I received a PhD in Computer Science in 2010 with a thesis on combinatorial problems in studies of genetic variations under the supervision of Prof. Paola Bonizzoni.
I received my master degree in Computer Science in 2006 working on a thesis on problem difficulty measurement in Genetic Programming under the supervision of Leonardo Vanneschi and Giancarlo Mauri.
I am working on combinatorial problems arising from bioinformatics and computational biology.
My main interests involve the study of the computational complexity of optimization problems, the design of exact/approximation/parametrized algorithms for their resolution, and their implementation and experimentation.
My Curriculum Vitae provides an up-to-date and detailed overview of my scientific interests and activities (Italian, last update October 3, 2011).
My education includes a summer school organized by CINECA on Parallel and Scientific Computing which I attended in 2006 (information on new editions are available here) and the Lipari International Summer School on Bioinformatics and Computational Biology of June 2008.
I have been a Visiting Scholar at University of California, Riverside (Dept. of Computer Science and Engineering) advised by Prof. Tao Jiang from February to July 2009.
More about me
PhD Activities
My PhD thesis in Computer Science was titled “Combinatorial Problems in Studies of Genetic Variations: Haplotyping and Transcript Analysis”, and is freely available for download from the institutional repository. Notice that the content has been submitted to international conferences and accepted for publication. Please refer to the list of my publications.
The presentation I held for the admission to the final exam is available here (English) and the one for the final PhD thesis defense is available here (English).
The progress of my research at the end of the 2nd year is described here (Italian) and the slides that I used to present it at the “Collegio Docenti” are here (English).
A draft of my PhD thesis proposal can be found here (Italian). The presentation of the proposal at the “Collegio Docenti” is here (Italian).
A summary of my activities during my first year as a PhD student can be found here (Italian) while the activities of my second year are summarized here (Italian).
The presentations that I held at the end of a few PhD courses are (in reverse chronological order):
- course: “Biomolecular Computing: Theory and Experiments”, teacher: Natasha Jonoska (visiting researcher). The final assignment was the analysis of an article: I prepared a written report and an oral presentation;
- course: “Teoria e Applicazioni del Calcolo Evoluzionistico”, teacher: Leonardo Vanneschi, presentation here (Italian). See below for the source code of the program used for the experimentation;
- course: “Web Services: concetti, applicazioni e problemi aperti”, teacher: Flavio De Paoli, presentation here (Italian).
Master Thesis
The title of my master thesis was “Analisi della neutralità degli spazi di ricerca booleani in Programmazione Genetica” (English: “Analysis of Neutrality in GP Boolean Fitness Landscapes”).
A copy of the abstract in English and in Italian is available. The presentation that I used to “defend” my thesis can be found here (Italian).
Talks
- PIntron: a fast method for gene structure prediction via maximal pairings of a pattern and a text, ICCABS 2011 (slides).In this work, we propose a novel pipeline for computational gene-structure prediction based on spliced alignment of expressed sequences (ESTs and mRNAs). This pipeline, called PIntron, is composed by four steps: Firstly, alternative alignments of expressed sequences to a reference genomic sequence are implicitly computed and represented in a graph (called embedding graph) by a novel fast spliced alignment procedure. Secondly, biologically meaningful alignments are extracted. Then, a consensus gene structure induced by the previously computed alignments is determined based on a parsimony principle. Finally, the resulting introns are reconciliated and classified according to general biological criteria. The software, released under the GNU Affero General Public License, can be freely downloaded from this page.
- Haplotype Inference on Pedigrees with Recombinations and Mutations, WABI 2010 (slides).The work proposes a new combinatorial formulation for haplotype inference on general pedigrees that generalizes the existing combinatorial ones to a more realistic settings. We prove an approximation-preserving reduction from this problem, called Minimum Change Haplotype Configuration (MCHC), to a well-known coding theory problem, namely the Nearest Codeword Problem. This reduction automatically implies the approximability of MCHC within a factor O(n/log n) and, more importantly, it leads to a new very efficient heuristic algorithm that has been experimentally compared with other state-of-the-art HI methods.
- Minimum Factorization Agreement of Spliced ESTs, WABI 2009 (slides).The work presents a new parsimony-based formulation for the problem of choosing the best alignment of an expressed sequence against a genomic sequence exploiting the redundancy of current expressed sequence databases. A preliminary experimental evaluation of the formulation and the related algorithm shows their applicability on real instances.
- Pure Parsimony Xor Haplotyping, ISBRA 2009 (slides).In this work we addressed the problem of haplotype inference from xor genotypes under the pure parsimony assumption. Exact algorithms for restricted instances, a fixed parameter algorithm, an approximation algorithm, and an effective heuristic have been proposed.
Software
The development of most of the software projects is based on GitHub. Please refer to my GitHub profile or to the AlgoLab GitHub profile for a more complete description of the projects, along with their documentation.
Recently, I contributed to the following projects:
- PXH-GA, an implementation of Genetic Algorithms to solve the Pure Parsimony Xor-Haplotyping Problem, written for the PhD course on Evolutionary Algorithms.
- PIntron, a computational gene-structure prediction pipeline.
- Heu-MCHC, a fast and accurate heuristic algorithm for the haplotype inference problem on pedigree data with recombinations and mutations.
Teaching
Publications
(A preprint version of the following papers and articles is available upon request)
2012 |
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Pirola, Yuri; Bonizzoni, Paola; Jiang, Tao An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations (Article) IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9, 1, Page(s): 12-25, 2012. |
2011 |
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Bonizzoni, Paola; Vedova, Gianluca Della; Pirola, Yuri; Rizzi, Raffaella PIntron: a fast method for gene structure prediction via maximal pairings of a pattern and a text (Inproceeding) Proc. of the 1st IEEE Int. Conf. on Computational Advances in Bio and medical Sciences, ICCABS 2011, Orlando, FL, USA, Feb. 3-5, 2011, Page(s): 33-39, IEEE Computer Society, 2011. |
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Bonizzoni, Paola; Vedova, Gianluca Della; Dondi, Riccardo; Pirola, Yuri Parameterized Complexity of k-Anonymity: Hardness and Tractability (Inproceeding) Iliopoulos, Costas S.; Smyth, William F. (Ed.): Revised selected papers of the 21st Int. Workshop on Combinatorial Algorithms, IWOCA 2010, London, UK, Jul. 26-28, 2010, Page(s): 242-255, Springer, 2011. |
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Vanneschi, Leonardo; Pirola, Yuri; Mauri, Giancarlo; Tomassini, Marco; Collard, Philippe; Verel, Sebastien A Study of Neutrality of Boolean Function Landscapes in Genetic Programming (Article) Theoretical Computer Science, 2011. |
2010 |
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Bonizzoni, Paola; Vedova, Gianluca Della; Dondi, Riccardo; Pirola, Yuri; Rizzi, Romeo Pure Parsimony Xor Haplotyping (Article) IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7, 4, Page(s): 598-610, 2010. |
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Bonizzoni, Paola; Vedova, Gianluca Della; Dondi, Riccardo; Pirola, Yuri Variants of constrained longest common subsequence (Article) Information Processing Letters, 110, 20, Page(s): 877-881, 2010. |
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Vedova, Gianluca Della; Dondi, Riccardo; Jiang, Tao; Pavesi, Giulio; Pirola, Yuri; Wang, Lusheng Beyond Evolutionary Trees (Article) Natural Computing, 9, 2, Page(s): 421-435, 2010. |
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Pirola, Yuri Combinatorial Problems in Studies of Genetic Variations: Haplotyping and Transcript Analysis (PhD Thesis) Univ. degli Studi di Milano-Bicocca, 2010. |
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Pirola, Yuri; Bonizzoni, Paola; Jiang, Tao Haplotype Inference on Pedigrees with Recombinations and Mutations (Inproceeding) Moulton, Vincent; Singh, Mona (Ed.): Proc. of the 10th Int. Workshop on Algorithms in Bioinformatics, WABI 2010, Liverpool, UK, Sept. 6-8, 2010, Page(s): 148-161, Springer, 2010. |
2009 |
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Bonizzoni, Paola; Mauri, Giancarlo; Pesole, Graziano; Picardi, Ernesto; Pirola, Yuri; Rizzi, Raffaella Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach (Article) Journal of Computational Biology, 16, 1, Page(s): 43-66, 2009. |
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Bonizzoni, Paola; Vedova, Gianluca Della; Dondi, Riccardo; Pirola, Yuri; Rizzi, Romeo Pure Parsimony Xor Haplotyping (Inproceeding) Mandoiu, I.; Narasimhan, G.; Zhang, Y. (Ed.): Proc. of the 5th Int. Symp. on Bioinformatics Research and Applications, ISBRA 2009, Fort Lauderdale FL, USA, May~13-16, 2009, Page(s): 186-197, Springer, 2009. |
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Bonizzoni, Paola; Vedova, Gianluca Della; Dondi, Riccardo; Pirola, Yuri; Rizzi, Raffaella Minimum Factorization Agreement of Spliced ESTs (Inproceeding) Salzberg, S.; Warnow, T. (Ed.): Proc. of the 9th Int. Workshop on Algorithms in Bioinformatics, WABI 2009, Philadelphia PA, USA, Sept. 12-13, 2009, Page(s): 1-12, Springer, 2009. |
2007 |
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Vanneschi, Leonardo; Tomassini, Marco; Collard, Philippe; Verel, Sebastien; Pirola, Yuri; Mauri, Giancarlo A Comprehensive View of Fitness Landscapes with Neutrality and Fitness Clouds (Inproceeding) Ebner, M.; O'Neill, M.; Ekart, A.; Vanneschi, L.; Esparcia-Alcazar, A. I. (Ed.): Proc. of the 10th European Conf. on Genetic Programming, EuroGP 2007, Valencia, Spain, Apr. 11-13, 2007, Page(s): 241-250, Springer, 2007. |
2006 |
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Vanneschi, Leonardo; Pirola, Yuri; Collard, Philippe A quantitative study of neutrality in GP boolean landscapes (Inproceeding) Proc. of the 8th Annual Conf. on Genetic and evolutionary computation, GECCO 2006, Seattle, WA, USA, Jul. 8-12, 2006, Page(s): 895-902, ACM, 2006. |
Contacts
Address:
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Phone: +39 02 6448 7879
Email: 
Links
- Preprints of some submitted papers (on arXiv)
- My GitHub profile and my GitHub page (sources and documentation of the software projects that I am contributing to)
- My LinkedIn Profile
- Some posts that I’ve found worth-reading
License
This page and all the material here available are licensed under the
Creative Commons Attribuzione-Non commerciale-Non opere derivate 2.5 Italia License.
