Fabio Vandin's Publications

Fabio Vandin's Home Page

My publications

Conference papers

A. Pietracaprina, and F. Vandin. Efficient Incremental Mining of Top-K Frequent Closed Itemsets. In Proc. International Conference on Discovery Science (DS) 2007, LNCS 4755, pages 275-280, 2007.
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A. Kirsch, M. Mitzenmacher, A. Pietracaprina, G. Pucci, E. Upfal, and F. Vandin. An Efficient Rigorous Approach for Identifying Statistically Significant Frequent Itemsets. In Proc. of 28th ACM Symposium on Principles of Database Systems (PODS'09), pages 117-226, 2009.
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R. Grossi, A. Pietracaprina, N. Pisanti, G. Pucci, E. Upfal, and F. Vandin. MADMX: A Novel Strategy for Maximal Dense Motif Extraction. In Proc. 9th Workshop on Algorithms in Bioinformatics, (WABI 2009), LNCS 5724, pages 362-374.
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software
F. Vandin, E. Upfal, and B. J. Raphael. Algorithms for Detecting Significantly Mutated Pathways in Cancer. In Proc. 14th International Conference on Research in Computational Molecular Biology (RECOMB) 2010, LNCS 6044, pages 506-521, Lisbon (Portugal), 2010.
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F. Vandin, E. Upfal, and B. J. Raphael. De novo Discovery of Mutated Driver Pathways in Cancer. In Proc. 15th International Conference on Research in Computational Molecular Biology (RECOMB), LNCS 6577, pages 499-500, 2011.
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F. Vandin, E. Upfal, and B. J. Raphael. Finding Driver Pathways in Cancer: Models and Algorithms. In Proc. 11th Workshop on Algorithms in Bioinformatics (WABI 2011), LNCS 6833, pages 314-325.
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F. Vandin, P. Clay, E. Upfal, and B. J. Raphael. Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer. In Proc. Pacific Symposium on Biocomputing (PSB), 2012.
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A. Anagnostopoulos, R. Kumar, M. Mahdian, E. Upfal, and F. Vandin. Algorithms on Evolving Graphs. In Proc. of 3rd Innovations in Theoretical Computer Science (ITCS), pages 149-160, 2012.
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L. He, F. Vandin, G. Pandurangan, and C. Bailey-Kellogg. Ballast: A Ball-based Algorithm for Structural Motifs. In Proc. 16th International Conference on Research in Computational Molecular Biology (RECOMB), LNCS 7262, pages 79-93, 2012.
publisher link
F. Vandin, A. Papoutsaki, B. Raphael, and E. Upfal. Genome-Wide Survival Analysis of Somatic Mutations in Cancer. In Proceedings 17th International Conference on Research in Computational Molecular Biology (RECOMB), LNCS 7821, 2013, pp 285-286.
Best Paper Award
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A. Pietracaprina, G. Pucci, F. Silvestri, F. Vandin. Space-Efficient Parallel Algorithms for Combinatorial Search Problems. In Proceedings 38th International Symposium on Mathematical Foundations of Computer Science (MFCS), 2013, accepted for publication.
full version on Arxiv (with omitted proofs)
B.J. Raphael, F. Vandin. Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. In Proceedings 7th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2014, accepted for publication.
M. Riondato, F. Vandin. Finding the True Frequent Itemsets. In Proceedings SIAM International Conference on Data Mining (SDM), 2014, accepted for publication.

Journals

A. Pietracaprina, M. Riondato, E. Upfal, F. Vandin. Mining Top-K Frequent Itemsets Through Progressive Sampling. Data Mining and Knowledge Discovery, ECML PKDD 2010 special issue, Volume 21, Number 2, 2010.
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F. Vandin, E. Upfal, and B. J. Raphael. Algorithms for Detecting Significantly Mutated Pathways in Cancer. Journal of Computational Biology, March 2011, 18(3): 507-522.
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R. Grossi, A. Pietracaprina, N. Pisanti, G. Pucci, E. Upfal, and F. Vandin. MADMX: A Strategy for Maximal Dense Motif Extraction. Journal of Computational Biology, April 2011, 18(4): 535-545.
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F. Vandin, E. Upfal, and B. J. Raphael. De novo Discovery of Mutated Driver Pathways in Cancer. Genome Research 22(2):375-85, 2012. Epub 2011 Jun 7.
pdf preprint
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The Cancer Genome Atlas Project Research Network. Integrated Genomic Analyses of Ovarian Carcinoma. Nature, 2011 Jun. 30;474(7353):609-15.
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F. Vandin, E. Upfal, B.J. Raphael. Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer. IEEE Computer, March 2012 (vol. 45, no. 3) pp.39-46.
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A. Kirsch, M. Mitzenmacher, A. Pietracaprina, G. Pucci, E. Upfal, and F. Vandin. An Efficient Rigorous Approach for Identifying Statistically Significant Frequent Itemsets. Journal of the ACM. 59(3):12:1-12:22.
C. Grasso , Y.Wu , D. Robinson , X. Cao , S. Dhanasekaran , A. Khan , M. Quist , X. Jing , R. Lonigro , J.C. Brenner , I. Asangani , B. Ateeq , S. Chun , J. Siddiqui , L. Sam , M. Anstett , R. Mehra , J. Prensner , N. Palanisamy , G. Ryslik , F. Vandin , B. Raphael , L. Kunju , D. Rhodes , K. Pienta , A. M. Chinnaiyan, S.A. Tomlins. The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer. Nature, 2012 Jul 12;487(7406):239-43.
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F. Vandin, E. Upfal, and B. J. Raphael. Finding Driver Pathways in Cancer: Models and Algorithms. Algorithms for Molecular Biology, 2012 Sep 6;7(1):23.
L. He, F. Vandin, G. Pandurangan, and C. Bailey-Kellogg. BALLAST: A Ball-based Algorithm for Structural Motifs. Journal of Computational Biologyi, 20(2): 137-151 (2013).
The Cancer Genome Atlas Research Network. Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. New England Journal of Medicine , May 1st 2013.
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The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature, 2013 Jul 4; 499(7456):43-9.
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The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics, 2013, 45(10):1113-20.
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C.Kandoth*, M.D. McLellan*, F. Vandin, K.Ye, B. Niu, C. Lu, M. Xie, Q. Zhang, J.F. McMichael, M.A. Wyczalkowski, M.D.M. Leiserson, C.A. Miller, J.S. Welch, M.J. Walter, M.C. Wendl, T.J. Ley, R.K. Wilson, B.J. Raphael, L. Ding. Mutational landscape and significance across 12 major cancer types. Nature, 2013, 502, 333-339.
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Abstracts/Posters

F. Vandin, E. Upfal, and B. J. Raphael. Identification of Significantly Mutated Pathways in Cancer. (Abstract) Annual RECOMB Satellite 2009 MIT, Boston, MA, December 2009.
F. Vandin, E. Upfal, and B. J. Raphael. Detection of Mutated Pathways in Cancer. (Poster) 18th International Conference on Intelligent Systems for Molecular Biology (ISMB) 2010, Boston, MA, 2010.
L. He, F. Vandin, G. Pandurangan, and C. Bailey-Kellogg. Ball-based Algorithms for Structural Motifs. (Poster) 3DSIG 2011, Structural Bioinformatics and Computational Biophysics, ISMB Satellite Meeting, Vienna (Austria), 2011.
F. Vandin, H-T. Wu, E. Upfal, and B. J. Raphael. Algorithms for Automated Discovery of Mutated Pathways in Cancer. (Poster/Abstract) The Cancer Genome Atlas' 1st Annual Scientific Symposium, Washington DC, 2011.
F. Vandin, E. Upfal, and B. J. Raphael. Algorithms for Discovery of Mutated Pathways in Cancer. (Abstract) 2nd Workshop on Computational Advances for Next Generation Sequencing (CANGS) 2012, Las Vegas, NV, 2012.
F. Vandin, H-T. Wu, E. Upfal, and B. J. Raphael. Algorithms to Find Mutated Pathways in Cancer. 16th International Conference on Research in Computational Molecular Biology (RECOMB) 2012, (Poster/Abstract) Barcelona, Spain, 2012.
M. Leiserson, H.-T. Wu, D. Blokh, F. Vandin, R. Sharan, B. J. Raphael. Methods for Identifying Driver Pathways in Cancer. (Poster) 3rd Annual Beyond the Genome Conference, Boston, USA, 2012.
M. Leiserson, H.-T. Wu, F. Vandin and B. J. Raphael. Network analysis of mutations across cancer types. (Poster) 17th International Conference on Research in Computational Molecular Biology (RECOMB), (Poster/Abstract) Beijing, China, 2013.
F. Vandin, A. Papoutsaki, B. Raphael, and E. Upfal. Accurate Genome-Wide Survival Analysis of Somatic Mutations in Cancer. (Poster) ISMB ECCB 2013, Berlin, Germany, 2013.

Theses

Laurea Triennale Final Project: "Models and Methods for the Evaluation of Runway Capacity", Advisor: Prof. Lorenzo Brunetta. University of Padova, 2004
Laurea Specialistica Thesis: "On the Top-K Frequent Closed Itemsets Mining Problem", Advisors: Prof. Andrea Pietracaprina, Prof. Geppino Pucci. University of Padova, 2006 (officially deemed as distinguished by the thesis committee)
Ph.D. Thesis: "Mining Significant Patterns: Theory and Practice", Advisor: Prof. Andrea Pietracaprina. University of Padova, 2010. pdf

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