Scientific Programme Overview

BITS 2009 aims at:

• presenting some of the most recent and interesting bioinformatics achievements
• presenting the most interesting achievements of Italian bioinformatics research
• presenting a landscape of Italian bioinformatics research
• allowing young researchers to present their work in a collaborative and supporting atmosphere
• training young researchers on the most innovative tools, technologies and methods in the field
• allowing for as much discussion as possible

The workshop will therefore include:

• keynote lectures
• oral communications
• posters presentations
• tutorials

The workshop is also meant to build a friendly atmosphere among participants, enabling a better reciprocal knowledge. It will therefore also include several social events:

• welcome reception
• guided tour of the old city center
• social dinner

Invited Lectures

• Predicting biological function at different spatial scales
  Peer Bork, EMBL, Heidelberg, Germany
  A short CV, research interests and an abstract of the presentation will be added shortly here.
  
  
• Predicting protein-peptide binding sites and peptide-mediated interactions
  Rob Russell, EMBL, Heidelberg, Germany
  A short CV, research interests and an abstract of the presentation will be added shortly here.
  
  
• Pfam: 10,000 families for the molecular biologist
  Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  Alex Bateman is a Senior Investigator at the Wellcome Trust Sanger Institute. He manages the Pfam, Rfam and MEROPS databases as well as acting as an Executive Editor for Bioinformatics.
  Pfam, the protein families databases, contains over 10,000 families based on the sequences found in the UniProt sequence database. This data provides a framework for understanding molecular protein biology. He will discuss Pfam clans that provide information about superfamilies of proteins. He will also describe the development and use of the HMMER 3 software written by Sean Eddy that provides large speed and sensitivity gains.
  
  
• Lessons learned from 2nd generation sequencing of entire transcriptomes
  Stefan Haas, Max Planck Institute for Molecular Genetics, Berlin, Germany
  Stefan Haas is group leader in the Department of Computational Molecular Biology at the Max-Planck-Institute for Molecular Genetics in Berlin. Stefan studied Biology and did his PhD on large-scale primer design for sequencing at the German Cancer Research Center.
  His research focuses on the computational analysis of gene expression data (ESTs), alternative splicing, and the tissue-specific regulation of gene expression.
  Next-generation sequencing methods are currently revolutionizing genomics research. The ability to sequence hundreds of millions of bases a day opens up a variety of potential applications but also challenges current data storage technologies. The presentation will summarize basic applications of 2nd generation sequencing techniques and will give a rough overview of the related computational infrastructure at the MPI. A transcriptome sequencing (RNA-Seq) project aiming to detect alternative splicing events will be described in detail providing insight into the quality of Solexa/Illumina sequencing data.
  
  

Tutorials

Two tutorials will be held in the afternoon of Friday, March 20, 2009. Participation in tutorials will be free for all workshop registrants.

Tutorial 1: Next-generation sequencing

• Overview on next-generation sequencing technology
  Francesca CICCARELLI, European Oncology Institute, Milan, Italy
• Applications of next-generation sequencing techonology
  Anna DE GRASSI, European Oncology Institute, Milan, Italy

• Perspectives of the application of semantic technologies in Bioinformatics
  Paolo ROMANO, National Cancer Research Institute, Genova, Italy
• Building semantic web tools for Bioinformatics
  Andrea SPLENDIANI, Rothamsted Research, United Kingdom

Agenda "at-a-glance"

	Wednesday, March 18, 2009		Thursday, March 19, 2009		Friday, March 20, 2009
		8:30	Registration and poster hang-up	8:30	Registration and poster hang-up
9:00	Registration and poster hang-up	9:00	Scientific session 3	9:00	Scientific session 6
10:30	Opening Session
		10:50	Poster session (with coffee break)	10:50	Poster session (with coffee break)
		11:50	Scientific session 4	11:50	Scientific session 7
12:50	Lunch break	12:50	Lunch break	12:50	Free time for lunch
14:00	Poster session	14:00	Scientific session 5	14:00	Tutorial 1: Next-generation sequencing
15:00	Scientific session 2
		15:50	Coffee break
				16:00	Coffee break
		16:20	BITS General Assembly
				16:30	Tutorial 2: Semantic Web applications and tools
16:45	Social activities
				18:00
		19:00	Free time
19:30	Welcome party and Music Concert in the church of Santa Maria di Castello
		20:00	Social dinner

Detailed Scientific Programme

This programme is still subject to changes!

Wednesday, March 18, 2009
Session type	Start	End	Title	Speaker	Duration
Registration	9:00	10:30	Registration and poster hang-up		1:30
Scientific Session	10:30	12:50	Opening Session		2:20
			Welcome and Introduction	Organizing Chairs and BITS President	20
			"Giuliano Preparata" Lecture Pfam: 10,000 families for the molecular biologist Alex Bateman, Sanger Center, Hinxton, UK		1:00
			Session 1: Clinical Bioinformatics and Biomedical Informatics Unsupervised joint analysis of arrayCGH, gene expression data and supplementary features Steinhoff C, Pardo M, Vingron M Identifying the Hypoxia Signature of Neuroblastoma via Regularization Barla A, Fardin P, Rosasco L, Mosci S, Verri A, Varesio L Ultra-deep Sequencing of a Human Ultraconserved Region Reveals Somatic and Constitutional Genomic Instability De Grassi A, Segala C, Volorio S, Bertario L, Radice P, Bernard L, Ciccarelli FD		1:00
Break	12:50	14:00	Lunch break		1:10
Scientific Session	14:00	15:00	Poster session (Group 1, see list of posters)		1:40
Scientific Session	15:00	16:20	Session 2: Databases, ontologies, tools and applications Improved Gene Ontology annotation predictions through Bayesian network post-processing Tagliasacchi M, Masseroli M engineDB: a repository of functional analogue gene products De Sario G, Tulipano A, Gisel A An integrated bioinformatic platform for SNPs detection: the test case of the pig genome Fronza R, Fontanesi L, Russo V, Casadio R Enhancing Graph Database Indexing By Suffix Tree Structure Bonnici V, Di Natale R, Ferro A, Giugno R, Mongiovi M, Pigola G, Pulvirenti A, Shasha D		1:20
Social	16:45	19:15	Guided tour of the old city center of Genoa		2:30
Social	19:30	20:30	Welcome party		1:00
Social	20:45	21:45	Music Concert in the church of Santa Maria di Castello		1:00
Thursday, March 19, 2009
Session type	Start	End	Title	Speaker	Duration
Registration	8:30	9:00	Registration and poster hang-up		30
Scientific Session	9:00	10:50	Session 3: Networks and Systems Biology I Keynote Lecture Predicting biological function at different spatial scales Peer Bork, EMBL, Heidelberg, Germany Estimating the solution space of Metabolic Networks Braunstein A, Mulet R, Pagnani A Multiplexing and demultiplexing signals by E. coli Pasotti L, Quattrocelli M, Galli D, Cusella De Angelis MG, Magni P Simulating signaling pathways: the motile photoresponse of H. salinarum as a case study Felicioli C, Cangelosi D, Cercignani G, Chiarugi D, Deiana N, Fabbiano S, Freschi L, Fulgentini L, Lucia S, Marangoni R		1:50
Break / Scientific Session	10:50	11:50	Coffee break and Poster session (Group 2, see list of posters)		1:00
Scientific Session	11:50	12:50	Session 4: Networks and Systems Biology II Genome-Wide Survey of mixed MicroRNA . Transcription Factor Feed-Forward Regulatory Circuits in Human Re A, Corà D, Taverna D, Caselle M Data fusion based gene function prediction using ensemble methods Re M, Valentini G Pathway analysis in proteomics Restuccia U, Fung E, Muzio M, Zubarev R, Bachi A		1:00
Break	12:50	14:00	Lunch break		1:10
Scientific Session	14:00	15:50	Session 5: Protein structure and function and Computational Proteomics Keynote Lecture Predicting protein-peptide binding sites and peptide-mediated interactions Rob Russel, EMBL, Heidelberg, Germany Identification of residue contacts in protein/protein interaction from multi-species data Weigt M, White RA, Szurmant H, Hoch JA, Hwa T Comparison of proteins flexibilities by self-organizing maps: the test case of SH3 and its mutants Fraccalvieri D, Pandini A, Bonati L 3D-Structure Prediction of the Modular Protein Sialoadhesin Using a Multi-step Modelling Strategy Corrada D, D'Ursi P, Botti S, Luperini A, Milanesi L, Rovida E		1:50
Break	15:50	16:20	Coffee break		30
Social	16:20	19:00	BITS General Assembly		2:40
Social	20:00	23:00	Social dinner		3:00
Friday, March 20, 2009
Session type	Start	End	Title	Speaker	Duration
Registration	8:30	9:00	Registration and poster hang-up		30
Scientific Session	9:00	10:50	Session 6: Transcriptomics gene expression and microarray analysis I Keynote Lecture Lessons learned from 2nd generation sequencing of entire transcriptomes Stefan Haas, MPI Molecular Genetics, Berlin, Germany Detection of alternative splicing in Vitis vinifera and validation by short sequencing reads Picardi E, Horner D, Chiara M, Pesole G A transcriptional sketch of a human breast cancer by 454 deep sequencing Guffanti A, Iacono M, Pelucchi P, Kim N, Soldà G, Croft LJ, Taft RJ, Rizzi E, Askarian-Amiri M, Bonnal RJ, Callari M, Mignone F, Pesole G, Bertalot G, Rossi Bernardi L, Albertini A, Lee C, Mattick JS, Zucchi I, de Bellis G Presentation of the Best Bioinformatics Paper in 2008 by a young Italian researcher (Award to be announced)		1:50
Break / Scientific Session	10:50	11:50	Coffee break and Poster session (Group 3, see list of posters)		1:00
Scientific Session	11:50	12:50	Session 7: Transcriptomics gene expression and microarray analysis II A bioinformatics pipeline for microarray analysis: from cell models to breast cancer classification Isella C, Renzulli T, Medico E A new clustering approach for learning transcriptional regulatory networks Archetti F, Giordani I, Mauri G, Messina E Discovering Relational Association Rules for the Characterization of UTR cis-regulatory modules Logisci C, Salvemini E, Turi A, Grillo G, Malerba D, D'Elia D		1:00
Break	12:50	14:00	Free time for lunch		1:10
Tutorial	14:30	16:15	Tutorial 1: Next-generation sequencing		1:35
			Overview on next-generation sequencing technology Francesca CICCARELLI, European Oncology Institute, Milan, Italy		45
			Mini break		5
			Applications of next-generation sequencing techonology Anna DE GRASSI, European Oncology Institute, Milan, Italy		45
Break	16:05	16:25	Coffee break		20
Tutorial	16:25	18:00	Tutorial 2: Semantic Web applications and tools		1:35
			Perspectives of the application of semantic technologies in Bioinformatics Paolo ROMANO, National Cancer Research Institute, Genova, Italy		45
			Mini break		5
			Building semantic web tools for Bioinformatics Andrea SPLENDIANI, Rothamsted Research, United Kingdom		45

List of posters

Three poster sessions will be held. See the programme above for date and time.
Each poster has been assigned to one of the three sessions.

See the list of posters and of their allocations.

Presentations

Presentations of invited lectures, oral communications, selected posters and tutorials will be available here after the conclusion of the workshop.

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