BIBM 2014
Program Schedule
Overview
Overview
Venue and Banquet
Presentation format
Conference schedule
Keynotes and Invited Talks
Main conference paper presentation
Workshops
Posters
Tutorials
Industrial Track
International Collaboration Forum
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p7
p12
p20
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p35
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Venue and Banquet
Venue and Banquet
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
WiFi Access:
Username: hhonors
Password: hilton11
Car Park (special rate, contact
Concierge team at reception):
£12.00 from 8am – 8pm
£18.00 for 24 hours
Banquet (Tuesday, November 4, 2014)
18:00
Buses depart from Hilton Hotel to Titanic Museum
18:30
Titanic Experience
19.15 – 19.45
Titanic Suite drinks reception
19:45 – 22.30
Gala Dinner, prize presentation
22:30
Buses leave from Titanic Museum to Hilton Hotel
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)
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Conference schedule
Conference schedule
November 1
November 1, 2014 (Saturday)
16:0020:00
Registration: Hilton Hotel, lobby (gound floor)
November 2
November 2, 2014 (Sunday)
08:00-18:00
Venue:
08:3012:30
Registration
Foyer in Hilton Hotel (Floor 2)
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
Boardroom
Coffee break: 10:30-10:50
12:30-13:30
Lunch at Hotel restaurant (provided by the conference)
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
CANCELLED
Zhao
Weidong Tian
HY Wang
H Wang
Venue:
Lagan A
Lagan B
Glenbank
Boardroom
Lisburn
Brookfield
o
Break : 15:30-15:50
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November 3
November 3, 2014 (Monday)
08:00-18:00 Registration
Venue:
Foyer in Hilton Hotel (Floor 2)
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
Haiying
Wang
Raymond Richard
Bond
Davies
Boardroom
Broadway
Lisburn
Session 7
Genomics and
molecular
structure, function
and evolution
Session 8
( T1)
Biological
data mining
and
visualization
Haiying Wang
Benjamin Li Raymond Richard
Bond
Davies
Boardroom
Broadway
WS16
Taesung Park
Brookfield Glenbank
13:00-14:00 Lunch at Hilton Restaurant
Poster Session Foyer (Floor 2)
14:00-15:00 Session Chair: Prof. Maurice Mulvenna
Keynote 2: Prof. Henggui Zhang
Venue:
Lagan
15:00-15:20 Break
15:20-17:30 Session 5
Biomedical
signal/image
analysis
Session
Chair
Bing Nan Li
Session 6
Biomedical
intelligence, clinical
data Analysis, and
electronic health
record
Paul Walsh
Venue:
Lagan A
Lagan B
4
Lisburn
(WS1)
(WS16)
Taesung Park
Brookfield Glenbank
November 4
November 4, 2014 (Tuesday)
08:0018:00
Venue:
09:0010:30
Registration
Venue:
Lagan
10:3010:50
Break
10:50 13:00
Session 9
Session 10
Biomedical
signal/image
analysis,
biomedical text
mining and
ontologies
Transcriptomics: GenomeMicroarray data phenome
analysis
analysis,
biomarker
discovery
Healthcare
information
systems,
healthcare
informatics
Session
Chair
Yun Su
Arinze Akutekwe Jinbo Bi
Venue:
Lagan A
Lagan B
13:0014:00
Lunch (provided by the conference)
Foyer in Hilton Hotel (Floor 2)
Session Chair: Prof. Werner Dubitzky
Feature talk 1: Prof. Bryan Scotney,
Keynote 1: Prof. Martin Kuiper
Session 11
Session 12
Tutorial2
Industrial
Track
Networking/
Meeting/
Discussion
Mahua
Bhattacharya
Serghei
Mangul
Drs. Carlos
Open
Toro and Paul
Walsh
Boardroom
Broadway
Brookfield Lisburn
GlenBank
Session 15
Session 16
(Tutorial2) Industrial
Track
Networking/
Poster Session Floor 2 foyer
14:0015:00
Venue:
Session Chair: Prof. Chris Nugent
Invited talk 3: Prof. Fangxiang Wu
Invited talk 4: Dr. Timothy Davison
Lagan
15:0015:20
Break
15:2017:30
Session 13
Session 14
Gene regulation, Highalternative
performance
splicing,
computing
network/pathway
analysis
Biomedical text Proteomics,
mining and
PTMs,
ontologies
metabolomics,
epigenomics,
non-coding RNA
analysis, DNA
methylation
analysis
Fangxiang Wu Ricardo de
Serghei
Matos Simoes
Mangul
Session
Chair
Wooyoung Kim
Chi-Ren Shyu
Venue:
Lagan A
Lagan B
18:0022:00
Banquet (Best Paper Award, Best Student Paper Award, Best Workshop Paper Award, Best Poster
Award)
Boardroom
Broadway
Drs. Carlos
Open
Toro and Paul
Walsh
Brookfield Lisburn
(Titanic Experience and Museum, Drink Reception and Gala Dinner. Buses leave Hilton Hotel at
6.00pm)
5
Meeting/
Discussion
GlenBank
November 5
November 5, 2014 (Wednesday)
08:0015:00
Venue:
Registration:
Foyer in Hilton Hotel (Floor 2)
9:00-10:30 Session Chair: Prof. George Thoma
Feature talk 2: Prof. James
McLaughlin
Invited talk 1: Dr. Carlos Toro
Venue:
Lagan
10:3010:50
Break
10:3013:00
Session 17
Session 18
Session 20
Computational Healthcare
modeling and informatics
data
integration
Genomics and
molecular
structure,
function and
evolution
Computational
modeling and
data integration
Session
Chair
Ricardo de
Matos Simoes
Lucia Vaira
Ding Cheng Li
Hong Yue
Morcous M. Dr. Fiona
Yassa
Browne
Open
Venue
Lagan A
Lagan B
Boardroom
Broadway
Brookfield
GlenBank
13:0014:00
Lunch (provided by the conference)
14:0015:30
Session 21
Session 23
Networking/
(Tutorial 3) Int’l Forum Networking/
Meeting/
Session 22
Tutorial 3
Int’l Forum Networking/
Meeting/
Horizon
Session 19
2020
Lisburn
Discussion
Health data
acquisition,
analysis and
mining
Chi-Ren Shyu
Clinical decision
support and
informatics
Computational
systems biology
Meeting/
Sameer Antani
Inanç Birol
Open
Morcous M. Dr. Fiona
Yassa
Browne
Open
Venue:
Lagan A
Lagan B
Boardroom
Broadway
Brookfield
GlenBank
15:3015:50
Break
Session
Chair
Conference Closing
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Discussion
US-Ireland
R&D
Lisburn
Discussion
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
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.
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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, Ulster University, 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 Ulster University 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 Ulster University 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/
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, Ulster University, UK
Abstract
This talk will survey ongoing work in healthcare technologies and bioinformatics in the Computer Science
Research Institute (CSRI) at the Ulster University. 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 phone- and
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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
Ulster University. He joined the Ulster University 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, Ulster University, 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
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 Ulster
University. 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
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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).
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.
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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: An Integrated Framework of Model Selection for Robust Biomarker Development
Speaker: Timothy Davison, B. Math, Ph.D. – VP of Bioinformatics and Biostatistics, Almac Diagnostics,
Northern Ireland
Abstract
In recent years, thousands of diagnostic, prognostic and predictive gene signatures have been reported in the
literature, however, only a handful have been developed into tests available for application in routine clinical
practice. In this presentation I will outline the best practices for biomarker development with a view to
creating a product with biological relevance, statistical, analytical and clinical utility. I will describe how this
can be achieved by integrating the evaluation of data and prior knowledge including standard clinical
covariates, gene ontology and biological processes, technical replication and model permutation within crossvalidation at the biomarker discovery stage. Biomarkers discovered with such a framework result in products
with an increased likelihood of clinical and analytical validation. I will conclude with an example of how this
framework was used to discover a 44-gene signature for the identification of a molecular subgroup of breast
cancer patients with DNA-damage repair deficiency which has been independently validated for predicting
pathological response to neoadjuvant chemotherapy and relapse free survival to adjuvant chemotherapy.
Biography
Dr. Timothy Davison is VP of Bioinformatics and Biostatistics within Almac Diagnostics. In this role, Timothy
leads a team of scientists, supporting technology benchmarking and the development of diagnostic, prognostic
and predictive tests. He has a range of experience in the academic, biotechnology and pharmaceutical
industries, having previously been employed at Janssen PRD (Centocor), Asuragen Inc., the University Health
Network Clinical Informatics research center and Hospital for Sick Children (Toronto) bioinformatics
supercomputing center. Timothy received his bachelor of Applied Mathematics from the University of
Waterloo and Ph.D. in Medical Biophysics from the University of Toronto. He spent 2 years as a post-doctoral
research scientist, joint appointed to the Max Planck Institute for Biological Cybernetics, Department of
Empirical Inference for Machine Learning and Perception, and the Institute for Developmental Biology,
Department of Molecular Biology.
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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
November 3, 10:50 – 13:00, Lagan A
Chair: Iona Kifer
Regular Efficient and Accurate Clustering for Large-Scale Genetic Mapping
B306
Veronika Strnadova, Aydin Buluc, Jarrod Chapman, Joseph Gonzalez, Stefanie Jegelka, John Gilbert, Daniel
Rokshar, and Leonid Oliker
Regular Identification and characterization of accessory genomes in bacterial species based on genome comparison and
B333
metagenomic recruitment
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
November 3, 10:50 – 13:00, Lagan B
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
November 3, 10:50 – 13:00, Boardroom
Chair: Fiona Browne
Regular Identifying Hypertrophic Cardiomyopathy Patients by Classifying Individual Heartbeats from 12-lead ECG Signals
B287
Quazi Abidur Rahman, Larisa Tereshchenko, Matthew Kongkatong, Theodore Abraham, M. Roselle Abraham, and
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
November 3, 10:50 – 13:00, Broadway
Chair: Haiying Wang
Regular Selection of preprocessing methodology for multivariate regression of cellular FTIR and Raman spectra in
B365
radiobiological analyses
Aidan Meade, Colin Clarke, Hugh Byrne, and Fiona Lyng
Regular Morphometric Analysis of Sciatic Nerve Images: A Directional Gradient Approach
B368
Inês V. Rodrigues, Pedro M. Ferreira, Ana R. Malheiro, Pedro Brites, Eduardo M. Pereira, and Hélder P. Oliveira
Regular Model-free Expectation Maximization for Divisive Hierarchical Clustering of Multicolor Flow Cytometry Data
B379
Başak Esin Köktürk and Bilge Karaçalı
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
November 3, 15:20 – 17:30, Lagan A
Chair: Bing Nan Li
Regular Two-step segmentation of Hematoxylin-Eosin stained histopathological images for prognosis of breast cancer
B278
Aiping Qu, Jiamei Chen, Linwei Wang, Jingping Yuan, Fang Yang, Qingming Xiang, Ninu Maskey, Guifang Yang,
Juan Liu, and Yan Li
Regular Covariate Shift-Adaptation Using a Transductive Learning Model for Handling Non-Stationarity in EEG based
B330
Brain- Computer Interfaces
Haider Raza, Girijesh Prasad, Yuhua Li, and Hubert Cecotti
Regular Fractal Descriptor Applied to the Classification of HEp-2 Cell Patterns
B344
Rudan Xu, Yuanyuan Sun, Zhihao Yang, Bo Song, and Xiaopeng Hu
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
13
Session 6: Biomedical intelligence, clinical data analysis, and electronic health records
Session 6: Biomedical intelligence, clinical data analysis, and electronic health records
November 3, 15:20 – 17:30, Lagan B
Chair: Paul Walsh
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
November 3, 15:20 – 17:30, Boardroom
Chair: Haiying Wang
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
November 3, 15:20 – 17:30, Broadway
Chair: Benjamin Li
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
B357
Qiang Yu, Hongwei Huo, Xiaoyang Chen, Haitao Guo, Jeffrey Scott Vitter, and Jun Huan
Regular Ensemble-based semi-supervised learning approaches for imbalanced splice site datasets
B423
Ana Stanescu and Doina Caragea
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
November 4, 10:50 – 13:00, Lagan A
Chair: Yun Su
Regular Muscle Tissue Labeling of Human Lower Extremities in Multi-Channel mDixon MR Imaging: Concepts and
B391
Applications
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
November 4, 10:50 – 13:00, Lagan B
Chair: Arinze Akutekwe
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
November 4, 10:50 – 13:00, Boardroom
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
November 4, 10:50 – 13:00, Broadway
Chair: Mahua Bhattacharya
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
B445
Digital Asset Management For Heterogeneous Biomedical Data in an Era of Data-Intensive Science
Robert Schuler, Carl Kesselman, and Karl Czajkowski
Short
B480
GUI based Smart Breast Cancer Identification System Using 2nd Level Secured Combined Crypto-Watermarking
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
November 4, 15:20 – 17:30, Lagan A
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 Predicting Drug-Target Interaction for New Drugs Using Enhanced Similarity Measures and Super-Target
B390
Clustering
Jian-Yu Shi, Siu-Ming Yiu, Yiming Li, Henry C. M. Leung, and Francis Y. L. Chin
Short
B432
ESclassifier: A random forest classifier for detection of exon skipping events from RNA-Seq data
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
November 4, 15:20 – 17:30, Lagan B
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
B401
Minutes
Qiao Wang, Fan Shi, Andrew Kowalczyk, Richard Campbell, Benjamin Goudey, David Rawlinson, Aaron Harwood,
Herman Ferra, and Adam Kowalczyk
Regular
B421
Adaptive Parallel Simulation of a Two-Timescale Model for Apoptotic Receptor-Clustering on GPUs
Alexander Schoell, Claus Braun, Markus Daub, Guido Schneider, and Hans-Joachim Wunderlich
Short
B470
MRSMRS: Mining Repetitive Sequences in a MapReduce Setting
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
16
Session 15: Biomedical text mining and ontologies
Session 15: Biomedical text mining and ontologies
November 4, 15:20 – 17:30, Boardroom
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
November 4, 15:20 – 17:30, Broadway
Chair: Ricardo de Matos Simoes
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
B465
Ruimin Sun, Ye Tian, and Xin Chen
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
November 5, 10:30 – 13:00, Lagan A
Chair: Ricardo de Matos Simoes
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
November 5, 10:30 – 13:00, Lagan B
Chair: Lucia Vaira
Regular EmotionO+: Physiological Signals Knowledge Representation and Emotion Reasoning Model for Mental Health
B382
Monitoring
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
November 5, 10:30 – 13:00, Boardroom
Chair: Ding Cheng Li
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
November 5, 10:30 – 13:00, Broadway
Chair: Hong Yue
Regular ENISI MSM: A Novel Multi-Scale Modeling Platform for Computational Immunology
B355
Yongguo Mei, Adria Carbo, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Pinyi Lu, Casandra Philipson, and Josep
Bassaganya-Riera
Regular Network-Constrained Forest for Regularized Omics Data Classification
B413
Michael Andel, Jiri Klema, and Zdenek Krejcik
Regular Simulation of Ventricular Automaticity Induced by Reducing Inward-rectifier K+ Current
B449
Yue Zhang, Kuanquan Wang, and Henggui Zhang
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
November 5, 14:00 – 15:30, Lagan A
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
November 5, 14:00 – 15:30, Lagan B
Chair: TBC
Regular A Symp-Med Matching Framework for Modeling and Mining Symptom and Medication Relationships from Clinical
B276
Notes
Yuan Ling, Yuan An, and Xiaohua Hu
Short
B233
Deep Learning for Diagnosis and Healthcare Decision Making
Zhaohui Liang, Jimmy Xiangji Huang, Gang Zhang, Honglai Zhang, and Jianhua Zhang
Short
B420
Admission Duration Model for Infant Treatment (ADMIT)
Keith Feldman and Nitesh Chawla
Short
B476
Automatic and Fast Registration Method for Image-Guided Surgery
Xi Wen, Hong Wang, and Weiming Zhai
Session 23: Computational systems biology
Session 23: Computational systems biology
November 5, 14:00 – 15:30, Boardroom
Chair: Inanc Birol
Regular RMA with quantile normalization mixes biological signals between different sample groups in microarray data
B377
analysis
Chang Sik Kim, Seungwoo Hwang, and Shu-Dong Zhang
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
Regular Sampling-based Methods for a Full Characterization of Energy Landscapes of Small Peptides
B367
Didier Devaurs, Amarda Shehu, Thierry Siméon, and Juan Cortés
Regular Microbiome Data Integration by Robust Similarity Network Fusion
B418
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
Session 1: 10:50 – 12:45
Chair: Richard Davies, Maurice Mulvenna
10:50 – 11:00
Open
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 medicine through optimal design of experimentation and computational
modelling (ESM)
November 2nd, 2014: 08:30 – 12:30
Location: Lobby in Hilton Hotel
Session 1: 08:30 – 10:30
Chair: Hong Yue
08:30 – 08:40
Open
Time
08:40 – 09:05
Paper ID
S3201
Paper title / authors
LogisticCrypt - a Logistic Model of Intestinal Crypt Structure
Irina A. Roznovat and Heather J. Ruskin
09:05 – 09:30
B295
On Structural Identifiability of S-system
Choujun Zhan, Benjamin Y. S. Li, and Lam Fat Yeung
09:30 – 09:55
S3202
Mechanisms of Cisapride–Induced Cardiac Pro-arrhythmia: A Simulation Study
Yongfeng Yuan, Songjun Xie, Kuanquan Wang, and Henggui Zhang
09:55 – 10:20
S3204
Modelling the Role of Spontaneous and Collision Induced Catastrophe in the Self
Organisation of Cortical Microtubules
Alex Mace and Wenjia Wang
10:20 – 10:50
Coffee Break
Session 2: 10: 50:00 – 12:30
Chair: Irina A. Roznovat
Time
10:50 – 11:15
Paper ID
S3205
Paper title / authors
Time Scale Analysis of Receptor Enzyme Activity
Tao You and Hong Yue
11:15 – 11:40
B416
Analysis of a Computational Model of Dopamine Synthesis and Release through
Perturbation
Maell Cullen and KongFatt Wong-Lin
11:40 – 12:05
S3207
A Computational Analysis on Methylation Inhibition during Intestinal Cancer Initiation
Irina A. Roznovat and Heather J. Ruskin
12:05 – 12:30
B430
Building Cross-Scale Models of Epigenetic Mechanisms
Heather J. Ruskin, Dimitri Perrin, and Irina A. Roznovat
12:30
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
09:30 – 09:40
Time
09:40 – 10:10
Open
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
18:00
Close
23
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
9:00 – 9:15am
Open
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
24
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
09:00 – 09:15
Open
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
10:30 – 10:50
Break
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
25
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
13:30 – 13:40
Open
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
26
WS10: Workshop on Computational Translational Medicine (CTM)
November 2, 2014: 13:30 – 18:30
Location: Boardroom
Session 1: 13:30 – 15:20
Chair: Graham Ball, Xing-Ming Zhao
13:30 – 13:40
Open
Time
13:40 – 14:00
Paper ID
SA209
Paper title / authors
Motif Discovery in Cancer Gene Regulation Network
Matthew Carson, Jianlei Gu, Guangjun Yu, and Hui Lu
14:00 – 14:20
SA207
Revisiting Topological Properties of Protein-Protein Interaction Networks from the
Perspective of Dataset Evolution
Mingyu Shao, Shuigeng Zhou, and Jihong Guan
14:20 – 14:40
SA206
Protein-protein interaction network constructing based on text mining and reinforcement
learning with application to prostate cancer
Fei Zhu, Quan Liu, Xiaofang Zhang, and Bairong Shen
14:40 – 15:00
SA201
Accelerating Protein Interaction Networks Alignment using GPU
Jiang Xie, Jin Ma, Zhonghua Zhou, Qianfei Xue, Huiran Zhang, and Qing Nie
15:00 – 15:20
SA208
A survey of pattern classification-based methods for predicting survival time of lung cancer
patients
Bin Gan, Chun-Hou Zheng, and Hong-Qiang Wang
15:20 – 15:40
Break
Time
Session 2: 15:40 – 17:30
Chair: Graham Ball, Xing-Ming Zhao
Paper title / authors
Evidence of positive selection on D-lactate dehydrogenases in Lactobacillus delbrueckii
subsp. bulgaricus
Jifeng Zhang, Guangyu Gong, Xiao Wang, Hao Zhang, and Weidong Tian
15:40 – 16:00
Paper ID
SA210
16:00 – 16:20
SA205
Link-based Identification of Survival Time-related Biological Pathways
Hong-Mei Zheng, Gao-Jian Jing, Zirui Zhang, and Hong-Qiang Wang
16:20 – 16:40
SA204
Study of acupuncture therapy on hypertension based on text mining
Yanqin Bian
16:40 – 17:00
SA203
PFGD: A systematic functional genomics resource for Poplar
Jingna Si
17:00 – 17:20
SA202
Prediction of Human Disease-specific Phosphorylation Sites with Combined Feature
Selection Approach and Support Vector Machine
Xiaoyi Xu, Ao Li, and Minghui Wang
17:00 – 17:30
Discussion
Xing-Ming Zhao
17:30
Close
27
WS11: High Performance Computing on Bioinformatics (HPCB 2014)
November 2, 2014: 8:30 – 12:30
Location: Broadway
Session 1: 8:30 – 10:30
Chair: Che-Lun Hung
08:30 – 09:00
Open
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 – 12:55
SB206
A fast and lightweight filter-based algorithm for circular pattern matching
Md. Aashikur Rahman Azim, Costas S. Iliopoulos, M. Sohel Rahman, and M. Samiruzzaman
12:30
Close
28
WS12: The Fifth International Workshop on Information Technology for Chinese Medicine (ITCM 2014)
CANCELLED
29
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
30
WS15: Semantic Data Analytics and Bioinformatics (SDAB)
November 02, 2014: 09:00 – 18:00
Location: Lisburn
Session 1: 09:00 – 12:30
Chair: Haiying Wang
09:00 – 09:15
Time
09:15 – 10:05
Open
Haiying Wang/Hui Wang
Paper ID
Paper title / authors
Who needs semantics when you have big data?
Phillip Lord (Invited Talk)
Improving the detection of biologically meaningful clusters in protein interaction networks
through integrated functional analysis
10:05 – 10:30
Huiru (Jane) Zheng
10:30 – 10:50
Break
10:50 – 11:15
SF201
Applied Semantic Technologies in ECG Interpretation and Cardiovascular Diagnosis
DuyHoa Ngo and Bharadwaj Veeravalli
11:15 – 11:40
B392
Assessing Ancestral Genome Reconstruction Methods by Resampling
Jun Zhou, Fei Hu, William Hoskins, and Jijun Tang
11:40 – 12:05
B343
Biases in Information Content Measurement of Gene Ontology Terms
Pietro Hiram Guzzi, Marianna Milano, Agapito GIuseppe, and Cannataro Mario
10:05 – 10:30
B458
Validation of minimum data of archetyped telehealth clinical record for attendance of
prenatal care
Danielle Alves, Valéria Times, and Magdala Novaes
12:30 – 13:30
Break
Session 2: 13:30 – 18:00
Chair: Hui Wang
Paper title / authors
On Knowledge Change and its Detection
David Bell (Invited talk)
Time
13:30 – 14:20
Paper ID
14:20 – 14:45
B307
A Framework for MicroRNAs Data Integration and Functional Comparison Based on
Ontologies
Mariana Sasazaki and Joaquim Cezar Felipe
14:45 – 15:10
B229
Improving Annotation Quality in Gene Ontology by Mining Cross-Ontology Weighted
Association Rules
Pietro Hiram Guzzi, Agapito Giuseppe, Marianna Milano, and Mario Cannataro
15:10 – 15:30
B451
MUDDIS: A MUlti-Dimensional semantic integrative approach to comparing genes for
knowledge DIScovery
Maryam Panahiazar
15:30 – 15:50
Break
15:50 – 17:30
17:30 – 18:00
AIARG presentation:
Tatiana Delgado: Semantic Web: from theory to practice
David Glass: Explaining and Explaining Away
Hui Wang: Standards based Approach to Video Archive Search and Analysis
Yanxin Bi: Evidential Fusion Sentiment Analysis for Social Media
Panel discussion
18:00
Close
31
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
Session 1: 10:50 – 12:55
Chair: Taesung Park
10:50 – 10:50
Open
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)
32
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
33
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
34
Tutorials
Tutorials
Tutorial 1:
Methods for Engineering and Evaluating the Usability of Medical Software & Medical Devices
Instructors: Prof. Jonathan Wallace (Ulster University), Dr Peter O’Hare (HeartSine Technologies),
Dr Raymond Bond (Ulster University)
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
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
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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.
Industrial track
Industrial Track
November 4, 2014, 10:50 – 13:00, 15:20 – 17:30, Lisburn Suite
Chair: Carlos Toro and Paul Walsh
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
Paul Barber
16:50 – 17:20
User led design to support successful product development in
assistive technology (N205)
Accelerating bioinformatics platforms (Analytic Engines)
International R&D Foruml track
International R&D Forum
November 5, 2014, 10:30 – 13:00, 14:00 – 15:30, Lisburn Suite
Chair: Fiona Browne, Huiru Zheng
Time
Title / invited speaker
10:50 – 13:00
Horizon 2020 and Beyond
Teresa Lennon, Head of European Research Development, Ulster University
Panel discussion
14:00 – 15:30
US-Ireland R&D Programme
Dr Clive Wolsley, Programme Manager, HSC Research & Development Division, Public Health
Agency
Panel Discussion
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