2015 IEEE International Conference on Bioinformatics and

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2015 IEEE International Conference on

Bioinformatics and Biomedicine

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

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Sponsored by

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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

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IEEE BIBM 2015 Program Schedule

Program

• November 09, 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

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Monday, Nov 9 (Workshops and Tutorials)

7:20am – 6:30pm Registration Ballroom Foyer

10:30-10:50am

and 3:30-3:50pm

Coffee Break

Meeting Room Foyer

12:00-1:30pm Lunch (On Own)

1:30-6:00pm Poster Session (Set Up)

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

Workshop: The 2015 Computational Structural Bioinformatics Workshop Jing He, Amarda Shehu, Nurit

Haspel, Brian Chen Judiciary Suite

Workshop: 2015 International Workshop on Biomedical and Health

Informatics Illhoi Yoo Embassy/Patuxent

Workshop: COMputational Methods for Analyzing Metagenomics Data Catherine Putonti, Charlie Xia

and Erliang Zeng Diplomat/Ambassador

Workshop: The 6th Integrative Data Analysis in Systems Biology (IDASB

2015).

Rui Jiang, Huiru Jane Zheng,

Zhongming Zhao Cartier/Tiffany

Joint Workshop Schedule Data mining in translational biomedical informatics & Second International Workshop on the Role for Quantified Self for Personal

Healthcare

Qian Zhu, Hongfang Liu, Frank Hopfgartner, Na Li

Susquehanna

Workshop: Data mining from genomic variants and its application to genome-wide analysis

Taesung Park Baccarat

Tutorial: Integrative Genomic Big-Data Analytics for Translational Bioinformatics and Precision Medicine Research (10am-12noon)

Mary Yang and Kenji Yoshigoe

Haverford

1:30-6:00pm Workshops/Tutorials Session Chair Location

Workshop: Inaugural International Workshop on Biological Network Driven Analysis

Fione Brown Waterford

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

Workshop: The 2015 Computational Structural Bioinformatics Workshop Jing He, Amarda Shehu, Nurit

Haspel, Brian Chen Judiciary Suite

Workshop: 2015 International Workshop on Biomedical and Health

Informatics Illhoi Yoo Embassy/Patuxent

Tutorial: Introduction to computational analysis of microbiome shotgun

sequencing data (1:30-3:30pm) Daniel H. Huson Haverford

Tutorial: Human Microbiome Analysis: Computational Techniques and Challenges (4:00-6:00pm)

Serghei Mangul Haverford

Workshop: Semantic Data Analytics and Bioinformatics Haiying Wang Lalique

Joint Workshop Schedule

Nonnegative Matrix Factorization and Tensor Decomposition Techniques for High-Throughput Biological Data Analysis &

Computational Regulatory Genomics and Metagenomics

Michael Ochs, Elana Fertig,

Alieoune Ngom, Hongyu Zhang, Guoliang Li, Anyuan

Guo, Hongyu Ou and Xingpeng Jiang

Baccarat

Workshop: International Workshop on Biomolecular Interaction Network Analysis and Interactomics

Young-Rae Cho

Diplomat/Ambassador

Workshop: The 6th Integrative Data Analysis in Systems Biology (IDASB 2015).

Rui Jiang, Huiru Jane Zheng,

Zhongming Zhao Cartier/Tiffany

Workshop: Electronic Health Record: Implementation, Data Mining, Security and User Acceptance

Manuel Grana, Michel

Wozkniak, Konrad Jakowski Susquehanna

Workshop: Biomedical Visual Search and Deep Learning

Richard Conroy, Vinay Pai,

Todd Horowitz, Susan

Gregurick, Tom Radman

Potomac

Workshop: The 6h International Workshop on High Performance Computing in Bioinformatics

Che-Lun Hung et al. Severn

http://staff.icar.cnr.it/cannataro/hibb2015/

mailto:[email protected]



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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

9:00-10:00am

Keynote Lecture 1 (Chair: Satoru Miyano) “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


(including

Invited talks)

Session5: Biological Networks II Przytycka, Teresa Cabinet Suite

Session6: Translational Bioinformatics I Yang, Mary Diplomat/Ambassador

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


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

7:00-9:00pm

Banquet (Ticket required)

1. Introduction of BIBM 2016 Host City (Chairs: Xiaohua Tony Hu, Jianguo Lu)

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

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Wednesday, Nov 11

8:00am-6:00pm


9:00-10:00am

Keynote Lecture 2 (Chair: Sanguthevar Rajasekaran) 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

1:00-2:00pm

Keynote Lecture 3 (Chair: Luke Huan) Toward Personalized Pan-Omic Association Analysis under Complex Structure s and Big Data

Eric Xing Crystal Ballroom

Poster Session Meeting Room Foyer and Concours Terrace

2:00-3:40pm Panel

Federal Agencies and Industry

Crystal Ballroom

3:40-4:00pm Coffee Break

Meeting Room Foyer


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

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Thursday, Nov 12

8:00-10:00am


9:00-10:00am

Keynote Lecture 4 (Chair: Amarda Shehu)

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

Biology Fahad Saeed Old Georgetown

Workshop: Machine learning in decision making for biomedical

applications Mahua Bhattacharya Embassy/Patuxent

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Floor Plan

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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.

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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.

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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

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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.

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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.

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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

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Workshops

Inaugural International Workshop on Biological Network Driven Analysis

Session Chairs: Fiona Browne, Haiying Wang

Time Title Presenter/Author

13:30-14:15 Opening talk:

Biological Network Driven Analysis for discovering novel disease genes and pathways, biomarkers and drug targets

for disease. Fiona Browne

14:15 – 14:45 On the Comparison of State- and Transition-based Analysis of

Biological Relevance in Gene Co-expression Networks

Kathryn Cooper. Prasuna Vemuri, and

Hesham Ali

14:45-15:15 Network signatures based on gene pair expression ratios improve

classification and the analysis of muscle-invasive urothelial cancer

Ricardo de Matos, Simoes, Constantine

Mitsiades, Kate E Williamson, Frank

Emmert-Streib

15:30-16:00 Coffee Break

16:00 – 16:30 Visualizing the topology and re-analyzing the causes of small-world

property of amino acid network

Yongpan Hua, Xiuchan Xiao, Min Zhu,

Yangxu Wang and Menglong Liy

16:30 – 17:00 Functional Connectivity of Chinese Characters Processing:A Meta-

analysis

Yaoxin Nie, Jieyao Wei, Linlin Zhu, Qian

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


13:30-15:30

Session 1Nonnegative Matrix Factorization and Tensor Decomposition Techniques for High-Throughput Biological

Data Analysis

Elana Fertig Session Co-chair: Alioune Ngom

The Estimation of Dimensionality in Gene Expression Data using

Nonnegative Matrix Factorization Michael Ochs

A Hybrid Algorithm for Non-Negative Matrix Factorization Based on

Symmetric Information Divergence Karthik Devarajan

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)

16:00-17:25 Session 2: Computational Regulatory Genomics and Metagenomics

16:00-16:25 A New DP Algorithm for Comparing Gene Expression Data Using

Geometric Similarity Amir Vajdi, Nurit Haspel, and Hadi Banaee

16:25-16:50 Understanding Heterogeneity in Pregnancy Associated Breast Cancer Murlidharan Nair

16:50-17:15 A Novel Signature For Identification Of Upstream Alternative

Translation Initiation Sites Kritika Karri and Dhundy Bastola

17:15-17:40 Patho-finder – a Fast and Accurate Program for Pathogen

Identification through RNA-seq

Chin-Ting Wu, Tzu-Hung Hsiao, Yu-Chiao

Chiu, Yu-Ching Hsu, Eric Chuang, and

Yidong Chen


17

6th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB-2015) Session Chair: Mario Cannataro


09:00 – 10:30 Session 1 (15 minutes for talk and 5 minutes for Q and A)

Session Chair: Mario Cannataro

Opening Remarks

An LDA and Probability-based Classifier for the Diagnosis of

Alzheimer's Disease from Structural MRI Alexander Spedding

Time Series Discord Detection in Medical Data using a Parallel

Relational Database, Diane M. Woodbridge

Towards an Efficient Data Assimilation in Physically-Based Medical

Simulations Igor Peterlik

Overall Survival Analyzer: a software tool to analyze genotyping and

clinical data enriched with temporal events Giuseppe Agapito

10:30-11:00 Coffee Break – perhaps poster session

11:00-12:00 Session 2(15 minutes for talk and 5 minutes for Q and A)

Session Chair: Mario Cannataro

Conservation in Mitochondrial DNA: Parallelized Estimation and

Alignment Influence Jorge Álvarez-Jarreta

Ancestral Reconstruction under Weighted Maximum Matching Jijun Tang

High performance computing of a fusion gene detection pipeline on

the K computer Satoshi ITO

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


13:30 – 15:30 Session 1 (30 minutes for each talk)

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,

and Passing Medical Licensing Exams

Barry Robson and Srinidhi Boray

Selected Aspects of Electronic Health Record Analysis from the Big

Data Perspective

Boguslaw Cyganek, Manuel Grana, Andrzej

Kasprzak, Krzysztof Walkowiak, and Michal

Woznia

Tensor Based Representation and Analysis of the Electronic

Healthcare Record Data Boguslaw Cyganek and Michal Wozniak

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

09:00-09:20 Next Generation Sequence Assembler Mis-assembly of Phage

Genomes with Terminal Redundancy Julia Sommer

09:20-09:40 A Computational Framework for Integrative Analysis of Large

Microbial Genomics Data

Erliang Zeng, Wei Zhang, Scott Emrich, Dan

Liu, Josh Livermore, and Stuart Jones

09:40-10:00 Finding Function in the Unknown: Methods for Examining

Transcriptomes of Non-Model Organisms

Kelly Boyd, Emma Highland, Amanda

Misch, Amber Hu, Sushma Reddy, and

Catherine Putonti, Loyola

10:00-10:20 CoCo: an application to store High Throughput Sequencing data in

compact text and binary file formats

Kamil Khanipov, Georgiy Golovko, Mark

Rojas, Levent Albayrak, Otto Dobretsberger,

18

Maria Pimenova, Nels Olsen, Sergei

Chumakov, and Yuriy Fofanov


10:50-11:10 HAsh-MaP-ERadicator: Filtering Non-Target Sequences from Next

Generation Sequencing Reads Jonathon Brenner and Catherine Putont

11:00-11:30 Bipartite Graphs for Metagenomic Data Analysis and Visualization Karel Sedlar, Helena Skutkova, Petra

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


09:00 – 10:30 Session 1 (20 minutes for each talk, including Q and A)

Session Chair: Dr. Heejong Sung

09:00-09:10 Opening Remarks

Developing cancer prediction model based on stepwise selection by

AUC measure for proteomics data Yongkang Kim, Seungyeoun Lee, etc

Competitive pathway analysis using structural equation models (CPA-

SEM) for gene expression data Sungkyoung Choi, Sungyoung Lee, etc

Cross-validation and cross-study validation of chronic lymphocytic

leukemia with exome sequences and machine learning

Nihir Patel, Abdulrhman Aljouie, Bharati

Jhadav, and Usman Roshan

Dynamic regulation of RNA-editing in human brain development Taeyoung Hwang, JooHeon Shin, and Daniel

Weinberger


10:50-12:10 Session 2(20 minutes for each talk, including Q and A)

Session Chair: Prof. Taesung Park

VizEpis : a visualization and mapping tool for interpreting epistasis Min-Seok Kwon, Sungyoung Lee, Yongkang

Kim, and Taesung Park

Multi-purpose SNP Selection by the principal variables for a genetic

study Seunghyun Lee and Mira Park

Tiled regression reduces type I error rates in tests of association of rare

single nucleotide variants with non-normally distributed traits,

compared with simple linear regression

Heejong Sung, Alexa Sorant,etc

Genetic association tests for aggregated count data Haewon Choi, Hye-Young Jung, and

Taesung Park

11:20 Closing

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


09:00 – 10:30 Session 1 (15inutes for each talk, including Q and A)

Session Chair: Qian Zhu

Opening Remarks

Resting State Functional Connectivity Explains Individual Scores of

Multiple Clinical Measures for Major Depression Kosuke Yoshida, Yu Shimizu, etc

Acquisition of diabetes-related biological associations using a motif

based network: preliminary results

Iyanuoluwa Odebode, Aryya Gangopadhyay,

and Qian Zhu

BmQGen: Biomedical Query Generator for Knowledge Discovery Feichen Shen, Hongfang Liu, Sunghwan

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



19


Thermal Sensor Based Multi-occupancy Motion Tracking and

Visualisation in Smart Environments

Jun Zhou, Huiru (Jane) Zheng, Haiying

Wang,etc

Usability testing of a novel automated external defibril l ator user

interface: a pilot study

Peter O'Hare, Rebecca Di Maio, and

Raymond Bond

Outlier Detection in Weight Time Series of Connected Scales Saeed Mehrang, Elina Helander, Misha

Pavel, Angela Chieh, and Ilkka Korhonen

The Syndromes of Lung Cancer and Compatibility of Medicine in

Traditional Chinese Medicine Science Treatment Based on Clustering

Algorithm

Miao Wang, Mengying Wang, Dongyi

Wang,etc

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-

series Clusters

Abed Alkhateeb, Iman Rezaeian, Siva

Singireddy, and Luis Rueda

CancerVis: an Interactive Exploratory Tool for Cancer Biomarker

Analysis

Lei Zhang, Ying Zhu, and Sergey Klimov

ILP based screening applied to predicting carbonic anhydrase II

ligands

Tadasuke Ito, Masato Okada, Shotaro

Togami, Shinya Ariyasu, Shin Aoki, and

Hayato Ohwada

Exploration of Topological Torsion Fingerprints Petr Škoda and David Hoksza

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

Patients

Ali Azari, Vandana Janeja, and Scott Levin

Clinical Processes from Various Angles - Amplifying BPMN for

Integrated Hospital Management

Richard Braun, Martin Burwitz, Hannes

Schlieter, and Martin Benedict

Predictive and Preventive Models for Diabetes Prevention using

Clinical Information in Electronic Health Record

Ni Cao, SiSi Zeng, Feixia Shen, Chuandi

Pan, Chengshui Chen, Thanh Nguyen, and

Jake Chen

12:00-12:30 Poster Session

Risk Prediction of Stroke: A Prospective Statewide Study on Patients

in Maine

Le Zheng, Yue Wang, Shiying Hao, etc.

A GRReat Framework for Incident Response in Healthcare

Subrata Acharya, William Glenn, and

Matthew Carr

Patient Portal: Anytime Anywhere

Subrata Acharya, Gabriel Susai, and Manoj

Pillai

OWASP Inspired Mobile Security

Subrata Acharya, Branden Ehrenreich, and

James Marciniak



Simple Objects Tracking System for Smart Homes

Frederic Bergeron, Kevin Bouchard,

Sebastien Gaboury, Sylvain Giroux, and

Bruno Bouchard

20

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


09:00 – 10:30 Session 1 (15inutes for each talk, including Q and A)

Session Chair: Huiru Zheng Co-chair: Zhongming Zhao

Opening Remarks

The upregulation of Myb and Peg3 may mediate EGCG inhibition

effect on mouse lung adenocarcinoma

Hong Zhou, Joseph Manthey, Ekaterina

Lioutikova, etc

Construction of Dynamic Probabilistic Protein Interaction Networks

for Protein Complex Identification Yijia Zhang

Sketching the distribution of transcriptomic features on RNA

transcripts with Travis coordinates Xiaodong Cui, Zhen Wei,


11:00-11:30 Session 2

Session Chair: Huiru Zheng Co-chair: Zhongming Zhao

Integrating Prior Biological Knowledge and Graphical LASSO for

Network Inference

Yiming Zuo, Guoqiang Yu, and Habtom

Ressom

11:0\30-12:30 poster session


13:30-15:30 Session 3

Session Chair: Zhongming Zhao Session Co-chair: Huiru Zheng

Identification of Hot Regions in Protein-Protein Interactions Based on

SVM and Detecting Local Community Structure Xiaoli Lin

S-Fit: Knowledge guided Fitness Pattern Mining Framework

Ayush Sharma, Komal Agarwal, Rahul

Dubey, Sandip Bhaumik, and samudrala

nagaraju

ccKOPLS: Confounder-Correcting Kernel-based Orthogonal

Projections to Latent Structures

David Moore, Kellan Fluette, Heather Milne,

Andrew Shedlock, and Paul Anderson

Feature Selection and Classification of Speech under Long-term Stress

Bin Hu, Zhenyu Liu, Lihua Yan, Tianyang

Wang, Fei Liu, Xiaoyu Li, and Huanyu Kang

Direct Higher Order Fuzzy Rule-based Classification System:

Application in Mortality Prediction

Abolfazl Doostparast Torshizi, Linda

Petzold, and Mitchell Cohen



Design of a Real-time Morphology-based Anomaly Detection Method

from ECG Streams

DuyHoa NGO and Bharadwaj Veeravalli

Analyzing epileptogenic brain connectivity networks using clinical

EEG data

Abhijit Dasgupta, Ritankar Das, Losiana

Nayak, and Rajat K. De

Analysis of Machine Learning Algorithms on EEG Data for Brain

State Intelligence (short)

Alexander Chan, Christopher Early, Sishir

Subedi, Yuezhe Li, and Hong Lin

Shared Genetic Architecture In Autoimmune Disease - Preliminary

Analysis (short)

Leqi Liu, Ziyan Yang, Jia Tao, and Fadi

Towfic

Risk prediction for future 6-month healthcare resource utilization in

Maine (short)

Shiying Hao, Zhongkai Hu, Bo Jin, etc.

Entropy Chain Multi-Label Classifiers for Traditional Medicine

Diagnosing Parkinson’s Disease (short)

PENG Yue, FANG Ming, WANG Chongjun,

and XIE Junyuan

17:50 Closing Remark

21

Simulation of Effects of TBX18 on the Pacemaker Activity of Human

Ventricular Cells

Yue Zhang, Kuanquan Wang, Henggui

Zhang, and Wei Wang

15:30-16:00 Coffee Break, poster session (coffee: 15:30-15:50)

16:00-17:00 Session 4

Session Chair: Zhongming Zhao Co-chair: Huiru Zheng

Reconstructing Transcriptional Regulatory Networks Using Data

Integration and Text Mining

Rafael Pereira, Hugo Costa, Sónia Carneiro,

Miguel Rocha, and Rui Mendes

Prioritization Through Geometric-Inspired Kernel Data Fusion POOYA ZAKERI, Sara Elshal, and Yves

Moreau


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


09:30 – 10:30 Session 1 (20 mins for full papers and 15 mins for short papers)

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

Smart Mobile Phone based Approach

Herman Chan, Huiru (Jane) Zheng, Haiying

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

Support Systematic Reviews Abdulaziz Alamri and Mark Stevenson

SOLOMON: An Ontology for Sensory-Onset, Language-Onset and

Motor-Onset Dementias

Martin Skarzynski, Adam Craig, and Carl

Taswell

A Distributional Approach to Summarization of Radiology Reports Eamon Johnson, W Christopher Baughman,

and Gultekin Ozsoyoglu

Transcriptome analysis of HIV-1 virus in understanding the effect of

antiretroviral drugs (cART) and methamphetamine on the virus

Ishwor Thapa, Howard Fox, and Dhundy

Bastola


A Prototype for a Hybrid System to Support Systematic Review

Teams: A Case Study of Organ Transplantation

Tanja Bekhuis, Eugene Tseytlin, and Kevin

Mitchell

A systems chemical biology approach to identify targets of

antibacterial agents: a case study of Chelerythrine and Rhein Li-Da Zhu, Chang-Shou He, Ye-Mao Liu

Using Aggregate Taxonomies to Summarize SNOMED CT Evolution Christopher Ochs, Yehoshua Perl, James

Geller, and Mark Musen

A Path Based Approach to Quantifying the Progression of Alzheimer's

Disease Prabesh Kanel and Xiuwen Liu

Investigating gene expression array with outliers and missing data in

bladder cancer Stéphane Chrétien, Christophe Guyeux,etc

A semantic approach for knowledge capture of microRNA-target gene

interactions Jingshan Huang, Fernando,etc


A Systems Approach to Reducing Central Line Associated Blood

Stream Infections Eva Lee, Michael Callahan

Refining Disease Databases for Clinical Decision Support Systems -

Post-processing disease entries after integration of OMIM and

Orphanet

Takashi Okumura, Demi Menez, and

Theekshana Abayawickrama

Dealing with incompleteness in Multidimensional Analysis of Health

Records: an Experience on Fetal Growth Mario Bochicchio, Lucia Vaira,etc

Activity-Driven Exploration of Chemical Space with Morphing Matin Šícho, Daniel Svozil, and David

Hoksza

Comparative Utility of Time and Frequency HRV Domains for

Automated Classification of Exercise Exertion Level In cheol Jeong and Joseph Finkelstein

A Novel Automatic Tongue Image Segmentation Algorithm: Color

Enhancement Method Based on L*a*b* Color Space

Li Chen, Dongyi Wang, Yiqin Liu, Xiaohang

Gao, and Huiliang Shang

Directed Cyclic Graph-Based Feature Selection and Modeling of The Weifei Xu, Guoping Liu, Jianjun Yan, Yiqin

22

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


13:30-15:30 Session 1 (25-minute presentation and 5-minute Q & A.)

Session Chair: Young-Rae Cho

MODULA: A Network Module Based Local Protein Interaction

Network Alignment Method.

Pietro Hiram Guzzi, Pierangelo Veltri,

Swarup Roy, and Jugal K Kalita.

Diffusion Kernel to Identify Missing PPIs in Protein Network

Biomarker. Dominic Bett and Ananda Mondal.

Testing whether hot regions in protein–protein interactions are

conserved in different species Jing Hu and Xiaolong Zhang.

Mining Maximal Subnetworks from Interaction Network with Node

Attributes

Aditya Goparaju, Bassam Qormosh, and

Saeed Salem.


16:00-17:00 Session 2

Session Chair: Pierangelo Veltri

SRP: A Concise Non-parametric Similarity-Rank-based Model for

Predicting Drug-Target Interactions. Jian-Yu Shi and Siu-Ming Yiu.

Semantic mapping to align PPI networks and predict conserved

protein complexes. Lizhu Ma and Young-Rae Cho


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


13:30-17:15

Session Chair: Dr. Vinay Pai, NIBIB, NIH

13:30-13:35 Opening Remark(5mins)

13:35-14:20 Keynote Part 1

Visual Search in Biomedical Sciences Todd Horowitz, NCI, NIH.

14:20-14:40 Probabilistic Visual Search for Masses Within Mammography Images

using Deep Learning Mehmet Gunhan Ertosun and Daniel Rubin

14:40-15:10 Keynote Part 2

Deep Learning in Basic Biomedical Sciences Susan Gregurick, NIGMS, NIH.

15:10-15:30 Learning structure in gene expression data using deep architectures,

with an application to gene clustering

Aman Gupta, Haohan Wang, and Madhavi

Ganapathiraju


15:50-16:10 Deep Learning of Tissue Fate in Acute Ischemic Stroke Noah Stier, Nicholas Vincent, David

Liebeskind, and Fabien Scalzo

16:10-16:30 A deep learning-based segmentation method for brain tumor in MR

images

Yi Ding, Ruohan Huang, Tian Lan, Xinjie

Zhang, Wei Wang, and Zhiguang Qin

16:30-16:50 Detection of Hyperperfusion on Arterial Spin Labeling using Deep

Learning

Nicholas Vincent, Noah Stier, Songlin Yu,

David Liebeskind, Danny Wang, and Fabien

Scalzo

16:50-17:15 Open Discussion Tom, Radman, NIDA, NIH

23

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


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

Reconstruction Shang Gao

An Algorithm for Discovering Deep Order Preserving Submatrix in

Gene Expression Data

Qiuhua Kuang, Meizhen Zhang, Zhihao Ma, Bo

Ma, Zhiwen Liu, and Yun Xue


16:00-17:10 Session 2(25mins for each talk)

A Unified Approach to the Computation and Analysis of Strings of

Gene Expression States Jaime Seguel and Marie Lluberes

Leveraging the k-Nearest Neighbors Classification Algorithm for

Microbial Source Tracking Using a Bacterial DNA Fingerprint Library Jeffrey McGovern, Alexander Dekhtyar,etc

DNA Sequences Compression Algorithms Based on the Two bits

Codation Method Bacem SAADA and Jing Zhang,

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


09:00-10:30 Session 1 (30mins for each talk)

Session Chair: Che-Lun Hung

Opening Remarks

Innovative Approach for Porting Existing CPU Program to Its CUDA

Program

Yu Liu, Yang Hong, Chung-Hung Wang, Sheng-

Ta Lee, Chun-Yuan Lin, and Che-Lun Hung

Cloud Computing Framework for Bioinformatics Tools Guan-Jie Hua, Che-Lun Hung, Chuan Yi Tang,

and Yaw-Ling Lin

Biomarker Discovery, High Performance and Cloud Computing: A

Comprehensive Review

Jaine Blayney, Valeriia Haberland, Gaye

Lightbody, and Fiona Browne Combining AR filter and Sparse Wavelet representation for P300

speller Zhihua Huang and Huiru (Jane) Zheng

A Study of Genomic Data Provenance in NoSQL Document-Oriented

Database Systems

Valeria Guimarães, Fernanda Hondo, Rodrigo

Almeida, Harley Vera, Maristela Holanda,

Aleteia Araujo, Sérgio Lifschitz, and Maria

Emilia Walter


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,

24

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


9:00-10:30 Session 1(15mins for each talk)


Opening Remarks

Resting State Functional Connectivity Explains Individual Scores of

Multiple Clinical Measures for Major Depression Kosuke Yoshida, Yu Shimizu, etc.

Acquisition of diabetes-related biological associations using a motif

based network: preliminary results

Iyanuoluwa Odebode, Aryya Gangopadhyay,

and Qian Zhu

BmQGen: Biomedical Query Generator for Knowledge Discovery Feichen Shen, Hongfang Liu, Sunghwan 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


11:00-12:00 Session 2 (15mins for each talk)

Session Chair: Huiru(Jane) Zheng

Thermal Sensor Based Multi-occupancy Motion Tracking and

Visualisation in Smart Environments

Jun Zhou, Huiru (Jane) Zheng, Haiying Wang,

Jonathan Synnott, Chris Nugent, and Paul Jeffers Usability testing of a novel automated external defibril l ator user

interface: a pilot study

Peter O'Hare, Rebecca Di Maio, and Raymond

Bond

Outlier Detection in Weight Time Series of Connected Scales Saeed Mehrang, Elina Helander, Misha Pavel,

Angela Chieh, and Ilkka Korhonen

The Syndromes of Lung Cancer and Compatibility of Medicine in

Traditional Chinese Medicine Science Treatment Based on Clustering

Algorithm

Miao Wang, Mengying Wang, Dongyi Wang,

Shiyu Duan, Yisheng Wang, Yanjun Huang, and

Huiliang Shang

25

IEEE Workshop on Machine Learning in Decision Making for Biomedical Applications

Session Chair: .Mahua Bhattacharya


10:20-10:25 Welcome

10:25-10:40 Multi-VBE: A New Model for the Prediction of Hot Spots

at Protein-Protein Interaction Interface

Hui Peng, Quan Liu, Lei Wang, and Jinyan Li

10:40-10:55 Quantitative Clinical guidelines for Imaging Use in

Evaluation of Pediatric Cardiomyopathy

Yuzhe Liu, Shobhit Madan, MD, MPH, and Vanathi

Gopalakrishnan

10:55-11:10 Cross-validation and cross-study validation of chronic

lymphocytic leukaemia with exome sequences and machine

learning

Nihir Patel, Bharati Jhadav, and Usman Roshan

11:10-11:25 A New Compact Set of Biomarkers for Distinguishing

among Ten Breast Cancer Subtypes

Forough Firoozbakht, Iman Rezaeian, Alioune Ngom, and Luis

Rueda

11:25-11:40 A Longitudinal Support Vector Regression for Prediction of

ALS Score

Wei Du, Huey Cheung, Calvin Johnson, Ilya Goldberg, Madhav

Thambisetty, and Kevin Becker

11:40-11:55 Integration of Multimodal RNA-Seq Data for Prediction of

Kidney Cancer Survival

Matt Schwartz, Martin Park, John Phan, and May Wang

11:55:-12:10 EEG-based Seizure Detection Using Discrete Wavelet

Transform through Full-Level Decomposition

Duo Chen, Suiren Wan, and Forrest Bao

12:10-12:25 Effective Image Fusion Method to Study Alzheimer's

Disease using MR, PET Images

Arpita Das and Mahua Bhattacharya

12:25-12:40 A Genetic Algorithm for the Selection of Structural MRI Alexander Spedding,

26

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

27

Conference Paper Presentations

Session 1 Genomics

Regular

B461 "A novel dimensionality reduction algorithm based on Laplace matrix for microbiomie data

analysis"

Yetian Fan, Xingpeng Jiang, Xiaohua Hu, Bo Song, Yuan Ling, and Wei Wu

Regular

B503 "A New Algorithm for The LCS Problem with Application in Compressing Genome

Resequencing Data"

Richard Beal, Tazin Afrin, Aliya Farheen, and Don Adjeroh

Short B453 "Fast alignment filtering of nanopore sequencing reads using locality-sensitive hashing"

Jeremy Wang and Corbin Jones

Regular "SNVSniffer: An Integrated Caller for Germline and Somatic SNVs Based on Bayesian Models"

Yongchao Liu, Martin Loewer, Srinivas Aluru, and Bertil Schmidt

Short B338 "Short Read Error Correction using an Augmented FM-Index"

Seth Greenstein, James Holt, and Leonard McMillan

Short B352 “HapColor: A Graph Coloring Framework for Polyploidy Phasing”

Sepideh Mazrouee and Wei Wang

Session 2 Biological Networks I

Regular B293 "Constructing directed gene regulatory network solely by gene expression data"

Lu Zhang, Yen Kaow Ng, and Shuai Cheng Li

Regular B424 "Triple Imputation for Microarray Missing Value Estimation"

Chong He, Hui-Hui Li, Changbo Zhao, and Guo-Zheng Li

Short

B218 "Principle Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set

Enrichment Analysis Tool"

Neil Clark, Maciej Szymkiewicz, Zichen Wang, Caroline Monteiro, Matthew Jones, and Avi Ma'aya

Short

B311 "Hausdorff Distance and Global Silhouette Index as Novel Measures for Estimating Quality of

Biclusters"

Nishchal Verma, Esha Dutta, and Yan Cui

Regular

B227 "Integrative approach for inference of gene regulatory networks using lasso-based random

featuring and application to Psychiatric disorders"

Dong-Chul Kim, Mingon Kang, Ashis Biswas, Chunyu Liu, and Jean Gao

Short B470 "Gene Selection for Cancer Classification With the Help of Bees"

Johra Moosa, Rameen Shakur, Mohammad Kaykobad, and M Sohel Rahman

Short

B313 "Integrated Study to Infer Dynamic Protein-gene Interactions in human P53 Regulatory

Networks"

Junbai Wang, Qianqian Wu, and Tianhai Tian

28

Session 3 Medical Informatics I

Regular

B229 "RREV: Reconfigurable Rendering Engine for Cross-Cohort Visualization of Clinically Annotated

Polysomnograms"

Catherine Jayapandian, Wei Wang, Michael Morrical, Dennis Dean II, Daniel Mobley, Mathew Kim,

Michael Rueschman, Kenneth Loparo, Susan Redline, and Guo-Qiang Zhang

Short B230 "Feature-Level Fusion of Multimodal Physiological Signals for Emotion Recognition"

Jing Chen, Bin Hu, Lixin Xu, Philip Moore, and Yun Su

Regular B282 "Sparse Multidimensional Patient Modeling using Auxiliary Confidence Labels"

Eric Heim and Milos Hauskrecht

Short B382 "Survival Analysis via Transduction for Semi-Supervised Neural Networks in Medical Prognosis"

Faisal Khan and Casimir Kulikowski

Regular B263 "Context-learning Based Electroencephalogram Analysis for Epileptic Seizure Detection"

Guangxu Xun, Xiaowei Jia, and Aidong Zhang

Short

B395 "On Automated Flow Cytometric Analysis for MRD Estimation of Acute Lymphoblastic

Leukaemia: a comparison among different approaches"

Paolo Rota, Stefanie Groeneveld-Krentz, and Michael Reiter

Short

B275 "On Using Compressed Sensing and Peak Detection Method for the Dynamic Instability

Parameters Estimation for Microtubules Modeled in three States"

Shantia Yarahmadian, Vineetha Menon, and Vahid Rezania

Session 4 Semantics and Ontology I

Regular B222 "Learning to Rank for Biomedical Information Retrieval"

Bo Xu, Hongfei Lin, and Yuan Lin

Regular

B245 "Algorithmic Detection of Inconsistent Modeling among SNOMED CT Concepts by Combining

Lexical and Structural indicators"

Ankur Agrawal, Yehoshua Perl, Christopher Ochs, and Gai Elhanan

Short B203 "Semantic Rules for Extracting Proteins Functions Information from Biomedical Abstracts"

Kamal Taha

Regular B262 "Supporting HIV Literature Screening with Data Sampling and Supervised Learning"

Hayda Almeida, Marie-Jean Meurs, Leila Kosseim, and Adrian Tsang

Regular B271 "Implicit Knowledge Discovery in Biomedical Ontologies: Computing Interesting Relatednesses"

Tian Bai, Leiguang Gong, Casimir Kulikowski, and Lan Huang

Short B216 "A Transition-Based Model for Jointly Extracting Drugs, Diseases and Adverse Drug Events"

Fei Li and Donghong Ji

Short

B281 "A text mining application for linking functionally stressed-proteins to their post-translational

modifications"

Oliver Bonham-Carter and Dhundy Bastola

29

Session 5 Biological Networks II

Invited

Talk I

“Understanding Genotype-Phenotype effects in Cancer via Network Approaches”

Teresa Przytycka

Regular

B326 "Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features

in Glioblastoma Multiforme"

Yu-Chiao Chiu, Kai-Wen Liang, Tzu-Hung Hsiao, Yidong Chen, and Eric Chuang

Short B220 "On Observability of Singleton Attractors in Boolean Networks"

Yushan Qiu, Xiaoqing Cheng, Wai-Ki Ching, Hao Jiang, and Tatsuya Akutsu

Regular B292 "Construction of signaling networks with incomplete RNAi data"

Qiyao Wang, Yaunfang Ren, Mahmudul Hasan, Ahmet Ay, and Tamer Kahveci

Session 6 Translational Bioinformatics I

Invited

Talk II

“Developing Systems Genomics Approaches to Facilitate Precision Medicine research”

Mary Yang

Regular

B205 "Feature Selection of High-dimensional Biomedical Data using Improved SFLA for Disease

Diagnosis"

Yongqiang Dai, Bin Hu, Yun Su, Chengsheng Mao, Jing Chen, Xiaowei Zhang, Philip Moore, Hanshu

Cai, and Lixin Xu

Short

B469 "A new method for prioritizing drug repositioning candidates extracted by literature-based

discovery"

Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Dingcheng Li, Rashmi Prasad, and

Hongfang Liu

Short B482 "Detecting Adverse Drug Effects Using Link Classification on Twitter Data"

Satya Katragadda, Harika Karnati, Murali Pusala, Vijay Raghavan, and Ryan Benton

Session 7 Medical Imaging

Invited

Talk III

“Empowering self-management for chronic conditions through technology and analytics: Can machines

care for us?”

Huiru (Jane) Zheng

Regular B500 "Level Set Segmentation using Non-Negative Matrix Factorization of Brain MRI Images"

Dimah Dera, Nidhal Bouaynaya, and Hassan Fathallah-Shaykh

Regular B247 "Spatio-Temporal Diffusion-based Dynamic Cell Segmentation"

Fatima Boukari and Sokratis Makrogiannis

Short

B251 "Quantitative Assessment of the Parallel MRI Reconstruction Using Background Noise

Uniformity"

Fu-Hsing Wu and Hsin-Chih Lo

30

Session 8 Structure, Function and Evolution I

Invited

Talk IV

“Protein Match Making at Massive Scale”

Chi-Ren Shyu

Regular B258 "Computational Synteny Block: A framework to identify Evolutionary Events"

Jose A. Arjona-Medina and Oswaldo Trelles

Regular B435 "A Module tree of Wnt Signaling Pathways"

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

Regular B393 "Predicting microRNA-disease associations by integrating multiple biological information"

Wei Lan, Jianxin Wang, Min Li, Jin Liu, and Yi Pan

Regular

B458 "Model-Based and Context-Specific Background Correction and Differential Methylation

Testing for MBDCap-seq"

Yuanhang Liu, Desiree Wilson, Robin Leach, and Yidong Chen

Short

B483 "Human Absorbable Dietary microRNAs Prediction based on an Ensemble Manifold Ranking

Model"

Jiang Shu, Kevin Chiang, Dongyu Zhao, and Juan Cui

Regular B506 "Interpretable Deep Neural Networks for Enhancer Prediction"

Seong Kim, Nawanol Ampornpunt, Ananth Grama, and Somali Chaterji

Short B521 "A test for detecting differentially methylated regions"

Iksoo Huh, Soojin V. Yi Yi, and Taesung Park

Regular B413 "A two-step logistic regression algorithm for identifying individual-cancer-related genes"

Bolin Chen, Xuequn Shang, Min Li, Jianxin Wang, and Fang-Xiang Wu

Session 10 Healthcare Informatics I

Regular

B495 "A Grammar-based Approach to Model the Patient’s Clinical Trajectory after a mild Traumatic

Brain Injury"

Filip Dabek and Jesus Caban

Regular B310 "Facial Color Management for Mobile Health in the Wild"

Jinling Niu, Changbo Zhao, and Guozheng Li

Regular

B324 "Modeling Electronic Health Records in Ensembles of Semantic Spaces for Adverse Drug Event

Detection"

Aron Henriksson, Jing Zhao, Henrik Boström, and Hercules Dalianis

31

Short B477 "SmartStep 2.0 – A completely wireless, versatile insole monitoring system"

Nagaraj Hegde and Edward Sazonov

Regular

B265 "Automatic weighing attribute to retrieve similar lung cancer nodules"

David Jones Ferreira de Lucena, José Raniery Ferreira Junior, Marcelo Costa Oliveira, and Aydano

Pamponet Machado

Session 11 Cross-cutting Computational Methods I

Regular B447 "A novel approach to identify shared fragments in drugs and natural products"

Akshay Balasubramanya, Ishwor Thapa, Dhundy Bastola, and Dario Ghersi

Short B418 "A New Approach For Estimating Probability of Metastasis at Diagnosis"

Shuhao Sun, Fima Klebaner, and Tianhai Tian

Short B420 "TMDFM: A Data Fusion Model for Combined Detection of Tumor Markers"

Chi Yuan, Yongli Wang, Yanchao Li, Xiaohui Jiang, and Isma Masood

Regular

B462 "Integrating Omics Data for Identifying Disease Subtypes: a Multiplex Network-based

Approach"

Haiying Wang and Huiru Zheng

Regular

B353 "A generative model for correlation discover of genetic polymorphism and adverse drug

reactions"

Zhaohui Liang, Ziping Li, Gang Zhang, and Jimmy Huang

Short B276 "The effective diagnosis of schizophrenia by using 4-layer RBMs deep networks"

Chen Qiao

Short B201 "The Influence of EM Estimation of Missing Nodes in DCM on Model Ranking"

Shaza Zaghlool and Christopher Wyatt

Session 12 Structure, Function, and Evolution II

Regular B494 "Extending Rule-Based Methods to Model Molecular Geometry"

Brittany Hoard, Bruna Jacobson, Kasra Manavi, and Lydia Tapia

Regular B348 "Structure-Guided Selection of Specificity Determining Positions in the Human Kinome"

Mark Moll, Paul Finn, and Lydia Kavraki

Short B241 "Protein model quality assessment by learning-to-rank"

Xiaoyang Jing, Qiwen Dong, Xuan Liu, and Bin Liu

Regular B509 "Superposition of Protein Structures Using Electrostatic Isopotentials"

Ziyi Guo, Juliana Hong, Katya Scheinberg, and Brian Chen

Short

B463 "SphereGrinder - reference structure-based tool for quality assessment of protein structural

models"

Piotr Lukasiak, Maciej Antczak, Tomasz Ratajczak, and Jacek Blazewicz

Regular

B339 "Evolutionary Search Strategies for Efficient Sample-based Representations of Multiple basin

Protein Energy Landscapes"

Emmanuel Sapin, Kenneth De Jong, and Amarda Shehu

32

Session 13 Cross-cutting Computational Methods I

Invited

Talk V

Accurate and Fast RNAseq Analysis

Wei Wang

Regular B242 "Identification of DNA-binding proteins by auto-cross covariance transformation"

Qiwen Dong, Shanyi Wang, Kai Wang, Xuan Liu, and Bin Liu

Short B272 "MALBACsim: a Multiple Annealing and Looping Based Amplification Cycles Simulator"

Li Tengpeng, Zhang Changsheng, Bo Xu, Li Fuqiang, and Cai Hongmin

Regular B414 "Reference Sequence Selection for Motif Searches"

Qiang Yu, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter, and Jun Huan

Regular B511 "DiscMLA: AUC-Based Discriminative Motif Learning"

Hongbo Zhang, Lin Zhu, and De-Shuang Huang

Short B407 "Biomedical Named Entity Recognition Based on Extended Recurrent Neural Networks"

Lishuang Li, Liuke Jin, Zhenchao Jiang, and Dengen Huang

Session 14 Healthcare Informatics II

Regular

B321 "Classification with Imbalance: A Similarity based Method for Predicting Respiratory

Failure"

Harsh Shrivastava, Vijay Huddar, Sakyajit Bhattacharya, and Vaibhav Rajan

Short B479 "A Method for Imputation of Semantic Class in Diagnostic Radiology Text"

Eamon Johnson, W Christopher Baughman, and Gultekin Ozsoyoglu

Regular B334 "Framework for Workflow-driven Clinical Decision Support in Oncology"

Anca Bucur, Jasper van Leeuwen, and Norbert Graf

Short

B249 "Insight: Semantic Provenance and Analysis Platform for Multi-center Neurology

Healthcare Research"

Priya Ramesh, Annan Wei, Johnny Sams, Elisabeth Welter, Samden Lhatoo, Martha

Sajatovic, and Satya Sahoo

Regular B502 "Using Myoelectric Signals to Recognize Grips and Movements of the Hand"

Gene Shuman, Zoran Duric, Daniel Barbara, Jessica Lin, and Lynn H. Gerber

Regular

B285 "Collaborative and Trajectory Prediction Models of Medical Conditions by Mining Patients’

Social Data"

Xiang Ji, Soon Ae Chun, James Geller, and Vincent Oria

Short

B366 "Chronic Lymphocytic Leukemia Patient Classification Methodology Through Flow

Cytometry Analysis"

Evdoxia Papadopoulou, Konstantia Kotta, Panagiotis Moschonas, Vassiliki Douka, Achilles

Anagnostopoulos, Kostas Stamatopoulos, and Dimitrios Tzovaras

33

Session 15 Semantics and Ontology II

Regular

B314 "An integrative measure of graph- and vector-based semantic similarity using information

content distance"

Young-Rae Cho

Short

B277 "ImmPort: Shared Research Data for Bioinformatics and Immunology"

Patrick Dunn, Elizabeth Thomson, Henry Schaefer, John Campbell, Thomas Smith, Sanchita

Bhattacharya, Sandra Andorf, Vincent Desborough, Jeff Wiser, and Atul Butte

Regular B231 "A novel two-stage method for identifying miRNA-gene regulatory modules in breast cancer"

Wenwen Min, Juan Liu, Fei Luo, and Shihua Zhang

Regular B330 "On Stabbing Queries for Generalized Longest Repeat"

Bojian Xu

Short

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

Smith, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei

Wang, He Zhang, David Schmitt, and Ming Tan

Regular B336 "Integrating Association Mining into Relevance Feedback for Biomedical Literature Search"

Yanqing Ji, Hao Ying, John Tran, Peter Dews, and Michael Massanari

Short B297 "Training Word Embeddings for Deep Learning in Biomedical Text Mining Tasks"

Zhenchao Jiang, Lishuang Li, Degen Huang, and Liuke Jin

Session 16 Medical Imaging

Regular B283 "Analysis of Oddity in Facial Physiology of Children with Autism using 3D Imaging"

Manar Samad, Jonna Bobzien, John Harrington, and Khan Iftekharuddin

Short B254 "An Image Reconstruction Model and Hybrid Algorithm for Limited-angle Projection Data"

Hongxia Gao, Yinghao Luo, Kewei Chen, Ge Ma, and Lixuan Wu

Regular

B371 "A Seeding-Searching-Ensemble Method for Gland Segmentation and Detection"

Yizhe Zhang, Lin Yang, John MacKenzie, Rageshree Ramachandran, and Danny

Chen

Short

B268 "Segmentation of Multicolor Fluorescence In-Situ Hybridization (M-FISH) Image Using an

Improved Fuzzy C-Means

Clustering Algorithm While Incorporating Both Spatial and Spectral Information"

Jingyao Li, Dongdong Lin, and Yu-Ping Wang

Short

B456 "Segmentation-based Multi-scale Framework for the Classification of Epithelial and Stromal

Tissues in H&E Images"

Filiz Bunyak, Adel Hafiane, Zahraa Al-Milagi, Ilker Ersoy, Anoop Haridas, and

Kannappan Palaniappan

Short B349 "Robust landmark-based image registration using l1 and l2 norm regularizations"

Xuan Yang, Bo Wang, and Yan-Ran Li

34

Session 17 Biological Networks III

Regular

B419 "Protein-protein interaction network inference from multiple kernels with optimization based on

random walk by linear programming"

Lei Huang, Li Liao, and Cathy Wu

Regular B465 "GREAT: GRaphlet Edge-based network AlignmenT"

Joseph Crawford and Tijana Milenkovic

Regular B486 "petal: A Novel Co-Expression Network Modeling System"

Juli Petereit, Frederick C. Jr. Harris, and Karen Schlauch

Short B430 "Joint inference of tissue-specific networks with a scale free topology"

Somaye Hashemifar, Behnam Neyshabur, and Jinbo Xu

Regular B337 "EpiTracer – an algorithm for identifying epicenters in condition-specific biological networks"

Narmada Sambaturu, Madhulika Mishra, and Nagasuma Chandra

Short

B362 "Exhaustive analysis of dynamical properties of Biological Regulatory Networks with Answer

Set Programming"

Emna Ben Abdallah, Maxime Folschette, Olivier Roux, and Morgan Magnin

Session 18 Sequence, Structure, and Function

Regular B472 "Predicting Protein-Protein Interaction Using Co-Occurring Aligned Pattern Clusters"

Antonio Sze-To, Sanderz Fung, En-Shiun Annie Lee, and Andrew K. C. Wong

Regular B484 "Adaptive Local Learning in Sampling Based Motion Planning for Protein Folding"

Chinwe Ekenna, Shawna Thomas, and Nancy Amato

Short B515 "Imputation of ChIP-Seq Datasets via Low Rank Convex Co-Embedding"

Lin Zhu, De-Shuang Huang, and Canyi Lu

Regular

B376 "Computing Transition Paths in Multiple-Basin Proteins with a Probabilistic Roadmap

Algorithm Guided by Structure Data"

Tatiana Maximova, Erion Plaku, and Amarda Shehu

Short

B497 "Guilt-by association approach to identify novel human aging-related genes using protein

domains"

Jasjit Banwait, Schuyler Dougherty, Ishwor Thapa, and Dhundy Bastola

Regular

B372 "Identifying Inorganic Material Affinity Classes for Peptide Sequences Based on

Context Learning"

Guangxu Xun, Xiaoyi Li, Marc R. Knecht, Paras N. Prasad, Mark T. Swihart, Tiffany R. Walsh, and

Aidong Zhang

Short B490 "Quantifying Feed Efficiency of Dairy Cattle for Genome-wide Association Analysis"

Tingyang Xu, Jiangwen Sun, Erin Connor, and Jinbo Bi

35

Session 19 Medical Informatics

Regular B346 "A Generative Bayesian Model To Identify Cancer Driver Genes"

CHRISTOPHER MA

Short B480 "EEG Dynamic Source Localization using Marginalized Particle Filtering"

Bradley Ebinger, Nidhal Bouaynaya, Petia Georgieva, and Lyudmila Mihaylova

Short

B287 "Sparse Omics-network Regularization to Increase Interpretability and Performance of Linear

Classification Models"

Michael Andel, Filip Masri, Jiri Klema, Zdenek Krejcik, and Monika Belickova

Short B278 "Improved Brain Tumor Growth Prediction and Segmentation in Longitudinal Brain MRI"

Linmin Pei, Syed Mohammad Shamim Reza, and Khan Iftekharuddin

Short

B350 "Predicting Microbial Interactions by Using Network-constrained Regularization Incorporating

Covariate Coefficients and Connection Signs"

Hu Xiaohua and Wang yan

Short

B411 "Audio Signals Encoding for Cough Classification Using Convolutional Neural Networks: A

Comparative Study"

Hui-Hui Wang, Jia-Ming Liu, and Mingyu You

Regular B433 "On Frequency Dependencies of Sliding Window Correlation"

Sadia Shakil, Shella Keilholz, and Chin-Hui Lee

Session 20 Translational Bioinformatics

Regular B437 "Robust point matching by l1 regularization"

Jianbing Yi, Yan-Ran Li, Xuan Yang, and Guoliang Chen

Short

B427 "Using Hidden Markov Models to Capture temporal Aspects of Ultrasound Data in Prostate

Cancer"

Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron

Fenster, Aaron Ward, Purang Abolmaesumi, Parvin Mousavi, and Hagit Shatkay

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

Jing Zhao

Regular B385 "Identifying the pre-transition state during biological processes by hidden Markov model"

Pei Chen, Shuoyang Qiu, Yue Wang, and Yongjun Li

Short

B530 "Bayesian Classification with Local Probabilistic Model Assumption in Aiding Medical

Diagnosis"

Bin Hu, Chengsheng Mao, and Xiaowei Zhang

Regular

B386 "An Integrative Genomic Study for Multimodal Genomic Data Using Multi-Block Bipartite

Graph"

Mingon Kang, Juyoung Park, Dong-Chul Kim, Ashis Biswas, Chunyu Liu, and Jean Gao

36

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

Dan He

Session 21 Computational Systems Biology

Regular B286 "A Two-Stage Clustering Technique for Automatic Biaxial Gating of Flow Cytometry Data"

Maziyar Baran Pouyan, Vasu Jindal, Javad Birjandtalab, and Mehrdad Nourani

Regular B466 "Purification of LC/GC-MS based Biomolecular Expression Profiles Using a Topic Model"

Minkun Wang, Tsung-Heng Tsai, Guoqiang Yu, and Habtom Ressom

Short B394 "Sequential Data Selection for Predicting the Pathogenic Effects of Sequence Variation"

Mark Rogers, Hashem Shihab, Tom Gaunt, Matthew Mort, David Cooper, and Colin Campbell

Regular B340 "Improved Algorithms for Finding Edit Distance Based Motifs"

Soumitra Pal and Sanguthevar Rajasekaran

Regular B354 "Boosting Compound-Protein Interaction Prediction by Deep Learning"

Kai Tian, Mingyu Shao, Shuigeng Zhou, and Jihong Guan

Short

B347 "An efficient method to identify essential proteins for different species by integrating protein

subcellular localization information"

Xiaoqing Peng, Jianxin Wang, Jiancheng Zhong, Junwei Luo, and Yi Pan

Short B426 "An Efficient ACS Algorithm for Classification-based Peptide Identification"

Xijun Liang, Zhonghang Xia, Ling Jian, Xinnan Niu, and Andrew Link

Short B501 "RF-Phos: Random Forest-Based Prediction of Phosphorylation Sites"

Hamid Ismail, Ahoi Jones, Jung Kim, Robert Newman, and Dukka KC

Session 22 Bioinformatics Infrastructure

Regular

B280 "Accelerating Large-Scale Biological Database Search on Xeon Phi-based Neo-Heterogeneous

Architectures"

Haidong Lan, Weiguo Liu, Bertil Schmidt, and Bingqiang Wang

Short B344 "HPMA: High-performance Metagenomic Alignment Tool, on a Large-Scale GPU Cluster"

Ibrahim Savran and John Rose

Regular

B248 "Scalable Biobanking: A Modular Electronic Honest Broker and Biorepository for Integrated

Clinical, Specimen and Genomic Research"

Alex Felmeister, Tyler Rivera, Aaron Masino, Jeffrey Pennington, and Adam Resnick

Short B520 "Large scale multi-species palindrome study using distributed in-memory computing"

Devin Petersohn, Matt Spencer, Alex Fratila, and Chi-Ren Shyu

Short

B428 “Inference of Gene Regulatory Networks via Multiple Data Sources and a Recommendation

Method”

Makbule Gulcin Ozsoy, Faruk Polat, and Reda Alhajj

37

Session 23 Industry and Government

Regular N201 " A Highly Parallel Next-Generation DNA Sequencing Data Analysis Pipeline in Hadoop"

Kareem Aggour, Vijay Kumar, Dipen Sangurdekar, Lee Newberg, and Chinnappa Kodira

Regular N202 " Structuring Unstructured Clinical Narratives in OpenMRS with Medical Concept Extraction"

Ryan Eshleman, Hui Yang, and Barry Levine

Regular

N204 " The Medical Knowledge Cockpit: Real-time Analysis of Big Medical Data Enabling Precision

Medicine"

Matthieu-P. Schapranow

Outlook

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”

Yue Jiao, Dan Geary, Sheetal Chaudhuri, Mahathi Mothali, Terry Ketchersid, Dugan Maddux, John Larkin,

Scott Ash, Len Usvyat, Franklin Maddux, and Peter Kotanko

Outlook P221 “ZSeq 2.0: A Fully Automatic Preprocessing Method for Next Generation Sequencing Data”

Abed Alkhateeb, Iman Rezaeian, and Luis Rueda

Outlook P235 “A New DP Algorithm for Comparing Gene Expression Data Using Geometric Similarity”

Amir Vajdi, Nurit Haspel, and Hadi Banaee

Outlook P240 “PACH: Ploidy-AgnostiC Haplotyping”

Sepideh Mazrouee

38

Poster List

Poster

ID Poster Title

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

39

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

40

Conference WiFi Instruction

Instructions on connecting to Wireless Internet in meeting space

Network Name (SSID): @Hyatt_Meeting

Password: YENKDW

41

IEEE BIBM 2016 Call For Papers

Documents

2015 IEEE International Conference on Bioinformatics and