Proceedings

Keynote Lectures

• Towards an Algorithmic and Mathematical Exploration of Symbiosis
  Marie-France Sagot
• How not to Become a Systems Biologist
  Arthur Lesk
• Why we Keep Assembling...
  Bud Mishra
• Using the T-Coffee Multiple Sequence Aligner in the High Throughput Era
  Cedric Notredame

Oral Communications

• GapFiller: a Preprocessing Step for the De Novo Assembly Problem
  Nadalin F et Al.
• 454 Variant Detector: a New Blast-based Pipeline for Low Frequency INDEL Detections on 454 Amplicon Data
  Zara I et Al.

• In Silico Identification of New Biomolecular Annotations
  Quigliatti M et Al.
• ONCO-i2b2 Project: a Bioinformatics Tool to Integrate Biobank Information and Clinical Data to Support Translational Research in Oncology
  Segagni D et Al.
• OREMPdb: a Semantic Dictionary of Runnable Biological Circuits
  Umeton R et Al.
• Towards Linked Open Gene Mutations Data
  Zappa A et Al.

• Fine-tuning Anti-tumour Immunotherapies by Means of Stochastic Simulations
  d’Onofrio A et Al.
• Stochastic Simulations of Minimal Cell Model Systems
  Mavelli F et Al.

• Accurate Detection of Genomic Structural Variations Using High Throughput Resequencing Data
  Chiara M et Al.
• Large-scale Function Prediction Using Semantic Similarity of Weighted Gene Ontology Terms
  Falda M et Al.

• Phosphorylation Network Rewiring by Gene Duplication
  Freschi L et Al.
• Role of MicroRNAs in Regulating the Dosage of Duplicated Genes
  Pendino V et Al.
• BAR-PLUS: the Bologna Annotation Resource for Functional and Structural Annotation of Protein Sequences
  Piovesan D et Al.

• Intuitive Representation of Surface Properties of Biomolecules
  Andrei RM et Al.
• PDBBinder: a New Method for Binding Site Prediction in Protein Structures
  Bianchi V et Al.
• PhosTryp: a Novel Method for the Prediction of Phosphoprylation Sites in Trypanosomatids
  Palmeri A et Al.

• Efficient Phosphopeptide Identification from Tandem Mass Spectra
  Tiengo A et Al.

• Application of a Modular Verification Technique in Systems Biology
  Drabik P et Al.
• Modeling Gene Network Motifs Using Statecharts
  Fioravanti F et Al.
• A Stochastic Model of the Plant Circadian Clock in the Bio-PEPA Process Algebra
  Guerriero ML et Al.

• A User-friendly Web Bioinformatics Tool to Store, Analyse and Visualize Affymetrix Genechip Human Exon 1.0 St Array Data of Disease Experiments
  Consiglio A et Al.
• Stable Feature Selection for Biomarker Discovery: Use of Biological Information
  Sanavia T et Al.
• A Package for the Genome-wide Dissection of miRNA-mRNA Interactions Applied to the Plasma Cell Differentiation Process
  Uva P et Al.

Posters

• An Efficient Supervised Method to Integrate Multiple Biological Networks
  Bertoni A et Al.
• PyMod: a Tool for The Analysis of Protein Structures and Sequences in PyMOL
  Bramucci E et Al.
• Efficient Adaptive Strategy to Simulate Stochastically Biological Systems with Tau-leaping Algorithms
  Cangelosi D
• Intensive Comparison of Stochastic Simulation Algorithms Through Parallelization
  Cangelosi D et Al.
• Improved Singular Value Decomposition Method for Biomolecular Annotation Prediction
  Chicco D et Al.
• Digital Signal Processing of Quantitative Genomic Data
  Cittaro D et Al.
• A Diseases Classifier Based on a Data Mining Approach
  Evangelista D et Al.
• KungFQ: a Simple and Fast Approach to Compress Fastq Files
  Grassi E et Al.
• A Hierarchical Naïve Bayes Strategy for Genetic Association Studies
  Malovini A et Al.
• Anatomy of Parallel Stochastic Simulation of Biological Reactive Systems
  Mazza T
• GAIA: an R-Bioconductor Package for Identification of Recurrent Genetic Mutations
  Morganella S et Al.
• Biclustering of Gene Expression Data Based on GRASP-like Algorithms
  Musacchia F et Al.
• TReaDS: Tandem Repeats Discovery Service
  Renda ME et Al.
• A Novel Ensemble Approach for the Subcellular Localization of Proteins
  Rozza A et Al.
• GENS2: a Tool to Simulate Gene-gene and Gene-environment Interactions and Epistatsis
  Scala G et Al.
• Local Structure Similarity Within Protein Binding Pockets as a Tool to Infer their Ability to Bind Specific Functional Groups
  Truglio M et Al.

• Integration of Protein-protein Interaction Data in a Genomic and Proteomic Data Warehouse
  Canakoglu A et Al.
• A Method to Reveal and Handle Heterogeneities and Inconsistencies in Gene Ontology Annotation
  Facchinetti A et Al.
• More is Better, Different is Helpful: MitoZoa Database Improvements and the Usage of Mitochondrial Gene Order Diversity as Reannotation Criterion
  Lupi R et Al.
• GIDL: a Rule Based Expert System for Genbank Intelligent Data Loading into the Molecular Biodiversity Database
  Pannarale P et Al.
• More than a Decade of Bioinformatics Meetings in Italy: the BITS Virtual Library
  Romano P

• Brownian Dynamics Simulation of Natural Killer - Dendritic Cells Interaction in Draining Lymph Nodes
  Gritti N et Al.
• Characterization of the Emergent Properties of a Synthetic Quasi-cellular System
  Lazzerini-Ospri L et Al.
• Steps Towards the Design of Complex Quorum Sensing Networks Through Standard Biological Parts: Characterization of a Synthetic LuxR-HSL Repressible Promoter
  Politi N et Al.
• Realization of a Double Knob in Escherichia Coli to Optimize Fermentation of Lactose of Dairy Whey into Ethanol
  Zambianchi G et Al.
• Characterization of Promoter Strength at Different DNA Copy Numbers Using RPU Approach
  Zucca S et Al.

• A Draft de Novo Genome Assembly of the PCB-Degrader Pseudomonas Pseudoalcaligenes KF707
  Calabrese C et Al.
• SNP Arrays in Colorectal Cancer: a New Script to Reveal Broad and Focal Aberrations
  Capizzi C et Al.
• In Silico and in Vivo Analyses of Ests Databases Unveil Novel Mirnas from Carthamus and Cynara SPP
  Catalano D et Al.
• A Multi-signature Classifier Accurately Predicts Neuroblastoma Patients’ Outcome
  Cornero A et Al.
• Hypoxia Classifier is a New and Accurate Outcome Predictor for Neuroblastoma
  Fardin P et Al.
• SNP-Analyzer: Analysis of SNP Microarray Data
  Guzzi PH et Al.
• Coding Potential of the Products of Alternative Splicing in Human
  Leoni G et Al.
• Genome-wide DNA Conformational Flexibility in Yeast
  Menconi G et Al.
• Using SugarCRM in Streamlining a NGS Data Analysis Pipeline
  Muller H et Al.
• Improved Assembly Accuracy by Integrating Base-calling, Error Correction and Assembly
  Narzisi G et Al.
• An Integrated Computational Platform for Whole-Exome DNA-Seq Data Management and Analysis
  Nuzzo A et Al.
• Identification of Small Circular RNA Structures
  Tulipano A et Al.
• Long Range Cross Correlations Between Nucleotide Triplets in Human Chromosomes
  Vitale D et Al.
• SNPs Identification and Ranking Tool
  Viti F et Al.

• Evolution of Metazoan Mitochondrial Genomes: Bioinformatic Approaches to Detect the Impact of Evolutionary Forces on Protein Coding Genes
  Castellana S et Al.
• Evolution of DYX2: Dyslexia-associated Gene
  Karthik MVK et Al.
• Conserved Sequences in Ortologues CYP51 Promoters
  Mezzetti G et Al.
• Analysis of the Main Protein Families Involved in the Maintenance of Stem Cells
  Miele M et Al.
• Is Human Mitochondrial DNA Under Selection?
  Piredda R et Al.
• The Mammalian NumtS Compilations Available Through the UCSC Genome Browser
  Simone D et Al.

• Exploration of Pockets on Protein Surfaces
  Cammisa M et Al.
• Computational Biology Strategy for the Development of Ligands of GALK Enzyme as Potential Drugs for People with Classical Galactosemia
  Chiappori F et Al.
• Is it Biologically Relevant? An Evolutionary Method for Distinguishing Biological Interfaces from Crystal Contacts
  Duarte JM et Al.
• Bluues: a Program for Comprehensive Analysis of the Electrostatic Properties of Proteins Based on Generalized Born Radii
  Fogolari F et Al.
• Identification of Single Nucleotide Variants in Gastrointestinal Stromal Tumor KIT/PDGRFA Wild Type (WT GIST) with Massively Parallel Sequencing
  Indio V et Al.
• Detection of Allosteric Signal Transmission by Information-theoretic Analysis of Protein Dynamics
  Pandini A et Al.
• Structural and Functional Studies of the Human Selenium Binding Protein-1
  Raucci R et Al.
• Investigating the Physiological Role of Human Aryl Hydrocarbon Receptor
  Salzano M et Al.
• Structural Adaptations of Enzymes from Halophilic Organisms
  Siglioccolo A et Al.
• COCO Maps: a Web Application to Visualize Contacts at the Interface of Biomolecular Complexes
  Vangone A et Al.
• Elaboration of Protein Motion Using Blender Game Engine
  Zini MF et Al.

• Stochastic Linked Calculus of Looping Sequences
  Barbuti R et Al.
• A New Framework for Modeling Complex Biological Systems
  Cordero F et Al.
• High-dimensional Pareto Surfaces in the Genetic Design of Escherichia Coli
  Costanza J et Al.
• Multi-objective Optimization for the Mitochondrial Bioenergetics
  Costanza J et Al.
• Effects of Parameter Space Exploration within Dynamic Simulations of Pathways Dowstream of Erbb-family on Breast Cancer
  De Ambrosi C et Al.
• The Role of Noise and MicroRNAs-transcription Factors “Network Motifs” in the Onset and Progression of Rare, Complex Inherited Tumor Predisposing Disorder: the Multiple Endocrine Neoplasia Type 1 as a Model
  Luzi E et Al.
• BCL6 and LRF Crosstalk in Follicular Lymphoma
  Rizzo M et Al.
• Studying the Complete Interactome of Sirtuins
  Sharma A et Al.

• oneChannelGUI: Bringing RNA-seq/ChIP-seq Analysis Accessible to Wet Biologists
  Carrara M et Al.
• Gene Expression Profile in Hepatoma Cells Using Illumina Microarray: Bioinformatics Evaluation
  Costantini S et Al.
• Predicting Transcription Factor Binding Sites in Upstream and Intronic Regions of Rx1 Regulated Genes in Xenopus Laevis
  Degl’Innocenti A et Al.
• A Wavelet-based Approach for the Analysis of Exon-array Data
  Gandolfi F et Al.
• A Bioinformatics Resource to Detect and Classify Non-coding RNAs in Sequence Datasets from Deep-Sequencing Experiments
  Licciulli F et Al.
• Biological Interpretation of Microarray Gene Expression Data: Pathway Analysis and Data Mining Tools Face to Face
  Melissari E et Al.
• De Novo A-to-I RNA Editing Detection in Human mRNAs by RNA-Seq Data: Towards the Inosinome?
  Picardi E et Al.
• EasyCluster2: Clustering and Assembly of Large-scale Roche 454 Transcriptome Data for Gene Validation and Alternative Splicing Analysis
  Picardi E et Al.
• Exploring The Human “Inosinome” Through the Expedit Web Service
  Picardi E et Al.
• Identification of Tumor-associated Alternative Splicing Events in Human Cancer Through EST-based Computational Prediction and Experimental Validation
  Valletti A et Al.