Publications by Marco Pellegrini
(by subject in reverse chronological order)

  Bio-informatics

  1. M. Pellegrini, M. Elena Renda and A. Vecchio.
    Tandem Repeats Discovery Service (TReaDS) applied to finding novel Cis-acting factors in Repeat Expansion Diseases.
    BMC Bioinformatics. Supplement on the VIII Annual Meeting of the Bioinformatics Italian Society (BITS'11). Pisa, Italy. June 2011.
    In print.
  2. M. Pellegrini, M. Elena Renda and A. Vecchio.
    2. Ab Initio Detection of Fuzzy Amino Acid Tandem Repeats in Protein Sequences.
    BMC Bioinformatics. Supplement on the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM-BCB). Chicago, IL. August 1-3, 2011.
    In print.
  3. M. Pellegrini and M. Elena Renda and A. Vecchio.
    Detecting Fuzzy Amino Acid Tandem Repeats in Protein Sequences
    Proceedings of ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM-BCB), Chicago, IL. August 1-3, 2011. To appear.
  4. M. Pellegrini, M. Elena Renda and A. Vecchio.
    TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats
    Bioinformatics 26(12), pp. i358-366, 2010.
    Special issue on Proceedings of the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010). Boston, MA, July 11-13, 2010.
  5. F. Geraci and M. Pellegrini.
    ReHap: an Integrated System for the Haplotype Assembly Problem from Shotgun Sequencing Data
    Proceedings of Bionformatics 2010, INSTICC (Institute for Systems and Technologies of Information, Control and Communication). 2010.
    Valencia, Spain. 20-23 January 2010.
  6. F. Geraci, M. Pellegrini and M. Elena Renda.
    An Efficient Combinatorial Approach for Solving the DNA Motif Finding Problem
    Proceedings of the 9th International Conference on Intelligent Systems Design and Applications (ISDA 09).
    Pisa, Italy, November 30- December 2, 2009. 335-340.
  7. F. Geraci, M. Leoncini, M. Montangero, M. Pellegrini and M. Elena Renda.
    K-boost: A Scalable Algorithm for High Quality Clustering of Microarray Gene Expression Data
    Journal of Computational Biology. Vol. 16, Num. 6 pp. 859-873, June 2009.
  8. L. M. Genovese, F. Geraci, M. Pellegrini.
    SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage IEEE/ACM Transactions on Computational Biology and Bioinformatics 5(4), pp. 492-502, 2008. IEEE Computer Society. DOI: http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.67
  9. F. Geraci, M. Pellegrini, E. Renda. AMIC@: All MIcroarray Clusterings @ once.
    Nucleic Acids Research , Vol. 36, Web Server Issue W315~W319, 2008.
  10. L.M. Genovese, F. Geraci and M. Pellegrini.
    A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
    In Proceedings of the 7th Workshop on Algorithms in Bioinformatics (WABI 2007),
    Philadelphia, Pennsylvania, September 8-9, 2007.
  11. F. Geraci, M. Leoncini, M. Montangero, M. Pellegrini and M. Elena Renda.
    FPF-SB: A Scalable Algorithm for Microarray Gene Expression Data Clustering
    In Proceedings of HCI International 2007,
    Bejing, China, 22-27 July 2007.

  Information Retrieval on the World Wide Web

  1. M. Budinich, B. Codenotti, F. Geraci and M. Pellegrini.
    On the benefits of keyword spreading in sponsored search auctions: an experimental analysis
    Proceedings of the 11th International Conference on Electronic Commerce and Web Technologies (EC-Web 2010)
    Bilbao, Spain, Aug 30 - Sep 3, 2010. To appear
  2. M. Furini, F. Geraci, M. Montangero and M. Pellegrini.
    STIMO: STIll and MOving Video Storyboard for the Web Scenario
    Multimedia Tools and Applications , Vol. 46, Num. 1 pp. 47-69, 2010.
  3. Y. Dourisboure, F. Geraci and M. Pellegrini.
    Extraction and Classification of Dense Implicit Communities in the Web Graph
    ACM Transactions on the WEB, Vol 3, Num 2, Art 7, April 2009.
  4. F. Geraci and M. Pellegrini.
    Dynamic User-defined Similarity Searching in Semi-structured Text Retrieval.
    Proceedings of Infoscale 2008, The Third International ICST Conference on Scalable Information Systems.
    Vico Equense, Napoli, June 4-6, 2008. In print.
  5. M. Furini, F. Geraci, M. Montangero and M. Pellegrini.
    On Using Clustering Algorithms to Produce Video Abstracts for the Web Scenario
    In Proceedings of IEEE CCNC2008 Fifth IEEE Consumer Communications & Networking Conference,
    Las Vegas, Nevada, January 10-12, 2008. pages 1112-1116.
  6. F. Geraci, M. Pellegrini, F. Sebastiani and M. Maggini. Cluster Generation and Cluster Labelling for Web Snippets:A Fast and Accurate Hierarchical Solution.
    Internet Mathematics , 3(4) pp. 413-444, 2007. In print.
  7. M. Furini, F. Geraci, M. Montangero and M. Pellegrini.
    VISTO: VIsual STOryboard for Web Video Browsing
    In Proceedings of ACM CIVR International Conference on Image and Video Retrieval 2007,
    Amsterdam, The Netherlands, July 9-11, 2007.
  8. Y. Dourisboure, F. Geraci and M. Pellegrini.
    Extraction and classification of dense communities in the Web
    In Proceedings of the 16th International World Wide Web Conference (WWW2007),
    Banff, Alberta, Canada. May 2007.
  9. F. Geraci, M. Pellegrini, M. Maggini and F. Sebastiani.
    Cluster Generation and Cluster Labelling for Web Snippets: A Fast and Accurate Hierarchical Solution
    In Proceedings of the 13th Symposium on String Processing and Information Retrieval (SPIRE 2006), pages 25-36,
    Glasgow, UK. October 2006.
  10. F. Geraci, M. Pellegrini, F. Sebastiani and P. Pisati. A Scalable Algorithm for High-Quality Clustering of Web Snippets
    In Proceedings of the 21st Annual ACM Symposium on Applied Computing (SAC 2006)
    Dijon, France. April 2006.

  Data Structures for Internet Routing

  1. M. Pellegrini and G.Fusco. Efficient IP Table Lookup via Adaptive Stratified Trees with Selective Reconstructions .
    The ACM Journal of Experimental Algorithmics , Vol 12, Num 1.4, 2007.
  2. L. Galluccio, G. Morabito, S. Palazzo, M. Pellegrini, M. E. Renda and P. Santi. GEOROY: A Location-Aware Enhancement to Viceroy Peer-to-Peer Algorithm .
    Computer Networks , 51(8), pp. 1998-2014, 2007.
  3. F. Geraci, M. Pellegrini, P. Pisati and L. Rizzo. Packet Classification via Improved Space Decomposition Techniques.
    In Proceedings of IEEE Infocom 2005, volume 1, pages 304-312.
    Also Technical Report IIT TR-10/2004, Istituto di Informatica e Telematica del C.N.R. Pisa, Italy
    [Data and Code]
  4. M. Pellegrini and G. Fusco. "Efficient IP Table Lookup via Adaptive Stratified Trees with Selective Reconstructions.
    In Proceedings of the 12th European Symposium on Algorithms, Lecture Notes in Computer Science 3221, pages 772-783, 2004 .
    [Data and Code]
  5. M. Pellegrini. Fast Internet Packet Filtering on any Number of Attributes via Multi-dimensional Point Stabbing
    TR IMC B4-01-11, Istituto di Matematica Computazionale del CNR}, Area della Ricerca, Pisa, Italy. March 2001.

  Computational Geometry: Visibility and Intersection in 3D

  1. M. Pellegrini. Ray shooting and lines in space
    In Handbook of Discrete and Computational Geometry - second edition Jacob E. Goodman and Joseph O'Rourke (eds.). Chapman & Hall/CRC Press, Boca Raton, Florida, pp. 839-856, 2004.
  2. M. Pellegrini. Ray-shooting and lines in space.
    In The CRC Handbook of Discrete and Computational Geometry Jacob E. Goodman and Joseph O'Rourke (eds.). CRC Press, Boca Raton, Florida, pp. 599-614, 1997.
  3. M. Pellegrini. Repetitive Hidden Surface Removal for Polyhedra.
    Journal of Algorithms, 21, pp. 80-101, 1996.
  4. M. Pellegrini. On Lines Missing Polyhedral Sets in 3-space.
    Discrete & Computational Geometry, 12, pp. 203-221, 1994.
  5. M. Pellegrini. On Collision-Free Placements of Simplices and the Closest Pair of Lines in 3-Space.
    SIAM J. on Computing, 23 (1), pp. 133-153, 1994.
  6. B. Aronov, M. Pellegrini, and M. Sharir. On the zone of an algebraic surface in a hyperplane arrangement. Discrete & Computational Geometry, 9 (2), pp. 177-188, 1993.
  7. M. Pellegrini. Ray-shooting on triangles in 3-dimensional space.
    Algorithmica, 9, pp. 471-494, 1993.
  8. M. Pellegrini. Lower Bounds for Line Stabbing in 3-Space.
    Computational Geometry: Theory and Applications, 3, pp. 53-58, 1993.
  9. M. Pellegrini and P. Shor. Finding stabbing lines in 3-space.
    Discrete & Computational Geometry, 8, pp. 191-208, 1992.
  10. M. Pellegrini. Repetitive Hidden-Surface-Removal for Polyhedral Scenes
    In Proceedings of the 3rd Workshop on Algorithms and Data Structures,
    Number 709 in Lecture Notes in Computer Science, pages 541-552. Springer Verlag, 1993
  11. M. Pellegrini. On Lines Missing Polyhedral Sets in 3-space.
    In Proceedings of the 9th ACM Symposium on Computational Geometry, pages 19-28, 1993.
  12. M. Pellegrini. Incidence and nearest-neighbor problems for lines in 3-space.
    In Proceedings of the 8th ACM Symposium on Computational Geometry, pages 130-137, 1992.
  13. M. Pellegrini. Ray shooting and isotopy classes of lines in 3-dimensional space.
    In Proceedings of the 2nd Workshop on Algorithms and Data Structures,
    Number 519 in Lecture Notes in Computer Science, pages 20-31. Springer Verlag, 1991.
  14. M. Pellegrini. On the zone of a codimension p surface in a hyperplane arrangement.
    In Proceedings of the Third Canadian Conference on Computational Geometry, pages 233-238, 1991.
  15. M. Pellegrini and P. Shor. Finding stabbing lines in 3-dimensional space.
    In Proceedings of the Second SIAM-ACM Symposium on Discrete Algorithms, pages 24-31, 1991.
  16. M. Pellegrini. Stabbing and ray shooting in 3-dimensional space.
    In Proceedings of the 6th ACM Symposium on Computational Geometry, pages 177-186, 1990.

  Computational Geometry in Spaces of High Dimension.

  1. D. Finocchiaro and M. Pellegrini. On computing the diameter of a point set in high dimensional Euclidean space.
    Theoretical Computer Science , 287(2),pp. 501-514, September 2002
  2. M. Pellegrini. Randomized Combinatorial Algorithms for Linear Programming when the Dimension is Moderately High.
    In Proceedings of the 12th ACM-SIAM Symposium on Discrete Algorithms, pages 101-108, 2001.
  3. D. Finocchiaro and M. Pellegrini. On computing the diameter of a point set in high dimensional Euclidean space.
    In Proceedings of the Seventh Annual European Symposium on Algorithms. Lecture Notes in Computer Science 1643, pages 366-377, 1999.

  Computational Geometry: Point Location, Intersection Counting

  1. M. Pellegrini. On counting pairs of intersecting segments and off-line triangle range searching.
    Algorithmica 17 (4), pp. 380-398, April 1997.
  2. M. Pellegrini. On Point Location and Motion Planning in Arrangements of Simplices.
    SIAM J. on Computing, 25 (5), pp. 1061-1081, October 1996.
  3. M. Pellegrini. On Point Location and Motion Planning in Arrangements of Simplices.
    In Proceedings of the 26th ACM Symposium on Theory of Computing, pp. 95-104, 1994.
  4. P.K. Agarwal, M. Pellegrini, and M. Sharir. Counting circular arcs intersections.
    SIAM J. on Computing, 22 (4), 1993.
  5. M. Pellegrini. Point location and halfspace retrieval.
    AICA-Rivista d'informatica, 20(4):303-344, Ottobre-Dicembre 1990.

  Computer Graphics: Rendering

  1. M. Pellegrini. Analysis of Average and Worst case error in Hierarchical Radiosity matrices
    TR IMC B4-99-12, Istituto di Matematica Computazionale del CNR, via Santa Maria 46, Pisa, Italy. June 1999.
  2. M. Pellegrini. A Geometric Approach to Computing Higher Order Form Factors
    In Proceedings of the 15th ACM Symposium on Computational Geometry, pages 69-78, 1999.
  3. M. Pellegrini. Rendering equation revisited: how to avoid explicit visibility computations.
    In Proceedings of the 10th ACM-SIAM Symposium on Discrete Algorithms, pages 725-733, 1999.
  4. M. Pellegrini. Monte Carlo Approximation of Form Factors with Error Bounded a Priori.
    Discrete & Computational Geometry 17 (3), pp. 319-338, April 1997.
  5. M. Pellegrini. Monte Carlo Approximation of Form Factors with Error Bounded a Priori.
    In Proceedings of the 11th ACM Symposium on Computational Geometry, pages 287-296, 1995.

  Computational Physics: Numerical Electrostatics

  1. M. Pellegrini. Electrostatic Fields without Singularities: Theory, Algorithms and Error Analysis.
    Journal of the ACM. 45(6), 924-964, November 1998. Also TR IMC B4-97-15.
  2. D. Finocchiaro, M. Pellegrini and P. Bientinesi. On Numerical Approximation of Electrostatic Energy in 3D.
    Journal of Computational Physics 146/2, 707-725, 1998.
  3. M. Pellegrini. Electrostatic Fields without Singularities: Theory and Algorithms.
    In Proceedings of the 7th ACM-SIAM Symposium on Discrete Algorithms, pages 184-191, 1996.
  4. P. Bientinesi and M. Pellegrini Electrostatic fields without singularities: implementation and experiments.
    TR IMC B4-97-16, Istituto di Matematica Computazionale del CNR, via Santa Maria 46, Pisa, Italy. November 1997.

  Miscellaneous

  1. G. De Marco, M. Pellegrini and G. Sburlati. Faster Deterministic Wakeup in Multiple Access Channels
    Discrete Applied Mathematics , 155(8), pp. 898-903,, 2007.
  2. G. De Marco, M. Pellegrini and G. Sburlati Faster Deterministic Wakeup in Multiple Access Channels
    In Proceedings of the 9th Italian Conference on Theoretical Computer Science (ICTCS).
    Siena, Italy. October 2005. pages 196-204.
  3. M. Pellegrini Measuring Lines in Space - a Collection of Results
    In Homenatge al professor Lluís Santaló , Carles Barcelo i Vidal (ed). University of Girona, Girona, Spain, pp. 99-111, 2002.
  4. M. Pellegrini. Internet Protocol Table Lookup as a Geometric Problem
    ERCIM News No.50, July 2002.
  5. M. Pellegrini. A High Performance Computing Network for Protein Conformation Simulation
    ERCIM News No.43, October 2000.
  6. M. Pellegrini. From Computational Geometry to Computational Physics
    ERCIM News No.25, April 1996.
  7. M. Pellegrini and R. Sepe. Setlog, a tool for experimenting with new semantics.
    Sigplan Notices, 26(2):67-74, February 1991.
Last update: January 12th, 2012
[Marco's home page]