![IWBBIO 2015 Conference Program
Session A.2: ”SS12: Advances in Drug Discovery”
Improving activity prediction of Adenosine A2B receptor antagonists by machine
learning methods
Fahimeh Ghasemi, Alirezza Mehri, Jorge Pe˜na-Garc´ıa, Alfonso P´erez-Garrido,
Afshin Fassihi and Horacio P´erez-S´anchez
nBioChip (nano-Biofilm Chip)- A new technology platform for nano-scale microbial
culture with applications in high-throughput drug discovery of antimicrobial drugs and
diagnostics
Anand Srinivasan, Anand Ramasubramanian and Jose Lopez-Ribot
Support Vector Machines Prediction of drug solubility on GPUs
Gaspar Cano, Jos´e Garc´ıa-Rodr´ıguez, Jorge Pe˜na-Garc´ıa, Dharmendra
Kumar-Yadav, Alfonso P´erez-Garrido and Horacio P´erez-S´anchez
DIA-DB: a web-accessible database for the prediction of diabetes drugs
Antonia S´anchez-P´erez, Andr´es Mu˜n´oz, Jorge Pe˜na-Garc´ıa, Nick Bekas, Antigoni
Katsikoudi, Andreas G. Tzakos and Horacio P´erez-S´anchez
Molecular docking and Biological evaluation of functionalized benzo[h]quinolines as
Colon cancer agents
Ramendra Pratap, Dharmendra Kumar Yadav, Surjeet Singh, Reeta Rai, Naresh
Kumar, Han-Sup Uhm, Harpreet Singh and Horacio P´erez-S´anchez
Predicting cross-reactivity from computational studies for pre-evaluation of specific
hepatic glycogen phosphorylase inhibitors
V Badireenath Konkimalla
Session B.2: ”SS2: Quantitative and Systems Pharmacology - Thinking in a
wider ”systems-level” context accelerates drug discovery and enlightens our
understanding of drug action”
GESSE: Side Effects Prediction from GES Ligand-Target Relationships
Violeta Isabel Perez Nueno
Successes and Pitfalls in Scoring Molecular Interactions
Heloisa Muniz and Alessandro Nascimento
The use of Random Forest to predict binding affinity in docking
Hongjian Li, Kwong-Sak Leung, Man-Hon Wong and Pedro Ballester
Structural determinants in the binding of BB2 receptor ligands: in silico and
spectroscopic studies on PD176252 analogues
Antonio Carrieri, Danilo Belviso, Rocco Caliandro, Enza Lacivita, Mauro Nisio,
Piero Mastrorilli, Vito Gallo and Marcello Leopoldo
An integrated computational framework that predicts potential combinatorial targets
for personalized cancer treatment
Tapesh Santra, Melinda Halasz and Walter Kolch
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DEFINITIVE_PROGRAM_IWBBIO_2015
- 1. IWBBIO 2015 INTERNATIONAL WORK-CONFERENCE ON PPPRRROOOGGGRRRAAAMMM 15-17 April, 2015 Granada (SPAIN)
- 2. IWBBIO 2015 Short Program Wednesday, April 15, 2015 8:30-10:00 Session A.1: "Computational Genomics" Session B.1: "Computational Methods for Biomedical Image Analysis" 10:00-10:30 COFFEE BREAK 10:30-12:00 Session A.2: "SS12: Advances in Drug Discovery" Session B.2: "SS2: Quantitative and Systems Pharmacology" 12:00-13:00 OPENING PLENARY LECTURE: Prof. Xavier Estivill 13:00-15:00 LUNCH 15:00-16:00 Session A.3: "Computational Proteomics" Session B.3: "SS7 Part I: Interdisciplinary puzzles of measurements in biological systems" 16:00-17:00 Session A.4: "SS8: Biological Networks: Insight from interactions" Session B.4: "SS7 Part II: Interdisciplinary puzzles of measurements in biological systems" 17:00-18:00 Session A.5/B.5: Poster Session I 20:00 Light dinner at Carmen de los Mártires Thursday, April 16, 2015 8:30-10:00 Session A.6: "SS4: Advances in Computational Intelligence for Bioinformatics and Biomedicine" Session B.6: "Bioengineering and Bioinformatics for healthcare and diseases" 10:00-10:30 COFFEE BREAK 10:30-12:00 Session A.7: "SS5: Tools for Next Generation Sequencing data analysis" Session B.7: "e-Health" 12:00-13:00 PLENARY LECTURE: Prof. Alfonso Valencia 13:00-15:00 LUNCH 15:00-16:15 Session A.8: "Computational Applications in Genomics and NGS" Session B.8: "Applications of e-Health for diseases" 16:15-16:50 Session B.9: "SS14: Ambient Intelligence for Bioemotional Computing" 16:50-17:30 Session A.9: "Deciphering the human genome" 17:30-18:30 Session A.10/B.10: Poster Session II 20:00 Gala Dinner at Hotel Alhambra Palace
- 3. Friday, April 17, 2015 8:30-9:30 Session A.11: "SS1: Expanding Concept of Chaperone Therapy for Inherited Brain Disease" Session B.11: "SS10: Towards an effective telemedicine: an interdisciplinary approach" 9:30-10:30 Session A.12: "SS11-Part I: High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry" Session B.12: "SS6: Dynamics networks in system medicine" 10:30-11:00 COFFEE BREAK 11:00-12:30 Session A.13: "SS11-Part II: High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry" Session B.13: "Computational systems for modelling biological and biomedical processes" 12:30-13:30 CLOSING PLENARY LECTURE: Prof. Patrick Aloy 13:30-15:00 LUNCH 15:00-16:00 Session A.14: "Biological Sequence Analysis and Alignments" Session B.14: "Computational Methods for Biomedical Signal Analysis " 16:30 Visit to the Alhambra NOTES: • All Sessions A will be held in Salón de Grados, Edificio Mecenas (just 20 meters from the Facultad de Ciencias). • All Sessions B will be held in Salón de Grados, Facultad de Ciencias. • The Poster Sessions will be held in the Hall of Facultad de Ciencias. • The Plenary Lectures will be held at Aula Magna, Facultad de Ciencias.
- 4. MAIN ENTRANCE Hall POSTER SESSIONS Facultad de Ciencias Salón De Grados. SESSIONS B Facultad de Ciencias Salón De Grados. SESSIONS A Edificio Mecenas Aula Magna PLENARY LECTURES Facultad de Ciencias
- 5. IWBBIO 2015 Conference Program IWBBIO 2015 FULL PROGRAM Wednesday, April 15, 2015 Session A.1: ”Computational Genomics” Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species Bassam Alkindy, Huda Al-Nayyef, Christophe Guyeux, Jean-Francois Couchot, Michel Salomon and Jacques Bahi A Computational Method for the Rate Estimation of Evolutionary Transpositions Nikita Alexeev, Rustem Aidagulov and Max Alekseyev A unified integer programming model for genome rearrangement problems Giuseppe Lancia, Franca Rinaldi and Paolo Serafini MicroRNA Target Prediction Based upon Metastable RNA Secondary Structures Ouala Abdelhadi Ep Souki, Luke Day, Andreas A. Albrecht and Kathleen Steinhofel Strong Inhomogeneity in Triplet Distribution Alongside a Genome Michael Sadovsky and Xenia Nikititna Genome Structure of Organelles Strongly Relates to Taxonomy of Bearers Michael Sadovsky, Anna Chernyshova, Julia Putinzeva and Vaselina Fedotova Session B.1: ”Computational Methods for Biomedical Image Analysis” Accurate Microscopic Blood Cell Image Enhancement and Segmentation Syed Hamad Shirazi Hamad Shirazi and Imran Razzak A Novel Algorithm for Segmentation of Suspicious Microcalcification Regions on Mammograms Bur¸cin Kurt, Vasif Nabiyev and Kemal Turhan Analysis of Inter-Rater Reliability of the Evaluation of Radiologists Assessment After Image Processing Kemal Turhan, Bur¸cin Kurt, Sibel Kul and Asli Yazagan A 3D Voxel Neighborhood Classification Approach within a Multiparametric MRI Classifier for Prostate Cancer Detection Francesco Rossi, Alessandro Savino, Valentina Giannini, Anna Vignati, Simone Mazzetti, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano and Daniele Regge Fast Localized Active Contours for left ventricle segmentation in cardiac MRI Derraz Foued, Pinti Antonio and Miloud Bousahla Transcatheter Heterotopic Tricuspid Valves Flow Performances measured by 2D and 3D Particle Image Velocimetry Munirah Ismail, Hwa Liang Leo, Edgar Tay and Foad Kabinejadian 1
- 6. IWBBIO 2015 Conference Program Session A.2: ”SS12: Advances in Drug Discovery” Improving activity prediction of Adenosine A2B receptor antagonists by machine learning methods Fahimeh Ghasemi, Alirezza Mehri, Jorge Pe˜na-Garc´ıa, Alfonso P´erez-Garrido, Afshin Fassihi and Horacio P´erez-S´anchez nBioChip (nano-Biofilm Chip)- A new technology platform for nano-scale microbial culture with applications in high-throughput drug discovery of antimicrobial drugs and diagnostics Anand Srinivasan, Anand Ramasubramanian and Jose Lopez-Ribot Support Vector Machines Prediction of drug solubility on GPUs Gaspar Cano, Jos´e Garc´ıa-Rodr´ıguez, Jorge Pe˜na-Garc´ıa, Dharmendra Kumar-Yadav, Alfonso P´erez-Garrido and Horacio P´erez-S´anchez DIA-DB: a web-accessible database for the prediction of diabetes drugs Antonia S´anchez-P´erez, Andr´es Mu˜n´oz, Jorge Pe˜na-Garc´ıa, Nick Bekas, Antigoni Katsikoudi, Andreas G. Tzakos and Horacio P´erez-S´anchez Molecular docking and Biological evaluation of functionalized benzo[h]quinolines as Colon cancer agents Ramendra Pratap, Dharmendra Kumar Yadav, Surjeet Singh, Reeta Rai, Naresh Kumar, Han-Sup Uhm, Harpreet Singh and Horacio P´erez-S´anchez Predicting cross-reactivity from computational studies for pre-evaluation of specific hepatic glycogen phosphorylase inhibitors V Badireenath Konkimalla Session B.2: ”SS2: Quantitative and Systems Pharmacology - Thinking in a wider ”systems-level” context accelerates drug discovery and enlightens our understanding of drug action” GESSE: Side Effects Prediction from GES Ligand-Target Relationships Violeta Isabel Perez Nueno Successes and Pitfalls in Scoring Molecular Interactions Heloisa Muniz and Alessandro Nascimento The use of Random Forest to predict binding affinity in docking Hongjian Li, Kwong-Sak Leung, Man-Hon Wong and Pedro Ballester Structural determinants in the binding of BB2 receptor ligands: in silico and spectroscopic studies on PD176252 analogues Antonio Carrieri, Danilo Belviso, Rocco Caliandro, Enza Lacivita, Mauro Nisio, Piero Mastrorilli, Vito Gallo and Marcello Leopoldo An integrated computational framework that predicts potential combinatorial targets for personalized cancer treatment Tapesh Santra, Melinda Halasz and Walter Kolch 2
- 7. IWBBIO 2015 Conference Program Nucleic Acid-Drug Interactions: An Electrochemical Approach Dominika Janiszek, Monika Karpinska, Andrzej Niewiadomy, Agnieszka Girstun, Hanna Elzanowska, Magdalena Maj-Zurawska and Pawel Kulesza OPENING PLENARY LECTURE: Prof. Xavier Estivill Genomics and Disease group Centre for Genomic Regulation (CRG) Barcelona (SPAIN) Session A.3: ”Computational Proteomics” Skin mucus proteome map of European sea bass (Dicentrachus labrax): a non-invasive technique for the search of immune biomarkers Hector Cordero, Monica Brinchmann, Alberto Cuesta, Jose Meseguer and Maria Angeles Esteban A pseudo de Bruijn graph representation for discretization orders for distance geometry Antonio Mucherino Prediction of Functional Types of Ligands for G Protein-Coupled Receptors with Dynamically Discriminable States Embedded in Low Dimension Yu-Hsuan Chen and Jung-Hsin Lin P3D-SQL: Extending Oracle PL/SQL Capabilities Towards 3D Protein Structure Similarity Searching Dariusz Mrozek and Bozena Malysiak-Mrozek Session B.3: ”SS7 Part I: Interdisciplinary puzzles of measurements in biological systems” Noise and baseline filtration in mass spectrometry Jan Urban Standardization of experimental protocols and data management process Petr C´ısar, Dalibor Stys, Step´an Papacek and Jan Urban Mixture model based efficient method for magnetic resonance spectra quantification Franciszek Binczyk, Michal Marczyk and Joanna Polanska BioWes - from design of experiment, through protocol to repository: control, standardization, and back-tracking. Antonin Barta, Petr Cisar and Dmytro Soloviov 3
- 8. IWBBIO 2015 Conference Program Session A.4: ”SS8: Biological Networks: Insight from interactions” Deciphering the genetic architecture of Type 2 Diabetes through SNP-SNP interaction Asima Zia, Attya Bhatti, Amjad Ali and Peter John Inference of Circadian Regulatory Pathways based on Delay Differential Equations Catherine Higham and Dirk Husmeier Gene Expression vs Network Attractors Gianfranco Politano, Alessandro Vasciaveo and Alessandro Savino Insights into Human Mitochondrial Hypothetical Proteins: A Computational Structural Biology approach Anuj Kumar, Johny Ijaq, Krishna Pal Singh and Prashanth Suravajhala Session B.4: ”SS7 Part II: Interdisciplinary puzzles of measurements in biological systems” Measurement in biological systems from the self - or-ganisation point of view Dalibor Stys, Jan Urban and Petr Cisar High-resolution 3D reconstruction of organelles from bright-field transmission microscopic images Renata Rychtarikova, Tomas Nahlik and Dalibor Stys FRAP & FLIP: Two sides of the same coin? Stepan Papacek, Jiri Jablonsky, Ctirad Matonoha, Radek Kana and Stefan Kindermann BioWES: Scientific data management solution. Dmytro Soloviov, Petr Cisar and Dalibor Stys Session A.5/B.5: Poster Session I Pseudoknots Prediction on RNA Secondary Structure using Term rewriting Linkon Chowdhury and Mohammad Ibrahim Khan A Segmentation-Free Model for Heart Sound Feature Extraction Haiyang Wang, Guangpei Li and Mingchui Dong IMPACT OF HEALTH APPS IN HEALTH AND COMPUTER SCIENCE PUBLICATIONS. A SYSTEMATIC REVIEW FROM 2010 TO THE PRESENT DAY Guillermo Molina Recio, Laura Garcia-Hernandez, A. Castilla Melero, Juan M. Palomo-Romero, R. Molina Luque, A. A. S´anchez Mu˜noz, A. Arauzo-Azofra and L. Salas-Morera A Hyperanalytic Wavelet Based Denoising Technique for Ultrasound Images Cristina Stolojescu-Crisan DOCKFACE: an easy to use application programming interface(API) for virtual ligand screening (VLS) using AUTODOCK software. Amirhossein Sakhteman and Hamidreza Ghafouri 4
- 9. IWBBIO 2015 Conference Program From Single Fibre Action Potential to Surface Electromyographic Signal: A Simulation Study Messaoudi Noureddine and Bekka Rais El’Hadi Master Clock in Schizophrenic Subjects with VIPR2 Duplication Jesus Miro-Bueno and Anil K. Seth A flexible denormalization technique for data analysis above a deeply-structured relational database: biomedical applications Stanislav Stefanic and Matej Lexa PloidyQuantX: a quantitative microscopy imaging tool for telomere mapping at cell and organ level Xavier Sevillano, Marc Ferrer, Mary-Paz Gonz´alez-Garc´ıa, Irina Pavelescu and Ana I. Ca˜no-Delgado Bio-Inspired Devices and Multi-Agent Systems Olga Valenzuela Automated extraction of food intake indicators from continuous meal weight measurements Vasileios Papapanagiotou, Christos Diou, Billy Langlet, Ioannis Ioakimidis and Anastasios Delopoulos System Development Ontology to Discover Lifestyle Patterns Associated with NCD Mar´ıa Somodevilla-Garcia, Maria De La Concepcion Perez De Celis Herrero and Dr Ivo H. Pineda Torres Homology modeling, molecular dynamic simulation and docking based binding site analysis of human dopamine (D4) receptor Minasadat Khoddami, Amirhossein Sakhteman, Alireza Moradi and Hamid Nadri Local Search for Multiobjective Multiple Sequence Alignment Maryam Abbasi, Luis Paquete and Francisco B. Pereira Awareness, perception and usage of mobile applications for health and wellness Diogo Calada and Henrique M G Martins Health Technology Assessment Models Utilized in the Chronic Care Management Ondrej Gajdos, Ivana Jurickov´a and Radka Otawov´a Using Entropy Cluster-based Clustering for finding potential Protein Complexes Viet-Hoang Le and Sung-Ryul Kim Modelling the hippocampus in MRI using the alpha-stable distribution Diego Salas-Gonzalez, Elmar W. Lang, Juan M. G´orriz and Javier Ram´ırez Prediction of human gene - phenotype associations by exploiting the hierarchical structure of the Human Phenotype Ontology Giorgio Valentini, Sebastian Kohler, Matteo Re, Marco Notaro and Peter Robinson Using multivariate analysis and bioinformatic tools to elucidate the functions of a cyanobacterial global regulator from RNA-Seq data obtained in different genetic and environmental backgrounds Jose I. Labella, Francisco Rodr´ıguez-Mateo, Javier Espinosa and Asunci´on Contreras 5
- 10. IWBBIO 2015 Conference Program THE HYPERCHOLESTEROLEMIC SWINE TO STUDY EXPERIMENTAL ATHEROGENESIS: STATISTICAL-MODEL BASED ASSOCIATIONS BETWEEN MOLECULAR FACTORS AND PLAQUE MORPHOLOGY Silvia Rocchiccioli IVUS/micro-CT/histomorphometry integrated model for coronary profiling of plaque formation/progression: a proof of concept experimental study. Gualtiero Pelosi Fabrication of Wrinkle Surfaces on Bio-Polymeric Substrates by Using Ion Implantation Taejin Kang QT interval measurement using Empirical Mode Decomposition Hadj Slimane Zine-Eddine Bioinformatics and Molecular Studies the three Glyceralehyde-3-Phosphate Dehydrogenase (GAPDHs) of Pseudomonas Syringae pv tomato DC3000 Bouchra Elkhalfi, Aurelio Serrano and Abdelaziz Soukri Inhibitory role of coumarin analogues on P-glycoprotein mediated efflux in cancer stem cells Anushree Tripathi and Krishna Misra A genome browser for visualization and analysis of alternative polyadenylation Yumin Zhang, Chuang Zhao and Xiaohui Wu Molecular Modeling study of alkaloid from roots of Toddalia Asiatica as inhibitors of HIV1 Reverse Transcriptase: A Molecular Modeling Approach Asif Naqvi, Mayank Sharma, Aditi Mathur, Bharti Sisodia, Rashmi Pareek, Shabnam Saroj, Deeksha Gupta, Abhinav Rathi and Sonam Mishra Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) an extracellular infection-induced Protein of the phytopathogenic proteobacterium Pseudomonas syringae pv tomato DC3000 Bouchra El Khalfi, Aurelio Serrano and Abdelaziz Soukri Structure-Based Virtual screening of LuxT Quorum Sensing inhibitors against pathogenic Vibrio alginolyticus Sasikala Dakshinamurthy Molecular Insights of active site surface based screening in identifying potent inhibitors against the HCV-PR through Structural Mapping and Molecular Dynamics Simulation Chandrabose Selvaraj Application of Dempster-Schafer Method in Family-Based Association Studies Farid Rajabli, Unal Goktas and Gul Inal NEW ALGORITHM FOR ASSESSMENT OF FREQUENCY DURATION OF MURMURS USING HILBERT-HUANG TRANSFORM Omari Tahar and Bereksi-Reguig Fethi USSD technology a low cost asset in complementing Public Health Workers’ work processes Munyaradzi Zhou, Marlien Herselman and Alfred Coleman 6
- 11. IWBBIO 2015 Conference Program Genome wide study via in silico analysis and characterization of grapevine chloride channels Mohsen Hanana Inhibition of Ebola Virus by Potent anti-Ebola miRNAs in silico Prof. Omar Bagasra, Zhabiz Golkar and Roshan Battaria COMPARISON OF THE CYTOTOXIC EFFECTS OF RG108 (A DNA METHYLTRANSFERASE INHIBITOR) ALONE AND COMBINATION WITH NERVE GROWTH FACTOR ON PC-12 Adh CELLS Selin Engur, Elif Kaya, Miris Dikmen and Yusuf Ozturk A DNA METHYLTRANSFERASE INHIBITOR RG108 POTENTIATES NGF-INDUCED NEURITE OUTGROWTH OF PC-12 Adh CELLS Elif Kaya, Selin Engur and Miris Dikmen Capturing the mechanism of action of antipsychotic drugs at G protein-coupled receptors (GPCRs) by means of Markov State Model analysis Ismael Rodriguez-Espigares, Nuria Plattner, Juan Manuel Ramirez-Anguita, Frank Noe, Ferran Sanz-Carreras and Jana Selent GESSE: Side Effects Prediction from GES Ligand-Target Relationships Violeta Isabel Perez Nueno 7
- 12. IWBBIO 2015 Conference Program Thursday, April 16, 2015 Session A.6: ”SS4: Advances in Computational Intelligence for Bioinformatics and Biomedicine” A Weighted Cramers V Index for the Assessment of Stability in the Fuzzy Clustering of Class C G Protein-Coupled Receptors Alfredo Vellido, Christiana Halka and Angela Nebot Multigenetic risk quantification for SNP array based direct-to-consumer genomic services Svetlana Bojic and Stefan Mandic-Rajcevic MicroOn and MicroOndb: A software suite and a database for prediction and validation of miRs involved in cancer Sumit Biswas and Ram Kothandan Computational inference in systems biology Benn Macdonald and Dirk Husmeier A Price we Pay for Inexact Dimensionality Reduction Sarunas Raudys, Vytautas Valaitis, Zidrina Pabarskaite and Gene Biziuleviciene Finding unknown nodes in phylogenetic graphs Luis Evaristo Caraballo, Jos´e-Miguel D´ıaz-B´a˜nez and Edel P´erez-Castillo Session B.6: ”Bioengineering and Bioinformatics for healthcare and diseases” Parametric study of ventricular catheters for hydrocephalus ´Angel Gim´enez, Marcelo Galarza, Olga Pellicer, Jos´e Valero and Jos´e M. Amig´o Artificial Neural Networks in Acute Coronary Syndrome Screening M. Ros´ario Martins, Teresa Mendes, Jos´e Gra˜neda, Rodrigo Gusmo, Henrique Vicente and Jos´e Neves Multilayer clustering: Biomarker driven segmentation of Alzheimer’s disease patient population Dragan Gamberger, Bernard Zenko, Alexis Mitelpunkt and Nada Lavrac Mortality Prediction with Lactate and Lactate Dehydrogenase Yasemin Zeynep Avci, Kemal Turhan, Asli Yazagan and Asim Orem Building Bayesian Networks with Statistical Inference to Model Temporal Order and Dependencies of Somatic Mutations Ugur Toprak, Serbulent Unsal and Kemal Turhan Predicting human protein substrates for Toxoplasma gondii rhoptry kinases through multiple tests of spectral alignment Gladys Salcedo, Ailan Arenas and Andrey Montoya 8
- 13. IWBBIO 2015 Conference Program Session A.7: ”SS5: Tools for Next Generation Sequencing data analysis” ngsCAT: an easy-to-use tool to assess the efficiency of targeted enrichment sequencing Javier P.Florido, Francisco Javier L´opez-Domingo, Antonio Rueda, Joaquin Dopazo and Javier Santoyo-L´opez DEgenes Hunter - A self-customised gene expression analysis workflow for non-model organisms Isabel Gonz´alez Gayte, Roc´ıo Bautista Moreno and M. Gonzalo Claros Bioinformatics Analyses to Separate Highly Divergent mRNAs from Unknown Sequences in de novo Assembled Transcriptomes David Velasco, Pedro Seoane and M. Gonzalo Claros The FDA’s experience with emerging genomics technologies - past, present and future Weida Tong Evaluation of combined genome assemblies: a case study with fungal genomes Mostafa Abbas, Ponnuraman Balakrishnan and Qutaibah Malluhi INTEGRATED VARIABLE SELECTION FROM MULTI-OMICS EXPERIMENTS USING MACHINE LEARNING Sonia Tarazona, M´onica Clemente-C´ıscar and Ana Conesa Session B.7: ”e-Health” A Semantic Layer for Unifying and Exploring Biomedical Document Curation Results Pedro Sernadela, Pedro Lopes, David Campos, S´ergio Matos and Jos´e Luis Oliveira e-Health Informed Foreign Patient and Physician Communication: The Perspective of Informed Consent Echo Huang, Shao-Fu Liao and Shing-Lung Chen Empirical Analysis of the Effect of eHealth on Medical Expenditures of Patients with Chronic Diseases Masatsugu Tsuji and Yusuke Kinai A LOD-based service for extracting Linked Open Emergency Healthcare Data Mikaela Poulymenopoulou, Flora Malamateniou and George Vassilacopoulos Data Reduction for Medical Education Program Evaluation Questionnaire Kemal Turhan, Bur¸cin Kurt, Asli Yazagan, Ugur Toprak and Program Evaluation Working Group The Medical Information System - The Perspective Tool for Realization of Quality Assurance Programs Ekaterina Kldiashvili 9
- 14. IWBBIO 2015 Conference Program PLENARY LECTURE: Prof. Alfonso Valencia Structural Computational Biology group Spanish National Cancer Research Center (CNIO) Madrid (SPAIN) Session A.8: ”Computational Applications in Genomics and Next Generation Sequencing” Comprehensive study of bivalent chromatin marks on promoters in mammalian embryonic stem cells. Anna Mantsoki and Anagha Joshi Supporting Bioinformatics Applications with Hybrid Multi-Cloud Services Ahmed Abdullah Ali, Mohamed El-Kalioby and Mohamed Abouelhoda Computationally assessing RNA-protein binding affinity in lncRNAs Carmen Navarro, Carlos Cano, Marta Cuadros and Armando Blanco Integrative bioinformatic analyses of gene and miRNA expression genome-wide profiles from hippocampus of Alzheimer’s disease patients Francisco Jose Campos-Laborie, Sara Aibar, Rosana Chehin, Rita Raisman-Vozari, Dulce Papy-Garcia and Javier De Las Rivas Novel associations of closely related disorders with phenotypes, genes or chemicals using text and data mining Carol Perez-Iratxeta, Josef Priller, Eike Spruth, Miguel A. Andrade-Navarro and Jean-Fred Fontaine Applications of Proteochemometrics to Cancer Cell Line Sensitivity Modelling. Isidro Cortes-Ciriano, Gerard J.P. van Westen, Bouvier Guillaume, Michael Nilges, John P Overington, Andreas Bender and Therese E Malliavin Pharmacological deacetylation by HDAC inhibition Assam El-Osta Session B.8: ”Applications of e-Health for diseases” Development of a High Fundamental Frequency (HFF) Piezoelectric Immunosensor for early and sensitive detection of tuberculosis Angel Montoya, Carmen March, Yeison J. Montagut, Mar´ıa J. Moreno, Juan J. Mancl´us, Antonio Arnau, Yolanda Jim´enez, Marisol Jaramillo, Paula A. Mar´ın and R´obinson A. Torres 10
- 15. IWBBIO 2015 Conference Program Development of an Auditory Cueing System to Assist Gait in Patients with Parkinson’s Disease Vnia Guimares, Rui Castro, Ana Barros, Joo Cevada, ngels Bay´es, Sheila Garc´ıa and Berta Mestre Evolutionary Multiobjective Feature Selection in Multiresolution Analysis for BCI Julio Ortega, Javier Asensio-Cubero, John Q. Gan and Andr´es Ortiz The Mining Minds Platform: a Novel Person-Centered Digital Health and Wellness Framework Oresti Banos, Muhammad Bilal Amin, Wajahat Ali Khan and Sungyoung Lee Augmented Reality in Radiofrequency Ablation of the Liver Tumours Lucio Tommaso De Paolis, Francesco Ricciardi and Cosimo Luigi Manes Session A.9: ”Deciphering the human genome” Inference Of Distant Genetic Relations In Humans Using ’1000 Genomes’ Alexei Fedorov, Ahmed Al-Khudhair, Shuhao Qiu, Rajib Dutta and Larisa Fedorova Session B.9: ”SS14: Ambient Intelligence for Bioemotional Computing” Externalising Moods and Psychological States to Smooth Pet-robot/Child Interaction through Bluetooth Communication Ferran Larriba, Crist´obal Raya, Cecilio Angulo, Jordi Albo-Canals, Marta D´ıaz and Roger Bold´u Patient Lifecycle Management: An Approach for Clinical Processes Alberto Salido L´opez, Carmelo Del Valle Sevillano and Mar´ıa Jos´e Escalona Cuaresma Advertising liking recognition technique applied to neuromarketing by using low-cost eeg headset Luis Miguel Soria Morillo, Juan Antonio Alvarez-Garc´ıa, Luis Gonzalez-Abril and Juan Ortega Heart Rate Variability indicating Stress visualized by Correlations Plots Wilhelm Daniel Scherz, Juan Ortega, Natividad Martinez Madrid and Ralf Seepold Emotions and Diabetes Charrise M. Ramkissoon and Josep Veh´ı Session A.10/B.10: Poster Session II A genetic algorithm for motif finding based on statistical significance Josep Basha Gutierrez, Martin Frith and Kenta Nakai Energy Efficiency Study of representative Microcontrollers for Wearable Electronics Gregor Rebel, Francisco Estevez and Peter Gloesekoetter HvDBase: a web resource on Hydra Vulgaris transcriptome. Daniela Evangelista, Kumar Parijat Tripathi, Valentina Scuotto and Mario Rosario Guarracino 11
- 16. IWBBIO 2015 Conference Program Heart rate regularity changes in older people with orthostatic intolerance Marcos Hortelano, Richard B. Reilly, Lisa Cogan and Raquel Cervig´on Entropy analysis of atrial activity morphology to study atrial fibrillation recurrences after ablation procedure Raquel Cervig´on, Javier Moreno, Gast´on Schlotthauer and Mar´ıa Eugenia Torres Proposal of a magnetic resonance technique for the evaluation of the neurodegenerative disease Olga Valenzuela new advances in Computational Biology and bioinformatics using heterogenous data base Ignacio Rojas A new approach to obtain EFMs using graph methods based on the shortest path between end nodes Jose Francisco Hidalgo C´espedes, Francisco De As´ıs Guil Asensio and Jose Manuel Garc´ıa Carrasco Transcriptome-mining identification and in silico analysis of olive (Olea europaea L.) pollen NADPH oxidase homologous involved in allergy inflammation Maria J. Jimenez-Quesada, Jose A. Traverso, Adoracion Zafra, Jose C. Jimenez-Lopez, Rosario Carmona, M. Gonzalo Claros and Juan D. Alche Identification of distinctive variants of the olive pollen allergen Ole e 5 (Cu,Zn Superoxide Dismutase) throughout the analysis of the olive pollen transcriptome Adoracion Zafra, Rosario Carmona, Jose C. Jimenez-Lopez, M. Gonzalo Claros and Juan D. Alche Lupin allergy: uncovering structural features and epitopes of β-conglutin proteins in Lupinus angustifolius L. with a focus on cross-allergenic reactivity to peanut and other legumes Jose C. Jimenez-Lopez, Elena Lima-Cabello, Su Melser, Rhonda C. Foley, Karam B. Singh and Juan D. Alche A mobile application to enhance adherence to hormonal treatment in breast cancer survivors through a competitive social game Maria De La Concepcion Perez De Celis Herrero, Enrique Soto-Perez-De-Celis, Felipe Orihuela-Espina, Yanin Chavarri Guerra, Maria Teresa Gutierrez Martinez, Alejandro Herrera de La Luz, Maria J. Somodevilla and Ivo H. Pineda Torres Hierarchical Assembly of Pools Riccardo Vicedomini, Francesco Vezzi, Simone Scalabrin, Lars Arvestad and Alberto Policriti Statistical integration of p-values for enhancing discovery of radiotoxicity gene signatures. Anna Papiez, Sylwia Kabacik, Christophe Badie, Simon Bouffler and Joanna Polanska Non-canonical imperfect base pair predictor: the RNA 3D structure modeling process improvement. Jacek Smietanski A simple hair removal algorithm from dermoscopic images Damian Borys, Paulina Kowalska, Mariusz Frackiewicz and Ziemowit Ostrowski 12
- 17. IWBBIO 2015 Conference Program XTENS - a JSON-based digital repository for Biomedical Data Management Massimiliano Izzo, Gabriele Arnulfo, Maria Carla Piastra, Valentina Tedone, Luigi Varesio and Marco Massimo Fato Automatic segmentation system of emission tomography data based on classification system Sebastian Student, Marta Danch-Wierzchowska, Kamil Gorczewski and Damian Borys Cost-effectiveness studies in cardiology: application of medical devices Radka Otawova, Vojtech Kamensk, Pavla Hasenohrlova and Vladimir Rogalewicz Automated measurement of the density of vessels and Ki67-positive cells on whole slide images Christophe Deroulers, Mathilde Badoual, Volodia Dangouloff-Ros and Pascale Varlet SimpLiSMS: A Simple, Lightweight and Fast Approach for Structured Motifs Searching Ali Alatabbi, Shuhana Azmin, Md. Kawser Habib, Costas Iliopoulos and M. Sohel Rahman Predicting sub-cellular location of proteins based on hierarchical clustering and hidden Markov models Jorge Alberto Jaramillo-Garz´on, Jacobo Castro-Ceballos and C´esar Germ´an Castellanos Evaluation of example-based measures for multi-label classification performance Andr´es Felipe Giraldo Forero, Jorge Alberto Jaramillo-Garz´on and German Castellanos An event-driven architecture for biomedical data integration and interoperability Pedro Lopes and Jos´e Luis Oliveira New insights in echocardiography based left-ventricle dynamics assessment Susana Br´as, Augusto Silva, Jos´e Ribeiro and Jos´e Lu´ıs Oliveira Ontologies: A Basis for Integrating, Organizing and Representing Biological Data Muhammad Tariq Pervez, Masroor Ellahi Babar and Tanveer Hussain Intellectual Property Protection for Bioinformatics and Computational Biology Dennis Fernandez, Antonia Maninang, Shumpei Kobayashi, Shashank Bhatia and Carina Kraatz Medical Planning: Sterilization Department Design Khaled Sayed Inhibition of inflammatory reactions mediated by the CD36 receptor via Fyn kinase signaling pathway in the case of atherosclerosis Zineb Tarhda and Ibrahimi Azeddine Genome wide analyses and molecular characterization of Chloride channels and transporters in Cereals Mohsen Hanana Cluster Estimation on a Dendrogram Mohammad Sajjad Ghaemi, Bruno Agard and Vahid Partovi Nia 13
- 18. IWBBIO 2015 Conference Program Application of kappa statistics in sequential tests for family-based design Farid Rajabli A Practical Tool for Aligning Biological Signals using Various Warping Methods Ahmet Elbir, Mustafa Duran and Fethullah Karabiber Dose calculation in a mouse lung tumor and in secondary organs during radiotherapy treatment: A Monte Carlo study Mahdjoub Hamdi, Malika Mimi and M’Hamed Bentourkia A novel approach to identify GO terms without a fold-change threshold limitation Farid Rajabli, Fatih Emekci, Unal Goktas and Gulistan Ozdogan UX integrated cloud-based medical application for improving lifestyle in users Alexandru Serban, Mihaela Crisan-Vida, Maria-Corina Serban and Lacramioara Stoicu-Tivadar Reprogramming of cellular signalling networks following targeted mono- and combination anti-cancer therapy Alexey Goltsov, Yusuf Deeni, Hilal Khalil, Simon Langdon, David Harrison and James Bown IRALLER: a Comprehensive Web Server for Bioinformatics Allergenicity Assessment of Novel Proteins Najaf Allahyari Fard An Ontology for Dynamic Sensor Selection in Wearable Activity Recognition Claudia Villalonga, Oresti Banos, Hector Pomares and Ignacio Rojas Use of Flaviviral Genetic fragment-based Vaccine as a Potential Prevention Strategy for HIV-1: A Computational and Molecular Analyses of HIV-1 Silencing Human microRNAs Prof. Omar Bagasra, Mahmudul Hasan, Muhammad Sheraz, Mazhar Kanak and Roshan Bhattarai PROPOSAL FOR INTEROPERABILITY STANDARS APPLICATIONS IN THE HEALTH SECTOR Octavio Salcedo Parra and Brayan Reyes Determination of anti-proliferative effects of secondary metabolites isolated from halotolerant fungi, on colon cancer cells by Real Time Cell Analyze System (Xcelligence) Zerrin Canturk, Miris Dikmen and Semra Ilhan Investigation of Anti-Candidal Effect of Halotolerant Fungal Secondary Metabolites Mustafa Guclu Ozarda, Zerrin Canturk, Miris Dikmen, Selin Engur and Semra Ilhan In vitro evaluation of the cytotoxic, anti-proliferative, apoptotic and anti-migration properties of Fumagillin on C6 Glioma Cells Miris Dikmen 14
- 19. IWBBIO 2015 Conference Program Friday April 17, 2015 Session A.11: ”SS1: Expanding Concept of Chaperone Therapy for Inherited Brain Disease” Development of pharmacological chaperone candidates for Retinitis Pigmentosa and Niemann-Pick type C1 disease. Tomomi Noguchi-Yachide Non-cell autonomous therapeutic effects of molecular chaperones on polyglutamine disease models via its exosome-mediated intercellular transmission. Yoshitaka Nagai, Toshihide Takeuchi and Keiji Wada RECENT ADVANCES IN CHAPERONE DESIGN FOR LYSOSOMAL STORAGE DISRODERS Jos´e M. Garc´ıa Fern´andez and Carmen Ortiz Mellet Session B.11: ”SS10: Towards an effective telemedicine: an interdisciplinary approach” Simplifying tele-rehabilitation devices for their practical use in non-clinical environments. Daniel Cesarini, Davide Calvaresi, Pasquale Buonocunto, Mauro Marinoni and Giorgio Buttazzo Non-intrusive monitoring and data analysis for supporting general practitioners in following diseases evolution based on patients’ daily (motor) behaviour Davide Calvaresi, Daniel Cesarini, Mauro Marinoni, Pasquale Buonocunto and Giorgio Buttazzo Interactive business models for Telerehabilitation after Total Knee Replacement: Preliminary results from Tuscany. Francesco Fusco and Giuseppe Turchetti Ontological Personal Healthcare using Medical Standards Yeong-Tae Song and Neekoo Torkian Session A.12: ”SS11-Part I: High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry” Applications of High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry Horacio P´erez-S´anchez, Afshin Fassihi, Jos´e M. Cecilia, Hesham H. Ali and Mario Cannataro Mobile access to on-line analytic bioinformatics tools Sergio D´ıaz Del Pino, Tor Johan Mikael Karlsson, Juan Falgueras Cano and Oswaldo Trelles 15
- 20. IWBBIO 2015 Conference Program A GPU solution of the HP Protein Folding Problem based on UEGO Jos´e Mar´ıa Garc´ıa Mart´ınez, Ester Mart´ın Garz´on, Jos´e Mar´ıa Cecilia, Horacio Perez Sanchez and Pilar Mart´ınez Ortigosa Enhancing the parallelization of Non-Bonded Interactions Kernel for Virtual Screening on GPUs Baldomero Imbern´on, Antonio Llanes, Jorge Pe˜na-Garc´ıa, Horacio P´erez-S´anchez and Jos´e M Cecilia Session B.12: ”SS6: Dynamics networks in system medicine” Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues Hector Zenil, Narsis Kiani and Jesper Tegner Modeling of the Urothelium with an Agent Based Approach Angelo Torelli, Fabian Siegel, Philipp Erben and Markus Gumbel NEArender: a new R package for rendering ’omics’ data into pathway space using network enrichment analysis Andrey Alexeyenko, Ashwinipriya Jeggari and Simon Kebede Merid Flexible and fast linear program to infer signaling networks Marta Matos, Bettina Knapp, Fabian Theis and Lars Kaderali Session A.13: ”SS11-Part II: High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry” Identification of Biologically Significant Elements using Correlation Networks in High Performance Computing Environments Kathryn Dempsey, Sachin Pawaskar and Hesham Ali isDNA: A tool for real-time visualization of plasmid DNA Monte-Carlo simulations in 3D Adriano Raposo and Abel Gomes Computing Biological Model Parameters by Parallel Multi-Core Statistical Model Checking Toni Mancini, Enrico Tronci, Ivano Salvo, Federico Mari, Annalisa Massini and Igor Melatti Transport Properties of RNA Nanotubes using Molecular Dynamics Simulation Shyam Badu, Roderick Melnik and Sanjay Prabhakar Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach Xiaohua Zhang, Horacio Perez-Sanchez and Felice Lightstone Predicting atherosclerotic plaque location in an iliac bifurcation using a hybrid CFD/biomechanical approach Giulia Di Tomaso, Mona Alimohammadi, Obiekezie Agu and Vanessa Diaz-Zuccarini 16
- 21. IWBBIO 2015 Conference Program Session B.13: ”Computational systems for modelling biological and biomedical processes” The MetaboX library: building metabolic networks from KEGG database Francesco Maiorano, Luca Ambrosino and Mario Guarracino Logical Modeling and Analysis of Regulatory Genetic Networks in a Non Monotonic Framework Nicolas Mobilia, Alexandre Rocca, Samuel Chorlton, Eric Fanchon and Laurent Trilling Incorporating multiple recurrences in a flowgraph model for bladder carcinoma Gregorio Rubio, Belen Garcia-Mora, Cristina Santamaria and Jos´e Luis Pontones A Computational Domain-based Feature Grouping Approach for Prediction of Stability of SCF Ligases Mina Maleki, Mohammad Haj Dezfulian and Luis Rueda Identifiability of Nonlinear ODE Models in Systems Biology: Results from both Structural and Data-based methods Maria Pia Saccomani What makes a protein sequence a prion? Salvador Ventura CLOSING PLENARY LECTURE: Prof. Patrick Aloy Structural Bioinformatics and Network Biology Group Institute for Research in Biomedicine (IRB) Barcelona (SPAIN) Session A.14: ”Biological Sequence Analysis and Alignments” Alignment Free Frequency Based Distance Measures for Promoter Sequence Comparison Kouser, Lalitha Rangarajan, Darshan S Chandrashekar, Kshitish K Acharya and Emin Mary Abraham Relation between Insertion Sequences and Genome Rearrangements in Pseudomonas aeruginosa Huda Al-Nayyef, Christophe Guyeux, Marie Petitjean, Didier Hocquet and Jacques Bahi Biological Sequence Alignment and Compression via Shortest Unique Substring Identifiers Boran Adas, Ersin Bayraktar, Simone Faro, Ibrahem Moustafa and M. Oguzhan Kulekci 17
- 22. IWBBIO 2015 Conference Program Energy-Efficient Architecture For DP Local Sequence Alignment: Exploiting ILP and DLP Miguel Cruz, Pedro Tom´as and Nuno Roma Session B.14: ”Computational Methods for Biomedical Signal Analysis” Alpha Rhythm Dominance in Human Emotional Attention States: An Experimentation with ’idling’ and ’binding’ Rhythms. Mohammed G Al-Zidi, Jayasree Santhosh and Jamal Rajabi Optimal Elbow Angle for MMG Signal Classification of Biceps Brachii during Dynamic Fatiguing Contraction Mohamed Al-Mulla, Francisco Sepulveda and Mohammad Suoud Feature Selection for Best Identification of Congestive Heart Failure Using Artificial Neural Network Abdulnasir Yahya Hossen Hossen 18
- 23. IWBBIO 2015 Conference Program VIRTUAL PRESENTATIONS Virtual Presentation Session Preliminary Research on Combination of Exponential Wavelet and FISTA for CS-MRI Yudong Zhang, Shuihua Wang, Genlin Ji and Zhengchao Dong Towards a More Efficient Discovery of Biologically Significant DNA Motifs Aqil Azmi and Abdulrakeeb Al-Ssulami GA-based feature selection with ANFIS approach to breast cancer recurrence Hamza Turabieh and Muhanna Muhanna Blind and Visually Impaired students can perform computer-aided molecular design with an assistive molecular fabricator Valere Lounnas, Hoby Wedler, Tim Newman, Jon Black and Gerrit Vriend Detection of Pathological Brain in MRI scanning based on Wavelet-entropy and Naive Bayes Classifier Xingxing Zhou, Shuihua Wang, Wei Xu, Genlin Ji, Preetha Phillips, Ping Sun and Yudong Zhang Characterization of pneumonia incidence supported by a business intelligence system Maribel Yasmina Santos, Vera Leite, Antonio Carvalheira and Artur Teles de Ara´ujo Are wildfires and pneumonia spatially and temporally related? Maribel Yasmina Santos, Vera Leite, Antonio Carvalheira and Artur Teles de Ara´ujo An Ensemble of Cooperative Parallel Metaheuristics Gene Selection method for Cancer Classification Anouar Boucheham and Mohamed Batouche Linear accelerator bunkers: Shielding Verification Khaled Sayed and Shereen El-Metwally Portable Low-cost Heart Attack Detection System using ZigBee Wireless Technology Khaled Sayed and Shereen El-Metwally Towards exact segmentation of corneal endothelial cells Adam Piorkowski and Jolanta Gronkowska-Serafin Sliding box method for automated detection of the optic disc and macula in retinal images Dan Popescu, Loretta Ichim and Radu Dobrescu A model of the dynamics of a population of diabetics with and without complications with optimal control Wiam Boutayeb, Mohamed E.N. Lamlili, Mohammed Derouich and Abdesslam Boutayeb The impact of obesity on type 2 Diabetes: Mathematical model Wiam Boutayeb, Abdesslam Boutayeb and Mohamed E.N.Lamlili 19
- 24. IWBBIO 2015 Conference Program Systematic comparison of machine learning methods for identification of miRNA species as disease biomarkers Chihiro Higuchi, Toshihiro Tanaka and Yukinori Okada 20
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