Programme 2015

1. High Throughput Sequencing (HTS) data analysis
   Sapienza University, Rome, Italy - 5-7 October 2015
   The course constitutes a formal teaching activity of the BeMM PhD school and is primarily aimed at 2nd year students of the participating PhD courses. The programme consists of lectures, which will be open to approximately 100 students, and practicals that will be available only to 24 students. The aim of this course is to familiarise the participants with the primary analysis of datasets generated through two popular next-generation sequencing (NGS) assays: ChIP-seq and RNA-seq.


2. Gene Expression profiling with HTS: RNA-Seq data analysis
   CINECA Auditorium, via dei Tizii 2/C, Rome - 19-22 October 2015
   The aim of this course is to familiarize the participants with the primary analysis of datasets generated through the RNA-Seq assays. This course starts with a brief introduction to high-throughput sequencing (hts) technologies and their application to gene expression analysis (RNA-Seq). Next, we will present key steps in the data analysis pipeline (such as quality control, alignment, summarization) along with most commonly used software to accomplish them. Finally, we focus on dataset specific downstream analysis, including quantification of expression, transcriptome assembly and differential expression analysis.


3. NGS for evolutionary biologists: from basic scripting to variant calling
   CINECA Auditorium, via dei Tizii 2/C, Rome - 23-27 November 2015
   Recent advances in genome sequencing technologies provide unprecedented opportunities to characterise individual genomes and identify mutations relevant for the study of both evolutionary questions and diagnosis and therapy. This course will run over five days focusing on variant analysis of NGS data and is addressed to wet lab scientists with no previous knowledge of the use of a command line, statistical computing packages, and programming. Participants will be immersed in the experience of running a complete NGS data analysis workflow, from the retrieval of raw data from bioinformatics resources, to the downstream analysis of the processed data.


4. Protein Networks and Systems Biology
   Dept. of Computer Science and Engineering IT Room (University of Bologna) - Via Ranzani 14/C, Bologna, IT - 14-18 December 2015
   The aim of this course is to familiarise the participants with the different approaches to the study of protein-protein interactions (PPIs), protein interaction networks and systems biology, providing hands-on training sessions as well. The course is structured in four sessions. The first one focuses on bioinformatics databases, tools, and web resources dedicated to PPIs. The second one provides a molecular point of view on protein-protein interactions (PPI), including how to exploit structural information in analyses and predictions. The third session is about graph theory, network models and the tools to analyse them. Last session is about biomedical applications of PPI resources, methods and networks.