CV

Please find a formal PDF version of my CV here (last update on April, 2018).

Education

• Ph.D in Computer Science, approced with honours, University of Milano-Bicocca, Italy, 04/2017
• M.S. in Computer Science cum laude, University of Milano-Bicocca, Italy, 07/2013
• B.S. in Computer Science cum laude, University of Milano-Bicocca, Italy, 09/2011

Visiting

• 11/2015–12/2016, Brown University, Visiting Graduate student
• 07/2015, CWI with with Prof. Gunnar Klau and Prof. Nadia Pisanti, Amsterdam, Netherlands.
• 03/2013–-07/2013 Laboratory of Genominformatik, Research Fellow for master thesis with Prof. Jens Stoye, University of Bielefeld, Germany.

Publications

Preprints

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

S. Zaccaria and B.J. Raphael. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. bioRxiv, 2018 (https://doi.org/10.1101/496174)

Peer-reviewed journal

On the inversion-indel distance

E. Willing, S. Zaccaria et al. On the inversion-indel distance. BMC bioinformatics. Vol. 14. No. 15. BioMed Central, 2013

HAPCOL: accurate and memory-efficient haplotype assembly from long reads

Y. Pirola*, S. Zaccaria*, et al. HAPCOL: accurate and memory-efficient haplotype assembly from long reads. Bioinformatics 32.11 (2015): 1610-1617.

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes

P. Bonizzoni, R. Dondi, GW. Klau, Y. Pirola, N. Pisanti, and S. Zaccaria. On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. Journal of Computational Biology 23, no. 9 (2016): 718-736.

Complexity and algorithms for copy-number evolution problems

M. El-Kebir, B.J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi, and R. Zeira. Complexity and algorithms for copy-number evolution problems. Algorithms for Molecular Biology, 12(1), 13. 2017

Phylogenetic copy-number factorization of multiple tumor samples

S. Zaccaria et al. Phylogenetic copy-number factorization of multiple tumor samples. Journal of Computational Biology 25.7 (2018): 689-708.

HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads

S. Beretta, M.D. Patterson, S. Zaccaria, G. Della Vedova, and P. Bonizzoni. HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinformatics 19, no. 1 (2018): 252.

Peer-reviewed conference

On the fixed parameter tractability and approximability of the minimum error correction problem

P. Bonizzoni, R. Dondi, G.W. Klau, Y. Pirola, N. Pisanti, and S. Zaccaria. On the fixed parameter tractability and approximability of the minimum error correction problem. In Annual Symposium on Combinatorial Pattern Matching (CPM 2015), pp. 100-113. Springer, 2015.

Copy-number evolution problems: complexity and algorithms

M. El-Kebir, B.J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi, and R. Zeira. Copy-number evolution problems: complexity and algorithms. In International Workshop on Algorithms in Bioinformatics (WABI 2016), pp. 137-149. Springer, 2016.

The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data

S. Zaccaria et al. The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data. International Conference on Research in Computational Molecular Biology (RECOMB 2017). Springer, 2017.

Talks

On the inversion-indel distance

November 28, 2013

Talk at PRIN10-11 meeting, Politecnico di Milano, Milan, Italy

HAPCOL: Faster and memory-efficient Haplotype Assembly for Future-Generation-Reads

June 03, 2015

Talk at BITS 2015, Twelfth Annual Meeting of the Bioinformatics Italian Society, University of Milano-Bicocca, Milan, Italy

On the Fixed Parameter Tractability and Approximability of the Minimum ErrorCorrection problem

June 29, 2015

Talk at CPM 2015, 26th Annual Symposium on Combinatorial PatternMatching, Ischia Island, Italy

Copy-Number Evolution Problems: Complexity and Algorithms

August 21, 2016

Talk at WABI 2016, Inter-national Workshop on Algorithms in Bioinformatics, Aarhus, Denmark

The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data

May 03, 2017

Talk at RECOMB 2017, The 21st Annual InternationalConference on Research in Computational Molecular Biology, University of Hong Kong

HATCHet: Inference of Allele and Clone-specific Copy-Number Aberrations inTumor Samples

April 19, 2018

Talk at RECOMB CCB 2018, The 22st Annual International Conference onResearch in Computational Molecular Biology, Paris, France

Posters

HAPCOL: Faster and memory-efficient Haplotype Assembly forFuture-Generation-Reads

June 03, 2015

Poster at BITS 2015, Twelfth Annual Meeting of the BioinformaticsItalian Society, University of Milano-Bicocca, Milan, Italy

HAPCOL: Faster and memory-efficient Haplotype Assemblyfor Future-Generation-Reads

July 10, 2015

Poster at HiTSeq (ISMB) 2015, Conference on High ThroughputSequencing, Algorithms and Applications, Dublin, Ireland

Inference of Allele and Clone-specific Copy-Number Aberrations in Tumor Samples

February 07, 2018

Poster at Cancer Genomics and Mathematical DataAnalysis Symposium, Columbia University, NYC

HATCHet: Inference of Allele and Clone-specific Copy-Number Aberrations in Tumor Samples

April 21, 2018

Poster at RECOMB 2018, Paris, France

HATCHet: Inference of Allele and Clone-specific Copy-Number Aberrations in Tumor Samples

September 27, 2018

Poster at TCGA Legacy meeting, Washington DC, USA

Teaching

Teaching tutor for the courses of Algorithms and Operative Research

Teacher assistant for the course of Programming

Haplotype Assembly

Teacher assistant for the course of Programming

Teacher assistant for the course of Programming