Marco Previtali

I’m a PhD student in Computer Science at the department of Computer Science at the University of Milano-Bicocca (DISCo) since January 2014.

I’m currently focusing my research activity on computational problems arising from bioinformatics such as genome assembly, genomes indexing, and Genomic data compression.

Contacts:

Email: marco [dot] previtali [atsymbol] disco [dot] unimib [dot] it
Address: Stanza 1001, c/o Edificio U14, Dip. di Informatica Sistemistica e Comunicazione, Viale Sarca, 336, I-20126 Milano (Italy)
Phone Number: +39 02 6448 7917

Publications:

• Bonizzoni Paola, Della Vedova Gianluca, Pirola Yuri, Previtali Marco, Rizzi, Raffaella
  An External-Memory Algorithm for String Graph Construction
  (2016) Algorithmica, pp. 1-31. Article in Press.
• Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali
  Fully Dynamic de Bruijn Graphs. SPIRE 2016: 145-152
• 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
• Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi: Bidirectional Variable-Order de Bruijn Graphs. LATIN 2016:164-178
• 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 (JCB) 23(3):137-149 (2016)
• Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi: Constructing String Graphs in External Memory. WABI 2014:311-325. [doi link]

Talks:

• FSG: Fast String Graph Construction for De Novo Assembly of Reads Data
  12th International Symposium on Bioinformatics Research and Applications (ISBRA)
  Minsk, Belarus
  June 2016
• de Bruijn Compression
  The Finnish center of Excellence in Cancer Genetics Research
  Helsinki, Finland
  May 2016
• Fast String Graph Construction for De Novo Assembly of NGS Data
  Next Generation Sequencing Milano Meeting 2016
  Milan, Italy
  April 2016
• Moving backward in variable-order BOSS
  University of Helsinki, Finland
  September 2015
• An external memory BWT based assembler for next generation data
  Workshop clustering in Big Data (PRIN Workshop)
  Naples, Italy
  May 2015
• An external memory BWT-based assembler for Next Generation Data
  Workshop of Data Structures in Bioinformatics (DSB)
  Montpellier, France
  December 2014
• Constructing String Graphs in External Memory
  14th Workshop on Algorithms in Bioinformatics (WABI2014)
  Wrocław, Poland
  September 2014
• Lightweight assembling of splicing graphs from RNA-seq data using the Burrows-Wheeler Transform
  2nd NGS Milan Meeting (link in italian)
  Milan, Italy
  September 2013

Posters:

• Memory Efficient String Graph Construction
  11th Annual Meeting of the Bioinformatics Italian Society (BITS2014)
  Rome, Italy
  February 2014

Visiting Periods

• August 2016 – October 2016
  Medvedev Group, Pennsylvania State University.
  Supervisor: Paul Medvedev
• April 2016 – June 2016
  Genome-Scale algorithmics group, University of Helsinki.
  Supervisor: Veli Mäkinen
• August 2015 – October 2015
  Genome-Scale algorithmics group, University of Helsinki.
  Supervisor: Veli Mäkinen

Studies:

• October 2010 – March 2013: Master’s Degree (“Laurea Magistrale”) in Informatics (summa cum laude) from the University of Milano-Bicocca. Master’s Thesis: “Algoritmi per la predizione di eventi di splicing alternativo da dati NGS (Next Generation Sequencing)” Advisor: Prof.sa P. Bonizzoni Co-Advisors: Prof. G. Della Vedova, Dott.sa R. Rizzi
• October 2006 – November 2010: Bachelor’s Degree (“Laurea Triennale”) in Informatics from the University of Milano-Bicocca. Bachelor’s Thesis: “Strumenti testuali e grafici per la specifica delle reti di Petri” Advisor: Prof.sa L. Pomello Co-Advisor: Dott. L. Bernardinello

You can find some software I developed in the last years on my page at github.