SCOPE AND TOPICS

Next Generation Sequencing (NGS) methods are revolutionizing genomic and functional-genomics research. However, the manipulation and interpretation of the huge amounts of data produced present significant computational challenges.

To provide an overview of current ultra-high throughput sequencing platforms and introduce NGS data analysis strategies for genomic sequencing, transcriptome analysis ChIP-Seq and other applications, we have organized a workshop with practical sessions.

Topics will include:

Next Generation Sequencing platforms (Roche 454, Illumina Solexa, ABI SOLiD)
Strategies for mapping NGS reads to reference sequences
Genome re-sequencing and assembly, SNP discovery
Clustering of reads from expressed sequences (peak finding)
Integration of gene expression data and genome annotation
Estimation of gene expression levels and profiles
Analysis of splicing and alternative splicing
Small RNA discovery and characterization
Analysis of genome methylation
Chip-seq data analysis

The workshop will include seminars to illustrate the theoretical basis of the computational approaches and analysis workflows based on real examples.

Practical sessions will follow, where the participants will use state-of-the art tools for real data analysis.

Workshop Scientific and Organizing Committee

Graziano Pesole, University of Bari and ITB-CNR, Bari (Workshop Chair)
Ernesto Picardi, University of Bari
Elisabetta Sbisà, ITB-CNR, Bari
Sabino Liuni, ITB-CNR, Bari
Apollonia Tullo, ITB-CNR, Bari
Domenica D'Elia, ITB-CNR, Bari
Antonio Baldini, IGB-CNR, Naples
Tiziana Castrignanò, CASPUR, Rome
David Horner, University of Milan
Giulio Pavesi, University of Milan
Flavio Mignone, University of Milan

Workshop Secretary and Organization

Angela Evangelista, University of Bari

The number of participants is limited to 80 for the lectures and to 50 for the practical sessions. The registration form is available here.

For information please contact a.evangelista@biologia.uniba.it

Technical support

Nicola Losito, ITB, CNR-Bari
Flavio Licciulli, ITB, CNR-Bari
Massino Ianigro, ISSIA, CNR-Bari

Workshop Venue

Aula 1 - Facoltà di Scienze Biotecnologiche, Labobiotech, University of Bari
via Fanelli, 204 (map)

The practicals will be located at:
Aula Shannon - Dipartimento di Informatica, University of Bari
via Orabona, 4 (map)

WORKSHOP PROGRAM

16.9.2009 - NGS Platforms

15:00 - 15:40	Arrival and Registration
15:40 - 16:00	Workshop Opening and Introductory remarks
16:00 - 17:00	Michele Iacono (Roche Sequencing Specialist) Technology and applications of the Genome Sequencer Roche 454 FLX.
17:00 - 18:00	Marco Cappelletti (Illumina Product Marketing Manager - Europe) Innovations in Genomic Analysis: Downstream analysis of Illumina Sequencing Data.
18:00 - 19:00	Raimo Tanzi (AB Director, Next Gen Sequencing Europe) and Enrico Delle Piatte (AB SOLiD Manager) SOLiD technology: from Gigabases to Terabases.

17.9.2009 - NGS for Genomics

9:00 - 9:45	Tiziana Castrignanò (CASPUR, Rome) Hardware requirements and databases for NGS handling and analysis.
9:45 - 10:30	Ernesto Picardi (University of Bari) Bioinformatic tools for fast and accurate reads mapping.
10:30 - 11:00	Coffee Break and Discussion
11:00 - 11:45	Michele Morgante (University of Udine) High-throughput investigation of SNPs and genomic rearrangements through NGS data.
11:45 - 12:30	Giulio Pavesi (University of Milan) Bioinformatic stategies for the analysis of ChIP-seq Data.
14:30 - 18:00	Giulio Pavesi and Federico Zambelli (University of Milan) Practical Session 1 - (read more)

18.9.2009 - NGS for Metagenomics and Transcriptomics

9:00 - 9:45	Gabriel Valiente (Technical University of Catalonia and CRG, Barcelona) High-throughput metagenomics analysis
9:45 - 10:30	Flavio Mignone (University of Milan) Bioinformatic workflows for transcriptome profiling and analysis.
10:30 - 11:00	Coffee Break and Discussion
11:00 - 11:45	Graziano Pesole (University of Bari) Analysis of the alternative splicing pattern through NGS data.
11:45 - 12:30	David Horner (University of Milan) Small RNA discovery and characterization.
14:30 - 18:00	David Horner and Viviana Piccolo (University of Milan) Practical Session 2 - (read more)