2016

    51. Fabio Fassetti, Simona E. Rombo, Cristina Serrao Discovering Discriminative Graph Patterns from Gene Expression Data. In Proceedings of ACM/SIGAPP Symposium on Applied Computing (SAC 2016). In Press.

    50. Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E. Rombo, Adolfo Saiardi Discovering new Proteins in Plant Mitochondria by RNA Editing Simulation. In Proceedings of BIOINFORMATICS 2016. In Press.

2015

    49. Raffaele Giancarlo, Simona E. Rombo, Filippo Utro. Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning. Bioinformatics, 31(18), 2939-2946, Oxford Journals, 2015. Doi

    48. Simona Panni, Simona E. Rombo. Searching for repetitions in biological networks: methods, resources and tools. Briefings in Bioinformatics, 16(1), 118-136, Oxford Journals, 2015. Doi

2014

    47. Clara Pizzuti, Simona E. Rombo. An evolutionary restricted neighborhood search clustering approach for PPI networks. Neurocomputing, 145, 53-61, Elsevier, 2014. Doi

    46. Clara Pizzuti, Simona E. Rombo. Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods. Bioinformatics, 30(10), 1343-1352, Oxford Journals, 2014. Doi

    45. Raffaele Giancarlo, Simona E. Rombo, Filippo Utro. Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies. Briefings in Bioinformatics, 15(3), 390-406, Oxford Journals, 2014. Doi

    44. Laxmi Parida, Cinzia Pizzi, Simona E. Rombo. Irredundant tandem motifs. Theoretical Computer Science, 525, 89–102, ISSN 0304-3975, Elsevier, Amsterdam (Nederlands), 2014. Doi

    43. Laxmi Parida, Cinzia Pizzi and Simona E. Rombo. Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences. In Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, (WABI 2014), pp. 148-160, LNCS 8701. Springer 2014. Doi,

2013

    42. Simona E. Rombo. Finding repetitions in biological networks: challenges, trends and applications. In Algorithmic and AI Methods for Protein Bioinformatics (Y. Pan, J. Wang, and M. Li Eds.), Ch. 24, pp. 461-479, John Wiley & Sons, Inc., Hardbound, 2013.

    41. Erika De Francesco, Giuliana Di Santo, Luigi Palopoli and Simona E. Rombo. Genomic Databases Characteristics. In Encyclopedia of Systems Biology, , pp. 834-838, Springer, 2013.

    40. Luigi Palopoli, Simona E. Rombo, Giorgio Terracina, Giuseppe Tradigo and Pierangelo Veltri. Protein Structure Metapredictors. In Encyclopedia of Systems Biology, pp. 1781-1785, Springer, 2013 (To Appear).

    39. Clara Pizzuti and Simona E. Rombo. Restricted Neighborhood Search Clustering Revisited: An Evolutionary Computation Perspective. In Proceedings of the 8th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2013), pp. 59-68, LNCS 7986, Springer 2013. Doi, BibTex

    38. Angelo Furfaro, Maria Carmela Groccia and Simona E. Rombo. Image classification based on 2D feature motifs. In Proceedings of the Flexible Query Answering Systems (FQAS 2013), pp. 340-351, LNCS 8132, Springer 2013.

2012

    37. Simona E. Rombo. Extracting string motif bases for quorum higher than two. Theoretical Computer Science, 460, 94-103, ISSN 0304-3975, Elsevier, Amsterdam (Nederlands), 2012. Doi

    36. Clara Pizzuti and Simona E. Rombo. A co-clustering approach for mining large protein-protein interaction networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(3), 717-730, ISSN 1545-5963, IEEE Computer Society, Los Alamitos, CA (USA), 2012. Doi, BibTex

    35. Laxmi Parida, Cinzia Pizzi and Simona E. Rombo. Characterization and Extraction of Irredundant Tandem Motifs. In Proceedings of the 19th International Symposium on String Processing and Information Retrieval (SPIRE 2012), pp. 385-397, LNCS 7608. Springer 2012. Doi, BibTex

    34. Clara Pizzuti and Simona E. Rombo. Experimental Evaluation of Topological-based Fitness Functions to Detect Complexes in PPI Networks. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2012), pp. 193-200, ACM. Doi, BibTex

    33. Clara Pizzuti, Simona E. Rombo and Elena Marchiori. Complex detection in protein-protein interaction networks: a compact overview for researchers and practitioners. In Proceedings of the 10th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Computational Biology (EvoBio 2012), pp. 821-830, LNCS 7246 Springer 2012. Doi, BibTex

    32. Roberto De Virgilio and Simona E. Rombo. Approximate Matching over Biological RDF Graphs. In Proceedings of The 27th Symposium On Applied Computing (SAC 2012), Poster Session on Bioinformatics.

2011

    31. Nicola Ferraro, Luigi Palopoli, Simona Panni and Simona E. Rombo. Asymmetric Comparison and Querying of Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(4), 876-889, ISSN 1545-5963, IEEE Computer Society, Los Alamitos, CA (USA), 2011. Doi, BibTex

    30. Fabio Fassetti, Ofelia Leone, Luigi Palopoli, Simona E. Rombo and Adolfo Saiardi. IP6K gene identification in plant genomes by tag searching. BMC Proceedings, 5(Suppl 2), S1, ISSN 1753-6561, BioMed Central Ltd, London (United Kingdom), 2011. Doi, Draft, BibTex

    29. Alessia Amelio, Alberto Apostolico and Simona E. Rombo. Image Compression by 2D Motif Basis. In Proceedings of IEEE Data Compression Conference (DCC 2011), IEEE CS Press, Snowbird, UT, USA. Doi, Draft, BibTex

2010

    28. Francesco Bruno, Luigi Palopoli and Simona E. Rombo.New trends in graph mining: Structural and Node-colored network motifs. International Journal of Knowledge Discovery in Bioinformatics, 1(1): 81-99, 2010. Doi, BibTex

    27. Nicola Ferraro, Luigi Palopoli, Simona Panni and Simona E. Rombo. "Master-Slave" Biological Network Alignment. In Proceedings of 6th International symposium on Bioinformatics Research and Applications (ISBRA 2010), pp. 215-229, LNBI/LNCS 6053 Springer 2010, Connecticut, USA, May 23-26, 2010. Doi, Draft, BibTex

    26. Fabio Fassetti, Ofelia Leone, Luigi Palopoli, Simona E. Rombo and Adolfo Saiardi. IP6K gene identification in plant cells via tag discovery. In Proceedings of Seventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistic (CIBB 2010), Palermo, Italy, September 16-18, 2010. Draft, BibTex

    25. Fabio Fassetti, Ofelia Leone, Luigi Palopoli, Simona E. Rombo and Adolfo Saiardi. IP6K gene identification by tag search. In Proceedings of 6th International symposium on Bioinformatics Research and Applications (ISBRA 2010), Short Abstracts, Connecticut, USA, May 23-26, 2010. Draft, BibTex

    24. Nicola Ferraro, Luigi Palopoli, Simona Panni and Simona E. Rombo. Asymmetric Global Alignment of Protein-Protein Interaction Graph Databases (Extended Abstract). In Atti del Convegno Nazionale su Sistemi Evoluti per Basi di Dati (SEBD 2010), ISBN 978-88-7488-369-1, Rimini, Italy, June 20-23, 2010. Draft, BibTex

2009

    23. Simona E. Rombo. Optimal extraction of motif patterns in 2D. Information Processing Letters, 109(17): 1015-1020, 2009. Doi, Draft, BibTex

    22. Valeria Fionda, Simona Panni, Luigi Palopoli and Simona E. Rombo. A technique to search functional similarities in PPI networks. International Journal of Data Mining and Bioinformatics, 3(4): 431-453, ISSN 1748--5673, 2009. Doi, Draft, BibTex

    21. Luigi Palopoli, Simona E. Rombo, Giorgio Terracina, Giuseppe Tradigo and Pierangelo Veltri. Improving protein secondary structure predictions by prediction fusion. Information Fusion, 10(3): 217-232, 2009. Doi, Draft, BibTex

    20. Simona E. Rombo, Filippo Utro and Raffaele Giancarlo. Basic Statistical Indices for SeqAn. In Biological Sequence Analysis using the SeqAn C++ Library (Knut Reinert et al.), Ch. XVI, pp. 249-260, Chapman&Hall/CRC Mathematical & Computational Biology, ISBN 142007623X, United Kingdom, 2009. Doi, Draft, BibTex

    19. Clara Pizzuti and Simona E. Rombo. Discovering Protein Complexes in Protein Interaction Networks. In Biological Data Mining in Protein Interaction Networks (X. L. Li and S. K. Ng Eds.), Ch. IX, pp. 144-168, IGI Global, ISBN-10 1605663980, Hershey, Pennsylvania (USA), 2009. Doi, BibTex

    18. Erika De Francesco, Giuliana Di Santo, Luigi Palopoli and Simona E. Rombo. A summary of genomic databases: overview and discussion. In Biomedical Data and Applications (Amandeep S. Sidhu, Tharam S. Dillon and Elizabeth Chang Eds.), Ch. III, pp. 37-54, Springer, ISBN 978-3-642-02192-3, Heidelberg (Germany), 2009. Doi, Draft, BibTex

    17. Valeria Fionda, Simona Panni, Luigi Palopoli and Simona E. Rombo. Extracting similar sub-graphs across PPI Networks. In Proceedings of 24th International Symposium on Computer and Information Sciences (ISCIS 2009), pp. 183-188, IEEE CS Press, North Cyprus, September 14-16, 2009. Doi, Draft, BibTex

    16. Luca Miceli, Luigi Palopoli, Simona E. Rombo, Giorgio Terracina, Giuseppe Tradigo and Pierangelo Veltri. Experimental evaluation of protein secondary structure predictors. In Proceedings of the International Conference on Computational Science 2009 (ICCS 2009), pp. 848-857, LNCS 5544 Springer 2009, Baton Rouge, LA, USA, May 25-27, 2009. Doi, Draft, BibTex

2008

    15. Alberto Apostolico, Laxmi Parida and Simona E. Rombo. Motif Patterns in 2D. Theoretical Computer Science, 390(1): 40-55, ISSN 0304-3975, Elsevier, Amsterdam (Nederlands), 2008. Doi, Draft, BibTex

    14. Clara Pizzuti and Simona E. Rombo. Multi-functional Protein Clustering in PPI Networks. In Proceedings of the 2nd International Conference on Bioinformatics Research and Development (BIRD 2008), pp. 318-330, Communications in Computer and Information Science 13 Springer 2008, Vienna, Austria, July 7-9, 2008. Doi, Draft, BibTex

    13. Valeria Fionda, Simona Panni, Luigi Palopoli and Simona E. Rombo. Protein-protein interaction network querying by a "focus and zoom" approach. In Proceedings of the 2nd International Conference on Bioinformatics Research and Development (BIRD 2008), pp. 331-346, Communications in Computer and Information Science 13 Springer 2008, Vienna, Austria, July 7-9, 2008. Doi, Draft, BibTex

    12. Clara Pizzuti and Simona E. Rombo. Discovering meaningful protein-protein interaction modules by a co-clustering based approach. In Atti del Convegno Nazionale su Sistemi Evoluti per Basi di Dati (SEBD 2008), pp. 294-301, Palermo, Italy, June 22-24, 2008. Draft, BibTex

    11. Valeria Fionda, Luigi Palopoli, Simona Panni and Simona E. Rombo. Singling out functional similarities in graph databases. In Atti del Convegno Nazionale su Sistemi Evoluti per Basi di Dati (SEBD 2008), pp. 271-278, Palermo, Italy, June 22-24, 2008. Draft, BibTex

2007

    10. Simona E. Rombo and Luigi Palopoli. Pattern Discovery In Biosequences: From Simple To Complex Patterns, in Data Mining Patterns: New Methods and Applications (Florent Masseglia, Pascal Poncelet and Maguelonne Teisseire Eds.), Ch. IV, pp. 85-105, IGI Global, ISBN 978-159904162-9, Hershey, Pennsylvania (USA), 2007. Doi, BibTex

    9. Valeria Fionda, Simona Panni, Luigi Palopoli and Simona E. Rombo. Bi-GRAPPIN: Bipartite graph based protein-protein interaction networks similarity search. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007), pp. 355-361, IEEE CS Press, Silicon Valley, USA, November 2-4, 2007. Doi, Draft, BibTex

    8. Clara Pizzuti and Simona E. Rombo. PINCoC: a Co-Clustering based Method to Analyze Protein-Protein Interaction Networks. In Proceedings of the 8th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2007), pp. 821-830, LNCS 4881 Springer 2007, Birmingham, UK, December 16-19, 2007. Doi, Draft, BibTex

    7. Fabrizio Angiulli, Valeria Fionda and Simona E. Rombo. PProtein Data Condensation for Effective Quaternary Structure Classification. In Proceedings of the 8th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2007), pp. 810-820, LNCS 4881 Springer 2007, Birmingham, UK, December 16-19, 2007. Doi, Draft, BibTex

2006

    6. Luigi Palopoli, Simona E. Rombo, Giorgio Terracina, Giuseppe Tradigo and Pierangelo Veltri. JSSPrediction: a Framework to Predict Protein Secondary Structures Using Integration. In Proceedings of the 19-th IEEE Symposium on Computer-Based Medical Systems (CBMS 2006), pp. 931-935, IEEE CS Press, Salt Lake City, Utah, June 22-23, 2006. Doi, Draft, BibTex

    5. Luigi Palopoli, Simona E. Rombo, Giorgio Terracina, Giuseppe Tradigo and Pierangelo Veltri. Protein Secondary Structure Prediction: How to Improve Accuracy by Integration. Third International Meeting of Bioinformatics and Biostatistic (CIBB 2006), in Proceedings of the 7-th Int. FLINS Conf., pp. 579--586, World Scientific Printers, Genova, Italy, August 29-31, 2006. Draft, BibTex

2005

    4. Luigi Palopoli, Simona Rombo and Giorgio Terracina. Flexible Pattern Discovery with (Extended) Disjunctive Logic Programming. In Proceedings of the International Syposium on Methodologies for Intelligent Systems (ISMIS 2005), pp. 504-513, LNCS 3488 Springer 2005, New York, USA, May 25-28, 2005. Doi, Draft, BibTex

2004

    3. Simona Rombo and Giorgio Terracina. Discovering Representative Models in Large Time Series Databases. In Proceedings of the International Conference On Flexible Query Answering Systems (FQAS 2004), pp. 84-97, LNCS 3055 Springer 2004, Lyon, France, June 24-26, 2004. Doi, Draft, BibTex

    2. Pasquale Grimaldi, Simona E. Rombo, Giorgio Terracina e Luigi Palopoli. Derivazione Efficiente di Pattern Strutturati Frequenti da Database di Natura Biologica. In Atti del Convegno Nazionale su Sistemi Evoluti per Basi di Dati (SEBD 2004), pp. 106-117, S. Margherita di Pula, Cagliari, Italy, June 21-23, 2004. Draft, BibTex

    1. Francesco Buccafurri, Gianluca Lax e Simona E. Rombo. Riduzione del Traffico nei Sistemi P2P: un Approccio Semantico. In Atti del Convegno Nazionale su Sistemi Evoluti per Basi di Dati (SEBD 2004), pp. 370-381, S. Margherita di Pula, Cagliari, Italy, June 21-23, 2004. Draft, BibTex



My DBLP entry (thanks to Michael Ley)



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