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 6 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. 11 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
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