NETTAB 2011 Workshop: Scientific Programme

NETTAB 2011 workshop focused on
Clinical Bioinformatics
October 12-14, 2011, Pavia, Italy

The workshop is held under the patronage of the Bioinformatics Italian Society

National Cancer Research Institute of Genoa

University of Pavia

Scientific Programme Overview

NETTAB 2011 will include keynote lectures given by leading experts in the field, oral communications from selected contributions, open discussion, selected software demonstrations and posters, as well as tutorials.

Scientific Programme

Wednesday, October 12, 2011
Tutorials and Opening Sessions at "Aula Magna", Ghislieri College, Pavia

Session type Start End Title Speaker Duration

Tutorial 9:00 10:30 Data Warehouse Carlo Combi,
Department of Computer Science, University of Verona, Verona, Italy 1^h30'

Break 10:30 11:00 Coffee break 30'

Tutorial 11:00 12:30 Bio Search Computing Marco Masseroli,
Dipartimento di Elettronica e Informazione, Politecnico di Milano, Milan, Italy 1^h30'

Break 12:30 13:30 Lunch Break 1^h00'

Tutorial 13:30 15:00 Natural Language Processing Pierre Zweigenbaum,
LIMSI - CNRS, Orsay, France 1^h30'

Scientific
Session 15:00 16:00 Opening Session
Chairperson Riccardo Bellazzi, University of Pavia, Italy

Welcome and Introduction Riccardo Bellazzi, University of Pavia, Italy, and
Paolo Romano, National Cancer Research Institute, Genoa, Italy 15'

Network Models of Mesophenotypes in Personal Genomics and Targeted Therapies
(Invited lecture) Yves A. Lussier,
Institute for Translational Medicine, University of Chicago, USA 45'

Break 16:00 16:30 Coffee break 30'

Scientific
Session 16:30 18:00 Session 2
Chairperson Carlo Combi, University of Verona, Italy

Formal Modelling and Performance Analysis of Clinical Pathway Rui Han, Xian Yang, Rowe Anthony, and Yike Guo 25'

EVA: Exome Variation Analyzer, a convivial tool for filtering strategies Sophie Coutant, Arnaud Lefebvre, Martine Léonard, Elise Prieur-Gaston, Dominique Campion, Thierry Lecroq, and Hélène Dauchel 25'

Spell-checking queries by combining Levenshtein and Stoilos distances Zied Moalla, Lina F. Soualmia, Élise Prieur-Gaston, Thierry Lecroq, and Stéfan J. Darmoni 10'

An integrated annotation system to support whole exome sequencing experiments design and data management Ivan Limongelli, Angelo Nuzzo, Riccardo Bellazzi, Annalisa Vetro, Erika Della Mina, Roberto Ciccone, and Orsetta Zuffardi 10'

Bio Search Computing: Exploration and Global Ranking of Distributed BioMedical-Molecular Data Marco Masseroli, Giorgio Ghisalberti, and Stefano Ceri 10'

Drug Interaction Information Extraction from Free Text Using Conditional Random Fields Stefania Rubrichi and Silvana Quaglini 10'

Thursday, October 13, 2011
Scientific Sessions at "Aula Magna", Ghislieri College, Pavia

Session type Start End Title Speaker Duration

Break 8:45 9:15 Breakfast 30'

Scientific
Session 9:15 10:00 Session 3
Chairperson Jan-Eric Litton, Karolinska Institutet, Sweden

From Omics to Systems Biology - an Approach to Individualized Medicine
(Invited lecture) Thomas Illig,
Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany 45'

Scientific
Session 10:00 12:30 Poster Session with coffee break 2^h30'

Break 12:30 13:30 Lunch break 1^h00'

Scientific
Session 13:30 14:15 Session 4
Chairperson Paolo Romano, National Cancer Research Institute, Italy

ICT Architectures for Biobanks to Support Clinical Research Jan-Eric Litton,
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden 45'

Scientific
Session 14:15 15:15 Session 5
Chairperson Thomas Illig, Helmholtz Zentrum München, Germany

Towards a wiki system for human and animal cell lines Dan Bolser and Paolo Romano 10'

Formal Analysis of Bone Clinical Pathologies Pietro Liò, Emanuela Merelli, and Nicola Paoletti 10'

Bag of Naïve Bayes: biomarker selection and classification from Genome-Wide SNP data Francesco Sambo, Emanuele Trifoglio, Barbara Di Camillo, Gianna Toffolo, and Claudio Cobelli 10'

Design of neural network models for screening anticancer activities in taxol analogues Stan Svojanovsky, Swapan Chakrabarti, Gunda Georg, and Peter Smith 10'

A novel method for proteomic analysis of immunoglobulin light chains and attribution to a germline gene-based family Alessandra Tiengo, Francesca Lavatelli, Nicola Barbarini, Giampaolo Merlini, and Paolo Magni 10'

MURCIA: Fast parallel solvent accessible surface area calculation on GPUs and application to drug discovery and molecular visualization Eduardo J. Cepas Quiñonero, Horacio Pérez-Sánchez, Wolfgang Wenzel, and José M. García 10'

Special
Session 15:15 16:00 Why clinicians need e-Health Terry Hannan,
University of Tasmania, Launceston, Australia 45'

Break 16:00 16:30 Coffee break 30'

Special
Session 16:30 18:00 Interoperability - HL7 Amnon Shabo,
IBM Research Lab, Haifa, Israel 1^h30'

Social
Activity 20:00 23:00 Social Dinner at Ristorante Bardelli, Via Lungoticino Visconti, 2, Pavia
(tickets on sell at the reception at 20.00 €) 3^h00'

Friday, October 14, 2011
Applications day at Lardirago Castle, Lardirago. Bus leaving Pavia at 8:45

Session type Start End Title Speaker Duration

Scientific
Session 9:15 10:00 Session 6
Chairperson Riccardo Bellazzi, University of Pavia, Italy

Computing our Patients' Future Using Data from our Healthcare Institutions
(Invited lecture) Shawn Murphy,
Harvard Medical School, Boston, USA 45'

Break 10:00 10:30 Coffee break 30'

Scientific
Session 10:30 11:30 Panel Discussion
Chairperson Riccardo Bellazzi, University of Pavia, Italy, and
Paolo Romano, National Cancer Research Institute, Italy

Technology challenges for Clinical Bioinformatics
Marco Masseroli, Politecnico di Milano, Milan, Italy
Shawn Murphy, Harvard Medical School, Boston, USA
Amnon Shabo, IBM Research Lab, Haifa, Israel
Pierre Zweigenbaum, LIMSI - CNRS, Orsay, France 1^h00'

Scientific
Session 11:30 12:30 Session 7
Chairperson Pierre Zweigenbaum, LIMSI - CNRS, France

GePhCARD & BioMIMS: a combined platform that support research on hereditary diseases Marina Mordenti, Alexander Melament, Elena Pedrini, Valentina Filomena Gentile, Manuela Locatelli, Sergio D'Ascia, Giuseppe Frangiamone, Yardena Peres, and Luca Sangiorgi 25'

Ad2BioDB as Open Source Bioinformatics Platform for High-Throughput Data Management Amitava Bhattacharyya, Andrea Calabria, Maurizio Mercurio, and Daniele Cusi 10'

A New Cross-Platform Multi-Signature Classifier Approach To Predict Neuroblastoma Patients Outcome Massimo Acquaviva, Andrea Cornero, Paolo Fardin, Fabiola Blengio, Maria Luisa Belli, and Luigi Varesio 10'

Spatial pharmacokinetic-toxicokinetic modelling Paola Lecca 10'

Scientific
Session 12:30 13:00 Conclusions, State of Art of ONCO-i2b2 and Announcement of NETTAB 2012 30'

Break 12:30 14:00 Lunch break 1^h30'

Social
Activity 14:00 17:30 Visit to La Certosa di Pavia 3^h30'

Invited speakers

For the list of Invited speakers, see the related page.

Tutorials

For the list of Tutorials, see the related page.

List of poster abstracts

Extend the life of your poster
NETTAB 2011, in cooperation with Faculty of 1000, invites poster presenters to deposit their poster into the new open access poster repository, 1000 Posters to enable those who could not make the meeting to see your novel work.
F1000's expert Faculty of 10,000 members will then view these submissions to identify those they wish to select for positive evaluation in the award winning F1000 service. To deposit your poster, simply go to the deposit page and upload your poster file.

Posters that have already been uploaded to F1000 are available on-line HERE.

P1	Antonio D'Acierno, Giuseppe De Pietro and Massimo Esposito Introducing jFKD: a java Fuzzy Knowledge Discoverer
P2	Daniel Pastor-Rubia, Maria Del Mar Roldán-García, Ismael Navas-Delgado and Jose F Aldana Montes DTEKT - Semantic Classification for Medical Diagnosis
P3	Matteo Gabetta, Cristiana Larizza, Giuseppe Milani, Valentina Favalli, Eloisa Arbustini and Riccardo Bellazzi An alternative approach for Case-Based Reasoning with flexible case definition
P4	Vince Roberts, Rory Mullin, Martha Lemin, Edward Hoisington and Madhu Sasidhar. Short cycle business intelligence methodology to guide and improve process and outcomes during weaning from mechanical ventilation
P5	Wu-Lung R. Yang, Ming-Ying Lan, Kun-Mao Chao and Chi-Ying F. Huang. Discover new combination therapies using Semantic Web technology
P6	Irene Sánchez-Linares, Horacio Pérez-Sánchez, José M. Cecilia and José M. García. BINDSURF: a fast blind Virtual Screening methodology on GPUs
P7	Sumedha Gunewardena An Efficient Algorithm for Motif Count Analysis of Whole Genome Sequences
P8	Paola Russo, Carlo Russo, Stefania Rubrichi, Giovanni Palladini, Paolo Milani, Francesca Lavatelli, Riccardo Bellazzi, Giampaolo Merlini and Silvana Quaglini An ontology-based decision support system for the diagnosis of systemic amyloidosis
P9	Francesca Lavatelli, Riccardo Ferrari, Paolo Tormene, Paola Russo, Veronica Valentini, Stefania Rubrichi, Giampaolo Merlini, Riccardo Bellazzi and Silvana Quaglini The Pavia project for the integration of clinical data with a centralized biobank for systemic amyloidosis
P10	Nicola Barbarini, Carla Rognoni, Alberto Malovini, Fernando Fondra and Riccardo Bellazzi In-Silico Model of Diabetic Nephropathy Based on Dynamic Bayesian Networks
P11	Francesca Mulas, Blaz Zupan and Riccardo Bellazzi MeSHgoNET: Building gene association networks from high quality knowledge sources
P12	Elisa Del Fabbro, Francesca Mulas, Bla. Zupan and Riccardo Bellazzi A SPREADING ACTIVATION TECHNIQUE FOR DOCUMENT RETRIEVAL THROUGH INTERACTIVE NETWORKS IN PUBMED
P13	Tiziana Sanavia, Aler Crepaldi, Annalisa Barla and Barbara Di Camillo Gene Ontology based classification improves prediction and gene signature interpretability
P14	Francesca Nadalin, Alberto Policriti and Francesco Vezzi GapFiller
P15	Damiano Piovesan, Giuseppe Profiti and Rita Casadio The human .magnesome.: how to detect human proteins that can bind Mg ions
P16	Pietro Hiram Guzzi and Mario Cannataro miRNA-Analyzer: an extensible tool for Affymetrix miRNA data analysis
P17	Matteo Re and Giorgio Valentini Genes prioritization with respect to Cancer Gene Modules using functional interaction network data
P18	Ivan Merelli, Federica Viti and Luciano Milanesi IBDsite: an integrative database for supporting Inflammatory Bowel Disease clinical data analysis using high throughput techniques
P19	Vladan Mijatovic, Ilaria Iacobucci, Luciano Xumerle, Marco Sazzini, Antonio Mori, Pier Franco Pignatti, Giovanni Martinelli and Giovanni Malerba Verification of imputing efficiency with 2 different genotyping platforms
P20	Cristina De Ambrosi, Annalisa Barla, Lorenzo Tortolina, Nicoletta Castagnino, Raffaele Pesenti, Alessandro Verri, Alberto Ballestrero, Franco Patrone and Silvio Parodi DYNAMIC SIMULATIONS OF PATHWAY CROSS-TALKS, RELEVANT IN COLORECTAL CANCER: A QUANTITATIVE PARAMETER SENSITIVITY ANALYSIS
P21	Alex Graudenzi, Giovanni De Matteis, Artiom Alhazov, Giulio Caravagna, Giancarlo Mauri and Marco Antoniotti Multiscale multicellular modeling for the description of intestinal crypt dynamics and the colorectal cancer development
P22	Philippe Youkharibache, Jochen Supper, Korbinian Grote and Nancy Bretschneider NGS data analysis - from raw reads to biological interpretation. A step towards Personalized Medicine
P23	Lucia Sacchi, Allan Tucker, Steve Counsell, David Garway-Heath and Stephen Swift Do quality indicators help in classifying glaucoma severity and progression from Visual Field data?