Simone Zaccaria

I am a visiting PhD candidate at Brown University, in the Center for Computational Molecular Biology. Under the supervision of prof. Ben Raphael, I am currently working on problems arising from cancer genomics and my focus is on the reconstruction of phylogenies in the case of copy-number aberrations.
I am a PhD candidate in DiSCo, the department of Computer Science of the Università degli studi di Milano-Bicocca since 2013 under the supervision of prof. Paola Bonizzoni.

My research is on the border between computer science and biology, and my main research interest is the designing of algorithms to solve problems in computational biology. In fact, I focus on developing and applying computational methods and mathematical models in order to answer questions that arise from biological processes, with a predilection for the study of genome variants and their evolution in the case of normal and cancer genomes.

My main interests involve the study of computational complexity of optimization problems, the design of exact/approximation/parameterized algorithms for their resolution, and their implementation and experimentation. Other personal interests are mainly in the area of algorithms and theoretical computer science, including data structure and graph theory.

My current research works have concerned problems concerning copy-number aberrations in cancer genomes and haplotype assembly in human genomes.

Here, the english version of my curriculum vitae:  cv_simone_zaccaria_eng


Current Project at Brown University supervised by prof. Ben J. Raphael:

Cancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations are copy number aberrations that alter the number of copies of genomic regions. The number of copies of each position along a chromosome constitutes the chromosome’s copy-number profile. Understanding how such profiles evolve in cancer can assist in both diagnosis and prognosis.
My current focus is the reconstruction of this evolutionary process by the inference of phylogenetic trees from copy-number profiles. As such, the phylogenies allow to study the intra-tumor heterogeneity when different cancer clones are present.

Project at Universita’ di Milano-Bicocca (DISCo) supervised by prof. Paola Bonizzoni:

The genome of diploid organisms, such as humans, is composed of two distinct copies, called haplotypes, for each chromosome. The information provided by the two haplotypes may be of fundamental importance for many applications (especially in genome medicine), such as analyzing the relationships between genetic variation and gene function, or between genetic variation and disease susceptibility.
The haplotype assembly is the approach aiming at reconstructing the haplotypes starting from a collection of sequencing reads that are mapped to a reference genome. This involves dealing in some way with sequencing and possible mapping errors and leads to a computational task that is generally modeled as an optimization problem. The Minimum Error Correction (MEC) is one of the prominent combinatorial approaches for haplotype assembly.
I studied the computational complexity and the fixed-parameter tractability for several variants of MEC that are motivated from a practical point of view. In particular, I extended and explored MEC formulation to polyploid genomes, that are typical in the case of fish, plant, and yeast genomes.
Since haplotype assembly highly benefits from the advent of ‘future-generation’ sequencing technologies, I designed a new algorithm, called HapCol, for exploiting the new characteristics of these data. A comparison on both simulated and real data showed that HapCol overcomes the limits of state-of-the-art approaches and increases the accuracy of reconstructed haplotypes.


Publications

DBLP Profile
Google Scholar Profile

 

*The marked papers follow the typical convention of theoretical computer science publications where the authors are listed in alphabetical order.


My Projects and Tools


Talks

  • On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction problem
    CPM 2015, 26th Annual Symposium on Combinatorial Pattern Matching
    June 29-July 1, 2015. Ischia Island, Italy
    [slides]
  • On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction problem
    June 16, 2015. Università di Milano-Bicocca, Milan, Italy
    [slides]
  • HAPCOL: Faster and memory-efficient Haplotype Assembly for Future-Generation-Reads
    BITS 2015, Twelfth Annual Meeting of the Bioinformatics Italian Society
    June 3-5, 2015. Milan, Italy
    [slides]
  • On the inversion-indel distance
    PRIN10-11 meeting, November 28–29, 2013. Politecnico di Milano, Milan, Italy
    [slides]

Posters

  • HAPCOL: Accurate and Memory-efficient Haplotype Assembly from Long Reads
    HitSeq 2015, high-throughput sequencing algorithms&applications
    A SIG of ISMB/ECCB 2015
    July 10-11. 2015. Dublin, Irleand
    [poster]

Visiting

  • 11/2015 – 07/2016 (ongoing): visiting research fellow at Brown University in the Center for Computational Molecular Biology with prof. Ben Raphael.
  • 07/2015: research meeting at CWI, Amsterdam (Netherlands), with prof. Gunnar Klau and prof. Nadia Pisanti
  • 09/2012 – 02/2013: visiting student for master thesis in the laboratory of Genominformatik of the University of Bielefeld (Germany) with prof. Jens Stoye.

Schools

  • International School on Graph Theory, Algorithms and Applications with Prof. Raffaele Cerulli, Prof. Andrew Goldberg, Prof. Giuseppe, F. Italiano, and Prof. Robert E. Tarjan as directors, organized by Ettore Majorana Foundation and Centre for Scientific Culture in Erice, in September 2014.
  • Summer School on Advanced Approximation Algorithms with Prof. Grandoni, organized by Institute of Theoretical Computer Science, ETH Zürich, in June 2014.


Teaching

Contacts

email: simone.zaccaria .AT. disco .DOT. unimib .DOT. it
or: simone_zaccaria .AT. brown .DOT. edu
or: simozacca .AT. gmail .DOT. com
Office:    Room 1001  –  Dottorandi 1
Telephone:   02 6448 7917