:30 pm – (1:30 pm – (1:30 pm – (1:30 pm – 1 pm (1:20 pm – 5 pm) 5 pm) Tutorial 3 5:30 pm) 5:15 pm) BrainKDD 6 pm) (1 pm – (T3) 4 pm 5 pm) Tutorial 4 (T4) Student NetWorking and Social Event at the Seattle Great Wheel 6 pm Meet at the pre-event space on the 4th floor WORKSHOPS * CNB-MAC 3rd International Workshop on Computational NetWork Biology: Modeling, Analysis, and Control Organizers: Byung-Jun Yoon, Xiaoning Qian and Tamer Kahveci BigLS 4th ACM International Workshop on Big Data in Life Sciences Organizers: JaroslaW Zola and Ananth Kalyanaraman MAHA 1st International Workshop on Methods and Applications in Healthcare Analytics Organizers: Fei Wang, Jyotishman Pathak and Nigam Shah pSALSA 3rd Workshop on Parallel SoftWare Libraries for Sequence Analysis Organizers: Srinivas Aluru TDA-Bio 1st International Workshop on Topological Data Analysis in Biomedicine Organizers: Bala Krishnamoorthy and Bei Wang Phillips ParBio 5th International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine Organizers: Mario Cannataro and John A. Springer BrainKDD The 3rd International Workshop on Data Mining and Visualization for Brain Science Organizers: ShuiWang Ji, Lei Shi, Hanghang Tong, Shuai Huang and Paul Thompson * See page 12 for detailed workshop programs. TUTORIALS * Sunday, October 2 8:30-9:30 T1: Combinatorial methods for nucleic acid sequence analysis Presenters: Sreeram Kannan and Mark Chaisson, University of Washington 10:00-12:00 T2: NetWork Science meets Tissue-specific Biology Presenters: Shahin Mohammadi and Ananth Grama, Purdue University 1:30-3:30pm T3: Big Data for Discovery Science Presenters: Ben Heavner (Institute for Systems Biology), Ravi Madduri (Argonne National Lab), Jack Van Horn (University of Southern California), and Naveen Ashish (Fred Hutchinson Cancer Research Center) 4:00-6:00pm T4: Deep Learning for Bioinformatics and Health Informatics Presenter: Sungroh Yoon, Seoul National University 3 Monday, October 3 (Seattle II) 11:00-12:00pm T5: Data-Driven Analysis of Untargeted Metabolomics Datasets Presenter: Soha Hassoun, Tufts University 1:30-3:30pm T6: Evolutionary Algorithms for Protein Structure Modeling Presenters: Emmanual Sapin, Amarda Shehu, and Kenneth De Jong, George Mason University Tuesday, October 4 (Seattle II) 10:00-12:00pm T7: The ISB Cancer Genomics Cloud Presenter: Sheila Reynolds, Institute for Systems Biology 1:30-3:30pm T8: Living the DREAM: CroWdsourcing biomedical research through challenges and ensembles Presenters: Gaurav Pandey, Lara Mangravite, Solveig Sieberts, Robert Vogel, and Gustavo Stolovitzky, Icahn School of Medicine at Mount Sinai, SAGE Bionetworks * See page 19 for more information on individual tutorials. Student Networking and Social Event All students and postdocs are invited to the student-netWorking event, which will be held Sunday at 6pm. This year the event will include an excursion to The Seattle Great Wheel (the largest observation Wheel on the West coast). The student activity is focused on developing programs for student growth through educational and netWorking opportunities. This is the second year of a recognized student activity and last year improved the student relationships during the conference. The event Will begin at 6:00PM on Sunday, October 2, 2016 With scientific speed netWorking in the pre-event space on the 4th floor before the short Walk to Elliot Bay. (The netWorking event is free but please bring cash for a discounted admission to the Great Wheel.) 4 Monday, October 3, 2016 8:00 – Continental Breakfast 10:00 Location: Fourth Floor Breakstation Opening Remarks (Location: Seattle I & II) 8:15 – General Chairs: Ümit V. Çatalyürek, Georgia Institute of Technology & 8:30 Genevieve Melton-Meaux, University of Minnesota Program Chairs: John Kececioglu, University of Arizona & Adam Wilcox, University of Washington Keynote Talk 1 (Location: Seattle I & II) 8:30 – Don’t forget the notes: Why NLP is key to health care transformation 9:30 Wendy W. Chapman, University of Utah Session Chair: Genevieve Melton-Meaux, University of Minnesota 9:30 – Morning Break 10:00 Session 1A Session 1B Session 1C Location: Seattle I Location: Seattle II Location: Seattle III Systems Biology Demo Presentations & Tutorials Automated Diagnosis and Session Chair: Anna Ritz, Session Chair: Robert W. Cottingham, Prediction Reed College Oak Ridge National Laboratory Session Chair: JaroslaW Zola, University at Buffalo 10:00 Demo Presentations 10:00 Tin Nguyen, Diana Diaz, Sorin 10:00 Shou-Hsuan Stephen Huang, Ming- Draghici. “TOMAS: A novel “Software tools for sequence Chih Shih, Youli Zu. “A Multi- TOpology-aware Meta-Analysis comparison, sequence mapping, and Objective Flow Cytometry Profiling approach applied to System biology” for B-Cell Lymphoma Diagnosis” patient-specific healthcare outcome 10:30 prediction”. Presenter: Ankit Agrawal, 10:30 Huey Eng Chua, Sourav S. BhoWmick, Northwestern University Ying Sha, Janani Venugopalan, May Jie Zheng, Lisa Tucker-Kellogg. D. Wang. “A Novel Temporal “TAPESTRY: Network-centric Target 10:20 Similarity Measure for Patients Prioritization in Disease-related “The CMH Variant Warehouse – A Based on Irregularly Measured Data Signaling Networks” Catalog of Genetic Variation in Patients in Electronic Health Records” of a Children’s Hospital". Presenter: 11:00 11:00 10:00 – Byunggil Yoo, Children’s Mercy Hospital 12:00 Aisharjya Sarkar, Yuanfang Ren, Aydin Saribudak, Adarsha A. Subick, Rasha Elhesha, Tamer Kahveci. 10:40 Joshua A. Rutta, M. Ümit Uyar, “The “Counting independent motifs in “KBase: Developing collaborative Alzheimer's Disease Neuroimaging probabilistic networks” analyses of biological function using Initiative. Gene Expression Based Computation Methods for 11:30 Narratives and App Catalog”. Presenter: Alzheimer's Disease Progression Robert W. Cottingham, Oak Ridge Paola Pesantez-Cabrera, Ananth using Hippocampal Volume Loss Kalyanaraman. “Detecting National Laboratory and MMSE Scores” Communities in Biological Bipartite Tutorial Networks” 11:30 11:00 Qiuling Suo, Hongfei Xue, Jing Gao, T5: Data-Driven Analysis of Untargeted Aidong Zhang. “Risk factor analysis Metabolomics Datasets based on deep learning models” Presenter: Soha Hassoun, Tufts University 12:30 – Lunch 13:30 (On your own) 5 Session 2A Session 2B Session 2C Location: Seattle I Location: Seattle II Location: Seattle III Biological Modeling Tutorials Applications to Healthcare Processes Session Chair: Tamer Kahveci, Session Chair: Beth Britt, University of Florida University of Washington 13:30 13:30 Hanyu Jiang, Morisa Manzella, Luka Shital Kumar Mishra, Sourav S. BhoWmick, Djapic, Narayan Ganesan. Huey Eng Chua, Jie Zheng. Predictive “Computational Framework for in-Silico “Modeling of Drug Effects on Signaling Study of Virtual Cell Biology via Process Pathways in Diverse Cancer Cell Lines” Simulation and Multiscale Modeling” 14:00 14:00 Qian Cheng, Jingbo Shang, Joshua Juen, Muhibur Rasheed, Nathan Clement, JiaWei Han, Bruce Schatz. “Mining Abhishek Bhowmick, Chandrajit Bajaj. T6: Evolutionary Algorithms for Discriminative Patterns to Predict Health “Statistical Framework for Uncertainty Protein Structure Modeling Status for Cardiopulmonary Patients” Quantification in Computational Presenters: Emmanual Sapin, 13:30 – Molecular Modeling” 14:30 Amarda Shehu, and Kenneth De 15:30 Paul D. Martin, Michael Rushanan, 14:30 Jong, George Mason University