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BIBM 2014
Program Schedule
Overview
Overview
Venue
Presentation format
Conference schedule
Keynotes and Invited Talks
Main conference paper presentation
Workshops
Posters
Tutorials
Industrial Track
International Collaboration Forum
Venue
Venue
Hilton Belfast
4 Lanyon Place
Belfast, BT1 3LP
United Kingdom
Tel.: +44-28-90277000
Fax: +44-28-90277277
Rooms:
• Lagan A
• Lagan B
• Boardroom Suite
• Broadway Suite
• Brookfield Suite
• Glenbank Suite
• Lisburn Suite
• Sonama Restaurant
• Tower Suite
1
Presentation format
Presentation format
Keynote Lectures:
Invited Talks:
Regular papers:
Short papers:
Tutorials:
60 minutes (ca. 45 minutes for paper presentation and 15 for questions and answers)
40 minutes (ca. 30 minutes for paper presentation and 10 for questions and answers)
25 minutes (ca. 20 minutes for paper presentation and 5 for questions and answers)
20 minutes (ca. 16 minutes for paper presentation and 4 for questions and answers)
115 minutes (ca. 110 minutes for paper presentation and 5 for questions and answers)
Conference schedule
Conference schedule
November 1
November 1, 2014
16:0020:00
Registration: Hilton Hotel, lobby
November 2
November 2, 2014
Registration
Lobby in Hilton Hotel
08:00-18:00
Venue:
08:3012:30
WS2
WS5
WS3
WS7
WS8
WS11
WS15
CIBB
BHI
ESM
BNHD
QSPH
HPCB
SDAB
Session Stephen Smith Illhoi Yoo
Chairs
Speaker
Hong Yue
I Roznovat
S Watterson
J Wang
Na Li
Fangxiang Wu
Allen Hung
Haiying Wang
Hui Wang
Venue:
Brookfield
Glenbank
Broadway
Lisburn
Lagan A
Lagan B
TBC
Coffee break: 10:30-10:50
Lunch at Hotel restaurant (provided by the conference)
12:30-13:30
Set up Poster Session (the poster authors could start their poster set-up and the posters will be displayed until November 5)
13:3018:30
WS2
WS5
WS9
WS14
WS10
WS12
WS15
CIBB
BHI
IDASB
NEHB
CTM
ITCM
SDAB
Session
Chairs
Stephen
Smith
Illhoi Yoo Jane Zheng
Jinbo Bi
Rong Liu
Xing-Ming
S K.Poon
Zhao
ZH Liang
Weidong Tian N Zhang
GZ Li
HY Wang
H Wang
Venue:
Lagan A
Lagan B
Glenbank
Boardroom
Lisburn
Brookfield
Break : 15:30-15:50
2
Broadway
November 3
November 3, 2014
08:00-18:00 Registration
Venue:
Lobby in Hilton Hotel
09:00-09:30 Opening and welcome address
Opening Address: Prof. Hugh McKenna
Venue:
Lagan Suite
09:30-10:30 Session Chair: Dr. Huiru Jane Zheng and Prof. Xiaohua Tony Hu
Keynote 3: Prof. Tony Bjourson
Venue:
Lagan Suite
10:30-10:50 Break
10:50-13:00 Session 1
Genomics and
molecular
structure,
function and
evolution (1)
Session
Chair
Iona Kifer
Session 2
Transcriptomics:
microarray data
analysis, gene
regulation,
alternative splicing,
network/pathway
analysis (1)
Shu-Dong Zhang
Venue
Lagan A
Lagan B
Session 3
Biomedical
intelligence, clinical
data analysis, and
electronic health
record (1)
Session 4
Tutorial1
Biomedical
signal/image
analysis
WS1
Fiona Browne
TBC
Raymond Richard
Bond
Davies
Boardroom
Broadway
Lisburn
Session 7
Genomics and
molecular
structure, function
and evolution
Session 8
( T1)
Biological
data mining
and
visualization
TBC
TBC
Raymond Richard
Bond
Davies
Boardroom
Broadway
Lisburn
WS16
Taesung Park
Brookfield Glenbank
13:00-14:00 Lunch at Hilton Restaurant
Poster Session Lagan Foyer
14:00-15:00 Session Chair: TBC
Keynote 2: Prof. Henggui Zhang
Venue:
15:00-15:20 Break
15:20-17:30 Session 5
Biomedical
signal/image
analysis
Session
Chair
TBC
Session 6
Biomedical
intelligence, clinical
data Analysis, and
electronic health
record
TBC
Venue:
Lagan A
Lagan B
3
(WS1)
(WS16)
Taesung Park
Brookfield Glenbank
November 4
November 4, 2014
08:00-18:00 Registration
Venue:
09:00-10:30 Session Chair: Prof. Werner Dubitzky
Feature talk 1: Prof. Bryan Scotney,
Keynote 1: Prof. Martin Kuiper
Venue:
Lagan
10:30-10:50 Break
10:50 13:00
Session
Chair
Venue:
Session 9
Session 10
Session 11
Session 12
Biomedical
signal/image
analysis,
biomedical text
mining and
ontologies
TBC
Transcriptomics:
Microarray data
analysis
Genome-phenome Healthcare
analysis, biomarker information
discovery
systems, healthcare
informatics
TBC
Jinbo Bi
Lagan A
Lagan B
Boardroom
Moumita
Bhattacharya
Broadway
Tutorial2
Industrial Track
TBC
TBC
Brookfield
Lisburn
13:00-14:00 Lunch (provided by the conference)
Poster Session Floor 2 foyer
14:00-15:00 Session Chair: Prof. Chris Nugent
Invited talk 3: Prof. Fangxiang Wu
Venue:
Lagan
15:00-15:20 Break
15:20-17:30 Session 13
Session 14
Gene regulation, High-performance
alternative
computing
splicing,
network/pathway
analysis
Session
Chair
Venue:
Session 15
Biomedical text
mining and
ontologies
Wooyoung Kim
Chi-Ren Shyu
Fangxiang Wu
Session 16
(Tutorial2) Industrial Track
Proteomics, PTMs,
metabolomics,
epigenomics, noncoding RNA
analysis, DNA
methylation
analysis
TBC
TBC
TBC
Lagan A
Lagan B
Boardroom
Broadway
18:00-22:00 Banquet (Best Paper Award, Best Student paper Award, Best Poster Award)
(Titanic Experience and Museum)
4
Brookfield Lisburn
November 5
November 5, 2014
08:00-15:00 Registration:
Venue:
9:00-10:30
Session Chair: TBC
Feature talk 2: Prof. James
McLaughlin
Invited talk 1: Dr. Carlos Toro
Venue:
Lagan
10:30-10:50 Break
10:30-13:00 Session 17
Session
Chair
Venue
Session 18
Session 19
Computational
modeling and
data integration
Healthcare
informatics
Genomics and
Computational
molecular
modeling and data
structure, function integration
and evolution
Session 20
Tutorial 3
Int’l Forum
TBC
TBC
TBC
TBC
TBC
Lagan A
Lagan B
Boardroom
Broadway
Brookfield
Lisburn
(Tutorial 3)
Int’l Forum
Horizon 2020
13:00-14:00 Lunch (provided by the conference)
14:00-15:30 Session 21
Session
Chair
Venue:
Session 22
Session 23
Health data
acquisition,
analysis and
mining
Chi-Ren Shyu
Clinical decision
support and
informatics
Computational
systems biology
TBC
Inanç Birol
TBC
TBC
Lagan A
Lagan B
Boardroom
Broadway
Brookfield
15:30-15:50 Break
Conference Closing
5
US-Ireland
R&D
Lisburn
Keynotes, feature and invited talks
Keynotes and invited/feature talks
Keynotes
1. Title: Networks for knowledge
Speaker: Prof. Martin Kuiper, NTNU-Trondheim Norwegian University of Science and Technology, Norway
Abstract
Biological networks are exploited in many ways for gaining new knowledge about biological systems. Graph
analysis of networks may provide useful characteristics about the design principles and mechanisms of
pathways and regulation processes. Building networks as an object of scientific study, however, may prove to
be a painstaking task, calling for elaborate database and literature surveying in order to get a comprehensive
network representation in a topological correct format. We have used such elaborate approaches for instance
for building logical models with predictive power for anti-cancer drug efficacy. Alternatively, the Semantic Web
brings promises of enhanced sharing and use of biological knowledge. Semantic Systems Biology (SSB) aims to
utilise semantic web resources as an additional toolkit for integrative and modeling approaches aiming to
analyse and understand biological systems. The SSB group at the Norwegian University of Science and
Technology works towards ways to reach out to end-users/biologists in order to create some user-pull to
direct further implementations of semantic web resources. One of our efforts resulted in the construction of a
resource for gene expression regulation analysis: the Gene eXpression Knowledge Base GeXKB. GeXKB
provides a resource for finding novel network candidates potentially involved in gene expression regulation.
The construction of GeXKB prompted us to start efforts in the direction of ‘semantifying’ data from the source:
the curation of Transcription Factor information from scientific literature. This resulted in the TFcheckpoint
database (www.tfcheckpoint.org), and the publication of a set of curation guidelines for other volunteer
curators to join in this effort. This work inspired us to see if we could bring together the global community
interested in the domain of transcription regulation research, and we are in the process of initiating GRECO:
the Gene Regulation Consortium. GRECO aims to facilitate communication between resource and technology
providers, paving the way to develop one virtual integrated high quality knowledge resource that could be
used for instance in the field of regulatory network building and analysis.
Biography
Martin Kuiper received a M.Sc. degree in Molecular Biology and Biochemistry (1982), and a PhD degree (1987)
in Biology, at the University of Groningen, Netherlands. A nomadic post-doctoral existence allowed him to visit
virtually all of the Kingdoms of Nature. In 1992 he took a career change and went to industry, where he
worked at KeyGene NV, the Netherlands; GenScope bvba / Celera West, Belgium / California; and Aventis
CropScience, Belgium. In 2001 he returned to academia to develop systems biology approaches at the Flanders
Institute of Biotechnology in Belgium. In 2008 moved to Norway where he started a systems biology group at
the Department of Biology at NTNU, Trondheim, to promote the incorporation of systems biology and
semantic web concepts in the Life Sciences at NTNU. His research interests include the development of
approaches and tools for the modelling, analysis and visualisation of biological data, not only by
bioinformaticians but also by the biologists themselves. His current group focuses on the use of ontologies and
semantic web technologies for the integration of biological knowledge.
Semantic systems biology website: http://www.ntnu.edu/biology/semantic-systems-biology
NT Faculty website: http://www.ntnu.edu/nt/research/systemsbiology
Project website: http://www.semantic-systems-biology.org
2. Title: Virtual physiological heart of the human for the study of atrial fibrillation
Speaker: Prof. Henggui Zhang, Manchester University, UK
Abstract
Atrial fibrillation (AF) is the most common cardiac arrhythmias causing morbidity and mortality. Current
treatment of AF is unsatisfactory as the mechanisms underlying the genesis and control of AF are not yet
understood. Given the complexity of cardiac nonlinear dynamics, it is a grand challenge to underpin such
mechanisms by classic bio-medical research. Recent advances in bio-systems engineering and sciences that
uses multidisciplinary approaches shed light to study the functions of the heart. In this talk, I shall review
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recent progresses in the development of virtual physiological heart (e-Heart) and demonstrate its great
potentials to investigate the functional impacts of some gene mutations in genesis of AF.
Biography
Dr. Henggui Zhang is Professor, Chair of Biological Physics in the University of Manchester. He received his PhD
degree in Computational Physiology from the University of Leeds in 1994. Then he worked as postdoctoral
research fellow at Johns Hopkins University School of Medicine (1994-1995) and the University of Leeds (19962000), and then senior research fellow at the University of Leeds (2000-2001). In October 2001, he moved to
UMIST to take up a lecturership. From then, he worked as lecturer (2001-2004; UMIST), senior lecturer (20042006) and Reader (2006-2009) in the University of Manchester. In 2009, he was promoted to Chair, Professor
of Biological Physics. In 2013, he was appointed as a Chinese National 1000-Plan Scholar. Currently he holds a
position of Distinguished Professor in Harbin Institute of Technology. His current research interests cover
Predictive and Integrative biology, pioneering the development of a virtual heart - a large scale computer
model of physiologically detailed heart.
3. Title: Personalised Medicine N=1: Stakeholder Expectations and Challenges in delivering clinical utility
Speaker: Prof. Tony Bjourson, University of Ulster, UK
Abstract
Personalised medicine relies on discovery of different types of markers that can revise disease classification
and better inform prevention, diagnosis and treatment of disease for specific strata or even single patients.
The input of a plurality of multidisciplinary stakeholders is required to create a personalised medicine product
with clinical utility. The key sectorial stakeholders whose input is required includes patient as key beneficiaries,
clinicians as end users, regulators, commissioners, industry, academic researchers, economists, educators and
governments. Each sector has a major role to play, but a better understanding of each others expectations,
needs and priorities would hasten the delivery of personalized medicine products for patient and societal
benefit. This talk will discuss some key sectorial drivers, expectations, misconceptions, along with the clinical
and policy challenges in translating personalised medicine for disease prevention and treatment.
Biography
Tony Bjourson, is Professor of genomics and has held the post of Director of the Biomedical Sciences Research
Institute (BMSRI) at the University of Ulster since 2007 and he manages the 250 Researchers within the
Institute. He is also Director of the Northern Ireland Centre for Stratified Medicine which he established at
Altnagelvin hospital campus (based in C-TRIC) in 2013 with a £12M investment. He obtained his MSc in
Biological Sciences from the University of Ulster and his PhD from Queen’s University Belfast. He has over 30
years of research experience and prior to joining Ulster in 2001, he established and managed genomic
programmes for the DARDNI and Queens University Belfast and participated in the EU Yeast Genome
sequencing program 1994-1996. After joining Ulster he led the Pharmaceutical Biotechnology Research Group
and subsequently established and led the Biomedical Genomics Research Group. He was founder and serves as
a Director on the board of the Clinical Translation Research & Innovation Centre (C-TRIC) based in L/Derry
aimed at translating biomedical research outputs from laboratory bench to patient bedside. He has secured in
excess of £20M in research funding and has supervised >20 PhD students to successful completion.
Websites:
http://biomed.science.ulster.ac.uk/stratifiedmed/
http://study.ulster.ac.uk/prospectus/course/201415/2911
http://study.ulster.ac.uk/prospectus/course/201415/2963
http://biomed.science.ulster.ac.uk/bmsri/
7
Feature talks
1. Title: Supporting healthcare through technology and analytics
Speaker: Prof. Bryan Scotney, Professor of Informatics and Director of the Computer Science Research
Institute, University of Ulster, UK
Abstract
This talk will survey ongoing work in healthcare technologies and bioinformatics in the Computer Science
Research Institute (CSRI) at the University of Ulster. Research in CSRI is driving the development of novel
assistive technologies to improve healthcare, well-being and independence associated with ageing and
cognitive impairment, and to help prevention and management of long-term health conditions. Work in
sensor-based behavioural analysis and activity recognition and prediction is promoting community-orientated
models for independent living and “ageing in place”. Extensive engagement with healthcare professionals,
clinicians, social care providers and end-users is helping to define a technology roadmap for next generation
cognitive prosthetics. Focussing on methodologies for data collection, annotation and analytics, mobile phoneand home-based technologies for self-monitoring and self-management are being developed, along with
evaluation of factors influencing technology adoption. Methods to support predictive and modelling tasks,
information integration and visualisation in bioinformatics are being developed to facilitate understanding of
gene expression and discovery of disease biomarkers; probabilistic methods are being adapted to infer protein
complexes by exploring protein interactions; and research on combining prior domain knowledge and data
mining supports biomedical decision support.
Biography
Bryan W. Scotney is Professor of Informatics and Director of the Computer Science Research Institute at the
University of Ulster. He joined the University of Ulster in 1984 as a Lecturer in Mathematics after completing a
BSc in Mathematics at the University of Durham, UK, and a PhD in Mathematics at the University of Reading,
UK. He has over 250 publications, spanning a range of research interests in mathematical computation,
especially in digital image processing and computer vision, pattern recognition and classification, statistical
databases, reasoning under uncertainty, and applications to healthcare informatics, official statistics,
biomedical and vision sciences, and telecommunications network management. He is currently President of
the Irish Pattern Recognition and Classification Society, and Member of Council of the International Federation
of Classification Societies. He has published widely in the area of distributed data processing and analysis,
focusing on solving the problems of integration of heterogeneous data from distributed sources. Much of this
work has been supported by funding from four EU FP5 projects to address issues of harmonisation of Official
Statistics, and has involved the development of prototype systems to support interoperability of distributed
heterogeneous systems through efficient data and metadata models and processing, and methodologies to
handle imprecision and uncertainty in data. Most recently, he is an investigator on the EPSRC NETWORK in
Next Generation Networks Systems and Services (EP/F030118/1), the EPSRC–DST funded India-UK Advanced
Technology Centre (IU-ATC) of Excellence in Next Generation Networks Systems and Services (EP/G051674/1
and EP/J016748/1), an ESRC-funded project on Design for Ageing Well (RES-353-25-0004), and two projects
funded by the EU FP7 Security programme: the SAVASA project on a Standards-based Approach to Video
Archive Search and Analysis, and the Slandail project on a Security System for Language and Image Analysis.
2. Title: Wearable wireless sensing systems
Speaker: Prof. James McLaughlin, University of Ulster, UK
Abstract
This talk will focus on our capacity and expertise in the area of Healthcare Sensor Systems for clinical and
home-based monitoring. In particular the talk will highlight the importance of high sensitivity and high
specificity sensor specifications when integrated into mobile patient monitoring and the need to design
integrated robust systems with low false positives/negatives. Our expertise in vital signs multi-signal analysis,
sensor fabrication, nano-systems approach, algorithm development and blood diagnostics (Point of Care) will
be highlighted as well as our ability to transfer technology into spin out activity such as Intelesens, Heartscape
and Heartsine. I will provide an insight into our global success in the Qualcomm Tri-corder X Prize Competition.
Biography
Prof McLaughlin, a physicist, and a Fellow of the Institute of Physics and The Irish Academy of Engineering has
developed significant initiatives within research, technology transfer, outreach and teaching over these past 30
8
years. Presently, as a Professor in the School of Engineering he is also the Director of the Engineering Research
Institute and Director of the Nanotechnology and Integrated Bioengineering Centre (NIBEC) at the University
of Ulster. His salient disciplines address carbon based nano-materials associated with medical devices, related
bio-sensing applications and integrated electronic smart embedded interfaces. He has also developed
associated applied healthcare medical systems, whereby smart sensing systems, with embedded algorithms,
based on data analytics, have led to a wide range of technology transfer via licensing, spin-outs and successful
commercialisation of his work. He was recently awarded an OBE for his services to Research and Economic
Development in Northern Ireland and a Senior Distinguished Fellowship Award. He has attained in excess of
three hundred publications (H index 28) and he has been honored as an invited speaker at over forty
International Conferences. He has attracted over £43m of research funding from a wide range of prestigious
funding bodies including EPSRC, Wellcome Trust, NSF, NIH, DOH, EU, DEL (NI), SFI etc. In recent years Professor
McLaughlin’s over-arching strategy is to develop a strong Connected Health Platform within Northern Ireland
(as Chair of the European Connected Health Campus) and the EU. This work involves linking bioengineering
and computing sciences with sensor technology (including nanofabrication) developed within NIBEC and thus
facilitating clinically-led research initiatives to benefit the healthcare sector. A holder of over twenty patents,
including one for the world’s best selling disposable medical electrode, he has successfully co-founded a set of
spin-out companies including the highly successful Connected Heath company - Intelesens Ltd (Chief
Technology Officer) and more recently SiSaF (Chief Scientific Officer). Professor McLaughlin has held positions
on committees such: RAE 2008 Materials Assessment Panel; a Matrix sub-Panel chair; EPSRC College;
NanoIreland Task Force/Chaired the Nanomaterials Panel; Advisory panel to MSSI and Chair of European
Connected Health Campus.
Invite talks
1. Title: Some applications of knowledge engineering and smart systems in bioinformatics
Speaker: Dr. Carlos Toro, Vicomtech, Spain
Abstract
Clinical Decision Support Systems (CDSS) are technical solutions that can be used to help in complex decisionmaking and problem solving. CDSS are focused on how IT can improve the decision-making process in an
efficient and effective form in the clinical domain. Experiential knowledge and its management require
methodologies and tools in order to be fully operationalized. However, how to automate experience based on
intelligent techniques and software engineering methodologies is still research problem. This talk will be
divided in two parts: The first part will provide fundamentals on Knowledge Engineering and Smart Systems,
providing some background of different technologies that are being tested in the medical and bioinformatics
domains. The second part will present two case examples where the technologies discussed can be clearly
identified.
Biography
Dr. Carlos Toro received his Ph.D. in Computer Science from the University of the Basque Country (Spain) and
his master degree in Control Systems by the same university. He holds a Bachelor degree in Mechanical
Engineering (with honors) from EAFIT University (Colombia). In 1998 he was student researcher in the LSFA
(Large Scale Flexible Automation Lab) of the University of Illinois at Urbana-Champaign (USA). His bachelor
dissertation was selected between the candidates for the national excellence prize finalizing as one of the
runner-ups. Dr. Toro lectured at EAFIT University in CAD/CAM Systems (Computational Geometry) and
Conceptual Design between 2002 and 2003 and in 2003 moved to Spain to pursue a doctorate while at the
same time he started working for Vicomtech within the Industry and Advanced Manufacturing division, where
his main tasks are the application of AI and Semantic Technologies in Virtual Engineering, and the mixing of
computer graphics to different industrial scenarios. Dr Toro has been also supporting the eHealth department
of Vicomtech, were his work is focused in the application of artificial intelligence and knowledge engineering
to clinical decision support systems (CDSS), the early detection of Alzheimer and the gathering of medical
knowledge and experience for its re-use. He has published 50+ research papers in different scientific
international forums and journals. In 2007 he was invited researcher at the University of Newcastle (NSWAustralia) returning in 2011 with a Marie Curie research visitor grant. Dr. Toro is a member of the American
Society of Mechanical Engineers (ASME) and the International Association of ontologies and their application
(IAOA).
9
2. Title: The gene regulatory network of colorectal cancer
Speaker: Dr. Frank Emmert-streib , Queens University Belfast, UK
Abstract
Cancer is a complex disease that cannot be understood on the single-gene level. For this reason a functional
elucidation needs to take the concerted interactions among genes on a systems-level into account. In this talk,
I present results about an inferred colon cancer network and discuss structural and functional analysis aspects
of the network. Furthermore, I discuss relations to the hallmarks of cancer.
Biography
Dr. Frank Emmert-Streib is a Senior Lecturer at the Queen's University Belfast at the Center for Cancer
Research and Cell Biology leading the Computational Biology and Machine Learning Laboratory. Frank received
postdoctoral training in Computational Biology and Biostatistics from the University of Washington (Seattle,
USA) and the Stowers Institute for Medical Research (Kansas City, USA) and obtained his PhD in Theoretical
Physics from the University of Bremen (Germany). His research interests are in the deciphering of regulatory
networks to shed light on causal mechanisms underlying cancer and pathological phenotypes and their
application to translations research questions.
3. Title: Biomolecular network element analysis and its applications
Speaker: Prof. Fangxiang Wu, University of Saskatchewan, Canada
Abstract
The best way to understand the specialty and the importance of an individual biomolecule is placing it into a
proper biomolecular network, which describes interactions among biomolecules. Typical biomolecular
networks includes protein-protein interaction (PPI) networks, gene regulatory networks, metabolic networks,
gene-disease networks, and so on. A biomolecular network can be modelled as (un)directed graphs, where
nodes or vertices represent molecules while edges or arcs represent interactions between pairs of molecules.
To measure the importance of an element (node or edge) in networks, various centrality metrics have been
proposed for network element analysis in past years. In this talk, after reviewing several commonly used
centrality metrics I will represent some of results in identification of essential proteins, drug targets and
disease genes from biomolecular networks, based on network element analysis method.
Biography
Dr. FangXiang Wu received the B. Sc. degree and the M. Sc. degree in applied mathematics, both from Dalian
University of Technology, Dalian, China, in 1990 and 1993, respectively, the first Ph.D. in control theory and its
applications from Northwestern Polytechnical University, Xi’an, China, in 1998, and the second Ph.D. in
bioinformatics and systems biology from University of Saskatchewan, Saskatoon, Canada, in 2004. He worked
as a post-doctorial fellow with Laval University Medical Research Center, Quebec City, Quebec, during 20042005. Dr. Wu is currently a full professor and the graduate chair of the Division of Biomedical Engineering at
the University of Saskatchewan, Canada. His current research interests include systems biology, biomolecular
network analysis, genomic and proteomic data analysis, biological system identification and parameter
estimation, applications of control theory to biological systems. He has published more than 200 technical
papers in refereed journals and conference proceedings. Dr. Wu is serving as the editorial board member of
seven international journals (including Scientific Reports), the guest editor of several international journals,
and as the program committee chair or member of several international conferences. He has also reviewed
papers for many international journals. He is a senior member of IEEE and a registered Professional Engineer in
Canada.
4. Title: Computational identification of pathways from molecular interactions networks
Speaker: Prof. Xingming Zhao, Tongji University, Shanghai, China
Abstract
Molecular pathways play important roles in biology, and are involved in various processes, e.g. development
and diseases. Unfortunately, our knowledge about molecular pathways is far from complete. In this talk, I’ll
present our recent work on computational approaches that are able to identify signaling pathways from
protein-protein interaction networks. Moreover, with the power of these approaches, we identified
10
dysfunctional pathways in cancer and the causal pathways linking DNA mutations to differentially expressed
genes. In particular, we repositioned drugs for cancers based on the dysfunctional pathways.
Biography
Prof. Xing-Ming Zhao is with the School of Electronics and Information Engineering, Tongji University. He
received his Ph.D. degree from the University of Science and Technology of China in 2005. He was a postdoc
fellow at the University of Tokyo during 2006-2008, and joined the Institute of Systems Biology at Shanghai
University in 2008 as an Associate Professor. He was a postdoc fellow at the European Molecular Biology
Laboratory (EMBL) during 2010-2011. In 2012, he moved to the School of Electronics and Information
Engineering, Tongji University. His research focuses on inference and analysis of molecular interaction
networks, identification of signaling pathways, prediction of drug-protein interactions and drug combinations.
He is Senior Member of IEEE, and the member of IEEE SMC TC on Systems Biology and IAPR TC20 on Pattern
Recognition in Bioinformatics. He has published more than 50 journal papers, and is editorial board member of
several journals.
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Main conference paper presentations
Main conference paper presentations
Session 1: Genomics and molecular structure, function and evolution
Session 1: Genomics and molecular structure, function and evolution
Chair: Iona Kifer
Regular Efficient and Accurate Clustering for Large-Scale Genetic Mapping
Veronika Strnadova, Aydin Buluc, Jarrod Chapman, Joseph Gonzalez, Stefanie Jegelka, John Gilbert, Daniel
B306
Rokshar, and Leonid Oliker
Regular Identification and characterization of accessory genomes in bacterial species based on genome comparison and
metagenomic recruitment
B333
Mingjie Wang, Haixu Tang, and Yuzhen Ye
Short
B237
Quasispecies Reconstruction Based on Vertex Coloring Algorithm
Diyue Bu and Haixu Tang
Short
B310
Efficient algorithms for the compression of FASTQ files
Subrata Saha and Sanguthevar Rajasekaran
Short
B337
DExTaR: Detection of Exact Tandem Repeats based on the de Bruijn graph
Andreea Radulescu, Guillaume Fertin, Géraldine Jean, and Irena Rusu
Session 2: Transcriptomics
Session 2: Transcriptomics: Microarray data analysis, gene regulation, alternative splicing, network/pathway analysis
Chair: Shu-Dong Zhang
Regular Functional module-centric interpretation of transcriptomic change between human and chimpanzee cerebral
B440
cortex
Kimin Oh, Taeho Hwang, Kihoon Cha, and Gwan-Su Yi
Regular Heavy Path Mining Reveals Novel Protein-Protein Associations in the Malaria Parasite Plasmodium falciparum
B292
Xinran Yu, Turgay Korkmaz, Timothy Lilburn, Hong Cai, Jianying Gu, and Yufeng Wang
Regular Probabilistic Verification of ER Stress-induced Signaling Pathways
B479
Haijun Gong and Lu Feng
Short
B385
Exploring the relation between the characteristics of protein interaction networks and the performances of
computational complex detection methods
Xiaoxia liu, Zhihao Yang, Hongfei Lin, and Jian Wang
Short
B408
A logistic regression based algorithm for identifying human disease genes
Bolin Chen, Min Li, Jianxin Wang, and Fang-Xiang Wu
Session 3: Biomedical intelligence, clinical data analysis, and electronic health records
12
Session 3: Biomedical intelligence, clinical data analysis, and electronic health records
Chair: Fiona Browne
Regular Identifying Hypertrophic Cardiomyopathy Patients by Classifying Individual Heartbeats from 12-lead ECG Signals
Quazi Abidur Rahman, Larisa Tereshchenko, Matthew Kongkatong, Theodore Abraham, M. Roselle Abraham, and
B287
Hagit Shatkay
Short
B271
Semi-supervised Imputation for Microarray Missing Value Estimation
Hui-Hui Li, Feng-Feng Shao, and Guo-Zheng LI
Short
B335
Developing a Linguistically Annotated Corpus of Chinese Electronic Medical Record
Zhipeng Jiang, Fangfang Zhao, and Yi Guan
Short
B356
A Novel Disease Gene Prediction Method Based on PPI Network
Xiaohua Hu and Junmin Zhao
Short
B454
Using Unsupervised Learning to Determine Risk Level for Left Ventricular Diastolic Dysfunction
Kaidi Ma, Marco Canepa, James Strait, and Hagit Shatkay
Session 4: Biomedical signal / image processing and analysis
Session 4: Biomedical signal / image processing and analysis
Chair: TBC
Regular Selection of preprocessing methodology for multivariate regression of cellular FTIR and Raman spectra in
radiobiological analyses
B365
Aidan Meade, Colin Clarke, Hugh Byrne, and Fiona Lyng
Regular Morphometric Analysis of Sciatic Nerve Images: A Directional Gradient Approach
Inês V. Rodrigues, Pedro M. Ferreira, Ana R. Malheiro, Pedro Brites, Eduardo M. Pereira, and Hélder P. Oliveira
B368
Regular Model-free Expectation Maximization for Divisive Hierarchical Clustering of Multicolor Flow Cytometry Data
Başak Esin Köktürk and Bilge Karaçalı
B379
Short
B283
Tessellation-based Coarse Registration Method for 3D Reconstruction of the Female Torso
Pedro Costa, João P. Monteiro, Hooshiar Zolfagharnasab, and Hélder P. Oliveira
Short
B383
Normal breast identification in screening mammography: a study on 18 000 images
Sílvia Bessa, Inês Domingues, Jaime Cardoso, Pedro Passarinho, Pedro Cardoso, Vítor Rodrigues, and Fernando
Lage
Session 5: Biomedical signal / image processing and analysis
Session 5: Biomedical signal / image processing and analysis
Chair: TBC
Regular Two-step segmentation of Hematoxylin-Eosin stained histopathological images for prognosis of breast cancer
Aiping Qu, Jiamei Chen, Linwei Wang, Jingping Yuan, Fang Yang, Qingming Xiang, Ninu Maskey, Guifang Yang,
B278
Juan Liu, and Yan Li
Regular Covariate Shift-Adaptation Using a Transductive Learning Model for Handling Non-Stationarity in EEG based
Brain- Computer Interfaces
B330
Haider Raza, Girijesh Prasad, Yuhua Li, and Hubert Cecotti
Regular Fractal Descriptor Applied to the Classification of HEp-2 Cell Patterns
Rudan Xu, Yuanyuan Sun, Zhihao Yang, Bo Song, and Xiaopeng Hu
B344
Short
B257
Biomedical Image Segmentation for Semantic Visual Feature Extraction
Daekeun You, Sameer Antani, Dina Demner-Fushman, and George Thoma
Short
B264
Fitting of Superquadrics for Breast Modelling by Geometric Distance Minimization
Diogo Pernes, Jaime S. Cardoso, and Hélder P. Oliveira
Session 6: Biomedical intelligence, clinical data analysis, and electronic health records
13
Session 6: Biomedical intelligence, clinical data analysis, and electronic health records
Chair: TBC
Regular Prioritizing Disease-Causing Genes Based on Network Diffusion and Rank Concordance
B351
Xiaohua Hu and Minghong Fang
Short
B380
A Semi-informative Aware Approach using Topic Model for Medical Search
Qinmin Hu, Liang He, Mingyao Li, and E. Mark Haccke
Short
B396
Exploring Gaze-Motor Imagery Hybrid Brain-Computer Interface design
Darren O'Doherty, Yogesh Kumar Meena, Haider Raza, Hubert Cecotti, and Girijesh Prasad
Short
B372
Microbial Abundance Patterns of Host Obesity Inferred by the Structural Incorporation of Association Measures
into Interpretable Classifiers
Nancy Huang and Yen-Jen Oyang
Short
B462
Identifying Growth-Patterns in Children by Applying Cluster analysis to Electronic Medical Records
Moumita Bhattacharya, Deborah Ehrenthal, and Hagit Shatkay
Session 7: Genomics and molecular structure, function and evolution
Session 7: Genomics and molecular structure, function and evolution
Chair: TBC
Regular Dynamics and Controllability in Cell Cycle Specific Protein Interaction Networks
B342
Haiying Wang, Huiru Zheng, and Chaoyang Wang
Regular A Two-Stage Geometric Method for Detecting Unreliable Links in Protein-Protein Networks
B353
Lin Zhu, Su-Ping Deng, and De-Shuang Huang
Short
B247
Pairwise Input Neural Network for Large-Scale Target-Ligand Interaction Prediction
Caihua Wang, Juan Liu, Yafang Tan, Zixin Deng, and Qian-nan Hu
Short
B279
Detecting Functional Modules in Dynamic Protein-Protein Interaction Networks Using Markov Clustering and
Firefly Algorithm
Xiujuan Lei, Fei Wang, Fang-Xiang Wu, and Aidong Zhang
Short
B327
MultiP-SChlo: multi-label protein subchloroplast localization prediction
Xiao Wang, Guo-Zheng LI, Qiuwen Zhang, and De-Shuang Huang
Session 8: Data mining and visualization of biomedical data
Session 8: Data mining and visualization of biomedical data
Chair: TBC
Regular A Novel Method to Improve Recognition of Antimicrobial Peptides through Distal Sequence-based Features
B286
Daniel Veltri, Uday Kamath, and Amarda Shehu
Regular An Efficient Motif Finding Algorithm for Large DNA Data Sets
Qiang Yu, Hongwei Huo, Xiaoyang Chen, Haitao Guo, Jeffrey Scott Vitter, and Jun Huan
B357
Regular Ensemble-based semi-supervised learning approaches for imbalanced splice site datasets
Ana Stanescu and Doina Caragea
B423
Short
B302
Personalized microbial network inference via co-regularized spectral clustering
Sultan Imangaliyev, Bart Keijser, Wim Crielaard, and Evgeni Tsivtsivadze
Short
B374
Predicting Protein Localization Using a Domain Adaptation Naive Bayes Classifier with Burrows Wheeler
Transform Features
Nic Herndon, Karthik Tangirala, and Doina Caragea
Session 9: Biomedical signal processing / image analysis, biomedical text mining and ontologies
14
Session 9: Biomedical signal processing / image analysis, biomedical text mining and ontologies
Chair: TBC
Regular Muscle Tissue Labeling of Human Lower Extremities in Multi-Channel mDixon MR Imaging: Concepts and
Applications
B391
Matthias Becker and Nadia Magnenat-Thalmann
Regular Generating Features for Named Entity Recognition by Learning Prototypes in Semantic Space: The Case of DeB448
Identifying Health Records Aron Henriksson, Hercules Dalianis, and Stewart Kowalski
Short
B387
Liver segmentation based on SKFCM and Improved GrowCut for CT images
Hong Song, Qian Zhang, and Shuliang Wang
Short
B394
Deep Graph Search Based Disease Related Knowledge Summarization from Biomedical Literature
Xiaofang Wu, Zhihao Yang, Yuanyuan Sun, Hongfei Lin, and Jian Wang
Session 10: Transcriptomics: microarray data analysis
Session 10: Transcriptomics: microarray data analysis
Chair: TBC
Regular Integrative analysis of chemo-transcriptomic profiles for drug-feature specific gene expression signatures
B328
Chang Sik Kim, Qing Wen, and Shu-Dong Zhang
Regular A scale-free structure prior for Bayesian inference of Gaussian Graphical models
B358
Osamu Maruyama and Shota Shikita
Short
B422
Drug sensitivity prediction for cancer cell lines based on pairwise kernels and miRNA profiles
Mehmet Tan
Short
B336
Budgeted Transcript Discovery: A Framework For Joint Exploration And Validation Studies
Sheehan Khan and Russell Greiner
Short
B395
Identifying differentially expressed genes for ordinal phenotypes
Yongkang Kim and Taesung Park
Session 11: Genome-phenome analysis, biomarker discovery
Session 11: Genome-phenome analysis, biomarker discovery
Chair: Jinbo Bi
Regular Ranking of Cancer Genes In Markov Chain Model Through Integration of Heterogeneous Sources of Data
B352
Christopher Ma, Yixin Chen, and Dawn Wilkins
Regular Multi-marker developement for pancreatic ductal adenocarcinoma using integrated analysis of mRNA and miRNA
B386
expression
Min-Seok Kwon, Yongkang Kim, Seungyeoun Lee, Junghyun Namkung, Taegyun Yun, Sung Gon Yi, Meejoo Kang,
Sun Whe Kim, Jin-Young Jang, and Taesung Park
Short
B253
VISWES: a system for finding related vaccinia virus protein sequences in cancer immune therapy
SeungHeui Ryu, NaHyun Kwak, and DoHoon Lee
Short
B429
Identifying Heritable Composite Traits from Multivariate Phenotypes with Genome-Wide SNPs
Jiangwen Sun, Jinbo Bi, and Henry Kranzler
Short
B409
Discovering phenotype specific gene module using a novel biclustering algorithm in colorectal cancer
Jungrim Kim, Jeagyoon Ahn, Youngmi Yoon, Yunku Yeu, and Sanghyun Park
Session 12: Healthcare information systems, healthcare informatics
15
Session 12: Healthcare information systems, healthcare informatics
Chair: TBC
Regular Towards automatic sensor-based triage for individual remote monitoring during mass casualty incidents
B464
David Rodriguez, Stephan Heuer, Alexandre Guerra, Wilhelm Stork, Benedikt Weber, and Markus Eichler
Regular Human-Machine-Environment Cyber-Physical Systems and Hierarchical Task Planning to Support Independent
B309
Living
Shuo Xu, Guixin Wu, Dawei Tu, and Huiru Zheng
Regular
Digital Asset Management For Heterogeneous Biomedical Data in an Era of Data-Intensive Science
B445
Robert Schuler, Carl Kesselman, and Karl Czajkowski
Short
GUI based Smart Breast Cancer Identification System Using 2nd Level Secured Combined Crypto-Watermarking
B480
Mahua Bhattacharya, Koushik Pal, and Goutam Ghosh
Short
B324
MMSE: A generalized coherence measure for identifying linear patterns
Shuhua Chen, Juan Liu, and Tao Zeng
Session 13: Gene regulation, alternative splicing, network/pathway analysis
Session 13: Gene regulation, alternative splicing, network/pathway analysis
Chair: Wooyoung Kim
Regular Efficient Updates of network motif instances in the extended protein-protein interaction network
B332
Wooyoung Kim and Sheil Kurmar
Regular Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering
B350
En-Shiun Annie Lee, Ho-Yin Sze-To, Man-Hon Wong, Kwong-Sak Leung, Terrence Chi-Kong Lau, and Andrew K. C.
Wong
Regular
Data Integration and Supervised Learning Based Protein Complex Detection Method
B384
Fengying Yu, Zhihao Yang, Xiaohua Hu, Yuanyuan Sun, Hongfei Lin, and Jian Wang
Short
ESclassifier: A random forest classifier for detection of exon skipping events from RNA-Seq data
B432
Yang Bai, Shufan Ji, and Yadong Wang
Short
B437
Different cancer cell lines resistant to the same drug exhibit differences in folate pathway dynamics
Amrisha Bhosle and Nagasuma Chandra
Session 14: High-performance computing
Session 14: High-performance computing
Chair: Chi-Ren Shyu
Regular A Heterogeneous Compute Solution for Optimized Genomic Selection Analysis
B224
Trevor DeVore, Scott Winkleblack, Bruce Golden, and Chris Lupo
Regular GWISFI: a Universal GPU Interface for Exhaustive Search of Pairwise Interactions in Case-Control GWAS in
Minutes
B401
Qiao Wang, Fan Shi, Andrew Kowalczyk, Richard Campbell, Benjamin Goudey, David Rawlinson, Aaron Harwood,
Herman Ferra, and Adam Kowalczyk
Short
Adaptive Parallel Simulation of a Two-Timescale Model for Apoptotic Receptor-Clustering on GPUs
B421
Alexander Schoell, Claus Braun, Markus Daub, Guido Schneider, and Hans-Joachim Wunderlich
Short
MRSMRS: Mining Repetitive Sequences in a MapReduce Setting
B470
Hongfei Cao, Michael Phinney, Devin Petersohn, Benjamin Merideth, and Chi-Ren Shyu
Short
B473
XPFS: A New Parallel PROSITE Profile Search Algorithm on Xeon Phi
Quangang Zheng, Haidong Lan, and Weiguo Liu
Session 15: Biomedical text mining and ontologies
16
Session 15: Biomedical text mining and ontologies
Chair: Fangxiang Wu
Regular Improving Kernel-Based Protein-Protein Interaction Extraction by Unsupervised Word Representation
B323
Lishuang Li, Rui Guo, Zhenchao Jiang, and Degen Huang
Regular Mining Meaningful Topics from Massive Biomedical Literature
B433
Peiyan Zhu, Junhui Shen, Dezhi Sun, and Ke Xu
Regular Relation Extraction from Biomedical Literature with Minimal Supervision and Grouping Strategy
B439
Mengwen Liu, Yuan Ling, Yuan An, Xiaohua Hu, Alan Yagoda, and Rick Misra
Short
B346
The Protein-Protein Interaction Extraction Based on Full Texts
Lishuang Li, Liuke Jin, Jieqiong Zheng, Panpan Zhang, and Degen Huang
Short
B369
An General Instance Representation Framework for Protein-Protein Interaction Extraction
Lishuang Li, Zhenchao Jiang, and Degen Huang
Session 16: Proteomics, PTMs, metabolomics, epigenomics, non-coding RNA analysis, DNA methylation analysis
Session 16: Proteomics, PTMs, metabolomics, epigenomics, non-coding RNA analysis, DNA methylation analysis
Chair: TBC
Regular Optimizing analytical depth and cost efficiency of IEF-LC/MS proteomics
B244
Ilona Kifer, Rui M. Branca, Ping Xu, Janne Lehtio, and Zohar Yakhini
Regular NovoPair: De novo peptide sequencing for complementary spectra pair
B402
Yan Yan, Anthony J. Kusalik, and Fang-Xiang Wu
Regular CSF protein dynamic driver network: at the crossroads of brain tumorigenesis
B461
Changlin Fu, Zhou Tan, Rui Liu, Shiying Hao, Zhen Li, Pei Chen, Taichang Jang, Milton Merchant, John Whitin,
Oxford Wang, Minyi Guo, Harvey Cohen, Lawrence Recht, and Xuefeng Ling
Regular TAMeBS: A sensitive bisulfite-sequencing read mapping tool for DNA methylation analysis
Ruimin Sun, Ye Tian, and Xin Chen
B465
Short
469
A new approach to investigate the inter and intra relationships for multi-omics data integration
Yiming Zuo, Guoqiang YU, Chi Zhang, and Habtom Ressom
Session 17: Computational modeling and data integration
Session 17: Computational modeling and data integration
Chair: TBC
Regular Virtual screening, ADMET profiling, molecular docking and dynamics approaches to search for potent selective
B219
natural molecule based inhibitors against metallothionein-III to study Alzheimer’s disease
Sudeep Roy, Akhil Kumar, and Ivo Provazník
Regular Pathogen Host Interaction Prediction via Matrix Factorization
B223
Benjamin Y. S. Li, Lam Fat Yeung, and Genke Yang
Regular An Integrative Network-Driven Pipeline for the Prioritization of Alzheimer’s Disease Genes
B339
Fiona Browne, Haiying Wang, and Huiru Zheng
Short
B254
Arithmetic computation using self-assembly of DNA tiles: integer power over finite field GF(2n)
Yongnan Li
Short
B282
Exploring Potential Therapeutic Agents of Duhuo-Jisheng-Tang for Rheumatoid Arthritis
Guang Zheng
Session 18: Healthcare informatics
17
Session 18: Healthcare informatics
Chair: TBC
Regular EmotionO+: Physiological Signals Knowledge Representation and Emotion Reasoning Model for Mental Health
Monitoring
B382
Yun Su, Bin Hu, Lixin Xu, Hanshu Cai, Philip Moore, Xiaowei Zhang, and Jing Chen
Short
B345
Genetic Testing Knowledge Base (GTKB) towards Individualized Genetic Test Recommendation – An Experimental
Study
Qian Zhu, Hongfang Liu, Christopher chute, and Matthew ferber
Short
B415
Automatically Recommending Healthy Living Programs to Patients with Chronic Diseases through Hybrid ContentBased and Collaborative Filtering
Yizhou Zang, Yuan An, and Xiaohua Hu
Short
B463
Signaling Adverse Drug Reactions with Novel Feature-based Similarity Model
Fan Yang and George Karypis
Session 19: Genomics and molecular structure, function and evolution
Session 19: Genomics and molecular structure, function and evolution
Chair: TBC
Regular Konnector: Connecting paired-end reads using a Bloom filter de Bruijn graph
B456
Benjamin P Vandervalk, Shaun D Jackman, Anthony Raymond, Hamid Mohamadi, Chen Yang, Dean A Attali, Justin
Chu, René L Warren, and Inanç Birol
Regular A Dynamic Programming Algorithm For (1,2)-Exemplar Breakpoint Distance
B314
Zhexue Wei, Daming Zhu, and Lusheng Wang
Short
B398
COMMET: Comparing and combining multiple metagenomic datasets
Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, and Pierre Peterlongo
Short
B255
Gene Similarity-based Approaches for Determining Core-Genes of Chloroplasts
Bassam AlKindy, Christophe Guyeux, Jean-François Couchot, Michel Salomon, and Jacques M. Bahi
Short
B204
DMET-Miner: Efficient Learning of Association Rules from Genotyping Data for Personalized Medicine
Pietro Hiram Guzzi
Session 20: Computational modeling and data integration
Session 20: Computational modeling and data integration
Chair: TBC
Regular ENISI MSM: A Novel Multi-Scale Modeling Platform for Computational Immunology
Yongguo Mei, Adria Carbo, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Pinyi Lu, Casandra Philipson, and Josep
B355
Bassaganya-Riera
Regular Network-Constrained Forest for Regularized Omics Data Classification
Michael Andel, Jiri Klema, and Zdenek Krejcik
B413
Regular Simulation of Ventricular Automaticity Induced by Reducing Inward-rectifier K+ Current
Yue Zhang, Kuanquan Wang, and Henggui Zhang
B449
Short
B477
A multi-model reverse-engineering algorithm for large gene regulation networks
Alexandru Mizeranschi, Huiru Zheng, Paul Thompson, and Werner Dubitzky
Short
B297
Essential Protein Identification based on Essential Protein-Protein Interaction Prediction by Integrated Edge
Weights
Yuexu Jiang, Yan Wang, Wei Pang, Liang Chen, Huiyan Sun, Yanchun Liang, and Enrico Blanzieri
Session 21: Health data acquisition, analysis and mining
18
Session 21: Health data acquisition, analysis and mining
Chair: Chi-Ren Shyu
Regular A Visual Analysis Approach to Cohort Study of Electronic Patient Records
B331
Chun-Fu Wang, Kwan-Liu Ma, Chih-Wei Huang, and Yu-Chuan Li
Regular Detecting Adverse Drug Events with Multiple Representations of Clinical Measurements
B444
Jing Zhao, Aron Henriksson, Lars Asker, and Henrik Boström
Short
B218
Construct Validity of the Chinese version of WHOQOL-BREF & Disabilities Module in 1000 adults with disabilities:
an Item Response Theory analysis
Zehui He
Short
B291
Cough Detection Using Deep Neural Networks
Jia-Ming Liu, Mingyu You, Zheng Wang, Guo-Zheng LI, Xianghuai Xu, and Zhongmin Qiu
Short
B308
Hospital Pricing Estimation by Gaussian Conditional Random Fields Based Regression on Graphs
Athanasia Polychronopoulou and Zoran Obradovic
Session 22: Clinical decision support and informatics
Session 22: Clinical decision support and informatics
Chair: TBC
Regular A Symp-Med Matching Framework for Modeling and Mining Symptom and Medication Relationships from Clinical
Notes
B276
Yuan Ling, Yuan An, and Xiaohua Hu
Short
Deep Learning for Diagnosis and Healthcare Decision Making
B233
Zhaohui Liang, Jimmy Xiangji Huang, Gang Zhang, Honglai Zhang, and Jianhua Zhang
Short
Admission Duration Model for Infant Treatment (ADMIT)
B420
Keith Feldman and Nitesh Chawla
Short
Automatic and Fast Registration Method for Image-Guided Surgery
B476
Xi Wen, Hong Wang, and Weiming Zhai
Session 23: Computational systems biology
Session 23: Computational systems biology
Chair: Inanc Birol
Regular RMA with quantile normalization mixes biological signals between different sample groups in microarray data
analysis
B377
Chang Sik Kim, Seungwoo Hwang, and Shu-Dong Zhang
Regular
Predicting Drug-Target Interaction for New Drugs Using Enhanced Similarity Measures and Super-Target
B390
Clustering
Regular Jian-Yu Shi, Siu-Ming Yiu, Yiming Li, Henry C. M. Leung, and Francis Y. L. Chin
B367
Sampling-based Methods for a Full Characterization of Energy Landscapes of Small Peptides
Regular Didier Devaurs, Amarda Shehu, Thierry Siméon, and Juan Cortés
B418
Microbiome Data Integration by Robust Similarity Network Fusion
Xingpeng Jiang and Xiaohua Hu
19
Workshops
Workshops
WS1: Inaugural International Workshop on Assistive Technologies in Smart Environments
November 3, 2014: 10:50 – 17:30
Location: Brookfield
Open
10:50 – 11:00
Session 1: 10:50 – 12:45
Chair: Richard Davies, Maurice Mulvenna
Time
11:00 – 11:25
Paper ID
S1201
Paper title / authors
Assistance in Smart Homes: Combining Passive RFID Localization and Load Signatures of
Electrical Devices
Jean-Sébastien Bilodeau Turbide, Dany Fortin-Simard, Bruno Bouchard, Sébastien Gaboury,
Abdenour Bouzouane
11:25 – 11:50
S1202
Inferring Health Metrics from Ambient Smart Home Data
Lorcan Walsh, Andrea Kealy, John Loane, Julie Doyle, Rodd Bond
11:50 – 12:15
S1203
Using Embedded Systems to Spread Assistive Technology on Multiple Devices in Smart
Environments
Davide Mulfari, Antonio Celesti, Maria Fazio, Massimo Villari, Antonio Puliafito
12:15 – 12:40
B268
Natural human-robot Interaction for elderly and disabled healthcare application
Qijie Zhao, Qingxu Meng, Dawei Tu, Hui Shao, Shuo Xu
12:40 – 15:20
Break
Time
15:20 – 15:45
Paper ID
B263
Session 2: 15:20 – 17:00
Chair: Richard Davies, Maurice Mulvenna
Paper title / authors
EEG based Intelligent Robot Chair With Communication Aid Using Statistical Cross
Correlation Based Features
Sazali Bin Yaacob, Sathees Kumar Nataraj, Paulraj M P, Abdul Hamid Adom
15:45 – 16:10
N205
Development and testing of the inTouch video link for people with dementia - Design
approach and practical challenges
Hazel Boyd, Simon Jones, Nigel Harris, Niki Panteli, Jason Leake, Roy Jones
16:10 – 16:35
S1206
A Low Power and High Accuracy MEMS Sensor based Activity Recognition Algorithm
Shaolin Weng, Luping Xiang, Weiwei Tang, Hui Yang, Lingxiang Zheng, Hai Lu, Huiru Zheng
16:35 – 17:00
S1204
Design and evaluation of a tool for reminiscence of life-logged data
William Burns, Christopher Nugent, Paul McCullagh, and Huiru Zheng
17:00 – 17:30
Discussion
Richard Davies, Maurice Mulvenna
17:30
Close
20
WS2: Workshop on Computational Intelligence for Biomedicine and Bioinformatics (CIBB)
November 2, 2014: 08:45 – 17:00
Location: Lagan A
08:45 – 09:00
Session 1: 08:45 – 12:30
Chair: Stephen L. Smith
Workshop Opening Remarks
Time
Paper ID
09:00 – 09:30 S2201
Paper title / authors
IMRT Beam Angle Optimization using Differential Evolution
Joana Dias, Humberto Rocha, Brígida Ferreira, and Maria do Carmo Lopes
09:30 – 10:00 B406
Using Independent Component Analysis to Obtain Feature Space for Reliable ECG
Arrhythmia Classification
Mohammad Sarfraz, Ateeq Khan, and Francis LI
10:00 – 10:30 S2206
Ant Colony Optimisation of Decision Trees for the Detection of Gene-Gene Interactions
Ed Keedwell, and Tim Frayling
10:30 – 11:00
Break
11:00 – 11:30 S2208
LSL: A new measure to evaluate triclusters
David Gutiérrez-Avilés and Cristina Rubio-Escudero
11:30 – 12:00 B403
Particle Swarm Optimization-Based Bio-Network Discovery Method for the Diagnosis of
Colorectal Cancer
Arinze Akutekwe and Huseyin Seker
12:00 – 12:30 S2209
Meta-classification Model for Diabetes onset forecast: a proof of concept
Nonso Nnamoko, Farath Arshad, David England, and Jiten Vora
12:30 – 13:30
Lunch
Time
Paper ID
14:00 – 14:30 B318
Session 2: 14:00 – 17:00
Chair: Stephen L. Smith
Paper title / authors
Deploying Swarm Intelligence in Medical Imaging
Mohammad Majid al-Rifaie, Ahmed Aber, Robert Sayers, Edward Choke, and Mathew
Bown
14:30 – 15:00 B304
A Systems Biology Approach To Identify Proliferative Biomarkers and Pathways In Breast
Cancer
Devika Agarwal, Marie Kergosien, David Boocock, Robert Rees, and Graham Ball
15:00 – 15:30 B298
Exploration of Leukemia Gene Regulatory Networks Using A Systems Biology Approach
Dong Tong and Graham Ball
15:30 – 16:00
Break
16:00 – 16:30 S2211
GreMuTRRR: A Novel Genetic Algorithm to Solve Distance Geometry Problem for Protein
Structures
Md. Lisul Islam, Swakkhar Shatabda, and M. Sohel Rahman
16:30 – 17:00 S2203/B267
Protein Folding Structure Optimization Based on GAPSO Algorithm in the Off-Lattice
Model
Xiaoli Lin and Xiaolong Zhang
17:00
Workshop Close
21
WS3: Empowering systems bedicine through optimal design of experimentation and computational
modelling (ESM)
November 2, 2014: 13:30 – 17:30
Location: Brookfield
Session 1: 13:30 – 13:40
Chair: TBC
00:00 – 00:00
Time
00:00 – 00:00
Paper ID
S9205
00:00 – 00:00
Session 2: 00:00 – 00:00
Chair: TBC
Time
Paper ID
00:00 – 00:00 Nnnnn
00:00
Open
Paper title / authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Break
Paper title / authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Close
22
WS4: Advanced Healthcare Sensor Systems (merged with WS5)
WS5: 2014 International Workshop on Biomedical and Health Informatics (BHI 2014)
November 2, 2014: 09:30 – 18:00
Location: Lagan B
Session 1: 09:30 – 12:10
Chair: Illhoi Yoo
Open
00:00 – 00:00
Time
09:40 – 10:10
Paper ID
Paper title / authors
An Analysis of the Area Under the ROC Curve and its Use as a Metric for Comparing Clinical
Scorecards
Ed Keedwell
10:10 – 10:40
Cost decisions in the development of disease knowledge base : A case study
Takashi Okumura, Hiroaki Tanaka, Mai Omura, Maori Ito, Shin’ichi Nakagawa, and Yuka
Tateisi
10:40 – 11:10
BPMN4CP: Design and Implementation of a BPMN Extension for Clinical Pathways
Richard Braun, Hannes Schlieter, Martin Burwitz, and Werner Esswein
11:10 – 11:40
Predicting Xerostomia induced by IMRT treatments: A logistic regression approach
Inês Soares, Joana Dias, Humberto Rocha, Maria do Carmo Lopes, and Brígida Ferreira
11:40 – 12:10
Systems Modeling for Reducing Medication Errors
Eva Lee, Deniz Cinalioglu, Hyojung Kang, Niquelle Brown, Lisa Davis, and Gary Frank
12:10 – 13:30
Break
Time
13:30 – 00:00
Paper ID
Session 2: 13:30 – 00:00
Chair: Illhoi Yoo
Paper title / authors
Are static fetal growth charts still suitable for diagnostic purposes?
Mario Bochicchio and Lucia Vaira
14:00 – 00:00
Towards a Multi-level Framework for Supporting Systematic Review
Dingcheng Li
14:30 – 00:00
Non-Invasive Breathing Rate Detection Using a Very Low Power Ultra-wide-band Radar
15:00 – 15:20
Tayebeh Taheri and Anita Sant'Anna
Similar Patient Search Using the Results of Heartbeat Classification (short paper)
Juyoung Park and Kyungtae Kang
15:20 – 15:50
Break
Time
15:50 – 16:20
Paper ID
Session 3: 15:50 – 18:00
Chair: Illhoi Yoo
Paper title / authors
ECG monitoring techniques using advanced signal recovery and arm worn sensors
William lynn, Omar Escalona, and David McEneaney
16:20 – 16:50
Functional Network Disruption in Attention Deficit Hyperactivity Disorder
Zhijun Yao, Bin Hu, Yuanwei Xie, Wei Wang, Ruiyue Liu, Chuanjiang Liang, and Yun Su
16:50 – 17:10
A Framework for the Creation of Prediction Models for Serious Adverse Events
Monique Hendriks, Norbert Graf, and Njin-Zu Chen
17:10 – 17:40
Association Mining of Search Tags in PubMed Search Sessions
Abu Mosa and Illhoi Yoo
17:40 – 18:00
Remote Health Monitoring System for Detecting Cardiac Disorders
Sunil Kumar, Ayush Bansal, Vijay Tiwari, Mithun M Nayak, and Ranga Narayanan
23
18:00
Close
24
WS6: Workshop on Knowledge Extraction from Genomic Data (KEGD) (merged with WS16)
WS7: 2014 International Workshop on Biomolecular Networks and Human Diseases (BHND)
November 2, 2014: 09:00 – 12:30
Location: Glenbank
Open
9:00 – 9:15am
Session 1
Chairs: Jianxin Wang and Fang-Xiang Wu
Time
09:15 – 09:40
Paper ID
S7201
Paper title / authors
ELMDF: A new classification algorithm based on Data Field
Shuliang Wang and Dakui Wang
09:40 – 10:05
B281
Exploring the Potential Therapeutic Mechanism of Da-Fang-Feng-Tang for Rheumatoid
Arthritis
Guang Zheng
10:05 – 10:30
B316
A Novel Proteins Complex Identification Based on Connected Affinity and Multi-level Seed
Extension
Peng Li and Xiaohua Hu
Session 2
Chairs: Jianxin Wang and Fang-Xiang Wu
10:50 – 11:15
B321
A Novel Approach to Breast Cancer-Related Disease Genes Discovered Through Variation of
Density Modularity
Xianjun Shen and Yang Yi
11:15 – 11:40
B397
Correlating Interactions with Gene Expressions to Detect Protein Complexes in Protein
Interaction Networks
Huaxiong Yao
11:40 – 12:05
B431
Network Analysis of Metabolic Pathways across Bacterial Organisms in a Community
Jay Pedersen, Ryan Patch, Lotfollah Najjar, and Dhundy Bastola, PathwayLinks
12:05 – 12:30
B348
Identification of functional miRNA regulatory modules and their associations via dynamic
miRNA regulatory function
Shuang Cheng, Maozu Guo, Chunyu Wang, Xiaoyan Liu, and Yang Liu
12:30pm
Close
25
WS8: The Role of Quantified Self for Personal Healthcare (QSPH 2014)
November 2, 2014: 09:00 – 12:30
Location: TBC
Session 1: 09:00 – 10:30
Chair: Frank Hopfgartner
Open
09:00 – 09:15
Time
09:15 – 10:20
Paper ID
Paper title / authors
Keynote: Scoping the Role of Quantified Self for Personal Healthcare
Ruth Rettie
10:20 – 10:21
S8201
Activity monitoring as a tool for person-centered care: preliminary report
Anita Sant’Anna
10:21 – 10:22
S8202
Wellbeing as a proxy for a mHealth study
Chonlatee Khorakhun and Saleem Bhatti
10:22 – 10:23
S8203
Applying a User-Centered, Rapid-Prototyping Methodology with Quantified Self: a case study
with triathletes
Robin De Croon, Tom De Buyser, Joris Klerkx, and Erik Duval
10:23 – 10:24
S8204
Quantifying Brain Activity for Task Engagement
TBC
10:24 – 10:25
S8205
How affective computing could complement and advance the quantified self
Alphonsus Keary and Paul Walsh
10:25 – 10:26
S8206
Periodicity Detection in Lifelog Data with Missing and Irregularly Sampled Data
Feiyan Hu, Alan Smeaton, and Eamonn Newman
10:26 – 10:27
S8207
Towards a Generic Platform for the Self Management of Chronic Conditions
Timothy Patterson, Ian Cleland, Christopher Nugent, Norman Black, Paul McCullaugh, Huiru
Zheng, Mark Donnelly, and Suzanne McDonough
10:27 – 10:28
S8208
COPD Lifestyle Support Through Self-management (CALS)
Mark Beattie, Huiru Zheng, Christopher Nugent, and Paul McCullagh
10:28 – 10:29
S8210
Looking at our data – perspectives from Mindfulness Apps and Quantified Self as a daily
practice
Krista Lagus
Break
10:30 – 10:50
Session 2: 10:30 – 12:30
Chair: Frank Hopfgartner
Time
10:50 – 12:00
Paper ID
Paper title / authors
Poster session
12:00 – 12:30
Discussion
12:30
Close
26
WS9: The 5th International Workshop on Integrative Data Analysis in Systems Biology (IDASB 2014)
November 2, 2014: 13:30 – 17:30
Location: Brookfield
Session 1: 13:30 – 15:20
Chair: Jane Zheng
Open
13:30 – 13:40
Time
13:40 – 14:00
Paper ID
S9205
Paper title / authors
A Sparse Integrative Cluster Analysis for Understanding Soybean Phenotypes
Jinbo Bi
14:00 – 14:20
B270
RABBIC: Discover Gene Modules from Gene Expression Data
Linglin Huang, Qing Liu, Nan Yang, Yaping Li, Lin Xiao
14:20 – 14:40
B466
Constructing the co-expression network of differential genes related to cervical cancer based
on an ensembled method
Su-Ping Deng, Lin Zhu, De-Shuang Huang
14:40 – 15:00
S9202
Identifying Protein Complex Based on Communication Theory and Weighted Gene Ontology
PPI network
Yanli Zhao and Xianjun Shen
15:00 – 15:20
S9203
Prediction of hot regions in protein-protein interaction based on the Gi statistics and cascade
classifier
Bingqin Tan and Xiaolong Zhang
15:20 – 15:40
Break
Time
15:40 – 16:00
Paper ID
S9204
Session 2: 15:40 – 17:20
Chair: Jinbo Bi
Paper title / authors
Automated Reverse-Engineering of Gene Regulatory Networks based on Semi-Mechanistic
Rate Laws
Alexandru Mizeranschi, Noel Kennedy, Paul Thompson, Huiru Zheng, Werner Dubitzky
16:00 – 16:20
S9201
Identification of Protein Complexes and Functional Modules in Integrated PPI Networks
Yang Guo, Xuequn Shang, and Qingping Zhu
16:20 – 16:40
B303
Genomic Mutation Big Data Enable The Discovery of The Influence of Different Genes in 26
Human Cancers
Mohamad Al-Shammari, Yonghong Peng, Des Tobin
16:40 – 17:00
B407
LA2SNE: A Novel Stochastic Neighbor Embedding Approach for Microbiome Data Visualization
Weiwei Xu, Xingpeng Jiang, Xiaohua Hu
17:00 – 17:20
B441
Provenance data storage of genome project workflows with graph database
Rodrigo Pinheiro, Bruno Aires, Maristela Holanda, Maria Emília Walter, Sergio Lifschitz
17:30
Close
27
WS10: Workshop on Computational Translational Medicine (CTM) Boardroom
November 2, 2014: 13:30 – 17:30
Location: Tnnn
Session 1: 13:30 – 13:40
Chair: TBC
00:00 – 00:00
Time
00:00 – 00:00
Paper ID
S9205
00:00 – 00:00
Session 2: 00:00 – 00:00
Chair: TBC
Time
Paper ID
00:00 – 00:00 Nnnnn
00:00
Open
Paper title / authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Break
Paper title / authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Close
28
WS11: High Performance Computing on Bioinformatics (HPCB 2014)
November 3, 2014: 8:30 – 12:30
Location: Broadway
Session 1: 8:30 – 10:30
Chair: Che-Lun Hung
Open
08:30 – 09:00
Time
09:00 – 09:25
Paper ID
SB202
Paper title / authors
PhyloFlow: A Fully Customizable and Automatic Workflow for Phylogenetic Reconstruction
Jorge Alvarez-Jarreta, Gregorio de Miguel Casado, and Elvira Mayordomo
09:25 – 09:50
SB203
Efficient Parallel Algorithm for Compound Comparisons on Multi-GPUs
Chun-Yuan Lin, Chung-Hung Wang, Che-Lun Hung, and Yu-Shiang Lin
09:50 – 10:15
SB204
Genomic Data Persistency on a NoSQL Database System
Rodrigo Aniceto, Rene Xavier, Maristela Holanda, Maria Emilia Walter, and Sérgio Lifschitz
10:15 – 10:30
Discussion
Che-Lun Hung
10:30 – 10:50
Break
Session 2: 10:50 – 12:30
Chair: Inanç Birol
Paper title / authors
Fastq_clean: an optimized pipeline to clean the Illumina sequencing data with quality control
Mi Zhang, Feng Zhan, Honghe Sun, Xiujun Gong, Zhangjun Fei, and Shan Gao
Time
10:50 – 11:15
Paper ID
B211
11:15 – 11:40
B376
Adopting the MapReduce Framework to Pre-train 1-D and 2-D Protein Structure Predictors
with Large Protein Datasets
Jesse Eickholt and Suman Karki
11:40 – 12:05
B438
Accelerating Microbiomic Big Data Analysis by Spectral Interpolation
Bo Song, Xingpeng Jiang, and Xiaohua Hu
12:05 – 12:30
B453
Spaced Seed Data Structures
Inanç Birol, Hamid Mohamadi, Anthony Raymond, Karthika Raghavan, Justin Chu, Benjamin P
Vandervalk, Shaun Jackman, and René L Warren
12:30
Close
29
WS12: The Fifth International Workshop on Information Technology for Chinese Medicine (ITCM 2014)
November 2, 2014: 13:30 – 17:30
Location: Tnnn
Session 1: 13:30 – 13:40
Chair: TBC
00:00 – 00:00
Time
00:00 – 00:00
Paper ID
S9205
00:00 – 00:00
Session 2: 00:00 – 00:00
Chair: TBC
Time
Paper ID
00:00 – 00:00 Nnnnn
00:00
Open
Paper title / authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Break
Paper title / authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Close
30
WS13: Computational Modelling and Bioinformatics in Epigenetics (CMBE 2014) (merged with WS3)
WS14: Workshop on Nanoinformatics for Environmental Health and Biomedicine (NEHB)
November 2, 2014: 13:30 – 17:20
Location: Glenbank
Session 1: 13:30 – 15:30
Chair: Rong Liu
Time
13:30 – 14:00
Paper ID
Paper title / authors
caNanoLab: A nanomaterial data repository for biomedical research
Stephanie Morris, Sharon Gaheen, Michal Lijowski, Mervi Heiskanen, and Juli Klemm
14:00 – 14:30
Visual Data Exploration of Soil Bacteria Susceptible to Engineered Nanomaterials
Rong Liu, Yuan Ge, Patricia Holden, and Yoram Cohen
14:30 – 15:00
The first eNanoMapper prototype: a substance database to support safe-by-design
Nina Jeliazkova, Vedrin Jeliazkov, Egon Willighagen, Bart Smeets, Cristian Munteanu, Bengt
Fadeel, Roland Grafström, Pekka Kohonen, Haralambos Sarimveis, Georgia Tsiliki, Philip
Doganis, David Vorgrimmler, and Janna Hastings
15:00 – 15:30
The Desription of Nanomaterials: A multi-disciplinary Uniform Description System
John Rumble, Steve Freiman, and Clayton Teague
15:30 – 15:50
Break
Session 2: 15:50 – 17:20
Chair: Rong Liu
Time
15:50 – 16:20
Paper ID
Paper title / authors
Regional multimedia distribution of nanomaterials and associated exposures: A software
platform
Haoyang Haven Liu, Muhammad BIlal, Anastasiya Lazareva, Arturo Keller, and Yoram Cohen
16:20 – 16:50
Comparative study among three different artificial neural networks to infectious diarrhea
forecasting
Yongming Wang and Juzhong Gu
16:50 – 17:20
Nanotoxicity Modeling in Multidimentional Cube
Xiong Liu, Kaizhi Tang, Lemin Xiao, Mitchell Song, and Roger Xu
17:20
Close
31
WS15: Semantic Data Analytics and Bioinformatics (SDAB)
November 2, 2014: 13:30 – 17:30
Location: Tnnn
Session 1: 13:30 – 13:40
Chair: TBC
00:00 – 00:00
Time
00:00 – 00:00
Paper ID
S9205
00:00 – 00:00
Session 2: 00:00 – 00:00
Chair: TBC
Time
Paper ID
00:00 – 00:00 Nnnnn
00:00
Open
Paper title / authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Break
Paper title / authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Title
Authors
Close
32
WS16: 2014 Workshop on Data Mining from Genomic Rare Variants and its Application to Genome-wide
Analysis
November 3, 2014: 10:50 – 17:00
Location: Glenbank
Open
10:50 – 10:50
Session 1: 10:50 – 12:55
Chair: Taesung Park
Time
10:50 – 11:15
Paper ID
SG205
Paper title / authors
Genome-wide association analysis with matched samples discloses novel risk loci for type II
diabetes
Jungsoo Gim, Sungkyoung Choi, Jongho Im, Jae-Kwang Kim, and Taesung Park
11:15 – 11:40
SG203
Multifactor dimensionality reduction analysis for gene-gene interaction of multiple binary
traits
Iksoo Huh and Taesung Park
11:40 – 12:05
B452
Drug Resistance Gene Identification Algorithm for Next-Generation Sequencing Data
Guan-Jie Hua, Che-Lun Hung, Chuan Yi Tang, and Huiru Zheng
12:05 – 12:30
B261
A fast pattern matching algorithm for highly similar sequences
Nadia Ben Nsira, Thierry Lecroq, and Mourad Elloumi
12:30 – 12:55
SG204
A normalization method for multiple reaction monitoring (MRM) data
Jungsoo Gim and Taesung Park
12:55 – 14:00
Lunch at Hilton Restaurant
Time
15:20 – 15:45
Paper ID
B312
Session 2: 15:20 – 15:45
Chair: Taesung Park
Paper title / authors
Microbiome Dynamics Analysis Using a Novel Multivariate Vector Autoregression Model with
Weighted Fusion Regularization
Hu Xiaohua, Wang Yan, and Jiang Xingpeng
15:45 – 16:10
SG202
Estimating cancer gene pathway proximity using network interaction
Rama Srikanth Mallavarapu, TaeJin Ahn, Subhankar Mukherjee, Ajit S Bopardikar, Garima
Agarwal, and Taesung Park
16:10 – 16:35
B227
Sparse gene expression data analysis based on Truncated Power
Ningmin Shen, Jing Li, Cheng Jin, and Peiyun Zhou
16:35 – 17:00
B372
Combining Active Learning and Composite kernel for Protein-Protein Interaction Extraction
Jian Wang, Minjie Liu, Hongfei Lin, Zhihao Yang, and Yijia Zhang
17:00
Close
WS17: Simplicity – Enabling a Rapid Route to Publication (merged with Industrial Track)
33
Posters
Posters
#
ID
Title / authors
1.
P201
Comprehensive Assessment of Gait Signals Using Multiple Time Scale Features
Xi Wu, Huitong Ding, Bingnan Li, and Ning An
2.
P202
Accelerating Incremental Wrapper based Gene Selection with K-Nearest-Neighbor
Aiguo Wang, Ning An, Lian Li, and Gil Alterovitz
3.
P203
Modeling of Personal Thinking and Its Application to Studies of Group Thinking Over the Internet
Satoru Ozawa, Shigeyuki Murayama, Sarkar Barbaq Quarmal, Atsushi Minato, and Masanori Itaba
4.
P204
Missing value estimation for visualization of meridian data in Traditional Chinese Medicine
Jia-Chang Chen, Hui-Hui Li, Yang Zhimin, Yuan Jiamin, and Guo-Zheng Li
5.
P205
Targeted profiling of 5-(hydroxy)methylcytosine in genomic DNA from human livers
Maxim Ivanov, Mart Kals, Lili Milani, and Magnus Ingelman-Sundberg
6.
P206
A Linear Classification Approach to model the Early Cellular Responses Induced by Drugs
Dechang Xu, Zhiying Liang, Dayou Cheng, Cuihong Dai, Aiju Hou, and Jianzhong Li
7.
P207
Whole Cancer Genome Analysis Using an I/O Aware Job Scheduler on High Performance Computing Resource
Junehawk Lee, Hyojin Kang, Seokjong Yu, Chul Kim, and Sang-Jun Yea
8.
P208
Picking out herbs with analogous efficacy based on MeSH semantic similarity
Sang-Jun Yea, Chul Kim, IckTae Kim, and BoSeok Sung
9.
P209
K-mer clustering algorithm using MapReduce approach
Chang Sik Kim, Martyn D. Winn, Vipin Sachdeva, and Kirk E. Jordan
10. P210
Relation Between the Yin-cold or Yang-heat Syndrome Type of TCM and the EGFR Gene Status in Patients with
NSCLC
Yan-juan Zhu, Hai-bo Zhang, Li-rong Liu, Bin Yuan, Fu-li Zhang, Jian-ping Bai, Yong Li, Yi-hong Liu, Yan-chun Qu,
and Xin Qu
11. P211
How to build databases of traditional Chinese medicine
Huan Ma
12. P212
Genetic risk variants in schizophrenia: Identifying disease relevant interactions
Bathilde Ambroise, JTR Walters, JL Moran, SA McCarroll, MJ Owen, MC O’Donovan, V Escott-Price, and AJ
Pocklington
13. P213
Deep sequencing of Sugar Beet small RNAs identifies microRNAs involved in cold stress response
Dechang Xu, Zhiying Liang, Dayou Cheng, Cuihong Dai, Aiju Hou, and Jianzhong Li
14. P214
Scaffold-based chemical space exploration
David Hoksza and Petr Škoda
15. P215
A novel un-supervised clustering pipeline utilizing a two-step process to identify robust and objective subtypes
with the optimal starting feature set
Sinead Donegan, Andreas Winter, Steve Deharo, Nicholas Goffard, and Fionnuala Patterson
16. P216
Network Driven Analysis for Biomarker Discovery in Alzheimer’s Disease
Haiying Wang, Fiona Browne, and Huiru Zheng
17. P217
Template-Based Prediction of Ribosomal RNA Secondary Structure
Josef Pánek, Jan Hajič jr., and David Hoksza
18. P218
Coreference Resolution in Biomedical Texts
Lishuang Li, Liuke Jin, Zhenchao Jiang, Jing Zhang, and Degen Huang
19. P219
Muscle-invasive urothelial cancer gene regulatory network signatures inferred from large-scale gene
expression data
Ricardo de Matos Simoes, Sabine Dalleau, Kate Williamson, and Frank Emmert-Streib
20. P220
Three-dimensional (3D) model of the genomic regulatory network controlling epidermal keratinocyte
differentiation
Krzysztof Poterlowicz, Joanne Yarker, Natalia Naumova, Bryan Lajoie, Andrei Mardaryev, Job Dekker, Vladimir
Botchkarev, Andrey Sharov, and Michael Fessing
21. P221
Smart Food: Crowdsourcing of experts in nutrition and non-experts in identifying calories of meals using
smartphone as a potential tool contributing to obesity prevention and management
Anne Moorhead, Raymond Bond, and Huiru Zheng
34
22. P222
VGA : a method for viral quasispecies assembly from ultra-deep sequencing data
Serghei Mangul, Nicholas Wu, Nick Mancuso, Alex Zelikovsky, Ren Sun, and Eleazar Eskin
23. P223
Combining AR filter and Sparse Wavelet representation for P300 speller
Zhihua Huang
24. P224
Usability testing of a novel automated external defibrillator user interface: a pilot study
Peter O'Hare, Raymond Bond, and Rebecca Di Maio
25. P225
Binding Update No Sense Drop BCE in LMA (BUNSD-LMA)
Mohamed Geaiger, Aisha Hassan, Elsheikh Elsheikh, and Wan Haslin Hassan
35
Tutorials
Tutorials
Tutorial 1:
Methods for Engineering and Evaluating the Usability of Medical Software & Medical Devices
Instructors:
Prof. Jonathan Wallace (University of Ulster), Dr Peter O’Hare (HeartSine Technologies),
Dr Raymond Bond (University of Ulster)
Summary
Approximately 98,000 patients die every year as a result of an avoidable medical error and there are also one
million patient injuries due to such errors. Specifically, a number of these errors are a result of counterintuitive medical software and medical devices. Hence, the FDA and other regulatory bodies now require
medical device companies to validate the usability of their products before they are approved for use within
routine healthcare. However, there are a plethora of usability evaluation methods, techniques and approaches
a researcher or a medical device company can adopt. This tutorial looks to present these various usability
evaluation methods and to highlight good practice in evaluating the usability of medical software and medical
devices.
Intended Audience
Biomedical engineers, software developers, those involved in trials of medical devices, those who interact with
biomedical software and medical devices, academics and experts in human computer interaction studies.
Tutorial 2:
Viral Population Analysis: Detection of Rare Variants and Full-length Genomes from Next-generation
Sequencing Data
Instructor: Dr. Serghei Mangul (Computational Biosciences Institute, University of California, Los Angeles)
Summary
Next-generation sequencing technologies sequence viruses with ultra‐deep coverage, thus promising to
revolutionize our understanding of the underlying diversity of viral populations. While the sequencing
coverage is high enough that even rare viral variants are sequenced. The presence of sequencing errors makes
it difficult to distinguish between rare variants and sequencing errors. In this tutorial, we provide necessary
knowledge and skills allowing researchers to use contemporary sequencing technologies for viral population
analysis. We provide hands‐on guide on available sequencing protocols and computations software tools for
complete viral population analysis i.e. read mapping, reference consensus construction, detection of rare
variants and assembly of full-length genomes in viral population.
The proposed workflow helps to overcome the limitations of sequencing technologies and allows monitoring
and quantifying HIV population structure from ultra deep sequencing data. In addition to hands‐on guide the
tutorial discusses current next-­‐generation sequencing technologies and available computational tools for
viral population analysis. The main focus of the tutorial is to enable researchers to acquire expertise necessary
for using next‐ generation sequence data for viral population analysis. The tutorial is supplemented with many
hands‐on examples.
Tutorial 3:
Ontology-based information visualization for Collaborative Network Organization (CNOs) visualization Case
study: visualization of Healthcare CNO
Instructor: Dr. Morcous M. Yassa, Cairo University, Egypt
36
Summary
By combining virtual communities with Internet portal and content management technologies, Collaborative
Network Organization (CNOs) share, access and extend the tacit and explicit knowledge within and across
organizations. CNOs are a special kind of web-enabled communities of practice, where like-minded people
collaborate and work together towards a common goal, sharing the same vision and values. Information
visualization is a powerful tool for communicating complex ideas, but also for exploring data. Research in
information visualization has been fueled by the continued growth in the size and complexity of data sets, but
it has focused mainly on visualization techniques. Understanding the process of visualization from a wider
perspective would support both the development of visualization software, and the adaptation of information
visualization as an exploratory technique. This tutorial aims to study this process, and how it can be used to
support the exploration of inter-organizational networks in particular. In addition, a case study involving the
visualization of Healthcare CNO will discuss.
37
Industrial track
Industrial Track
Time
Presenter
Title
10:50 – 11:20
Kieran Daly
BioBussiness
11:20 – 11:50
Frank EmmertStreib,
The gene regulatory network of colorectal cancer (N201 Invited Talk 2)
11:50 – 12:20
Paul Walsh and
John Carroll
Simplicity – Enabling a Rapid Route to Publication (SH201)
15:20 – 15:50
Sinead Donegan
A novel un-supervised clustering pipeline utilizing a two-step process to
identify robust and objective subtypes with the optimal starting feature
set (P215)
15:50 – 16:20
Ibtihal Nafea, Noha Health Tracking Framework for Hajj Pilgrims using Electronic Health
Bhiary, and Zeidan Records for Hajj (N204)
Zeidan
16:20 – 16:50
Hazel Boyd, and
Nigel Harris
User led design to support successful product development in assistive
technology (N205)
38