Mini EURO Conference on Computational Biology, Bioinformatics and Medicine

Program (file PDF)

MONDAY 15: morning Aula Marconi 8:30 - 9:30   Registration 9:30 - 10:30   Invited talk: Alberto Apostolico 10:30-11:45   M1 Protein Structure Analysis M1.1 DomAnS - method used for domain boundaries prediction Maciej Antczak Institute of Computing Science, Poznan University of Technology, Jacek Blazewicz, Piotr Lukasiak, Maciej Milostan, Grzegorz Palik M1.2 Multimodal protein indexing, searching and retrieval Eric Paquet Visual Information Technology, Institute for Information Technology, National Research Council of Canada, Ottawa, Ontario, Canada; eric.paquet@nrc-cnrc.gc.ca, Herna L Viktor M1.3 Predicting Distance Constraints to Guide Protein Structure Simulations Pooja Jain School of Chemistry , The University of Nottingham, UK , pcxpj1@nottingham.ac.uk, Paolo Frasconi, Jonathan Hirst 11:45-12:00       Coffee break 12:00-13:15   M2 Protein Structure Prediction M2.1 Feedforward Neural Networks for Protein Structure Quality Forecasting E. Gatti Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, 20126 Milano, Italy, L. De Gioia, E. Fagiuoli,P. Mereghetti, F. Stella, G. Tuana M2.2 Evolving energy function for protein structure prediction Pawel Widera School of Computer Science, University of Nottingham, Natalio Krasnogor, Jonathan Garibaldi M2.3 Protein structural class prediction via milp Fadime Üney Yüksektepe College of Engineering, Koç University, Rumelifeneri Yolu, Sariyer, 34450 Istanbul, TURKEY, Metin Türkay 13:15-14:30       Lunch

MONDAY 15: afternoon Aula Marconi 14:30 - 15:30   Invited talk: Burak Erman 15:30-16:45   M3A Structural Bioinformatics M3A.1 A global optimization algorithm for protein surface alignment G. Liuzzi Istituto di Analisi dei Sistemi ed Informatica .A. Ruberti. - C.N.R. Rome, Italy, P. Bertolazzi, , C. Guerra M3A.2 DOCKANALYSE: an algorithm for protein-protein interaction analysis Gómez A Molecular Biology and Bioinformatics Dpt. Institut de Biotecnologia i Biomedicina (IBB)Universitat Autònoma de Barcelona ( SPAIN); eric.paquet@nrc-cnrc.gc.ca, Delicado P., Amela I., Cedano J, Querol E M3A.3 Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach Anna Marabotti Istituto di Scienze dell'Alimentazione (ISA) - CNR, Via Roma 64, 83100 Avellino, Antonio d'Acierno and Angelo Facchiano 16:45-17:15       Coffee break 17:15-18:55   M4A Dynamic Models M4A.1 Prion protein helices: studying their stability by molecular dynamics simulations Susan Costantini Laboratory of Bioinformatics and Computational Biology, ISA- CNR, via Roma 52 A/C, 83100 Avellino (IT) Angelo M. Facchiano M4A.2 Stability and phase transitions in a mathematical model of Duchenne Muscular Dystrophy Guido Dell'Acqua I.A.C. - C.N.R., viale del Policlinico 137, Roma, 00161, Italy Filippo Castiglione M4A.3 Formulation and analysis of different numerical mathematical models for breast cancer Mohammed Shuker Mahmooda Department of Applied Mathematics, Mechanical Engineering Faculty, University of Zilina, Slovakia, Silvia Mahmoodb M4A.4 Mathematical model for citric acid production from date refuse by Aspergillus niger M.Sharifzadeh BaeiIslamic Azad university, Ayatollah Amoli Branch , Amol IRAN, H.Yunesi

MONDAY 15: afternoon Aula Pentagono 15:30-16:45   M3B Motif Recognition M3B.1 A comparison of optimization models for the analysis of RNA sequences A. Ceselli, Dipartimento di Tecnologie dell'.Informazione, University of Milan G. Pavesi, G. Trucco M3B.2 Bayesian variable selection, phylogenetic information, replicated experiments: a productive marriage for the identification of transcription factors I. De Feis I.A.C. "M. Picone" CNR ITALY, C. Angelini, P. Liò 16:45-17:15       Coffee break 17:15-18:55   M4B Image Analysis M4B.1 Pharmacokinetic models for post-contrastographic DCE analysis Di Paola PRABB - Faculty of Biomedical Engineering, University of Campus Bio-Medico, via A. del Portillo, 21 - 00128 ROME A. Fasano, V. Russo M4B.2 Statistical Analysis of Retinal Tomographic Pseudoimages for Diagnostic Purpose Valentina Russo D.I.S, Via Ariosto 25, 00 185 Roma - University La Sapienza Carlo Bruni, Joaquín De Juan, Claudia Ferrone, Daniela Giannini, Norberto M Grzywacz, David Huang, Giorgio Koch, Ou Tan M4B.3 Distinctive compositional age of nonclassically secreted proteins form proteobacteria Inara Kampenusa University of Latvia, Institute of Microbiology and Biotechnology, Kronvalda Boulevard 4, LV1010, Riga, Latvia, Ieva Minicha and Peteris Zikmanis

TUESDAY 16: morning Aula Marconi 9:00 - 10:00   Invited talk: Martin Vingron 10:00-11:15   T1A Networks T1A.1 Some considerations on the quasi steady state approximations in large enzyme reaction networks Alberto Bersani Department Me.Mo.Mat, University of Rome "La Sapienza", Italy Enrico Bersani, Guido Dell'Acqua, Morten Gram Pedersen T1A.2 Prediction by Graph Theoretic Measures of Structural Effects of SNPs on metabolic pathways Tammy M. K. Cheng Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom, Yu-En Lu, Michele Vendruscolo, Pietro Lio' , Tom L. Blundell T1A.3 Modelling the dynamic behavior of deterministic biological systems Annegret K. Wagler Magdeburg Center of Systems Biology (MaCS), Otto-von-Guericke Universitat Magdeburg, Germany Luis M. Torres, Robert Weismantel 11:15-11:45       Coffee break 11:45-13:25   T2A Networks T2A.1 Spatial rmodelling and simulation of intracellular signal transduction A. Cangiani, Istituto per le Applicazioni del Calcolo (IAC-CNR), Rome E. Bersani, R. Natalini T2A.2 Comparing the efficiency of metabolic networks with multiple nutrients and multiple products Lorenzo Castelli, DEEI, University of Trieste, Italy, Raffaele Pesenti, Daniel Segrè T2A.3 Reconstruction of Phylogenies by Mapping Bio-Sequences into a Probability Vector Space J.F. Weng, Victoria Research Lab (VRL), National ICT Australia (NICTA) Melbourne School of Engineering, The University of Melbourne I. Mareels and D.A. Thomas T2A.4 Relational clustering in the inference of genetic regulatory networks Enza Messina Dipartimento di Informatica Sistemistica e Comunicazione, Università di Milano Bicocca, Francesco Archetti, Elisabetta Fersini, Ilaria Giordani, Giancarlo Mauri 13:25-14:30       Lunch

TUESDAY 16: morning Aula Pentagono 10:00-11:15   T1B Data Mining Methods T1B.1 Knowledge discovery in bioinformatics: identifying the right path A. Fazel Famil Institute for Information Technology, National Research Council Canada, 1200 Montreal Road, Bldg M-50, Ottawa, ON, Canada, K1A0R6, Sieu Phan, and Ziying Liu T1B.2 Knowledge regions for logic programming based classification and their application to computational biology Mario Guarracino Istituto di Calcolo e Reti ad Alte Prestazioni, ICAR-CNR Napoli, Giovanni Felici , Paola Bertolazzi T1B.3 Database for plant phenolic secondary metabolites mass spectra Marcin Borowsk Institute of Computing Science, Poznan University of Technology, Maciej Stobiecki Krzysztof Rosiak, Piotr Kachlick, Dorota Muth, Jacek Blazewicz 11:15-11:45       Coffee break 11:45-13:25   T2B DNA Sequencing T2B.1 A Logic-Based Approach to Polymer Sequence Analysis Renato Bruni, DIEI, Università di Perugia, Via G. Duranti, 93 - 06125 Perugia - Italy T2B.2 Classification of Microarray data: a concave programming approach for predictive gene selecetion F. Rinaldi Istituto di Analisi dei Sistemi ed Informatica, Consiglio Nazionale delle Ricerche, Viale Manzoni 30 - 00185 Rome - Italy F. Schoen, M. Sciandrone T2B.3 Non-classical sequencing by hybridization - problems and algorithms. Marcin Radom, Poznan University of Technology, Piotr Formanowicz T2B.4 Gene - environment networks under uncertainty. Erik Kropat University of Erlangen-Nuremberg, Germany, Gerhard -Wilhelm Weber 13:25-14:30       Lunch

TUESDAY 16: afternoon Aula Marconi 14:30-15:45   T3A Optimization and Feature Extraction methods T3A.1 GRASP algorithms for feature selection problems modelled as integer programs Paola Festa Dept. of Mathematics and Its Applications, University of Napoli FEDERICO II Paola Bertolazzi, Giovanni Felici T3A.2 Global Optimization of Binary LennardJones Clusters Fabio Schoen Dipartimento di Sistemi e Informatica, Via di S. Marta 3 - 50139 Firenze - Italy Andrea Cassioli, Marco Locatelli T3A.3 Radial basis functions for the identification of cell cycle regulated genes in human cancer cells L. Farina Dipartimento di Informatica e Sistemistica "A. Ruberti", Sapienza Università di Roma, Italy L. Grippo, S. Lucidi, G. Pazienza 16:15-16:45       Coffee break 16:45-18:25   T4A Protein Structure Analysis T4A.1 Using Domain, Function and Interaction data to improve prediction of residues properties Marc Vincent Dipartimento di Sistemi e Informatica Universita degli Studi di Firenze, Italy, Paolo Frasconi T4A.2 A Data Mining Driven Tabu Search Approach For Drug Discovery Michele Samorani Leeds School of Business, Bldg 4, UCB 419, Boulder, Colorado Kirk DeLisle, Daniel Weaver T4A.3 Structural analysis of human Sirt-1 and its complex with resveratrol Ida Autiero Dipartimento di Biochimica e Biofisica - SUN, via Costantinopoli 16, Napoli (IT), Susan Costantini, Giovanni Colonna

TUESDAY 16: afternoon Aula Pentagono 14:30-16:10   T3B BIOPTRAIN T3B.1 Gene prioritization through genomic data fusion Leon-Charles Tranchevent Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven (Belgium) Stein Aerts, Bernard Thienpont, Peter Van Loo, Shi Yu, Roland Barriot, Steven Van Vooren, Bassem Hassam, Yves Moreau T3B.2 Parallel computing in DNA assembly Piotr Gawron, Institute of Computing Science, Poznan University of Technology,Piotrowo 2, 60-965 Poznan, Poland Jacek Blazewicz, Marcin Bryja, Marek Figlerowicz, Marta Kasprzak, Darren Platt, Jakub Przybytek, Aleksandra Swiercz and Lukasz Szajkowski T3B.3 Application of clustering techniques to gene prioritization using Endeavour Francisco Bonachela Capdevila Informatics Department, University of Leuven campus Kortrijk Patrick de Causmaecker, Leon-Charles Tranchevent T3B.4 A priori gene prioritization Daniela Nitsch, SCD-ESAT Katholieke Universiteit Leuven Yves Moreau 16:15-16:45       Coffee break 16:45-18:25   T4B BIOPTRAIN T4B.1 In Silico Study of wild-type and Raltegravir-selected Mutants of HIV-1 : Structural Features and DNA Recognition Properties Luba Tchertanov LBPA, CNRS, Ecole Normale Supèrieure de Cachan, 61 av. Président Wilson, 94235 Cachan, France, Jean-François Mouscadet T4B.2 Genome assembly algorithm for short reads Aleksandra Swiercz Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Jacek Blazewicz, Piotr Gawron, Marta Kasprzak T4B.3 On classification of labeled graphs A. Kozak Institute of computing science, Poznan University of Technology, T. Glowacki, P. Formanowicz T4B.4 A DNA based algorithm for calculating the maxflow in networks Andrea Sackmann Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Piotr Formanowicz, Jacek Blazewicz

WEDENSDAY 17: morning Aula Marconi 9:30-10:45   W1A Networks W1A.1 Modelling Synchronous Activity Patterns in Biological Systems Alfredo Colosimo Department of Human Physiology and Pharmacology - Sapienza, Rome University Mauro Colafranceschi, Ole Brix and Neri Accornero W1A.2 Proteins as networks Alessandro Giuliani Environment and Healt Dept., Istituto Superiore di Sanità Rome Italy, Maria Concetta Palumbo, Arun Krishnan and Alfredo Colosimo W1A.3 Prediction of gene regulatory network motifs using the expression time course of targets genes Lorenzo Farina Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", CNR, Roma Alfredo Germani, Gabriella Mavelli and Pasquale Palumbo 10:45-11:15       Coffee break 11:15-13:00   W2A Microarray analysis W2A.1 Mining transcriptome data of the AD11 transgenic mouse model Ivan Arisi European Brain Research Institute Rita Levi-Montalcini, Roma, Italy, Paola Bertolazzi, Giovanni Felici, Alberto Bernacchia, Mara D'Onofrio, Rossella Brandi, Alessandra Di Mambro, Maria Giulia Bacalini, Armando Felsani, Simona Capsoni, Antonino Cattaneo W2A.2 Bayesian Models for the two-sample time-course microarray experiments D. De Canditiis I.A.C. "M. Picone" CNR ITALY, C. Angelini, M. Pensky W2A.3 Analysing DNA Microarray Data Using Techniques of Boolean Functions Petr Kucera , Faculty of Mathematics and Physics, Charles University in Prague, Ondrej Cepek, David Kronus W2A.4 A new classification procedure based on mathematical programming: Application to breast cancer classification Youssef Masmoudi LOGIQ Laboratory- Sfax Tunisia, Habib Chabchoub, Ahmed Rebaï 13:00-14:00       Lunch

WEDENSDAY 17: morning Aula Pentagono 9:30-10:45   W1B BIOPTRAIN W1B.1 GeVaDSs - support system for novel genetic vaccine development process Lukasiak Piotr Institute of Bioorganic Chemistry, Polish Academy of Sciences, Blazewicz Jacek, Borowski Marcin, Wojciechowski Pawel, Kedziora Pawel W1B.2 An approximation algorithm for the sequencing by hybridization problem Kamil Kwarciak Institute of Computing Science, Poznan University of Technology, Piotr Formanowicz W1B.3 Genome mapping via simplified partial digest method: handling measurement errors Alexandr Kovalev Institute of Computing Science, Poznan University of Technology, and Institute of Bioorganic Chemistry, Polish Academy of Sciences , Jacek Blazewicz, Edmund Burke, Marta Kasprza, Mikhail Y. Kovalyov 10:45-11:15       Coffee break 11:15-13:00   W2B BIOPTRAIN W2B.1 A Class Representative Model for Pure Parsimony Haplotyping Daniele Catanzaro Computer Science Department, Université Libre de Bruxelles (U.L.B.), Belgium, Alessandra Godi, and Martine Labbe W2B.2 Problems on evaluation of multiple sequence alignments Pawel Wojciechowski Institute of Computing Science, Poznan University of Technology, Jacek Blazewicz, Piotr Formanowicz W2B.3 Graph models in NMR structural analysis Marta Szachniuk, Institute of Computing Science, Poznan University of Technology W2B.4 Classification techniques for breast cancer data Soria Daniele School of Computer Science, University of Nottingham, UK, Elia Biganzoliy, Ian O. Ellis, Jonathan M. Garibaldi W2B.5 A bioinformatic system for marine metagenomic data retrieval from scientific papers Agnieszka Rybarczyk Institute of Computing Science, Poznan University of Technology, Poland, Marcin Radom, Piotr Formanowicz, Marta Szachniuk, Jacek Blazewicz 13:00-14:00       Lunch