Raffaella Rizzi

I am an assistant professor at the Department of Computer Science of the University of Milan-Bicocca.

I had a post-doc position at the Department of Biosciences of the University of Milan. The title of the project was “Design, development and realization of a software tool  for the computational analysis of alternative splicing in eukaryotic genes“.

My primary interests are in the field of algorithms in Bioinformatics with particular attention to the problem of Alternative Splicing prediction.

I am currently working on the problems of assemblying Next-Generation Sequencing (NGS) reads and on the problem of constructing the Burrows-Wheeler Transforms (BWT) and the Longest Common Prefix (LCP) array of a set of reads in external memory.

I have been working on the design and the implementation of the software tool ASPIC (Alternative Splicing PredICtion) that predicts the exon-intron structure of a gene from a set of ESTs (Expressed Sequence Tags) aligned to a genomic sequence, and I have collaborated to the design and development of its next release, named PIntron.

Publications

My publication list at DBLP and at Google Scholar

Recent works:

  • Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
    LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly. Journal of Computational Biology 23(3): 137-149 (2016)
  • Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
    FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. ISBRA 2016: 27-39
  • Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Marco Previtali, Raffaella Rizzi: A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings. CoRR abs/1607.08342 (2016)
  • Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi:
    Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs. Journal of Computational Biology 21(1): 16-40 (2014)
  • Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
    Constructing String Graphs in External Memory. WABI 2014: 311-325

Projects

  • CARIPLO 2013-0955 “Modulation of anti-cancer immune response by regulatory non-coding RNAs”
  • PIntron, intron prediction software
  • ASPIC-DB, alternative splicing prediction database

Contacts

Address:
Room 2047 (second floor) – U14 building
Dipartimento di Informatica Sistemistica e Comunicazione
Viale Sarca, 336
I-20126 Milano

Phone: +39 02 6448 7838

Email: rizzi [dot] disco.unimib.it