2015 IEEE International Conference on Bioinformatics and Biomedicine

Nov 9-12, 2015, Washington D.C. , USA

1

Sponsored by

2

IEEE BIBM 2015

IEEE BIBM 2015 Program Schedule ...... 4

Floor Plan ...... 9

Keynote Lectures ...... 10

Invited Talks ...... 12

Federal Agencies and Industry Panel ...... 15

Workshops ...... 16

Tutorials ...... 26

Conference Paper Presentations ...... 27

Poster List ...... 38

Conference WiFi Instruction ...... 40

IEEE BIBM 2016 Call For Papers ...... 41

3

IEEE BIBM 2015 Program Schedule

Program • November 09, 2015 • November 10, 2015 • November 11, 2015 • November 12, 2015

Keynote Lecture: 60 minutes((about 45 minutes for talk and 15 minutes for Q and A)

Invited Talk: 40 minutes (about 30 minutes for talk and 10 minutes for Q and A)

Tutorial: 115 minutes (about 100 minutes for talk and 15 minutes for Q and A)

Main Conference Regular Paper: 20 minutes (about 15 minutes for talk and 5 minutes for Q and A) Main Conference Short Paper: 15 minutes (about 12 minutes for talk and 3 minutes for Q and A)

Sunday, November 8 4:00– 8:00 pm Registration Ballroom Foyer

4

Monday, Nov 9 (Workshops and Tutorials)

7:20am – 6:30pm Registration Ballroom Foyer 10:30-10:50am and Coffee Break 3:30-3:50pm Meeting Room Foyer

12:00-1:30pm Lunch (On Own) Poster Session (Set Up) 1:30-6:00pm Meeting Room and Concours Terrace

8:00-12:00pm Workshops/Tutorials Session Chair Location Workshop: High Performance Bioinformatics and Biomedicine (HiBB) Mario Cannataro Waterford Workshop:2015 Workshop on Health Informatics and Data Science (HI-DS) Xiong Liu, Rong Liu Cabinet Suite Jing He, Amarda Shehu, Nurit Workshop: The 2015 Computational Structural Bioinformatics Workshop Judiciary Suite Haspel, Brian Chen Workshop: 2015 International Workshop on Biomedical and Health Illhoi Yoo Embassy/Patuxent Informatics Catherine Putonti, Charlie Xia Workshop: COMputational Methods for Analyzing Metagenomics Data Diplomat/Ambassador and Erliang Zeng Rui Jiang, Huiru Jane Zheng, Workshop: The 6th Integrative Data Analysis in Systems Biology (IDASB Zhongming Zhao Cartier/Tiffany 2015).

Joint Workshop Schedule Data mining in translational biomedical informatics & Qian Zhu, Hongfang Liu, Frank Susquehanna Second International Workshop on the Role for Quantified Self for Personal Hopfgartner, Na Li Healthcare Workshop: Data mining from genomic variants and its application to Taesung Park Baccarat genome-wide analysis Tutorial: Integrative Genomic Big-Data Analytics for Translational Mary Yang and Kenji Haverford Bioinformatics and Precision Medicine Research (10am-12noon) Yoshigoe 1:30-6:00pm Workshops/Tutorials Session Chair Location Workshop: Inaugural International Workshop on Biological Network Driven Fione Brown Waterford Analysis Workshop:2015 Workshop on Health Informatics and Data Science (HI-DS) Xiong Liu, Rong Liu Cabinet Suite Jing He, Amarda Shehu, Nurit Workshop: The 2015 Computational Structural Bioinformatics Workshop Judiciary Suite Haspel, Brian Chen Workshop: 2015 International Workshop on Biomedical and Health Illhoi Yoo Embassy/Patuxent Informatics Tutorial: Introduction to computational analysis of microbiome shotgun Daniel H. Huson Haverford sequencing data (1:30-3:30pm) Tutorial: Human Microbiome Analysis: Computational Techniques and Serghei Mangul Haverford Challenges (4:00-6:00pm) Workshop: Semantic Data Analytics and Bioinformatics Haiying Wang Lalique Michael Ochs, Elana Fertig, Joint Workshop Schedule Alieoune Ngom, Hongyu Nonnegative Matrix Factorization and Tensor Decomposition Techniques for Zhang, Guoliang Li, Anyuan Baccarat High-Throughput Biological Data Analysis & Guo, Hongyu Ou and Xingpeng Computational Regulatory Genomics and Metagenomics Jiang Young-Rae Cho Workshop: International Workshop on Biomolecular Interaction Network Diplomat/Ambassador Analysis and Interactomics

Rui Jiang, Huiru Jane Zheng, Workshop: The 6th Integrative Data Analysis in Systems Biology (IDASB Zhongming Zhao Cartier/Tiffany 2015).

Manuel Grana, Michel Workshop: Electronic Health Record: Implementation, Data Mining, Wozkniak, Konrad Jakowski Susquehanna Security and User Acceptance

Richard Conroy, Vinay Pai, Workshop: Biomedical Visual Search and Deep Learning Todd Horowitz, Susan Potomac Gregurick, Tom Radman Workshop: The 6h International Workshop on High Performance Computing Che-Lun Hung et al. Severn in Bioinformatics

5

Tuesday, November 10 8:00am-6:00pm Registration Ballroom Foyer

8:45-9:00am Welcome and Opening Session Chairs: Luke Huan, Satoru Miyano, Amarda Shehu, Sanguthevar Rajasekaran, Xiaohua Tony Hu Crystal Ballroom Keynote Lecture 1 (Chair: Satoru Miyano) 9:00-10:00am “Big Data in Biomedicine – an NIH Perspective” Philip Bourne Crystal Ballroom 10:00-10:20am Coffee Break Meeting Room Foyer 10:20-12:30pm Sessions Session Chair Location Session1: Genomics Browne, Fiona Cabinet Suite Session2: Biological Networks I Huang,Yufei Diplomat/Ambassador

Session3: Medical Informatics I Boucher,Christina Judiciary Suite Session4: Semantics and Ontology I Zeng, Erlinagn Embassy/Patuxent

10:20-7pm Poster Session Setup and Display Meeting Room and Concours Terrace 12:30-2:00pm Lunch provided by conference Embassy/Patuxent 2:00-3:40pm Sessions Session Chair Location Session5: Biological Networks II Przytycka, Teresa Cabinet Suite (including Session6: Translational Bioinformatics I Yang, Mary Diplomat/Ambassador Invited talks) Session7: Medical Informatics II Zheng, Huiru Judiciary Suite Session8: Structure, Function and Evolution I Shyu, Chi-Ren Embassy/Patuxent

3:40-4:00pm Coffee Break Meeting Room Foyer 4:00-6:40pm Sessions Session Chair Location Session 9: Epigenetics and Gene Regulation Ananda Modal Cabinet Suite Session 10: Healthcare Informatics I Cho, Young-Rae Diplomat/Ambassador

Session 11: Cross-cutting Computational Methods I Haspel, Nurit Judiciary Suite Session 12: Structure, Function and Evolution II He, Jing Embassy/Patuxent Banquet (Ticket required) 1. Introduction of BIBM 2016 Host City (Chairs: Xiaohua Tony Hu, Jianguo Lu) 7:00-9:00pm 2. Best Paper Award (Chairs: Luke Huan, Satoru Miyano, Amarda Shehu) 3. Best Student Paper Award (Chairs: Luke Huan, Satoru Miyano, Amarda Shehu) 4. Best Paper Runner-Up (Chairs: Luke Huan, Satoru Miyano, Amarda Shehu) Crystal Ballroom

6

Wednesday, Nov 11 8:00am-6:00pm Registration Ballroom Foyer Keynote Lecture 2 (Chair: Sanguthevar Rajasekaran) 9:00-10:00am Parallel Machine Learning Approaches for Reverse Engineering Genome-Scale Networks Srinivas Alurur Crystal Ballroom

10:00-10:20am Coffee Break Meeting Room Foyer 10:20am - 12:30pm Sessions Session Chair Location Session 13: Cross-cutting Computational Methods II Moll, Mark Cabinet Suite Session 14: Healthcare Informatics II Shehu, Amarda Diplomat/Ambassador

Session15: Semantics and Ontology II Huang, Jingshan Judiciary Suite Session16: Medical Imaging Miyano, Satoru Embassy/Patuxent

12:30-2:00pm Lunch provided by conference Crystal Ballroom Keynote Lecture 3 (Chair: Luke Huan) Toward Personalized Pan-Omic Association Analysis under Complex Structure s and Big Data Eric Xing 1:00-2:00pm Crystal Ballroom Poster Session Meeting Room Foyer and Concours Terrace Panel 2:00-3:40pm Federal Agencies and Industry Crystal Ballroom 3:40-4:00pm Coffee Break Meeting Room Foyer 4:00-6:20pm Sessions Session Chair Location Session 17: Biological Networks III Huo,Hongwei Cabinet Suite Session 18: Sequence, Structure, and Function III Chen, Brian Diplomat/Ambassador

Session 19: Medical Informatics III Bastola, Dhundy Judiciary Suite Session 20: Translational Bioinformatics I Ghersi, Dario Embassy/Patuxent

7

Thursday, Nov 12 8:00-10:00am Registration Ballroom Foyer Keynote Lecture 4 (Chair: Amarda Shehu) 9:00-10:00am Computational Challenges in Microbiome Research Mihai Pop Crystal Ballroom 10:00-10:20am Coffee break Meeting Room Foyer 10:00 - 10:20 am Poster Display Chesapeake Foyer 10:20am-12:30pm Sessions Session Chair Location Session 21: Computational Systems Biology Ricardo de Matos Simoes Cabinet Suite Session 22: Bioinformatics Infrastructure Ryan Benton Judiciary Suite Session 23: Industry and Government Session Matthieu Schapranow Diplomat/Ambassador Workshop: High Performance Computing for Big Data Computational Fahad Saeed Old Georgetown Biology Workshop: Machine learning in decision making for biomedical Mahua Bhattacharya Embassy/Patuxent applications

8

Floor Plan

9

Keynote Lectures

Keynote 1: Big Data in Biomedicine -- An NIH Perspective

Speaker: Philip E. Bourne PhD, Associate Director for Data Science (ADDS) at the National Institutes of Health

Abstract: Biomedical research is becoming increasingly data driven, analytical and hence digital. In recognition of this evolution NIH has established the Office for Data Science with trans NIH responsibility for maximizing the value of this digital enterprise. This effort brings together communities, policy changes and new infrastructure to be applied to existing and new areas of research such as precision medicine. We will review these changes from the perspective of research advances that are underway and highlight how this community can further engage in these activities.

Short Bio: Philip E. Bourne PhD is the Associate Director for Data Science (ADDS) at the National Institutes of Health. Formally he was Associate Vice Chancellor for Innovation and Industry Alliances, a Professor in the Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego, Associate Director of the RCSB Protein Data Bank and an Adjunct Professor at the Sanford Burnham Institute.

Bourne's professional interests focus on service and research. He serves the national biomedical community through contributing ways to maximize the value (and hence accessibility) of scientific data. His research focuses on relevant biological and educational outcomes derived from computation and scholarly communication. This implies algorithms, text mining, machine learning, metalanguages, biological databases, and visualization applied to problems in systems pharmacology, evolution, cell signaling, apoptosis, immunology and scientific dissemination. He has published over 300 papers and 5 books, one of which sold over 150,000 copies.

Bourne is committed to maximizing the societal benefit derived from university research. Previosuly he co-founded 4 companies: ViSoft Inc., Protein Vision Inc., a company distributing independent films for free and most recently SciVee.

Bourne is committed to furthering the free dissemination of science through new models of publishing and better integration and subsequent dissemination of data and results which as far as possible should be freely available to all. He is the co-founder and founding Editor-in-Chief of the open access journal PLOS Computational Biology.

Bourne is committed to professional development through the Ten Simple Rules series of articles and a variety of lectures and video presentations.

Bourne is a Past President of the International Society for Computational Biology, an elected fellow of the American Association for the Advancement of Science (AAAS), the International Society for Computational Biology (ISCB) and the American Medical Informatics Association (AMIA).

Awards include: the Jim Gray eScience Award (2010), the Benjamin Franklin Award (2009), the Flinders University Convocation Medal for Outstanding Achievement (2004), the Sun Microsystems Convergence Award (2002) and the CONNECT Award for new inventions (1996 & 97).

Keynote 2: Parallel Machine Learning Approaches for Reverse Engineering Genome-Scale Network

Speaker: Prof. Srinivas Aluru, School of Computational Science and Engineering, Georgia Institute of Technology

Abstract: Reverse engineering whole-genome networks from large-scale gene expression measurements and analyzing them to extract biologically valid hypotheses are important challenges in systems biology. While simpler models easily scale to large number of genes and gene expression datasets, more accurate models are compute intensive limiting their scale of applicability. In this talk, I will present our research on the development of parallel mutual information and Bayesian network based structure learning methods to eliminate such bottlenecks and facilitate genome-scale network inference. As a demonstration, we reconstructed genome-scale networks of the model plant Arabidopsis thaliana from 11,700 microarray experiments using 1.57 million cores of the Tianhe-2 Supercomputer. Such networks can be used as a guide to predicting gene function and extracting context-specific subnetworks.

Short Bio: Srinivas Aluru is a professor in the School of Computational Science and Engineering at Georgia Institute of Technology. He co-directs the Georgia Tech Strategic Initiative in Data Engineering and Science, and co-leads the NSF South Big Data Regional Innovation Hub. Earlier, he held faculty positions at Iowa State University, Indian Institute of Technology, New Mexico State University, and Syracuse University. Aluru conducts research in high performance computing, bioinformatics and systems biology, combinatorial scientific computing, and applied algorithms. He pioneered the development of parallel methods in computational biology, and contributed to the assembly and analysis of complex plant genomes. 10

Aluru serves on the editorial boards of the IEEE Transactions on Big Data, IEEE Transactions on Parallel and Distributed Systems, Journal of Parallel and Distributed Computing, and the International Journal of Data Mining and Bioinformatics. He is currently serving as the Chair of the ACM Special Interest Group on Bioinformatics, Computational Biology and Biomedical Informatics (SIGBIO). Aluru is a recipient of the NSF Career award, IBM faculty award, Swarnajayanti Fellowship from the Government of India, the mid-career and outstanding research achievement awards from Iowa State University, and the College of Computing Dean’s award for faculty excellence at Georgia Tech. He is a Fellow of the American Association for the Advancement of Science (AAAS) and the Institute of Electrical and Electronics Engineers (IEEE).

Keynote 3: Toward Personalized Pan-Omic Association Analysis under Complex Structure s and Big Data

Speaker: Prof. Eric Xing, School of Computer Science at Carnegie Mellon University

Abstract: A fundamental aim of modern medical genetics is to connect variations in clinical phenotypes with variations in the genome so that one can identify druggable genetic artifacts, predict clinical outcomes, and practice personalized medicine. The existing approaches for genetic analysis of complex human diseases remain inadequate in meeting many of the challenges toward this aim, such as, incorporating complex structural information to improve power; scaling up to ultra-high dimensionality to capture higher-order effects; adjusting the statistical model to allow personalizable inference; and furthermore, providing software and cloud API for easy computing. In this talk, I will discuss our recent efforts in developing mathematically rigorous, computationally tractable, and user-friendly tools for medical genetic inference and clinical prediction in presence of multiple confounders, rich prior knowledge, and needs for capturing both shared patterns and individual signatures in complex genetic effects. Our preliminary results promises to offer a practical basis for personalized medicine in the Big Data era of genomic healthcare.

Short Bio: Dr. Eric Xing is a Professor of Machine Learning in the School of Computer Science at Carnegie Mellon University, and Director of the CMU/UPMC Center for Machine Learning and Health. His principal research interests lie in the development of machine learning and statistical methodology, and large-scale computational system and architecture; especially for solving problems involving automated learning, reasoning, and decision-making in high-dimensional, multimodal, and dynamic possible worlds in artificial, biological, and social systems. Professor Xing received a Ph.D. in Molecular Biology from Rutgers University, and another Ph.D. in Computer Science from UC Berkeley. He servers (or served) as an associate editor of the Annals of Applied Statistics (AOAS), the Journal of American Statistical Association (JASA), the IEEE Transaction of Pattern Analysis and Machine Intelligence (PAMI), the PLoS Journal of Computational Biology, and an Action Editor of the Machine Learning Journal (MLJ), the Journal of Machine Learning Research (JMLR). He was a member of the DARPA Information Science and Technology (ISAT) Advisory Group, a recipient of the NSF Career Award, the Sloan Fellowship, the United States Air Force Young Investigator Award, and the IBM Open Collaborative Research Award. He was the Program Chair of ICML 2014.

Keynote 4: Computational challenges in microbiome research

Speaker: Prof. Mihai Pop, Department of Computer Science/ Center for Bioinformatics and Computational Biology, University of Maryland

Abstract: Millions of bacteria make our bodies their home. They help keep us healthy, and disruptions in the normal microbiota are believed to contribute to a number of diseases. Cost-effective sequencing technologies have made it possible to sequence the genomes of human-associated microbial communities, leading to the birth of a new scientific discipline - metagenomics. Analyzing the resulting data, however, poses significant computational challenges, in part due to the sheer size of the data-sets, and in part due to the fact that most of the existing computational framework has been established for single organisms. In my talk I will outline several analytical challenges posed by metagenomic applications, and will describe recent results from my lab in the development of tools for analyzing metagenomic data. In particular I will discuss insights from our analysis of diarrheal disease in developing countries, as well as the effective use of co-abundance approaches for linking together data from two large metagenomic studies.

Short Bio: Dr. Pop is an associate professor in the Department of Computer Science and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park (UMCP). Dr. Pop received his Ph.D. in Computer Science at Johns Hopkins University where he focused on algorithms for computer graphics and Geographic Information Systems (GIS) applications. He then joined The Institute for Genomic Research (TIGR) as a Bioinformatics Scientist, where he was responsible for the development of genome assembly algorithms. During this time, Dr. Pop participated in a number of bacterial and eukaryotic genome projects including important human pathogens such as Bacillus anthracis and Entamoeba hystolitica. Since joining the University of Maryland, Dr. Pop has continued to develop novel approaches for genome assembly and analysis, and has developed extensive expertise in the analysis of metagenomic data. His lab has developed a number of widely used open-source software tools, such as the assembly suite AMOS, the NGS aligner Bowtie, the taxonomic classifier Metaphyler, and the metagenomic assembly package MetAMOS. 11

Most recently he co-led the data analysis working group for the Human Microbiome Project and led the sub-group responsible for the assembly of the data generated in this project.

Invited Talks

Invited Talk 1: Understanding Genotype-Phenotype effects in Cancer via Network Approaches

Speaker: Dr. Teresa Przytycka, NCBI/NLM/NIH

Abstract: Uncovering and interpreting phenotype--genotype relationships are among the most challenging open questions in disease studies. In cancer, these relationships are additionally obscured by heterogeneity of the disease. Pathway-centric approaches have emerged as methods that can empower studies of heterogeneous diseases. Over the years, using such network based approaches we have designed methods that allow detection of subnetworks dysregulated in cancer, and to establish associations gene expression and genotype. Our approaches build on variety of algorithmic techniques including graph-theoretical techniques (module cover) and on machine learning topic model approach (probabilistic genotype-phenotype model) and information flow. I will demonstrate the utility of our methods using TCGA (The Cancer Genome Atlas) data.

Short Bio: Teresa Przytycka is a Senior Investigator in the Computational Biology Branch at National Center of Biotechnology Information, NIH and heads the Computational Methods in Molecular and Systems Biology section. Dr. Przytycka received her PhD in Computer Science Department at University of British Columbia Vancouver where she focused on theory of algorithms. She did her postdoctoral work in Department of Biophysics, Johns Hopkins University studying protein folding. She was a recipient of I.W. Killam Memorial Fellowship, Sloan Foundation and the U.S. Department of Energy Fellowship in Computational Biology, and Burroughs Wellcome Fellowship in Computational Biology. Dr. Przytycka serves as a Deputy Editor of the Bioinformatics Section of Nature Molecular Therapy Nuclide Acids and as an Associate Editor for PloS Computational Biology, BMC Bioinformatics, IEEE Transactions on Computational Biology and Bioinformatics, and Algorithms for Molecular Biology. Research in her group focuses on dynamical properties of biological systems including spatial, temporal and contextual variations and exploring how such variations are impacting gene expression, functioning of biological pathways, and the phenotype of organisms. Her group developed several new approaches to study pathways dysregulated in cancer, gene regulation, and analysis of massive HT-SELEX data.

Invited Talk 2: Developing systems genomics approaches to facilitate precision medicine research

Speaker: Dr. Mary Yang, University of Arkansas Little Rock George Washington Donaghey College of Engineering & Information Technology

Abstract: Technology developments have rapidly produced data that facilitates the emerging precision medicine research. In particular, high-throughput next- generation sequencing (NGS) technologies have brought unprecedented opportunities in translational genomics research. However, connection of the genomic and phenotypic information to cellular functions and disease mechanisms relies on the development of effective approaches at higher systems level. My Systems Genomics Laboratory and the MidSouth Bioinformatics Center aim to integrate different genomic data to study the mechanisms underlying initiation and progression of complex diseases such as cancer. In this talk, I will present our study of integrating gene expression profiles with protein interactions to identify cancer biomarkers and disease associated pathways. By further combing with genotype information, we discovered genetic mutations associated with poor survival rate in patients with ovarian cancer. Our integrative genomics research also incorporates the study of long non-coding RNAs (lncRNAs). We identified differentially expressed lncRNAs in cancer and revealed that many over-regulated lncRNAs were bidirectionally oriented with neighboring protein-coding genes. These protein-coding genes are enriched in biological processes implicated in cancer. The systems genomics approaches enable us to establish a computational framework to comprehensively identify biomarkers and dysregulated pathways, which will facilitate the precision medicine research

Short Bio: Dr. Mary Yang is the Director of MidSouth Bioinformatics Center and Director of the Joint Bioinformatics Ph.D. Program of University of Arkansas Little Rock George Washington Donaghey College of Engineering & Information Technology and University of Arkansas for Medical Sciences. After receiving her M.S.E.C.E, M.S., and Ph.D. degrees from Purdue University, she joined the National Human Genome Research Institute at the National Institutes of Health (NIH) in 2005 where she contributed to various large-scale projects in genomics and bioinformatics. During her tenure at NIH, she contributed to various large-scale genomics and systems biology research projects. She was recruited by the University of Arkansas in 2013 to lead the joint bioinformatics program. Dr. Yang has been Founding Editor-in-Chief of International Journal of Computational Biology and Drug Design, a NIH PubMed fully indexed journal and is on editorial broads of Journal of Supercomputing and International Journal of Pattern Recognition and Artificial Intelligence. She served as a Steering Committee Member of NIH funded Arkansas INBRE. She has been the recipient of NIH Fellows Award for Research Excellence, NIH Academic Research Enhancement Award, Bilsland Dissertation Fellowship, Purdue Research Foundation Fellowship, IEEE and ISIBM Bioinformatics and Bioengineering Outstanding Achievement Awards, and Basic Science Research Award of Arkansas Science and Technology Authority (ASTA). Dr. Yang’s research is supported by NIH, FDA and ASTA. She has published over 100 12

research articles in computer science and biomedical sciences.

Invited Talk 3: Empowering self-management for chronic conditions through technology and analytics: Can machines care for us?

Speaker: Huiru (Jane) Zheng, School of Computing and Mathematics, Ulster University, UK.

Abstract: Population aging is widespread across the world. The impact of an ageing population affects all countries. As people age, they are progressively more likely to live with complex co-morbidities, disability and frailty. People with long-term conditions are the most frequent users of health care services. Technologies are changing out everyday lives and transforming healthcare. In this talk I will overview state-of-the-art technologies in telecare, and present our research work on supporting chronic care through technology and analytics. In particular, it will focus on personalized care and self- management. The challenges and opportunities of healthcare informatics will be discussed.

Short Bio: Dr. Huiru (Jane) Zheng is a Reader in Computer Science with the School of Computing and Mathematics, Ulster University, UK. Dr. Zheng is an active researcher in healthcare informatics (including bioinformatics and medical informatics). Her research interests include machine learning, data mining and their applications to healthcare informatics. She is particularly interested in the following research areas: data integration, predictive data analysis, complex network analysis (PPI networks and drug target associations); and assistive technology to personalized healthcare. She has been a grant holder of research projects funded by EPSRC, TSB, DEL, NHS, Invest NI and European Commission including SMART Self Management, NOCTURNAL, CLARCH COPD Self Management, Self Management Platform for Connected Health, CardioWorkbench, mHealth4Africa, SenseCare and MetaPlat. She has 170+ publications in these areas.

Invited Talk 4: Protein Match Making at Massive Scale

Speaker: Dr. Chi-Ren Shyu, Department of Electrical and Computer Engineering, University of Missouri

Abstract: To investigate structure–function relationships, life sciences researchers typically utilize structure characteristics to study structurally similar proteins. One application is classifying proteins with similar substructures into the same fold, such as SCOP, a manually constructed database which is considered highly accurate; however, it is labor intensive. Another application is finding geometrically similar protein binding sites for understanding protein functions and providing valuable information for protein–protein docking and drug discovery. As of October 2015, there are 112,968 structures in the Protein Data Bank, with this number of structures growing at a rapid rate. A similar trend is also observed as the number of known protein–protein interaction structures has dramatically increased. The scale of the publicly available structure data makes the human curation process in comprehensive and in-depth studies challenging. It is essential to develop high-throughput and accurate protein structure analytics methods for structure match and binding site comparison. In this talk, I will discuss a series of system developments, including ProteinDBS, index- based protein substructure alignment (IPSA), PPSalign, PBSWords, and PBSalign with a suite of “non-traditional” computational methods in feature extraction, database indexing, information retrieval, GPU computing, and in-memory computing for massive structure match making in real-time or pseudo real-time efficiency.

Short Bio: Dr. Chi-Ren Shyu received his Ph.D. from the School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA. He is the director of the University of Missouri Informatics Institute and the chairman of the Electrical and Computer Engineering Department. Dr. Shyu holds the Paul K. and Dianne Shumaker Endowed Professorship of Biomedical Informatics. Since joining the University of Missouri in 2000, he has received several awards including the National Science Foundation CAREER award, Engineering Faculty Research Award, Engineering Teaching Excellence Award, the 2014 University of Missouri Faculty Entrepreneurial Award, and seven computer science teaching awards. He organized the IEEE HealthCom 2011 conference as general chair and is co-chairing the technical program committee of the Second IEEE International Conference on Multimedia Big Data (BigMM2016) in Taipei, Taiwan. He has published more than 130 refereed articles in biomedical informatics, mHealth and eHealth, visual knowledge reasoning, and search engine design. Project sponsors, in addition to the NSF, include the National Institutes of Health, the U.S. Department of Education, and other for-profit and nonprofit organizations.

13

Invited Talk 5: Accurate and Fast RNAseq Analysis

Speaker: Dr. Wei Wang, Department of Computer Science at University of California at Los Angeles

Abstract: High throughput sequencing technique has been demonstrated as a revolutionary means for modern biology because it provides deep coverage and base pair-level resolution. It produces vast amount of data which pose new computational challenges, because subsequent analyses often rely on a sequence alignment step that re-establishes the origin of each read, a process that is both time consuming and error prone. In this talk, we will present our latest accomplishment in methodology advances that dramatically accelerate the analysis by removing the necessity of sequence alignment. We will demonstrate through a concrete example of RNASeq quantification, in which we are able to achieve two orders of magnitude speedup and deliver competitive accuracy.

Short Bio: Wei Wang is a professor in the Department of Computer Science at University of California at Los Angeles and the director of the Scalable Analytics Institute (ScAi). She also serves as a co-director of the NIH BD2K Coordination Center. She received her PhD degree in Computer Science from the University of California at Los Angeles in 1999. Dr. Wang's research interests include big data, data mining, bioinformatics and computational biology, and databases. She has filed seven patents, and has published one monograph and more than one hundred research papers in international journals and major peer-reviewed conference proceedings. Dr. Wang received the IBM Invention Achievement Awards in 2000 and 2001. She was the recipient of a UNC Junior Faculty Development Award in 2003 and an NSF Faculty Early Career Development (CAREER) Award in 2005. She was named a Microsoft Research New Faculty Fellow in 2005. She was honored with the 2007 Phillip and Ruth Hettleman Prize for Artistic and Scholarly Achievement at UNC. She was recognized with an IEEE ICDM Outstanding Service Award in 2012 and an Okawa Foundation Research Award in 2013. Dr. Wang has been an associate editor of the IEEE Transactions on Knowledge and Data Engineering, IEEE Transactions on Big Data, ACM Transactions on Knowledge Discovery in Data, Journal of Knowledge and Information Systems, Journal of Data Mining and Knowledge Discovery, International Journal of Knowledge Discovery in Bioinformatics, and an editorial board member of the International Journal of Data Mining and Bioinformatics and the Open Artificial Intelligence Journal. She serves on the organization and program committees of international conferences including ACM SIGMOD, ACM SIGKDD, ACM BCB, VLDB, ICDE, EDBT, ACM CIKM, IEEE ICDM, SIAM DM, SSDBM, RECOMB, BIBM.

14

Federal Agencies and Industry Panel

Panelists:

Moderator: Luke Huan and Amarda Shehu 1. Susan Gregurick: NIH NIGMS 2. Wendy Nilsen: NSF CISE/IIS 3. Frank Olken: NSF CISE/IIS 4. Vinay Pai: NIH NIBIB

15

Workshops

Inaugural International Workshop on Biological Network Driven Analysis Session Chairs: Fiona Browne, Haiying Wang Time Title Presenter/Author Opening talk: 13:30-14:15 Biological Network Driven Analysis for discovering novel disease genes and pathways, biomarkers and drug targets for disease. Fiona Browne On the Comparison of State- and Transition-based Analysis of Kathryn Cooper. Prasuna Vemuri, and 14:15 – 14:45 Biological Relevance in Gene Co-expression Networks Hesham Ali Ricardo de Matos, Simoes, Constantine Network signatures based on gene pair expression ratios improve 14:45-15:15 Mitsiades, Kate E Williamson, Frank classification and the analysis of muscle-invasive urothelial cancer Emmert-Streib 15:30-16:00 Coffee Break Visualizing the topology and re-analyzing the causes of small-world Yongpan Hua, Xiuchan Xiao, Min Zhu, 16:00 – 16:30 property of amino acid network Yangxu Wang and Menglong Liy Functional Connectivity of Chinese Characters Processing:A Meta- Yaoxin Nie, Jieyao Wei, Linlin Zhu, Qian 16:30 – 17:00 analysis Zhou, Zhendong Niu 17:00 Closing Remarks

Joint Program Schedule Nonnegative Matrix Factorization and Tensor Decomposition Techniques for High-Throughput Biological Data Analysis & Computational Regulatory Genomics and Metagenomics Session Chairs: Michael Ochs, Elana Fertig, and Alioune Ngom Time Title Presenter/Author Session 1Nonnegative Matrix Factorization and Tensor Decomposition Techniques for High-Throughput Biological 13:30-15:30 Data Analysis Elana Fertig Session Co-chair: Alioune Ngom The Estimation of Dimensionality in Gene Expression Data using Michael Ochs Nonnegative Matrix Factorization A Hybrid Algorithm for Non-Negative Matrix Factorization Based on Karthik Devarajan Symmetric Information Divergence The Nonnegative Matrix Factorization and Atomic Deconvolution Amanda Landi Data Integration in Machine Learning Yifeng Li 15:30-16:00 Coffee Break, poster session (coffee: 15:30-15:50) Session 2: Computational Regulatory Genomics and Metagenomics 16:00-17:25

A New DP Algorithm for Comparing Gene Expression Data Using 16:00-16:25 Amir Vajdi, Nurit Haspel, and Hadi Banaee Geometric Similarity 16:25-16:50 Understanding Heterogeneity in Pregnancy Associated Breast Cancer Murlidharan Nair A Novel Signature For Identification Of Upstream Alternative 16:50-17:15 Kritika Karri and Dhundy Bastola Translation Initiation Sites Chin-Ting Wu, Tzu-Hung Hsiao, Yu-Chiao Patho-finder – a Fast and Accurate Program for Pathogen 17:15-17:40 Chiu, Yu-Ching Hsu, Eric Chuang, and Identification through RNA-seq Yidong Chen 17:40 Closing Remarks

16

6th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB-2015) Session Chair: Mario Cannataro Time Title Presenter/Author Session 1 (15 minutes for talk and 5 minutes for Q and A) 09:00 – 10:30 Session Chair: Mario Cannataro Opening Remarks An LDA and Probability-based Classifier for the Diagnosis of Alexander Spedding Alzheimer's Disease from Structural MRI Time Series Discord Detection in Medical Data using a Parallel Diane M. Woodbridge Relational Database, Towards an Efficient Data Assimilation in Physically-Based Medical Igor Peterlik Simulations Overall Survival Analyzer: a software tool to analyze genotyping and Giuseppe Agapito clinical data enriched with temporal events 10:30-11:00 Coffee Break – perhaps poster session Session 2(15 minutes for talk and 5 minutes for Q and A) 11:00-12:00 Session Chair: Mario Cannataro Conservation in Mitochondrial DNA: Parallelized Estimation and Jorge Álvarez-Jarreta Alignment Influence Ancestral Reconstruction under Weighted Maximum Matching Jijun Tang High performance computing of a fusion gene detection pipeline on Satoshi ITO the K computer Concluding Remarks 12:00-12:30 poster session 12:30-13:30 Lunch (on your own)

Electronic Health Record: implementation, data mining, security, and user acceptance Session Chairs: Manuel Graña, Michal Wozniak and Konrad Jakowski Time Title Presenter/Author Session 1 (30 minutes for each talk) 13:30 – 15:30 Session Chair: Michal Wozniak Opening Remarks Interesting Things for Computer Systems to Do: Keeping and Data Mining Millions of Patient Records, Guiding Patients and Physicians, Barry Robson and Srinidhi Boray and Passing Medical Licensing Exams Boguslaw Cyganek, Manuel Grana, Andrzej Selected Aspects of Electronic Health Record Analysis from the Big Kasprzak, Krzysztof Walkowiak, and Michal Data Perspective Woznia Tensor Based Representation and Analysis of the Electronic Boguslaw Cyganek and Michal Wozniak Healthcare Record Data Electronic Health Record: A review Manuel Grana and Konrad Jacowsk Closing Remarks

COMputational Methods for Analyzing Metagenomics Data Session Chairs:Catherine Putonti, Charlie Xia and Erliang Zeng Time Title Presenter/Author 08:00-8:15 Welcome 08:15-09:00 Computational Challenges Facing Environmental Metaviromics Catherine Putonti Next Generation Sequence Assembler Mis-assembly of Phage 09:00-09:20 Julia Sommer Genomes with Terminal Redundancy A Computational Framework for Integrative Analysis of Large Erliang Zeng, Wei Zhang, Scott Emrich, Dan 09:20-09:40 Microbial Genomics Data Liu, Josh Livermore, and Stuart Jones Kelly Boyd, Emma Highland, Amanda Finding Function in the Unknown: Methods for Examining 09:40-10:00 Misch, Amber Hu, Sushma Reddy, and Transcriptomes of Non-Model Organisms Catherine Putonti, Loyola CoCo: an application to store High Throughput Sequencing data in Kamil Khanipov, Georgiy Golovko, Mark 10:00-10:20 compact text and binary file formats Rojas, Levent Albayrak, Otto Dobretsberger,

17

Maria Pimenova, Nels Olsen, Sergei Chumakov, and Yuriy Fofanov 10:20-10:50 Coffee Break HAsh-MaP-ERadicator: Filtering Non-Target Sequences from Next 10:50-11:10 Jonathon Brenner and Catherine Putont Generation Sequencing Reads Karel Sedlar, Helena Skutkova, Petra 11:00-11:30 Bipartite Graphs for Metagenomic Data Analysis and Visualization Videnska, Ivan Rychlik, and Ivo Provaznik 11:30 Closing

2015 Workshop on Data mining from genomic rare variants and its application to genome-wide analysis Session Chair: Prof. Taesung Park Time Title Presenter/Author Session 1 (20 minutes for each talk, including Q and A) 09:00 – 10:30 Session Chair: Dr. Heejong Sung 09:00-09:10 Opening Remarks Developing cancer prediction model based on stepwise selection by Yongkang Kim, Seungyeoun Lee, etc AUC measure for proteomics data Competitive pathway analysis using structural equation models (CPA- Sungkyoung Choi, Sungyoung Lee, etc SEM) for gene expression data

Cross-validation and cross-study validation of chronic lymphocytic Nihir Patel, Abdulrhman Aljouie, Bharati leukemia with exome sequences and machine learning Jhadav, and Usman Roshan Taeyoung Hwang, JooHeon Shin, and Daniel Dynamic regulation of RNA-editing in human brain development Weinberger 10:30-10:50 Coffee Break Session 2(20 minutes for each talk, including Q and A) 10:50-12:10 Session Chair: Prof. Taesung Park Min-Seok Kwon, Sungyoung Lee, Yongkang VizEpis : a visualization and mapping tool for interpreting epistasis Kim, and Taesung Park Multi-purpose SNP Selection by the principal variables for a genetic Seunghyun Lee and Mira Park study Tiled regression reduces type I error rates in tests of association of rare single nucleotide variants with non-normally distributed traits, Heejong Sung, Alexa Sorant,etc compared with simple linear regression Haewon Choi, Hye-Young Jung, and Genetic association tests for aggregated count data Taesung Park 11:20 Closing

Data mining in translational biomedical informatics Session Chairs: Qian Zhu, Hongfang Liu

Time Title Presenter/Author Session 1 (15inutes for each talk, including Q and A) 09:00 – 10:30 Session Chair: Qian Zhu Opening Remarks Resting State Functional Connectivity Explains Individual Scores of Kosuke Yoshida, Yu Shimizu, etc Multiple Clinical Measures for Major Depression Acquisition of diabetes-related biological associations using a motif Iyanuoluwa Odebode, Aryya Gangopadhyay, based network: preliminary results and Qian Zhu Feichen Shen, Hongfang Liu, Sunghwan BmQGen: Biomedical Query Generator for Knowledge Discovery Sohn, David Larson, and Yugyung Lee Collaborative Data Mining For Clinical Trial Analytics Jay Gholap, Vandana Janeja, etc Parallel Group ICA for Multimodal Biomedical Data Analyses jingyu Liu, Jiayu Chen, and Vince Calhoun 10:30-11:00 Coffee Break – perhaps poster session 11:00-12:00 Session 2(15 minutes for each talk, including Q and A) 18

Session Chair: Qian Zhu Thermal Sensor Based Multi-occupancy Motion Tracking and Jun Zhou, Huiru (Jane) Zheng, Haiying Visualisation in Smart Environments Wang,etc Usability testing of a novel automated external defibril l ator user Peter O'Hare, Rebecca Di Maio, and interface: a pilot study Raymond Bond Saeed Mehrang, Elina Helander, Misha Outlier Detection in Weight Time Series of Connected Scales Pavel, Angela Chieh, and Ilkka Korhonen The Syndromes of Lung Cancer and Compatibility of Medicine in Miao Wang, Mengying Wang, Dongyi Traditional Chinese Medicine Science Treatment Based on Clustering Wang,etc Algorithm

2015 Workshop on Health Informatics and Data Science (HI-DS) Session Chairs: Xiong Liu, Rong Liu

Time Title Author 08:30 – 10:20 Session 1 (25 minutes for each talk) 8:30-8:40 Opening Obtaining Biomarkers in Cancer Progression from Outliers of Time- Abed Alkhateeb, Iman Rezaeian, Siva series Clusters Singireddy, and Luis Rueda CancerVis: an Interactive Exploratory Tool for Cancer Biomarker Lei Zhang, Ying Zhu, and Sergey Klimov Analysis Tadasuke Ito, Masato Okada, Shotaro ILP based screening applied to predicting carbonic anhydrase II Togami, Shinya Ariyasu, Shin Aoki, and ligands Hayato Ohwada

Petr Škoda and David Hoksza Exploration of Topological Torsion Fingerprints 10:20 – 10:45 Coffee Break 10:45 – 12:00 Session 2(25 minutes for each talk, including Q and A) Imbalanced Learning to Predict Long Stay Emergency Department Ali Azari, Vandana Janeja, and Scott Levin Patients Richard Braun, Martin Burwitz, Hannes Clinical Processes from Various Angles - Amplifying BPMN for Schlieter, and Martin Benedict Integrated Hospital Management

Ni Cao, SiSi Zeng, Feixia Shen, Chuandi Predictive and Preventive Models for Diabetes Prevention using Pan, Chengshui Chen, Thanh Nguyen, and Clinical Information in Electronic Health Record Jake Chen

12:00-12:30 Poster Session Risk Prediction of Stroke: A Prospective Statewide Study on Patients Le Zheng, Yue Wang, Shiying Hao, etc. in Maine Subrata Acharya, William Glenn, and A GRReat Framework for Incident Response in Healthcare Matthew Carr

Subrata Acharya, Gabriel Susai, and Manoj Patient Portal: Anytime Anywhere Pillai

Subrata Acharya, Branden Ehrenreich, and OWASP Inspired Mobile Security James Marciniak

12:30-13:30 Lunch (on your own) 13:30-15:35 Session 3(25 minutes for each talk, including Q and A) Frederic Bergeron, Kevin Bouchard, Sebastien Gaboury, Sylvain Giroux, and Simple Objects Tracking System for Smart Homes Bruno Bouchard

19

Ayush Sharma, Komal Agarwal, Rahul Dubey, Sandip Bhaumik, and samudrala S-Fit: Knowledge guided Fitness Pattern Mining Framework nagaraju

David Moore, Kellan Fluette, Heather Milne, ccKOPLS: Confounder-Correcting Kernel-based Orthogonal Andrew Shedlock, and Paul Anderson Projections to Latent Structures Bin Hu, Zhenyu Liu, Lihua Yan, Tianyang Feature Selection and Classification of Speech under Long-term Stress Wang, Fei Liu, Xiaoyu Li, and Huanyu Kang

Abolfazl Doostparast Torshizi, Linda Direct Higher Order Fuzzy Rule-based Classification System: Petzold, and Mitchell Cohen Application in Mortality Prediction 15:35-16:00 Coffee Break 16:00-17:50 Session 4(25 minutes for each talk, including Q and A) Design of a Real-time Morphology-based Anomaly Detection Method DuyHoa NGO and Bharadwaj Veeravalli from ECG Streams Abhijit Dasgupta, Ritankar Das, Losiana Analyzing epileptogenic brain connectivity networks using clinical Nayak, and Rajat K. De EEG data Alexander Chan, Christopher Early, Sishir Analysis of Machine Learning Algorithms on EEG Data for Brain Subedi, Yuezhe Li, and Hong Lin State Intelligence (short)

Leqi Liu, Ziyan Yang, Jia Tao, and Fadi Shared Genetic Architecture In Autoimmune Disease - Preliminary Towfic Analysis (short) Risk prediction for future 6-month healthcare resource utilization in Shiying Hao, Zhongkai Hu, Bo Jin, etc. Maine (short) PENG Yue, FANG Ming, WANG Chongjun, Entropy Chain Multi-Label Classifiers for Traditional Medicine and XIE Junyuan Diagnosing Parkinson’s Disease (short) 17:50 Closing Remark

Workshop IDASB Session Chairs: Rui Jiang, Huiru Zheng, and Zhongming Zhao

Time Title Presenter/Author Session 1 (15inutes for each talk, including Q and A) 09:00 – 10:30 Session Chair: Huiru Zheng Co-chair: Zhongming Zhao Opening Remarks The upregulation of Myb and Peg3 may mediate EGCG inhibition Hong Zhou, Joseph Manthey, Ekaterina effect on mouse lung adenocarcinoma Lioutikova, etc Construction of Dynamic Probabilistic Protein Interaction Networks Yijia Zhang for Protein Complex Identification Sketching the distribution of transcriptomic features on RNA Xiaodong Cui, Zhen Wei, transcripts with Travis coordinates 10:30-11:00 Coffee Break – perhaps poster session Session 2 11:00-11:30 Session Chair: Huiru Zheng Co-chair: Zhongming Zhao Integrating Prior Biological Knowledge and Graphical LASSO for Yiming Zuo, Guoqiang Yu, and Habtom

Network Inference Ressom 11:0\30-12:30 poster session 12:30-13:30 Lunch (on your own) Session 3 13:30-15:30 Session Chair: Zhongming Zhao Session Co-chair: Huiru Zheng Identification of Hot Regions in Protein-Protein Interactions Based on Xiaoli Lin SVM and Detecting Local Community Structure 20

Simulation of Effects of TBX18 on the Pacemaker Activity of Human Yue Zhang, Kuanquan Wang, Henggui

Ventricular Cells Zhang, and Wei Wang 15:30-16:00 Coffee Break, poster session (coffee: 15:30-15:50) Session 4 16:00-17:00 Session Chair: Zhongming Zhao Co-chair: Huiru Zheng Reconstructing Transcriptional Regulatory Networks Using Data Rafael Pereira, Hugo Costa, Sónia Carneiro, Integration and Text Mining Miguel Rocha, and Rui Mendes

POOYA ZAKERI, Sara Elshal, and Yves Prioritization Through Geometric-Inspired Kernel Data Fusion Moreau 17:00 Closing Remarks

2015 Biomedical & Health Informatics (BHI) Session Chair: Illhoi Yoo

Time Title Presenter/Author Session 1 (20 mins for full papers and 15 mins for short papers) 09:30 – 10:30 Session Chair: Illhoi Yoo Opening Remarks Annotating Evidence-Based Argumentation in Biomedical Text Nancy Green Assessment of Gait Patterns of Chronic Low Back Pain Patients: A Herman Chan, Huiru (Jane) Zheng, Haiying Smart Mobile Phone based Approach Wang, and Dave Newell Foreign Object Detection in Chest X-rays Zhiyun Xue, Sema Candemir, etc 10:50-12:00 Session 2 (20 mins for full papers and 15 mins for short papers) Automatic Identification of Potentially Contradictory Claims to Abdulaziz Alamri and Mark Stevenson Support Systematic Reviews SOLOMON: An Ontology for Sensory-Onset, Language-Onset and Martin Skarzynski, Adam Craig, and Carl Motor-Onset Dementias Taswell

Eamon Johnson, W Christopher Baughman, A Distributional Approach to Summarization of Radiology Reports and Gultekin Ozsoyoglu Transcriptome analysis of HIV-1 virus in understanding the effect of Ishwor Thapa, Howard Fox, and Dhundy antiretroviral drugs (cART) and methamphetamine on the virus Bastola 13:30-15:30 Session 3 (20 mins for full papers and 15 mins for short papers) A Prototype for a Hybrid System to Support Systematic Review Tanja Bekhuis, Eugene Tseytlin, and Kevin Teams: A Case Study of Organ Transplantation Mitchell A systems chemical biology approach to identify targets of Li-Da Zhu, Chang-Shou He, Ye-Mao Liu antibacterial agents: a case study of Chelerythrine and Rhein Christopher Ochs, Yehoshua Perl, James Using Aggregate Taxonomies to Summarize SNOMED CT Evolution Geller, and Mark Musen

A Path Based Approach to Quantifying the Progression of Alzheimer's Prabesh Kanel and Xiuwen Liu Disease Investigating gene expression array with outliers and missing data in Stéphane Chrétien, Christophe Guyeux,etc bladder cancer A semantic approach for knowledge capture of microRNA-target gene Jingshan Huang, Fernando,etc interactions 15:50-18:30 Session 4 (20 mins for full papers and 15 mins for short papers) A Systems Approach to Reducing Central Line Associated Blood Eva Lee, Michael Callahan Stream Infections Refining Disease Databases for Clinical Decision Support Systems - Takashi Okumura, Demi Menez, and Post-processing disease entries after integration of OMIM and Theekshana Abayawickrama Orphanet Dealing with incompleteness in Multidimensional Analysis of Health Mario Bochicchio, Lucia Vaira,etc Records: an Experience on Fetal Growth

Matin Šícho, Daniel Svozil, and David Activity-Driven Exploration of Chemical Space with Morphing Hoksza Comparative Utility of Time and Frequency HRV Domains for In cheol Jeong and Joseph Finkelstein Automated Classification of Exercise Exertion Level A Novel Automatic Tongue Image Segmentation Algorithm: Color Li Chen, Dongyi Wang, Yiqin Liu, Xiaohang Enhancement Method Based on L*a*b* Color Space Gao, and Huiliang Shang Directed Cyclic Graph-Based Feature Selection and Modeling of The Weifei Xu, Guoping Liu, Jianjun Yan, Yiqin

21

Dampness Syndrome of Chronic Gastritis Wang, Xiong Lu, and Tao Zhong Finding Frequent Approximate Subgraphs in Medical Image Database Linlin Gao, Haiwei Pan,etc

International Workshop on Biomolecular Interaction Network Analysis and Interactomics (IWBNA) Session Chairs: Young-Rae Cho, Pietro H Guzzi, and Pierangelo Veltri

Time Title Presenter/Author Session 1 (25-minute presentation and 5-minute Q & A.) 13:30-15:30 Session Chair: Young-Rae Cho MODULA: A Network Module Based Local Protein Interaction Pietro Hiram Guzzi, Pierangelo Veltri, Network Alignment Method. Swarup Roy, and Jugal K Kalita. Diffusion Kernel to Identify Missing PPIs in Protein Network Dominic Bett and Ananda Mondal. Biomarker.

Testing whether hot regions in protein–protein interactions are Jing Hu and Xiaolong Zhang. conserved in different species Mining Maximal Subnetworks from Interaction Network with Node Aditya Goparaju, Bassam Qormosh, and Attributes Saeed Salem. 15:30-16:00 Coffee Break Session 2 16:00-17:00 Session Chair: Pierangelo Veltri SRP: A Concise Non-parametric Similarity-Rank-based Model for Jian-Yu Shi and Siu-Ming Yiu. Predicting Drug-Target Interactions.

Semantic mapping to align PPI networks and predict conserved Lizhu Ma and Young-Rae Cho protein complexes. 17:00 Closing Remarks

IEEE Workshop on Biomedical Visual Search and Deep Learning Session Chairs: Richard Conroy, Vinay M. Pai,, Susan Gregurick, Tom Radman, and Todd Horowitz

Time Title Presenter/Author

13:30-17:15 Session Chair: Dr. Vinay Pai, NIBIB, NIH 13:30-13:35 Opening Remark(5mins) Keynote Part 1 13:35-14:20 Todd Horowitz, NCI, NIH. Visual Search in Biomedical Sciences Probabilistic Visual Search for Masses Within Mammography Images 14:20-14:40 Mehmet Gunhan Ertosun and Daniel Rubin using Deep Learning Keynote Part 2 14:40-15:10 Susan Gregurick, NIGMS, NIH. Deep Learning in Basic Biomedical Sciences Learning structure in gene expression data using deep architectures, Aman Gupta, Haohan Wang, and Madhavi 15:10-15:30 with an application to gene clustering Ganapathiraju 15:30-15:50 Coffee Break Noah Stier, Nicholas Vincent, David 15:50-16:10 Deep Learning of Tissue Fate in Acute Ischemic Stroke Liebeskind, and Fabien Scalzo A deep learning-based segmentation method for brain tumor in MR Yi Ding, Ruohan Huang, Tian Lan, Xinjie 16:10-16:30 images Zhang, Wei Wang, and Zhiguang Qin Nicholas Vincent, Noah Stier, Songlin Yu, Detection of Hyperperfusion on Arterial Spin Labeling using Deep 16:30-16:50 David Liebeskind, Danny Wang, and Fabien Learning Scalzo 16:50-17:15 Open Discussion Tom, Radman, NIDA, NIH

22

Workshop on Semantic Data Analytics and Bioinformatics Session Chair: Dr. Haiying Wang

Time Title Presenter/Author 13:30-13:40 Opening Remarks 13:40-14:40 Invited talk: Talk title (TBC) 14:40-15:30 Session I (25mins for each talk) Integrating Multiple Sources of Genomic Data by Multiplex Network Shang Gao Reconstruction

An Algorithm for Discovering Deep Order Preserving Submatrix in Qiuhua Kuang, Meizhen Zhang, Zhihao Ma, Bo Gene Expression Data Ma, Zhiwen Liu, and Yun Xue 15:30-16:00 Coffee Break 16:00-17:10 Session 2(25mins for each talk) A Unified Approach to the Computation and Analysis of Strings of Jaime Seguel and Marie Lluberes Gene Expression States

Leveraging the k-Nearest Neighbors Classification Algorithm for Jeffrey McGovern, Alexander Dekhtyar,etc Microbial Source Tracking Using a Bacterial DNA Fingerprint Library DNA Sequences Compression Algorithms Based on the Two bits Bacem SAADA and Jing Zhang, Codation Method 17:10 – 17:15 Closing Remarks

The second International Workshop on High Performance Computing on Bioinformatics (HPCB 2015) Session Chairs: Che-Lun Hung, Huiru Zheng, Chuan Yi Tang, Chun-Yuan Lin

Time Title Presenter/Author Session 1 (30mins for each talk) 09:00-10:30 Session Chair: Che-Lun Hung Opening Remarks Innovative Approach for Porting Existing CPU Program to Its CUDA Yu Liu, Yang Hong, Chung-Hung Wang, Sheng- Program Ta Lee, Chun-Yuan Lin, and Che-Lun Hung Guan-Jie Hua, Che-Lun Hung, Chuan Yi Tang, Cloud Computing Framework for Bioinformatics Tools and Yaw-Ling Lin Biomarker Discovery, High Performance and Cloud Computing: A Jaine Blayney, Valeriia Haberland, Gaye Comprehensive Review Lightbody, and Fiona Browne Combining AR filter and Sparse Wavelet representation for P300 Zhihua Huang and Huiru (Jane) Zheng speller Valeria Guimarães, Fernanda Hondo, Rodrigo A Study of Genomic Data Provenance in NoSQL Document-Oriented Almeida, Harley Vera, Maristela Holanda, Database Systems Aleteia Araujo, Sérgio Lifschitz, and Maria Emilia Walter 10:30 Closing Remarks

IEEE Workshop on High Performance Computing for Big Data Computational Biology (HPC-BCB 2015) Session Chairs: Fahad Saeed, Ajay Gupta and Elise DeDoncker

10:00 -12:30 Session Chair: Fahad Saeed Opening Remarks 10:00 – 10:05 10:05 – 10:25am FPGA Acceleration of the Pair-HMMs Forward Algorithm for DNA Sequence Analysis, 23

Shanshan Ren, Vlad-Mihai Sima, and Zaid Al-Ars

10:30 -11:15 Keynote Lecture: Genomes Galore: Parallel Methods and Software for Tackling NGS Big Data Challenges Srinivas Aluru 11:15 – 11:35 am Cluster-Based Apache Spark Implementation of the GATK DNA Analysis Pipeline Hamid Mushtaq and Zaid Al-Ars 11:35 – 11:55 am Hybrid Multi-threaded Simulation of Agent-Based Pandemic Modeling using Multiple GPUs Barzan Shekh, Elise de Doncker, and Diana Prieto 11:55 – 12:15 pm NGS Read Data Compression using Parallel Computing Algorithm Biji C.L., Arun P.R., Jojo George, and Achuthsankar S. Nair 12:15 – 12:35 pm Parallel Merging Method to Integrate Different Genome Assemblies Kirill Romanenkov Closing Remarks

Merged Workshop: Data mining in translational biomedical informatics & Second International Workshop on the Role for Quantified Self for Personal Healthcare Session Chairs: Qian Zhu, Hongfang Liu, Frank Hopfgartner, Na Li Time Title Presenter/Author Session 1(15mins for each talk) 9:00-10:30 Session Chair: Qian Zhu Opening Remarks Resting State Functional Connectivity Explains Individual Scores of Kosuke Yoshida, Yu Shimizu, etc. Multiple Clinical Measures for Major Depression Acquisition of diabetes-related biological associations using a motif Iyanuoluwa Odebode, Aryya Gangopadhyay, based network: preliminary results and Qian Zhu Feichen Shen, Hongfang Liu, Sunghwan Sohn, BmQGen: Biomedical Query Generator for Knowledge Discovery David Larson, and Yugyung Lee Collaborative Data Mining For Clinical Trial Analytics Jay Gholap, Vandana Janeja, etc. Parallel Group ICA for Multimodal Biomedical Data Analyses Jingyu Liu, Jiayu Chen, and Vince Calhoun 10:30-11:00 Coffee Break Session 2 (15mins for each talk) 11:00-12:00 Session Chair: Huiru(Jane) Zheng Thermal Sensor Based Multi-occupancy Motion Tracking and Jun Zhou, Huiru (Jane) Zheng, Haiying Wang, Visualisation in Smart Environments Jonathan Synnott, Chris Nugent, and Paul Jeffers Usability testing of a novel automated external defibril l ator user Peter O'Hare, Rebecca Di Maio, and Raymond interface: a pilot study Bond Saeed Mehrang, Elina Helander, Misha Pavel, Outlier Detection in Weight Time Series of Connected Scales Angela Chieh, and Ilkka Korhonen The Syndromes of Lung Cancer and Compatibility of Medicine in Miao Wang, Mengying Wang, Dongyi Wang, Traditional Chinese Medicine Science Treatment Based on Clustering Shiyu Duan, Yisheng Wang, Yanjun Huang, and Algorithm Huiliang Shang

24

IEEE Workshop on Machine Learning in Decision Making for Biomedical Applications Session Chair: .Mahua Bhattacharya Time Title Presenter/Author 10:20-10:25 Welcome 10:25-10:40 Multi-VBE: A New Model for the Prediction of Hot Spots Hui Peng, Quan Liu, Lei Wang, and Jinyan Li at Protein-Protein Interaction Interface 10:40-10:55 Quantitative Clinical guidelines for Imaging Use in Yuzhe Liu, Shobhit Madan, MD, MPH, and Vanathi Evaluation of Pediatric Cardiomyopathy Gopalakrishnan 10:55-11:10 Cross-validation and cross-study validation of chronic Nihir Patel, Bharati Jhadav, and Usman Roshan lymphocytic leukaemia with exome sequences and machine learning 11:10-11:25 A New Compact Set of Biomarkers for Distinguishing Forough Firoozbakht, Iman Rezaeian, Alioune Ngom, and Luis among Ten Breast Cancer Subtypes Rueda 11:25-11:40 A Longitudinal Support Vector Regression for Prediction of Wei Du, Huey Cheung, Calvin Johnson, Ilya Goldberg, Madhav ALS Score Thambisetty, and Kevin Becker 11:40-11:55 Integration of Multimodal RNA-Seq Data for Prediction of Matt Schwartz, Martin Park, John Phan, and May Wang Kidney Cancer Survival 11:55:-12:10 EEG-based Seizure Detection Using Discrete Wavelet Duo Chen, Suiren Wan, and Forrest Bao Transform through Full-Level Decomposition 12:10-12:25 Effective Image Fusion Method to Study Alzheimer's Arpita Das and Mahua Bhattacharya Disease using MR, PET Images 12:25-12:40 A Genetic Algorithm for the Selection of Structural MRI Alexander Spedding,

25

Tutorials

1. Introduction to computational analysis of microbiome shotgun sequencing data Daniel H. Huson, University of Tübingen, Germany.

2. Integrative Genomic Big-Data Analytics for Translational Bioinformatics and Precision Medicine Research Mary Yang and Kenji Yoshigoe, Univ. Arkansas at Little Rock

3. Human Microbiome Analysis: Computational Techniques and Challenges by Serghei Mangul, University of California at Los Angeles

26

Conference Paper Presentations

Session 1 Genomics B461 "A novel dimensionality reduction algorithm based on Laplace matrix for microbiomie data Regular analysis" Yetian Fan, Xingpeng Jiang, Xiaohua Hu, Bo Song, Yuan Ling, and Wei Wu B503 "A New Algorithm for The LCS Problem with Application in Compressing Genome Regular Resequencing Data" Richard Beal, Tazin Afrin, Aliya Farheen, and Don Adjeroh

B453 "Fast alignment filtering of nanopore sequencing reads using locality-sensitive hashing" Short Jeremy Wang and Corbin Jones

"SNVSniffer: An Integrated Caller for Germline and Somatic SNVs Based on Bayesian Models" Regular Yongchao Liu, Martin Loewer, Srinivas Aluru, and Bertil Schmidt

B338 "Short Read Error Correction using an Augmented FM-Index" Short Seth Greenstein, James Holt, and Leonard McMillan

B352 “HapColor: A Graph Coloring Framework for Polyploidy Phasing” Short Sepideh Mazrouee and Wei Wang

Session 2 Biological Networks I B293 "Constructing directed gene regulatory network solely by gene expression data" Regular Lu Zhang, Yen Kaow Ng, and Shuai Cheng Li B424 "Triple Imputation for Microarray Missing Value Estimation" Regular Chong He, Hui-Hui Li, Changbo Zhao, and Guo-Zheng Li B218 "Principle Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Short Enrichment Analysis Tool" Neil Clark, Maciej Szymkiewicz, Zichen Wang, Caroline Monteiro, Matthew Jones, and Avi Ma'aya B311 "Hausdorff Distance and Global Silhouette Index as Novel Measures for Estimating Quality of Short Biclusters" Nishchal Verma, Esha Dutta, and Yan Cui B227 "Integrative approach for inference of gene regulatory networks using lasso-based random Regular featuring and application to Psychiatric disorders" Dong-Chul Kim, Mingon Kang, Ashis Biswas, Chunyu Liu, and Jean Gao B470 "Gene Selection for Cancer Classification With the Help of Bees" Short Johra Moosa, Rameen Shakur, Mohammad Kaykobad, and M Sohel Rahman B313 "Integrated Study to Infer Dynamic Protein-gene Interactions in human P53 Regulatory Short Networks" Junbai Wang, Qianqian Wu, and Tianhai Tian

27

Session 3 Medical Informatics I B229 "RREV: Reconfigurable Rendering Engine for Cross-Cohort Visualization of Clinically Annotated Polysomnograms" Regular Catherine Jayapandian, Wei Wang, Michael Morrical, Dennis Dean II, Daniel Mobley, Mathew Kim, Michael Rueschman, Kenneth Loparo, Susan Redline, and Guo-Qiang Zhang

B230 "Feature-Level Fusion of Multimodal Physiological Signals for Emotion Recognition" Short Jing Chen, Bin Hu, Lixin Xu, Philip Moore, and Yun Su

B282 "Sparse Multidimensional Patient Modeling using Auxiliary Confidence Labels" Regular Eric Heim and Milos Hauskrecht

B382 "Survival Analysis via Transduction for Semi-Supervised Neural Networks in Medical Prognosis" Short Faisal Khan and Casimir Kulikowski B263 "Context-learning Based Electroencephalogram Analysis for Epileptic Seizure Detection" Regular Guangxu Xun, Xiaowei Jia, and Aidong Zhang

B395 "On Automated Flow Cytometric Analysis for MRD Estimation of Acute Lymphoblastic Short Leukaemia: a comparison among different approaches" Paolo Rota, Stefanie Groeneveld-Krentz, and Michael Reiter

B275 "On Using Compressed Sensing and Peak Detection Method for the Dynamic Instability Short Parameters Estimation for Microtubules Modeled in three States" Shantia Yarahmadian, Vineetha Menon, and Vahid Rezania

Session 4 Semantics and Ontology I B222 "Learning to Rank for Biomedical Information Retrieval" Regular Bo Xu, Hongfei Lin, and Yuan Lin B245 "Algorithmic Detection of Inconsistent Modeling among SNOMED CT Concepts by Combining Regular Lexical and Structural indicators" Ankur Agrawal, Yehoshua Perl, Christopher Ochs, and Gai Elhanan B203 "Semantic Rules for Extracting Proteins Functions Information from Biomedical Abstracts" Short Kamal Taha B262 "Supporting HIV Literature Screening with Data Sampling and Supervised Learning" Regular Hayda Almeida, Marie-Jean Meurs, Leila Kosseim, and Adrian Tsang B271 "Implicit Knowledge Discovery in Biomedical Ontologies: Computing Interesting Relatednesses" Regular Tian Bai, Leiguang Gong, Casimir Kulikowski, and Lan Huang B216 "A Transition-Based Model for Jointly Extracting Drugs, Diseases and Adverse Drug Events" Short Fei Li and Donghong Ji B281 "A text mining application for linking functionally stressed-proteins to their post-translational Short modifications" Oliver Bonham-Carter and Dhundy Bastola 28

Session 5 Biological Networks II Invited “Understanding Genotype-Phenotype effects in Cancer via Network Approaches” Talk I Teresa Przytycka B326 "Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features Regular in Glioblastoma Multiforme" Yu-Chiao Chiu, Kai-Wen Liang, Tzu-Hung Hsiao, Yidong Chen, and Eric Chuang B220 "On Observability of Singleton Attractors in Boolean Networks" Short Yushan Qiu, Xiaoqing Cheng, Wai-Ki Ching, Hao Jiang, and Tatsuya Akutsu B292 "Construction of signaling networks with incomplete RNAi data" Regular Qiyao Wang, Yaunfang Ren, Mahmudul Hasan, Ahmet Ay, and Tamer Kahveci

Session 6 Translational Bioinformatics I Invited “Developing Systems Genomics Approaches to Facilitate Precision Medicine research” Talk II Mary Yang B205 "Feature Selection of High-dimensional Biomedical Data using Improved SFLA for Disease Diagnosis" Regular Yongqiang Dai, Bin Hu, Yun Su, Chengsheng Mao, Jing Chen, Xiaowei Zhang, Philip Moore, Hanshu Cai, and Lixin Xu B469 "A new method for prioritizing drug repositioning candidates extracted by literature-based discovery" Short Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Dingcheng Li, Rashmi Prasad, and Hongfang Liu B482 "Detecting Adverse Drug Effects Using Link Classification on Twitter Data" Short Satya Katragadda, Harika Karnati, Murali Pusala, Vijay Raghavan, and Ryan Benton

Session 7 Medical Imaging “Empowering self-management for chronic conditions through technology and analytics: Can machines Invited care for us?” Talk III Huiru (Jane) Zheng B500 "Level Set Segmentation using Non-Negative Matrix Factorization of Brain MRI Images" Regular Dimah Dera, Nidhal Bouaynaya, and Hassan Fathallah-Shaykh B247 "Spatio-Temporal Diffusion-based Dynamic Cell Segmentation" Regular Fatima Boukari and Sokratis Makrogiannis

B251 "Quantitative Assessment of the Parallel MRI Reconstruction Using Background Noise Short Uniformity" Fu-Hsing Wu and Hsin-Chih Lo

29

Session 8 Structure, Function and Evolution I Invited “Protein Match Making at Massive Scale” Talk IV Chi-Ren Shyu

B258 "Computational Synteny Block: A framework to identify Evolutionary Events" Regular Jose A. Arjona-Medina and Oswaldo Trelles

B435 "A Module tree of Wnt Signaling Pathways" Regular Losiana Nayak, Nitai P. Bhattacharyya, and Rajat K. De Short B400 "Accurate Simulation of Large Collections of Phylogenetic Trees" Suzanne Matthews

Session 9 Epigenetics and Gene Regulation B393 "Predicting microRNA-disease associations by integrating multiple biological information" Regular Wei Lan, Jianxin Wang, Min Li, Jin Liu, and Yi Pan B458 "Model-Based and Context-Specific Background Correction and Differential Methylation Regular Testing for MBDCap-seq" Yuanhang Liu, Desiree Wilson, Robin Leach, and Yidong Chen

B483 "Human Absorbable Dietary microRNAs Prediction based on an Ensemble Manifold Ranking Short Model" Jiang Shu, Kevin Chiang, Dongyu Zhao, and Juan Cui

B506 "Interpretable Deep Neural Networks for Enhancer Prediction" Regular Seong Kim, Nawanol Ampornpunt, Ananth Grama, and Somali Chaterji

B521 "A test for detecting differentially methylated regions" Short Iksoo Huh, Soojin V. Yi Yi, and Taesung Park

B413 "A two-step logistic regression algorithm for identifying individual-cancer-related genes" Regular Bolin Chen, Xuequn Shang, Min Li, Jianxin Wang, and Fang-Xiang Wu

Session 10 Healthcare Informatics I B495 "A Grammar-based Approach to Model the Patient’s Clinical Trajectory after a mild Traumatic Regular Brain Injury" Filip Dabek and Jesus Caban

B310 "Facial Color Management for Mobile Health in the Wild" Regular Jinling Niu, Changbo Zhao, and Guozheng Li

B324 "Modeling Electronic Health Records in Ensembles of Semantic Spaces for Adverse Drug Event Regular Detection" Aron Henriksson, Jing Zhao, Henrik Boström, and Hercules Dalianis

30

B477 "SmartStep 2.0 – A completely wireless, versatile insole monitoring system" Short Nagaraj Hegde and Edward Sazonov

B265 "Automatic weighing attribute to retrieve similar lung cancer nodules" Regular David Jones Ferreira de Lucena, José Raniery Ferreira Junior, Marcelo Costa Oliveira, and Aydano Pamponet Machado

Session 11 Cross-cutting Computational Methods I B447 "A novel approach to identify shared fragments in drugs and natural products" Regular Akshay Balasubramanya, Ishwor Thapa, Dhundy Bastola, and Dario Ghersi

B418 "A New Approach For Estimating Probability of Metastasis at Diagnosis" Short Shuhao Sun, Fima Klebaner, and Tianhai Tian

B420 "TMDFM: A Data Fusion Model for Combined Detection of Tumor Markers" Short Chi Yuan, Yongli Wang, Yanchao Li, Xiaohui Jiang, and Isma Masood B462 "Integrating Omics Data for Identifying Disease Subtypes: a Multiplex Network-based Regular Approach" Haiying Wang and Huiru Zheng B353 "A generative model for correlation discover of genetic polymorphism and adverse drug Regular reactions" Zhaohui Liang, Ziping Li, Gang Zhang, and Jimmy Huang B276 "The effective diagnosis of schizophrenia by using 4-layer RBMs deep networks" Short Chen Qiao

B201 "The Influence of EM Estimation of Missing Nodes in DCM on Model Ranking" Short Shaza Zaghlool and Christopher Wyatt

Session 12 Structure, Function, and Evolution II B494 "Extending Rule-Based Methods to Model Molecular Geometry" Regular Brittany Hoard, Bruna Jacobson, Kasra Manavi, and Lydia Tapia B348 "Structure-Guided Selection of Specificity Determining Positions in the Human Kinome" Regular Mark Moll, Paul Finn, and Lydia Kavraki

B241 "Protein model quality assessment by learning-to-rank" Short Xiaoyang Jing, Qiwen Dong, Xuan Liu, and Bin Liu B509 "Superposition of Protein Structures Using Electrostatic Isopotentials" Regular Ziyi Guo, Juliana Hong, Katya Scheinberg, and Brian Chen B463 "SphereGrinder - reference structure-based tool for quality assessment of protein structural Short models" Piotr Lukasiak, Maciej Antczak, Tomasz Ratajczak, and Jacek Blazewicz B339 "Evolutionary Search Strategies for Efficient Sample-based Representations of Multiple basin Regular Protein Energy Landscapes" Emmanuel Sapin, Kenneth De Jong, and Amarda Shehu 31

Session 13 Cross-cutting Computational Methods I Invited Accurate and Fast RNAseq Analysis Talk V Wei Wang B242 "Identification of DNA-binding proteins by auto-cross covariance transformation" Regular Qiwen Dong, Shanyi Wang, Kai Wang, Xuan Liu, and Bin Liu B272 "MALBACsim: a Multiple Annealing and Looping Based Amplification Cycles Simulator" Short Li Tengpeng, Zhang Changsheng, Bo Xu, Li Fuqiang, and Cai Hongmin

B414 "Reference Sequence Selection for Motif Searches" Regular Qiang Yu, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter, and Jun Huan

B511 "DiscMLA: AUC-Based Discriminative Motif Learning" Regular Hongbo Zhang, Lin Zhu, and De-Shuang Huang

B407 "Biomedical Named Entity Recognition Based on Extended Recurrent Neural Networks" Short Lishuang Li, Liuke Jin, Zhenchao Jiang, and Dengen Huang

Session 14 Healthcare Informatics II B321 "Classification with Imbalance: A Similarity based Method for Predicting Respiratory Regular Failure" Harsh Shrivastava, Vijay Huddar, Sakyajit Bhattacharya, and Vaibhav Rajan B479 "A Method for Imputation of Semantic Class in Diagnostic Radiology Text" Short Eamon Johnson, W Christopher Baughman, and Gultekin Ozsoyoglu B334 "Framework for Workflow-driven Clinical Decision Support in Oncology" Regular Anca Bucur, Jasper van Leeuwen, and Norbert Graf B249 "Insight: Semantic Provenance and Analysis Platform for Multi-center Neurology Healthcare Research" Short Priya Ramesh, Annan Wei, Johnny Sams, Elisabeth Welter, Samden Lhatoo, Martha Sajatovic, and Satya Sahoo B502 "Using Myoelectric Signals to Recognize Grips and Movements of the Hand" Regular Gene Shuman, Zoran Duric, Daniel Barbara, Jessica Lin, and Lynn H. Gerber B285 "Collaborative and Trajectory Prediction Models of Medical Conditions by Mining Patients’ Regular Social Data" Xiang Ji, Soon Ae Chun, James Geller, and Vincent Oria

B366 "Chronic Lymphocytic Leukemia Patient Classification Methodology Through Flow Cytometry Analysis" Short Evdoxia Papadopoulou, Konstantia Kotta, Panagiotis Moschonas, Vassiliki Douka, Achilles Anagnostopoulos, Kostas Stamatopoulos, and Dimitrios Tzovaras

32

Session 15 Semantics and Ontology II B314 "An integrative measure of graph- and vector-based semantic similarity using information Regular content distance" Young-Rae Cho B277 "ImmPort: Shared Research Data for Bioinformatics and Immunology" Short Patrick Dunn, Elizabeth Thomson, Henry Schaefer, John Campbell, Thomas Smith, Sanchita Bhattacharya, Sandra Andorf, Vincent Desborough, Jeff Wiser, and Atul Butte

B231 "A novel two-stage method for identifying miRNA-gene regulatory modules in breast cancer" Regular Wenwen Min, Juan Liu, Fei Luo, and Shihua Zhang

B330 "On Stabbing Queries for Generalized Longest Repeat" Regular Bojian Xu

B289 "Non-Coding RNA Ontology: A comprehensive resource for unification of non-coding RNA biology"

Jingshan Huang, Karen Eilbeck, Judith Blake, Dejing Dou, Darren Natale, Alan Ruttenberg, Barry Short Smith, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, David Schmitt, and Ming Tan B336 "Integrating Association Mining into Relevance Feedback for Biomedical Literature Search" Regular Yanqing Ji, Hao Ying, John Tran, Peter Dews, and Michael Massanari

B297 "Training Word Embeddings for Deep Learning in Biomedical Text Mining Tasks" Short Zhenchao Jiang, Lishuang Li, Degen Huang, and Liuke Jin

Session 16 Medical Imaging B283 "Analysis of Oddity in Facial Physiology of Children with Autism using 3D Imaging" Regular Manar Samad, Jonna Bobzien, John Harrington, and Khan Iftekharuddin B254 "An Image Reconstruction Model and Hybrid Algorithm for Limited-angle Projection Data" Short Hongxia Gao, Yinghao Luo, Kewei Chen, Ge Ma, and Lixuan Wu B371 "A Seeding-Searching-Ensemble Method for Gland Segmentation and Detection" Regular Yizhe Zhang, Lin Yang, John MacKenzie, Rageshree Ramachandran, and Danny Chen B268 "Segmentation of Multicolor Fluorescence In-Situ Hybridization (M-FISH) Image Using an Improved Fuzzy C-Means Short Clustering Algorithm While Incorporating Both Spatial and Spectral Information" Jingyao Li, Dongdong Lin, and Yu-Ping Wang B456 "Segmentation-based Multi-scale Framework for the Classification of Epithelial and Stromal Tissues in H&E Images" Short Filiz Bunyak, Adel Hafiane, Zahraa Al-Milagi, Ilker Ersoy, Anoop Haridas, and Kannappan Palaniappan

B349 "Robust landmark-based image registration using l1 and l2 norm regularizations" Short Xuan Yang, Bo Wang, and Yan-Ran Li

33

Session 17 Biological Networks III B419 "Protein-protein interaction network inference from multiple kernels with optimization based on Regular random walk by linear programming" Lei Huang, Li Liao, and Cathy Wu B465 "GREAT: GRaphlet Edge-based network AlignmenT" Regular Joseph Crawford and Tijana Milenkovic

B486 "petal: A Novel Co-Expression Network Modeling System" Regular Juli Petereit, Frederick C. Jr. Harris, and Karen Schlauch

B430 "Joint inference of tissue-specific networks with a scale free topology" Short Somaye Hashemifar, Behnam Neyshabur, and Jinbo Xu B337 "EpiTracer – an algorithm for identifying epicenters in condition-specific biological networks" Regular Narmada Sambaturu, Madhulika Mishra, and Nagasuma Chandra

B362 "Exhaustive analysis of dynamical properties of Biological Regulatory Networks with Answer Short Set Programming" Emna Ben Abdallah, Maxime Folschette, Olivier Roux, and Morgan Magnin

Session 18 Sequence, Structure, and Function B472 "Predicting Protein-Protein Interaction Using Co-Occurring Aligned Pattern Clusters" Regular Antonio Sze-To, Sanderz Fung, En-Shiun Annie Lee, and Andrew K. C. Wong B484 "Adaptive Local Learning in Sampling Based Motion Planning for Protein Folding" Regular Chinwe Ekenna, Shawna Thomas, and Nancy Amato B515 "Imputation of ChIP-Seq Datasets via Low Rank Convex Co-Embedding" Short Lin Zhu, De-Shuang Huang, and Canyi Lu B376 "Computing Transition Paths in Multiple-Basin Proteins with a Probabilistic Roadmap Regular Algorithm Guided by Structure Data" Tatiana Maximova, Erion Plaku, and Amarda Shehu B497 "Guilt-by association approach to identify novel human aging-related genes using protein Short domains" Jasjit Banwait, Schuyler Dougherty, Ishwor Thapa, and Dhundy Bastola B372 "Identifying Inorganic Material Affinity Classes for Peptide Sequences Based on Context Learning" Regular Guangxu Xun, Xiaoyi Li, Marc R. Knecht, Paras N. Prasad, Mark T. Swihart, Tiffany R. Walsh, and Aidong Zhang B490 "Quantifying Feed Efficiency of Dairy Cattle for Genome-wide Association Analysis" Short Tingyang Xu, Jiangwen Sun, Erin Connor, and Jinbo Bi

34

Session 19 Medical Informatics B346 "A Generative Bayesian Model To Identify Cancer Driver Genes" Regular CHRISTOPHER MA

B480 "EEG Dynamic Source Localization using Marginalized Particle Filtering" Short Bradley Ebinger, Nidhal Bouaynaya, Petia Georgieva, and Lyudmila Mihaylova B287 "Sparse Omics-network Regularization to Increase Interpretability and Performance of Linear Short Classification Models" Michael Andel, Filip Masri, Jiri Klema, Zdenek Krejcik, and Monika Belickova B278 "Improved Brain Tumor Growth Prediction and Segmentation in Longitudinal Brain MRI" Short Linmin Pei, Syed Mohammad Shamim Reza, and Khan Iftekharuddin B350 "Predicting Microbial Interactions by Using Network-constrained Regularization Incorporating Short Covariate Coefficients and Connection Signs" Hu Xiaohua and Wang yan

B411 "Audio Signals Encoding for Cough Classification Using Convolutional Neural Networks: A Short Comparative Study" Hui-Hui Wang, Jia-Ming Liu, and Mingyu You

B433 "On Frequency Dependencies of Sliding Window Correlation" Regular Sadia Shakil, Shella Keilholz, and Chin-Hui Lee

Session 20 Translational Bioinformatics B437 "Robust point matching by l1 regularization" Regular Jianbing Yi, Yan-Ran Li, Xuan Yang, and Guoliang Chen B427 "Using Hidden Markov Models to Capture temporal Aspects of Ultrasound Data in Prostate Cancer" Short Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron Ward, Purang Abolmaesumi, Parvin Mousavi, and Hagit Shatkay

B446 "Temporal Weighting of Clinical Events in Electronic Health Records for Pharmacovigilance" Regular Jing Zhao

B385 "Identifying the pre-transition state during biological processes by hidden Markov model" Regular Pei Chen, Shuoyang Qiu, Yue Wang, and Yongjun Li

B530 "Bayesian Classification with Local Probabilistic Model Assumption in Aiding Medical Short Diagnosis" Bin Hu, Chengsheng Mao, and Xiaowei Zhang B386 "An Integrative Genomic Study for Multimodal Genomic Data Using Multi-Block Bipartite Regular Graph" Mingon Kang, Juyoung Park, Dong-Chul Kim, Ashis Biswas, Chunyu Liu, and Jean Gao

35

B441 "Does Encoding Matter? A Novel View On The Quantitative Genetic Trait Prediction Problem" Short Dan He

Session 21 Computational Systems Biology B286 "A Two-Stage Clustering Technique for Automatic Biaxial Gating of Flow Cytometry Data" Regular Maziyar Baran Pouyan, Vasu Jindal, Javad Birjandtalab, and Mehrdad Nourani

B466 "Purification of LC/GC-MS based Biomolecular Expression Profiles Using a Topic Model" Regular Minkun Wang, Tsung-Heng Tsai, Guoqiang Yu, and Habtom Ressom B394 "Sequential Data Selection for Predicting the Pathogenic Effects of Sequence Variation" Short Mark Rogers, Hashem Shihab, Tom Gaunt, Matthew Mort, David Cooper, and Colin Campbell B340 "Improved Algorithms for Finding Edit Distance Based Motifs" Regular Soumitra Pal and Sanguthevar Rajasekaran B354 "Boosting Compound-Protein Interaction Prediction by Deep Learning" Regular Kai Tian, Mingyu Shao, Shuigeng Zhou, and Jihong Guan B347 "An efficient method to identify essential proteins for different species by integrating protein Short subcellular localization information" Xiaoqing Peng, Jianxin Wang, Jiancheng Zhong, Junwei Luo, and Yi Pan B426 "An Efficient ACS Algorithm for Classification-based Peptide Identification" Short Xijun Liang, Zhonghang Xia, Ling Jian, Xinnan Niu, and Andrew Link B501 "RF-Phos: Random Forest-Based Prediction of Phosphorylation Sites" Short Hamid Ismail, Ahoi Jones, Jung Kim, Robert Newman, and Dukka KC

Session 22 Bioinformatics Infrastructure B280 "Accelerating Large-Scale Biological Database Search on Xeon Phi-based Neo-Heterogeneous Regular Architectures" Haidong Lan, Weiguo Liu, Bertil Schmidt, and Bingqiang Wang

B344 "HPMA: High-performance Metagenomic Alignment Tool, on a Large-Scale GPU Cluster" Short Ibrahim Savran and John Rose

B248 "Scalable Biobanking: A Modular Electronic Honest Broker and Biorepository for Integrated Regular Clinical, Specimen and Genomic Research" Alex Felmeister, Tyler Rivera, Aaron Masino, Jeffrey Pennington, and Adam Resnick

B520 "Large scale multi-species palindrome study using distributed in-memory computing" Short Devin Petersohn, Matt Spencer, Alex Fratila, and Chi-Ren Shyu B428 “Inference of Gene Regulatory Networks via Multiple Data Sources and a Recommendation Short Method” Makbule Gulcin Ozsoy, Faruk Polat, and Reda Alhajj

36

Session 23 Industry and Government N201 " A Highly Parallel Next-Generation DNA Sequencing Data Analysis Pipeline in Hadoop" Regular Kareem Aggour, Vijay Kumar, Dipen Sangurdekar, Lee Newberg, and Chinnappa Kodira

N202 " Structuring Unstructured Clinical Narratives in OpenMRS with Medical Concept Extraction" Regular Ryan Eshleman, Hui Yang, and Barry Levine

N204 " The Medical Knowledge Cockpit: Real-time Analysis of Big Medical Data Enabling Precision Regular Medicine" Matthieu-P. Schapranow

P216 “Development and Testing of Prediction Models for End Stage Kidney Disease Patient Nonadherence to Renal Replacement Treatment Regimens Utilizing Big Data and Healthcare Informatics” Outlook Yue Jiao, Dan Geary, Sheetal Chaudhuri, Mahathi Mothali, Terry Ketchersid, Dugan Maddux, John Larkin, Scott Ash, Len Usvyat, Franklin Maddux, and Peter Kotanko P221 “ZSeq 2.0: A Fully Automatic Preprocessing Method for Next Generation Sequencing Data” Outlook Abed Alkhateeb, Iman Rezaeian, and Luis Rueda P235 “A New DP Algorithm for Comparing Gene Expression Data Using Geometric Similarity” Outlook Amir Vajdi, Nurit Haspel, and Hadi Banaee P240 “PACH: Ploidy-AgnostiC Haplotyping” Outlook Sepideh Mazrouee

37

Poster List

Poster Poster Title ID P202 Ruihuan Pan, Mingfeng He, Lechang Zhan, Zhen Huang, Jie Zhan, and Hongxia Chen, Bo’s Abdominal Acupuncture mitigate post-stroke fatigue: a clinical center retrospective analysis P203 Wen-Chen Lin, Tieh-Cheng Fu, Sheng-Cheng Huang, Cheng-Lun Tsai, Wen-Chi Lin, and Kang-Ping Lin, Influence of Heart Rate Variability in Healthy Subjects with Respiratory Manipulation P205 Reda Rawi, Khalid Kunji, Abdelali Haoudi, and Halima Bensmail, Residue-Residue Contact Prediction in the HIV-1 Envelope Glycoprotein Complex P208 Thomas Joseph, Vangala Govindakrishnan Saipradeep, Sujatha Kotte, Aditya Rao, and Rajgopal Srinivasan, Plugin for concept-assisted search and navigation on PubMed P209 Gladys Andino, Michael Gribskov, Denis Anderson, Jay Evans, and Greg Hunt, Differential gene expression in Varroa jacobsoni mites following a host shift to European honey bees (Apis mellifera) P211 Lishuang Li, Jieqiong Zheng, Dingxin Song, Rui Guo, and Degen Huang, Protein-Protein Interaction Extraction Based on Actively Transfer Learning P212 Insung Ahn and Jin-Wha Jang, Comparative Study of Middle East respiratory syndrome coronavirus using Bioinformatics Techniques - Based on the codon variation patterns P215 Seok Won Jeong, Myungguen Chung, Soo-Jung Park, and Seong Beom Cho, Genome-Wide Association Study of Biochemical traits based on eQTL-SNPs in Korean. P216 Yue Jiao, Dan Geary, Sheetal Chaudhuri, Mahathi Mothali, Terry Ketchersid, Dugan Maddux, John Larkin, Scott Ash, Len Usvyat, Franklin Maddux, and Peter Kotanko, Development and Testing of Prediction Models for End Stage Kidney Disease Patient Nonadherence to Renal Replacement Treatment Regimens Utilizing Big Data and Healthcare Informatics P217 PENG Yue, FANG Ming, WANG Chongjun, and XIE Junyuan, Entropy Chain Multi-Label Classifiers for Traditional Medicine Diagnosing Parkinson’s Disease P219 Atsushi matsumoto, Tadasuke Ito, Yurie Nishi, Tatsuro Teraoka, Shin Aoki, and Hayato Ohwada, Prediction of Radioprotectors Targeting p53 for Suppression of Acute Effect of Cancer Radiotherapy using Machine Learning P220 Songjian Lu, Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets P222 ZhiWei LIANG, LiWen ZHOU, Ning XU, JianBiao XU, QianRong LIANG, XiaoYang ZHANG, ZhongXun YUAN, Jing AN, XueLian MO, JuanHong ZENG, CanDong LI, Yi ZHOU, XiaoYan LUO, DongXu JIANG, XiaoPing LAI, Ye YUAN, and ShouZeng ZHENG, Cooperative Service Model Innovation and Pilot Application in the Prevention and Control on Diabetic Retinopathy with Web-movable Hand-hold Fundus Camera in Regional Health and Medicine of Digitization P223 V. B. Surya Prasath, Kiichi Fukuma, Bruce J. Aronow, and Hiroharu Kawanaka, Cell Nuclei Segmentation in Glioma Histopathology Images with Color Decomposition Based Active Contours P224 Xiangzhou Huang, Yin Zhang, Baogang Wei, and Liang Yao, A Question-Answering System over Traditional Chinese Medicine P227 V. B. Surya Prasath and Hiroharu Kawanaka, Vascularization Features for Polyp Localization in Capsule Endoscopy

38

P232 Juyoung Park, Mingon Kang, Younghoon Kim, and Kyungtae Kang, Heartbeat Classification for Detecting Arrhythmia Using Normalized Beat Mophology Features P235 Amir Vajdi, Nurit Haspel, and Hadi Banaee, A New DP Algorithm for Comparing Gene Expression Data Using Geometric Similarity P238 Jun Tan and Donald Adjeroh, A New Encoding Scheme for Protein Structure Representation P241 ZhiWei LIANG, YongYun WANG, XiaoYan LUO, QianRong LIANG, Ye YUANG, LiNi WANG, Yi ZHOU, and CanDong LI, An Algorithm for the Diversity of XML Document Based on the Model of the Rights- Distribution for Ancestral Property and its Testing Application in the Field of Health and Chinese Medicine P206 Joe Chalfoun, Michael Majurski, Tim Blattner, Walid Keyrouz, Peter Bajcsy, and Mary Brady, MIST: Microscopy Image Stitching Tool P214 Myungguen Chung, Seok Won Jeong, Soo-Jung Park, and Seong Beom Cho, A Case-Control Genome-Wide Association Study of Metabolic Syndrome in Korean. P218 Balachandran Manavalan, Structure-based protein folding type classification and folding rate prediction P221 Abed Alkhateeb, Iman Rezaeian, and Luis Rueda, ZSeq 2.0: A Fully Automatic Preprocessing Method for Next Generation Sequencing Data P225 Mingzhen Zhao, Bo Xu, Hongfei Lin, Jian Wang, and Zhihao Yang, Discover potential adverse drug reactions using the skip-gram model P228 Joseph Crawford, Yihan Sun, and Tijana Milenkovic, Fair Evaluation of Global Network Aligners P229 Sagar Patel, Padmapriya Swaminathan, Anne Fennell, and Erliang Zeng, De novo genome assembly tool comparison for highly heterozygous species Vitis vinifera cv. Sultanina P230 Aditya Rao, Thomas Joseph, Vangala Govindakrishnan Saipradeep, and Rajgopal Srinivasan, UIMA based Solution in Pharma Text P234 NUHAD MALALLA, Pengfei Sun, Ying Chen, Michael Lipkin, Glenn Preminger, and Jun Qin, Preliminary Study on C-arm Technique for Nephrolithiasis and Kidney Stones Detection P236 Henry Fabian Tobar Tosse, Sebastian Florido Sarria, Eliana Ocampo Toro, Pedro Miguel Hernandez, Andres Zuniga, and Paula Margarita Hurtado, Rare diseases clustering based on structural regularities at the gene structure P237 Mehdi Kchouk and Mourad Elloumi, Error Correction and DeNovo Genome Assembly for the MinION Sequencing Reads mixing Illumina Short Reads P240 Sepideh Mazrouee, PACH: Ploidy-AgnostiC Haplotyping

39

Conference WiFi Instruction

Instructions on connecting to Wireless Internet in meeting space

Network Name (SSID): @Hyatt_Meeting

Password: YENKDW

40

IEEE BIBM 2016 Call For Papers

41