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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
• 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
Registration
4:00– 8:00 pm
Ballroom Foyer
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Monday, Nov 9 (Workshops and Tutorials)
7:20am – 6:30pm
Registration
10:30-10:50am
and
3:30-3:50pm
Meeting Room Foyer
12:00-1:30pm
Lunch (On Own)
1:30-6:00pm
Meeting Room and Concours Terrace
Ballroom Foyer
Coffee Break
Poster Session (Set Up)
8:00-12:00pm
Workshops/Tutorials
Session Chair
Location
Workshop: High Performance Bioinformatics and Biomedicine (HiBB)
Workshop:2015 Workshop on Health Informatics and Data Science (HI-DS)
Mario Cannataro
Xiong Liu, Rong Liu
Jing He, Amarda Shehu, Nurit
Haspel, Brian Chen
Waterford
Cabinet Suite
Workshop: The 2015 Computational Structural Bioinformatics Workshop
Workshop: 2015 International Workshop on Biomedical and Health
Informatics
Workshop: COMputational Methods for Analyzing Metagenomics Data
Workshop: The 6th Integrative Data Analysis in Systems Biology (IDASB
2015).
Joint Workshop Schedule
Data mining in translational biomedical informatics &
Second International Workshop on the Role for Quantified Self for Personal
Healthcare
Workshop: Data mining from genomic variants and its application to
genome-wide analysis
Tutorial: Integrative Genomic Big-Data Analytics for Translational
Bioinformatics and Precision Medicine Research (10am-12noon)
1:30-6:00pm
Workshops/Tutorials
Workshop: Inaugural International Workshop on Biological Network Driven
Analysis
Workshop:2015 Workshop on Health Informatics and Data Science (HI-DS)
Workshop: The 2015 Computational Structural Bioinformatics Workshop
Workshop: 2015 International Workshop on Biomedical and Health
Informatics
Tutorial: Introduction to computational analysis of microbiome shotgun
sequencing data (1:30-3:30pm)
Tutorial: Human Microbiome Analysis: Computational Techniques and
Challenges (4:00-6:00pm)
Workshop: Semantic Data Analytics and Bioinformatics
Joint Workshop Schedule
Nonnegative Matrix Factorization and Tensor Decomposition Techniques for
High-Throughput Biological Data Analysis &
Computational Regulatory Genomics and Metagenomics
Workshop: International Workshop on Biomolecular Interaction Network
Analysis and Interactomics
Workshop: The 6th Integrative Data Analysis in Systems Biology (IDASB
2015).
Workshop: Electronic Health Record: Implementation, Data Mining,
Security and User Acceptance
Workshop: Biomedical Visual Search and Deep Learning
Workshop: The 6h International Workshop on High Performance Computing
in Bioinformatics
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Illhoi Yoo
Catherine Putonti, Charlie Xia
and Erliang Zeng
Rui Jiang, Huiru Jane Zheng,
Zhongming Zhao
Judiciary Suite
Embassy/Patuxent
Diplomat/Ambassador
Cartier/Tiffany
Qian Zhu, Hongfang Liu, Frank
Hopfgartner, Na Li
Susquehanna
Taesung Park
Baccarat
Mary Yang and Kenji
Yoshigoe
Haverford
Session Chair
Location
Fione Brown
Waterford
Xiong Liu, Rong Liu
Jing He, Amarda Shehu, Nurit
Haspel, Brian Chen
Cabinet Suite
Judiciary Suite
Illhoi Yoo
Embassy/Patuxent
Daniel H. Huson
Haverford
Serghei Mangul
Haverford
Haiying Wang
Michael Ochs, Elana Fertig,
Alieoune Ngom, Hongyu
Zhang, Guoliang Li, Anyuan
Guo, Hongyu Ou and Xingpeng
Jiang
Young-Rae Cho
Lalique
Baccarat
Diplomat/Ambassador
Rui Jiang, Huiru Jane Zheng,
Zhongming Zhao
Cartier/Tiffany
Manuel Grana, Michel
Wozkniak, Konrad Jakowski
Susquehanna
Richard Conroy, Vinay Pai,
Todd Horowitz, Susan
Gregurick, Tom Radman
Che-Lun Hung et al.
Potomac
Severn
Tuesday, November 10
Registration
8:00am-6:00pm
Ballroom Foyer
Welcome and Opening Session
8:45-9:00am
Chairs: Luke Huan, Satoru Miyano, Amarda Shehu, Sanguthevar Rajasekaran, Xiaohua Tony Hu
Crystal Ballroom
Keynote Lecture 1 (Chair: Satoru Miyano)
“Big Data in Biomedicine – an NIH Perspective”
Philip Bourne
Crystal Ballroom
9:00-10:00am
Coffee Break
10:00-10:20am
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
12:30-2:00pm
Lunch provided by conference
Meeting Room and Concours Terrace
Embassy/Patuxent
2:00-3:40pm
(including
Invited talks)
Sessions
Session Chair
Location
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
Coffee Break
3:40-4:00pm
Meeting Room Foyer
4:00-6:40pm
7:00-9:00pm
1.
2.
3.
4.
Sessions
Session Chair
Location
Session 9: Epigenetics and Gene Regulation
Session 10: Healthcare Informatics I
Session 11: Cross-cutting Computational Methods I
Session 12: Structure, Function and Evolution II
Ananda Modal
Cho, Young-Rae
Haspel, Nurit
He, Jing
Cabinet Suite
Diplomat/Ambassador
Judiciary Suite
Embassy/Patuxent
Banquet (Ticket required)
Introduction of BIBM 2016 Host City (Chairs: Xiaohua Tony Hu, Jianguo Lu)
Best Paper Award (Chairs: Luke Huan, Satoru Miyano, Amarda Shehu)
Best Student Paper Award (Chairs: Luke Huan, Satoru Miyano, Amarda Shehu)
Best Paper Runner-Up (Chairs: Luke Huan, Satoru Miyano, Amarda Shehu)
Crystal Ballroom
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Wednesday, Nov 11
Registration
8:00am-6:00pm
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
Coffee Break
10:00-10:20am
10:20am 12:30pm
Meeting Room Foyer
Sessions
Session Chair
Location
Session 13: Cross-cutting Computational Methods II
Session 14: Healthcare Informatics II
Session15: Semantics and Ontology II
Session16: Medical Imaging
Moll, Mark
Shehu, Amarda
Huang, Jingshan
Miyano, Satoru
Cabinet Suite
Diplomat/Ambassador
Judiciary Suite
Embassy/Patuxent
Lunch provided by conference
12:30-2:00pm
Crystal Ballroom
Keynote Lecture 3 (Chair: Luke Huan)
1:00-2:00pm
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
Panel
2:00-3:40pm
Federal Agencies and Industry
Crystal Ballroom
Coffee Break
3:40-4:00pm
4:00-6:20pm
Meeting Room Foyer
Sessions
Session Chair
Location
Session 17: Biological Networks III
Session 18: Sequence, Structure, and Function III
Session 19: Medical Informatics III
Session 20: Translational Bioinformatics I
Huo,Hongwei
Chen, Brian
Bastola, Dhundy
Ghersi, Dario
Cabinet Suite
Diplomat/Ambassador
Judiciary Suite
Embassy/Patuxent
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Thursday, Nov 12
Registration
8:00-10:00am
Ballroom Foyer
Keynote Lecture 4 (Chair: Amarda Shehu)
Computational Challenges in Microbiome Research
Mihai Pop
Crystal Ballroom
9:00-10:00am
Coffee break
10:00-10:20am
Meeting Room Foyer
Poster Display
10:00 - 10:20 am
10:20am-12:30pm
Chesapeake Foyer
Sessions
Session Chair
Location
Session 21: Computational Systems Biology
Session 22: Bioinformatics Infrastructure
Session 23: Industry and Government Session
Workshop: High Performance Computing for Big Data Computational
Biology
Workshop: Machine learning in decision making for biomedical
applications
Ricardo de Matos Simoes
Ryan Benton
Matthieu Schapranow
Cabinet Suite
Judiciary Suite
Diplomat/Ambassador
Fahad Saeed
Old Georgetown
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 nextgeneration 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 selfmanagement. 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, indexbased 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
13:30-14:15
14:15 – 14:45
14:45-15:15
15:30-16:00
16:00 – 16:30
16:30 – 17:00
17:00
Title
Presenter/Author
Opening talk:
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
Biological Relevance in Gene Co-expression Networks
Hesham Ali
Ricardo de Matos, Simoes, Constantine
Network signatures based on gene pair expression ratios improve
Mitsiades, Kate E Williamson, Frank
classification and the analysis of muscle-invasive urothelial cancer
Emmert-Streib
Coffee Break
Visualizing the topology and re-analyzing the causes of small-world
Yongpan Hua, Xiuchan Xiao, Min Zhu,
property of amino acid network
Yangxu Wang and Menglong Liy
Yaoxin Nie, Jieyao Wei, Linlin Zhu, Qian
Functional Connectivity of Chinese Characters Processing:A MetaZhou, Zhendong Niu
analysis
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
13:30-15:30
15:30-16:00
16:00-17:25
16:00-16:25
16:25-16:50
16:50-17:15
17:15-17:40
17:40
Title
Presenter/Author
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
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
Coffee Break, poster session (coffee: 15:30-15:50)
Session 2: Computational Regulatory Genomics and Metagenomics
A New DP Algorithm for Comparing Gene Expression Data Using
Geometric Similarity
Understanding Heterogeneity in Pregnancy Associated Breast Cancer
A Novel Signature For Identification Of Upstream Alternative
Translation Initiation Sites
Patho-finder – a Fast and Accurate Program for Pathogen
Identification through RNA-seq
Closing Remarks
16
Amir Vajdi, Nurit Haspel, and Hadi Banaee
Murlidharan Nair
Kritika Karri and Dhundy Bastola
Chin-Ting Wu, Tzu-Hung Hsiao, Yu-Chiao
Chiu, Yu-Ching Hsu, Eric Chuang, and
Yidong Chen
6th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB-2015)
Session Chair: Mario Cannataro
Time
09:00 – 10:30
10:30-11:00
11:00-12:00
12:00-12:30
12:30-13:30
Title
Presenter/Author
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
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
Coffee Break – perhaps poster session
Session 2(15 minutes for talk and 5 minutes for Q and A)
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
poster session
Lunch (on your own)
Electronic Health Record: implementation, data mining, security, and user acceptance
Session Chairs: Manuel Graña, Michal Wozniak and Konrad Jakowski
Time
13:30 – 15:30
Title
Presenter/Author
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,
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
08:00-8:15
08:15-09:00
Welcome
Computational Challenges Facing Environmental Metaviromics
Next Generation Sequence Assembler Mis-assembly of Phage
Genomes with Terminal Redundancy
A Computational Framework for Integrative Analysis of Large
Microbial Genomics Data
09:00-09:20
09:20-09:40
09:40-10:00
10:00-10:20
Presenter/Author
Finding Function in the Unknown: Methods for Examining
Transcriptomes of Non-Model Organisms
CoCo: an application to store High Throughput Sequencing data in
compact text and binary file formats
17
Catherine Putonti
Julia Sommer
Erliang Zeng, Wei Zhang, Scott Emrich, Dan
Liu, Josh Livermore, and Stuart Jones
Kelly Boyd, Emma Highland, Amanda
Misch, Amber Hu, Sushma Reddy, and
Catherine Putonti, Loyola
Kamil Khanipov, Georgiy Golovko, Mark
Rojas, Levent Albayrak, Otto Dobretsberger,
Maria Pimenova, Nels Olsen, Sergei
Chumakov, and Yuriy Fofanov
10:20-10:50
10:50-11:10
11:00-11:30
Coffee Break
HAsh-MaP-ERadicator: Filtering Non-Target Sequences from Next
Generation Sequencing Reads
Bipartite Graphs for Metagenomic Data Analysis and Visualization
11:30
Jonathon Brenner and Catherine Putont
Karel Sedlar, Helena Skutkova, Petra
Videnska, Ivan Rychlik, and Ivo Provaznik
Closing
2015 Workshop on Data mining from genomic rare variants and its application to genome-wide
analysis
Session Chair: Prof. Taesung Park
Time
09:00 – 10:30
09:00-09:10
10:30-10:50
10:50-12:10
11:20
Title
Presenter/Author
Session 1 (20 minutes for each talk, including Q and A)
Session Chair: Dr. Heejong Sung
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 (CPASungkyoung 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
Coffee Break
Session 2(20 minutes for each talk, including Q and A)
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
Closing
Data mining in translational biomedical informatics
Session Chairs: Qian Zhu, Hongfang Liu
Time
09:00 – 10:30
10:30-11:00
11:00-12:00
Title
Presenter/Author
Session 1 (15inutes for each talk, including Q and A)
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
Coffee Break – perhaps poster session
Session 2(15 minutes for each talk, including Q and A)
18
Session Chair: Qian Zhu
Thermal Sensor Based Multi-occupancy Motion Tracking and
Visualisation in Smart Environments
Usability testing of a novel automated external defibril l ator user
interface: a pilot study
Outlier Detection in Weight Time Series of Connected Scales
The Syndromes of Lung Cancer and Compatibility of Medicine in
Traditional Chinese Medicine Science Treatment Based on Clustering
Algorithm
Jun Zhou, Huiru (Jane) Zheng, Haiying
Wang,etc
Peter O'Hare, Rebecca Di Maio, and
Raymond Bond
Saeed Mehrang, Elina Helander, Misha
Pavel, Angela Chieh, and Ilkka Korhonen
Miao Wang, Mengying Wang, Dongyi
Wang,etc
2015 Workshop on Health Informatics and Data Science (HI-DS)
Session Chairs: Xiong Liu, Rong Liu
Time
08:30 – 10:20
8:30-8:40
Title
Author
Session 1 (25 minutes for each talk)
Opening
Obtaining Biomarkers in Cancer Progression from Outliers of TimeAbed Alkhateeb, Iman Rezaeian, Siva
series Clusters
Singireddy, and Luis Rueda
Lei Zhang, Ying Zhu, and Sergey Klimov
CancerVis: an Interactive Exploratory Tool for Cancer Biomarker
Analysis
Tadasuke Ito, Masato Okada, Shotaro
Togami, Shinya Ariyasu, Shin Aoki, and
ILP based screening applied to predicting carbonic anhydrase II
ligands
Hayato Ohwada
Exploration of Topological Torsion Fingerprints
10:20 – 10:45
10:45 – 12:00
Coffee Break
Session 2(25 minutes for each talk, including Q and A)
Ali Azari, Vandana Janeja, and Scott Levin
Imbalanced Learning to Predict Long Stay Emergency Department
Patients
Richard Braun, Martin Burwitz, Hannes
Clinical Processes from Various Angles - Amplifying BPMN for
Schlieter, and Martin Benedict
Integrated Hospital Management
Predictive and Preventive Models for Diabetes Prevention using
Clinical Information in Electronic Health Record
12:00-12:30
Poster Session
Risk Prediction of Stroke: A Prospective Statewide Study on Patients
in Maine
A GRReat Framework for Incident Response in Healthcare
12:30-13:30
13:30-15:35
Petr Škoda and David Hoksza
Ni Cao, SiSi Zeng, Feixia Shen, Chuandi
Pan, Chengshui Chen, Thanh Nguyen, and
Jake Chen
Le Zheng, Yue Wang, Shiying Hao, etc.
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
Lunch (on your own)
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
S-Fit: Knowledge guided Fitness Pattern Mining Framework
ccKOPLS: Confounder-Correcting Kernel-based Orthogonal
Projections to Latent Structures
Feature Selection and Classification of Speech under Long-term Stress
Direct Higher Order Fuzzy Rule-based Classification System:
Application in Mortality Prediction
15:35-16:00
16:00-17:50
Ayush Sharma, Komal Agarwal, Rahul
Dubey, Sandip Bhaumik, and samudrala
nagaraju
David Moore, Kellan Fluette, Heather Milne,
Andrew Shedlock, and Paul Anderson
Bin Hu, Zhenyu Liu, Lihua Yan, Tianyang
Wang, Fei Liu, Xiaoyu Li, and Huanyu Kang
Abolfazl Doostparast Torshizi, Linda
Petzold, and Mitchell Cohen
Coffee Break
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
Analysis of Machine Learning Algorithms on EEG Data for Brain
State Intelligence (short)
Shared Genetic Architecture In Autoimmune Disease - Preliminary
Analysis (short)
Risk prediction for future 6-month healthcare resource utilization in
Maine (short)
Entropy Chain Multi-Label Classifiers for Traditional Medicine
Diagnosing Parkinson’s Disease (short)
17:50
Alexander Chan, Christopher Early, Sishir
Subedi, Yuezhe Li, and Hong Lin
Leqi Liu, Ziyan Yang, Jia Tao, and Fadi
Towfic
Shiying Hao, Zhongkai Hu, Bo Jin, etc.
PENG Yue, FANG Ming, WANG Chongjun,
and XIE Junyuan
Closing Remark
Workshop IDASB
Session Chairs: Rui Jiang, Huiru Zheng, and Zhongming Zhao
Time
09:00 – 10:30
10:30-11:00
11:00-11:30
11:0\30-12:30
12:30-13:30
13:30-15:30
Title
Presenter/Author
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
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
Coffee Break – perhaps poster session
Session 2
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
poster session
Lunch (on your own)
Session 3
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
15:30-16:00
16:00-17:00
17:00
Simulation of Effects of TBX18 on the Pacemaker Activity of Human
Yue Zhang, Kuanquan Wang, Henggui
Ventricular Cells
Zhang, and Wei Wang
Coffee Break, poster session (coffee: 15:30-15:50)
Session 4
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
Closing Remarks
2015 Biomedical & Health Informatics (BHI)
Session Chair: Illhoi Yoo
Time
09:30 – 10:30
10:50-12:00
13:30-15:30
15:50-18:30
Title
Presenter/Author
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
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
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
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
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
Finding Frequent Approximate Subgraphs in Medical Image Database
Wang, Xiong Lu, and Tao Zhong
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
13:30-15:30
15:30-16:00
16:00-17:00
17:00
Title
Presenter/Author
Session 1 (25-minute presentation and 5-minute Q & A.)
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.
Coffee Break
Session 2
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.
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
13:30-17:15
13:30-13:35
13:35-14:20
14:20-14:40
14:40-15:10
15:10-15:30
15:30-15:50
15:50-16:10
16:10-16:30
16:30-16:50
16:50-17:15
Title
Presenter/Author
Session Chair: Dr. Vinay Pai, NIBIB, NIH
Opening Remark(5mins)
Keynote Part 1
Todd Horowitz, NCI, NIH.
Visual Search in Biomedical Sciences
Probabilistic Visual Search for Masses Within Mammography Images
Mehmet Gunhan Ertosun and Daniel Rubin
using Deep Learning
Keynote Part 2
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
with an application to gene clustering
Ganapathiraju
Coffee Break
Noah Stier, Nicholas Vincent, David
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
images
Zhang, Wei Wang, and Zhiguang Qin
Nicholas Vincent, Noah Stier, Songlin Yu,
Detection of Hyperperfusion on Arterial Spin Labeling using Deep
David Liebeskind, Danny Wang, and Fabien
Learning
Scalzo
Open Discussion
Tom, Radman, NIDA, NIH
22
Workshop on Semantic Data Analytics and Bioinformatics
Session Chair: Dr. Haiying Wang
Time
13:30-13:40
13:40-14:40
14:40-15:30
15:30-16:00
16:00-17:10
17:10 – 17:15
Title
Presenter/Author
Opening Remarks
Invited talk: Talk title (TBC)
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
Coffee Break
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
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
09:00-10:30
10:30
Title
Presenter/Author
Session 1 (30mins for each talk)
Session Chair: Che-Lun Hung
Opening Remarks
Innovative Approach for Porting Existing CPU Program to Its CUDA
Yu Liu, Yang Hong, Chung-Hung Wang, ShengProgram
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
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
9:00-10:30
10:30-11:00
11:00-12:00
Title
Presenter/Author
Session 1(15mins for each talk)
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
Coffee Break
Session 2 (15mins for each talk)
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
10:20-10:25
10:25-10:40
10:40-10:55
10:55-11:10
11:10-11:25
11:25-11:40
11:40-11:55
11:55:-12:10
12:10-12:25
12:25-12:40
Title
Presenter/Author
Welcome
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
Quantitative Clinical guidelines for Imaging Use in
Yuzhe Liu, Shobhit Madan, MD, MPH, and Vanathi
Evaluation of Pediatric Cardiomyopathy
Gopalakrishnan
Cross-validation and cross-study validation of chronic
Nihir Patel, Bharati Jhadav, and Usman Roshan
lymphocytic leukaemia with exome sequences and machine
learning
A New Compact Set of Biomarkers for Distinguishing
Forough Firoozbakht, Iman Rezaeian, Alioune Ngom, and Luis
among Ten Breast Cancer Subtypes
Rueda
A Longitudinal Support Vector Regression for Prediction of
Wei Du, Huey Cheung, Calvin Johnson, Ilya Goldberg, Madhav
ALS Score
Thambisetty, and Kevin Becker
Integration of Multimodal RNA-Seq Data for Prediction of
Matt Schwartz, Martin Park, John Phan, and May Wang
Kidney Cancer Survival
EEG-based Seizure Detection Using Discrete Wavelet
Duo Chen, Suiren Wan, and Forrest Bao
Transform through Full-Level Decomposition
Effective Image Fusion Method to Study Alzheimer's
Arpita Das and Mahua Bhattacharya
Disease using MR, PET Images
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
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
Regular
Session 2 Biological Networks I
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
Short
B470 "Gene Selection for Cancer Classification With the Help of Bees"
Johra Moosa, Rameen Shakur, Mohammad Kaykobad, and M Sohel Rahman
B313 "Integrated Study to Infer Dynamic Protein-gene Interactions in human P53 Regulatory
Networks"
Junbai Wang, Qianqian Wu, and Tianhai Tian
27
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
Parameters Estimation for Microtubules Modeled in three States"
Shantia Yarahmadian, Vineetha Menon, and Vahid Rezania
Regular
Regular
Short
Instability
Session 4 Semantics and Ontology I
B222 "Learning to Rank for Biomedical Information Retrieval"
Bo Xu, Hongfei Lin, and Yuan Lin
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
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
28
Invited
Talk I
Session 5 Biological Networks II
“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
Short
Invited
Talk III
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
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
“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
29
Invited
Talk IV
Session 8 Structure, Function and Evolution I
“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
Regular
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"
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
30
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, JoséRaniery 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
Regular
B462 "Integrating Omics Data for Identifying Disease Subtypes: a Multiplex Network-based
Approach"
Haiying Wang and Huiru Zheng
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
Short
Regular
B509 "Superposition of Protein Structures Using Electrostatic Isopotentials"
Ziyi Guo, Juliana Hong, Katya Scheinberg, and Brian Chen
B463 "SphereGrinder - reference structure-based tool for quality assessment of protein structural
models"
Piotr Lukasiak, Maciej Antczak, Tomasz Ratajczak, and Jacek Blazewicz
B339 "Evolutionary Search Strategies for Efficient Sample-based Representations of Multiple basin
Protein Energy Landscapes"
Emmanuel Sapin, Kenneth De Jong, and Amarda Shehu
31
Invited
Talk V
Session 13 Cross-cutting Computational Methods I
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
Regular
Session 14 Healthcare Informatics II
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
32
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
Regular
Session 16 Medical Imaging
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
33
Regular
Session 17 Biological Networks III
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
Regular
Short
Regular
Short
Regular
Short
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
B484 "Adaptive Local Learning in Sampling Based Motion Planning for Protein Folding"
Chinwe Ekenna, Shawna Thomas, and Nancy Amato
B515 "Imputation of ChIP-Seq Datasets via Low Rank Convex Co-Embedding"
Lin Zhu, De-Shuang Huang, and Canyi Lu
B376 "Computing Transition Paths in Multiple-Basin Proteins with a Probabilistic Roadmap
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
domains"
Jasjit Banwait, Schuyler Dougherty, Ishwor Thapa, and Dhundy Bastola
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
B490 "Quantifying Feed Efficiency of Dairy Cattle for Genome-wide Association Analysis"
Tingyang Xu, Jiangwen Sun, Erin Connor, and Jinbo Bi
34
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
35
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
Regular
Session 22 Bioinformatics Infrastructure
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
36
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
37
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
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Songjian Lu, Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive
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ZhiWei LIANG, LiWen ZHOU, Ning XU, JianBiao XU, QianRong LIANG, XiaoYang ZHANG, ZhongXun
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V. B. Surya Prasath, Kiichi Fukuma, Bruce J. Aronow, and Hiroharu Kawanaka, Cell Nuclei Segmentation in
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Xiangzhou Huang, Yin Zhang, Baogang Wei, and Liang Yao, A Question-Answering System over Traditional
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V. B. Surya Prasath and Hiroharu Kawanaka, Vascularization Features for Polyp Localization in Capsule
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38
P232
Juyoung Park, Mingon Kang, Younghoon Kim, and Kyungtae Kang, Heartbeat Classification for Detecting
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Myungguen Chung, Seok Won Jeong, Soo-Jung Park, and Seong Beom Cho, A Case-Control Genome-Wide
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Aditya Rao, Thomas Joseph, Vangala Govindakrishnan Saipradeep, and Rajgopal Srinivasan, UIMA based
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39
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IEEE BIBM 2016 Call For Papers
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