:: Publications

  1. Direct vs 2-Stage Approaches to Structured Motif Finding
    M. Federico, M. Leoncini M. Montangero, P. Valente
    Algorithms for Molecular Biology, 2012 Aug;7(1):20. (Epub ahead of print).
     
  2. Composite Motif Finder: a combinatorial tool for finding cis-regulatory modules
    M. Leoncini, M. Montangero, M. Pellegrini, K. Tillan
    Technical report IIT TR-08/2012. July 2012.
     
  3. Tandem Repeats Discovery Service (TReaDS) applied to finding novel Cis-acting factors in Repeat Expansion Diseases
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    BMC Bioinformatics 2012, Vol. 13(Suppl 4):S3, doi:10.1186/1471-2105-13-S4-S3. March 2012.
     
  4. Ab initio detection of fuzzy amino acid tandem repeats in protein sequences
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    BMC Bioinformatics 2012, Vol. 13(Suppl 3):S8, doi:10.1186/1471-2105-13-S3-S8. March 2012.
     
  5. Spaced Seeds Design Using Perfect Rulers
    L. Egidi, G. Manzini
    Proc. 18th International Symposium on String Processing and Information Retrieval, Pisa Italy, October 2011.
     
  6. Detecting Fuzzy Amino Acid Tandem Repeats in Protein Sequences
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB). Chicago, USA. August 2011.
     
  7. A High Performing Tool for Residue Solvent Accessibility Prediction using Sequence Homology
    L. Palmieri, M. Federico, M. Leoncini and M. Montangero
    Proc. of the 2nd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2011), LNCS 6865, pp. 138-152. August 2011.
     
  8. TReaDS: Tandem Repeats Discovery Service
    M. Elena Renda, Alessio Vecchio, Marco Pellegrini
    VIII Annual Meeting of the Bioinformatics Italian Society (BITS'11), pp 102-104. Pisa, Italy. June 2011.
     
  9. A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem
    Filippo Geraci
    Bioinformatics, Published by Oxford Journals, Vol. 26, Issue 18, pp 2217-2225, July 2010, doi: 10.1093/bioinformatics/btq411.
     
  10. TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    Bioinformatics. Published by Oxford University Press, Volume 26, Issue 12, pp i358-i366. June 2010. doi: 10.1093/bioinformatics/btq209.
     
  11. ReHap: an Integrated System for the Haplotype Assembly Problem from Shotgun Sequencing Data
    Filippo Geraci, Marco Pellegrini
    Proc. of Bionformatics 2010, INSTICC. Valencia, Spain, 20-23 January 2010.
     
  12. An Efficient Combinatorial Approach for Solving the DNA Motif Finding Problem
    Filippo Geraci, Marco Pellegrini, M. Elena Renda
    Proc. of the 9th International Conference on Intelligent Systems Design and Applications (ISDA'09), pp 335-340. Pisa, Italy, Nobember 30 - December 2 2009. doi: http://doi.ieeecomputersociety.org/10.1109/ISDA.2009.41.
     
  13. TRStalker: an Efficient Heuristic for Finding NP-Complete Tandem Repeats
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    Tech. Rep. n. 2009-TR-08, Istituto di Informatica e Telematica - CNR, Pisa, October 2009.
     
  14. An efficient algorithm for planted structured motif extraction
    Maria Federico, Paolo Valente, Mauro Leoncini, Manuela Montangero, Roberto Cavicchioli
    Proc. of the 1st ACM Workshop on Breaking Frontiers of Computational Biology (CompBio'09). Ischia, Italy, May 18 - 20 2009. ACM, New York, NY, 1-6, doi: doi.acm.org/10.1145/1531780.1531782.
     
  15. K-Boost: a Scalable Algorithm for High-Quality Clustering of Microarray Gene Expression Data
    Filippo Geraci, Mauro Leoncini, Manuela Montangero, Marco Pellegrini, M. Elena Renda
    Journal of Computational Biology, Published by Mary Ann Liebert, Vol. 16, Issue 6, pp 859-873, June 2009, doi:10.1089/cmb.2008.0201.
    Also Tech. Rep. n. 2007-TR-15, Istituto di Informatica e Telematica - CNR, Pisa, December 2007.
     
  16. SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
    Loredana M. Genovese, Filippo Geraci, Marco Pellegrini
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE Computer Society Digital Library, June 2008, doi.ieeecomputersociety.org/10.1109/TCBB.2008.67
     
  17. AMIC@: All MIcroarray Clusterings @ once
    Filippo Geraci, Marco Pellegrini, M. Elena Renda
    Nucleic Acids Research (NAR), May 2008, Vol. 36, Web Server Issue W315–W319, doi:10.1093/nar/gkn265.
     
  18. TReaDS: Tandem Repeats Discovery Service
    Alessio Vecchio, M. Elena Renda, Marco Pellegrini
    Tech. Rep. n. 2008-TR-06, Istituto di Informatica e Telematica - CNR, Pisa, May 2008.
     
  19. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment
    Paolo Ferragina, Raffaele Giancarlo, Valentina Greco, Giovanni Manzini, Gabriel Valiente
    BMC Bioinformatics, July 2007, doi:10.1186/1471-2105-8-252
     
  20. A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
    Loredana M. Genovese, Filippo Geraci, Marco Pellegrini
    in Proc. 7th Workshop on Algorithms in Bioinformatics (WABI'07), Philadelphia, USA, September 2007.
    Also Tech. Rep. n. 2007-TR-5, Istituto di Informatica e Telematica - CNR, Pisa, May 2007.
     
  21. FPF-SB: a Scalable Algorithm for Microarray Gene Expression Data Clustering
    Filippo Geraci, Mauro Leoncini, Manuela Montangero, Marco Pellegrini, M. Elena Renda
    in Proc. 12th International Conference on Human-Computer Interaction (HCI'07), Beijing, P.R. China, July 2007.
    Also Tech. Rep. n. 2007-TR-1, Istituto di Informatica e Telematica - CNR, Pisa, February 2007.
     
  22. High-Throughput Analysis of Gene Expression Data for Personalized Medicine
    Filippo Geraci, Mauro Leoncini, Manuela Montangero, Marco Pellegrini, M. Elena Renda
    ERCIM News No. 69, April 2007.
     
Styled and mantained by:
Geraci Filippo, M. Elena Renda