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.

Recent Award:

BEST POSTER AWARD – recomb2018

Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali and Paola Bonizzoni
ASGAL: Aligning RNA-Seq Data to a Splicing Graph to Detect Novel Alternative Splicing Events


My publication list at DBLP and at Google Scholar

Recent works:

  • ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. BMC Bioinformatics 19(1): 444:1-444:21 (2018)
  • 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


  • Prof. Graziano Pesole (Istituto of Biomembrane e Bioenergetica – CNR of Bari,
    Dipartimento di Biochimica e di Biologia Molecolare – University of Bari). Realization of the tool PIntron and the ASPicDB database (for gene structure prediction and transcript reconstruction).


  • CARIPLO 2013-0955 “Modulation of anti-cancer immune response by regulatory non-coding RNAs”
  • PIntron, intron prediction software
  • ASPIC-DB, alternative splicing prediction database
  • FFABR 2017
  • Progetto di Ateneo 2017 – Disegno e sperimentazione di approcci algoritmici per problemi computazionali in Bioinformatica


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