Compositional approaches for the characterization and mining of omics data

International Journals:

• S.Girotto, M.Comin, C.Pizzi: Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads BMC Genomics, 18(10):971, 6th December, 2017
• U. Ferraro-Petrillo, C.Guerra, C.Pizzi: A new distributed alignment-free approach to compare whole proteomes Theoretical Computer Science, 698:100-112, 2017
• S.Girotto, M.Comin, C.Pizzi: Metagenomic reads binning with spaced seeds Theoretical Computer Science, 698:88-99, 2017

International Conferences:

• S.Girotto, M.Comin, C.Pizzi: Fast Spaced Seed Hashing 17th Workshop on Algorithms in Bioinformatics - WABI 2017
• S.Girotto, M.Comin, C.Pizzi: Binning metagenomic reads with probabilistic sequence signatures based on spaced seeds IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology - CIBCB 2017
• M.Samory, C.Pizzi, E.Peserico: How user condition affects community dynamics in a forum on autism In proceedings of the 11th International Conference on Web and Social Media - ICWSM 2017, Montreal, Canada, May 15-18, 2017, pages 220-229.

International Journals:

• C.Pizzi, M.Ornamenti, S.Spangaro, S.E.Rombo, L.Parida: Efficient Algorithms for Sequence Analysis with Entropic Profiles accepted at IEEE Transaction in Computational Biology and Bioinformatics, advanced access available
• S.Girotto, C.Pizzi, M. Comin: MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures. Bioinformatics 2016 32 (17): i567-i575, special issue ECCB2016
• A.Apostolico, C.Guerra, G.M.Landau, C.Pizzi: Sequence Similarity Measures based on Bounded Hamming distance. Theoretical Computer Science, 638:76-90, 2016
• C.Pizzi: MissMax: alignment-free sequences comparison with mismatches through filtering and heuristics. Algorithms for Molecular Biology, 2016, 11:6
• M. Comin, M. Antonello: On the comparison of regulatory sequences with multiple resolution Entropic Profiles. BMC Bioinformatics 17: 130 (2016)
• F.Angiulli, F.Fassetti: Towards generalizing the unification with statistical outliers: the Gradient Outlier Factor measure. ACM Transactions on Knowledge Discovery from Data (TKDD), 10(3): article 27, 2016

International Conferences:

• S.Girotto, M.Comin, C.Pizzi: Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads. 6th IEEE International Conference on Computational Advances in Bio- and Medical Science
• F.Fassetti, S.E.Rombo, C.Serrao: Discovering Discriminative Graph Patterns from Gene Expression Data. ACM/SIGAPP Symposium on Applied Computing (SAC 2016). In Press.
• F.Fassetti, C.Giallombardo, O.Leone, L.Palopoli, S.E. Rombo, A.Saiardi: Discovering new Proteins in Plant Mitochondria by RNA Editing Simulation. BIOINFORMATICS 2016. In Press.

International Journals:

• R.Giancarlo, S.E.Rombo, F.Utro: ``Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning''. Bioinformatics 31(18): 2939-2946, 2015
• S. Panni, S.E.Rombo: ``Searching for repetitions in biological networks: methods, resources and tools''. Briefings in bioinformatics 16(1):118-136, 2015.
• M.Comin, A.Leoni, M.Schimd: ``Clustering of reads with alignment-free measures and quality values''. Algorithms for Molecular Biology 10:4, 2015

International Conferences:

• C.Pizzi: ``A Filtering Approach for Alignment-Free Biosequences Comparison with Mismatches''. Proceedings of WABI 2015, Lecture Notes in Computer Science 9289, 231-242, Springer, 2015
• M. Comin, M. Antonello: ``Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles''. Proceedings of Bioinformatics 2015, pp. 171-177, 2015

International Journals:

• C. Pizzuti, S.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. 2014.
• R. Giancarlo, S.E. Rombo, F. Utro. : ``Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies''. Briefings in bioinformatics 15 (3), 390-406. 2014
• C. Pizzuti, S.E. Rombo: ``An evolutionary restricted neighborhood search clustering approach for PPI networks''. Neurocomputing 145, 53-61. 2014.
• M. Comin, M. Antonello: ``Fast Entropic Profiler: An Information Theoretic Approach for the Discovery of Patterns in Genomes''. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(3), 500-509, 2014
• M. Comin, M. Farreras: ``Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes''. Journal of Computational Biology 21(4), 330-344, 2014

International Conferences:

• L. Parida, C. Pizzi, S.E. Rombo: ``Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences'' in proceedings of Workshop on Algorithms in Bioinformatics - WABI 2014, LNCS pp. 148-160, 2014.
• A. Apostolico, C. Guerra, C. Pizzi: ``Alignment Free Sequence Similarity with Bounded Hamming Distance''. In proceedings of Data Compression Conference - DCC2014, pp 183-192, IEEE 2014
• M. Comin, A. Leoni, M. Schimd: ``QCluster: Extending Alignment-Free Measures with Quality Values for Reads Clustering'', in proceedings of Workshop on Algorithms in Bioinformatics - WABI 2014, LNCS pp. 1-13, 2014.
• M.Comin, D. Verzotto: ``Beyond fixed-resolution alignment-free measures for mammalian enhancers sequence comparison''. Proceeding of the 12-th Asia Pacific Bioinformatics Conference 2014. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(4), 628-637, 2014
• M.Comin, M. Schimd: ``Assembly-free Genome Comparison based on Next-Generation Sequencing Reads and Variable Length Patterns''. Proceedings of the 4th Annual RECOMB Satellite Workshop at Massively Parallel Sequencing. BMC Bioinformatics, 15(9)S1, 2014