PINC project aims at laying the theoretical foundations of the new paradigm: from a linear reference to a pan-genome, by addressing the following main questions. How can one represent a pan-genome with data structures that are extremely space conscious and time efficient, while easing the comparative analysis of multiple genomes? How can one represent and analyze a pan-genome obtained from huge collections of data produced by sequencing technologies, i.e. several terabytes of short or long sequences which are fragments of different genomes? What are the main theoretical tools for the comparative analysis of pan-genomes? PINC project aims at developing new methodologies, combinatorial properties and data structures for taming the exploding complexity of the new kind of data.
Scientific structure
WP1 Pangenome representation and indexing
- Task 1.1: Language-theoretic and positional graph pangenome representations
- Task 1.2 Dynamic and compact data structures representations of pan-genomes
- Task 1.3. Highly compressed indexing structures for pangenomics
WP2 Comparative analysis of pangenomes and very large sequence collections
- Task 2.1 Sequence sketching based on Burrows-Wheeler Transform (BWT), Lyndon Words and minimal absent words
- Task 2.3 Alignment-free comparison of long reads
WP3 Pangenomics for biomedical research, from theory to applications
- Task 3.1 Detection of structural variants in pangenomes
- Task 3.2 Pan transcriptome variations in medically relevant genes
PINC Management structure
| Name | Members | Remit |
|---|---|---|
| Project PI | Paola Bonizzoni | – Organises and chairs the meetings of the Executive Committee; – Monitors the progress of the project; – Hosts the project website for coordination, administration, and dissemination |
| WP 1 leader WP 2 leader WP 3 leader | Marinella Sciortino Nadia Pisanti Paola Bonizzoni | – The leader of a WP organizes regular meeting for coordinating the joint activities; – Update of the web-site with publications and seminars and other activities related to the WP |
| Executive Committee | Project PI, all unit leaders, Headed by the project PI | – Holds a meeting, also via videoconference, at least once each three monts; – Monitors the scientific direction of the research activities; – Monitors dissemination and communication activities; – Coordinates the research activities with external (foreign) collaborators |