Optimal Discovery of Subword Associations in Strings. - Alberto Apostolico; Cinzia Pizzi; Giorgio Satta (Discovery Science, 2004)

Monotone Scoring of Patterns with Mismatches: (Extended Abstract). - Alberto Apostolico; Cinzia Pizzi (WABI, 2004)

A multistep bioinformatic approach detects putative regulatory elements in gene promoters. - Stefania Bortoluzzi; Alessandro Coppe; Andrea Bisognin; Cinzia Pizzi; Gian Antonio Danieli (BMC Bioinform., 2005)

On the Monotonicity of the String Correction Factor for Words with Mismatches. - Alberto Apostolico; Cinzia Pizzi (Combinatorial and Algorithmic Foundations of Pattern and Association Discovery, 2006)

Fast Search Algorithms for Position Specific Scoring Matrices. - Cinzia Pizzi; Pasi Rastas; Esko Ukkonen (BIRD, 2007)

Motif discovery by monotone scores. - Alberto Apostolico; Cinzia Pizzi (Discret. Appl. Math., 2007)

Scoring Unusual Words with Varying Mismatch Errors. - Alberto Apostolico; Cinzia Pizzi (Math. Comput. Sci., 2008)

Fast profile matching algorithms - A survey. - Cinzia Pizzi; Esko Ukkonen (Theor. Comput. Sci., 2008)

Expectation of Strings with Mismatches under Markov Chain Distribution. - Cinzia Pizzi; Mauro Bianco (SPIRE, 2009)

MOODS: fast search for position weight matrix matches in DNA sequences. - Janne H. Korhonen; Petri Martinmäki; Cinzia Pizzi; Pasi Rastas; Esko Ukkonen (Bioinform., 2009)

k-difference matching in amortized linear time for all the words in a text. - Cinzia Pizzi (Theor. Comput. Sci., 2009)

Efficient computation of statistics for words with mismatches. - Cinzia Pizzi (Structure Discovery in Biology: Motifs, Networks & Phylogenies, 2010)

Efficient algorithms for the discovery of gapped factors. - Alberto Apostolico; Cinzia Pizzi; Esko Ukkonen (Algorithms Mol. Biol., 2011)

Speedup for a periodic subgraph miner. - Alberto Apostolico; Manuel Barbares; Cinzia Pizzi (Inf. Process. Lett., 2011)

Finding Significant Matches of Position Weight Matrices in Linear Time. - Cinzia Pizzi; Pasi Rastas; Esko Ukkonen (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Characterization and Extraction of Irredundant Tandem Motifs. - Laxmi Parida; Cinzia Pizzi; Simona E. Rombo (SPIRE, 2012)

Efficient algorithms for the periodic subgraphs mining problem. - Alberto Apostolico; Péter L. Erdös; Ervin Györi; Zsuzsanna Lipták; Cinzia Pizzi (J. Discrete Algorithms, 2012)

Alignment Free Sequence Similarity with Bounded Hamming Distance. - Alberto Apostolico; Concettina Guerra; Cinzia Pizzi (DCC, 2014)

Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences. - Laxmi Parida; Cinzia Pizzi; Simona E. Rombo (WABI, 2014)

Irredundant tandem motifs. - Laxmi Parida; Cinzia Pizzi; Simona E. Rombo (Theor. Comput. Sci., 2014)

A Filtering Approach for Alignment-Free Biosequences Comparison with Mismatches. - Cinzia Pizzi (WABI, 2015)

Higher recall in metagenomic sequence classification exploiting Overlapping Reads. - Samuele Girotto; Matteo Comin; Cinzia Pizzi (ICCABS, 2016)

MissMax: alignment-free sequence comparison with mismatches through filtering and heuristics. - Cinzia Pizzi (Algorithms Mol. Biol., 2016)

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures. - Samuele Girotto; Cinzia Pizzi; Matteo Comin (Bioinform., 2016)

Sequence similarity measures based on bounded hamming distance. - Alberto Apostolico; Concettina Guerra; Gad M. Landau; Cinzia Pizzi (Theor. Comput. Sci., 2016)

Binning metagenomic reads with probabilistic sequence signatures based on spaced seeds. - Samuele Girotto; Matteo Comin; Cinzia Pizzi (CIBCB, 2017)

How User Condition Affects Community Dynamics in a Forum on Autism. - Mattia Samory; Cinzia Pizzi; Enoch Peserico (ICWSM, 2017)

Consensus-based anomaly detection for efficient heating management. - Francesco Carbone; Angelo Cenedese; Cinzia Pizzi (SmartWorld/SCALCOM/UIC/ATC/CBDCom/IOP/SCI, 2017)

Fast Spaced Seed Hashing. - Samuele Girotto; Matteo Comin; Cinzia Pizzi (WABI, 2017)

Metagenomic reads binning with spaced seeds. - Samuele Girotto; Matteo Comin; Cinzia Pizzi (Theor. Comput. Sci., 2017)

A new distributed alignment-free approach to compare whole proteomes. - Umberto Ferraro Petrillo; Concettina Guerra; Cinzia Pizzi (Theor. Comput. Sci., 2017)

FSH: fast spaced seed hashing exploiting adjacent hashes. - Samuele Girotto; Matteo Comin; Cinzia Pizzi (Algorithms Mol. Biol., 2018)

Efficient Algorithms for Sequence Analysis with Entropic Profiles. - Cinzia Pizzi; Mattia Ornamenti; Simone Spangaro; Simona E. Rombo; Laxmi Parida (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

MetaProb 2: Improving Unsupervised Metagenomic Binning with Efficient Reads Assembly Using Minimizers. - Francesco Andreace; Cinzia Pizzi; Matteo Comin (ICCABS, 2020)

Fast Approximation of Frequent k-Mers and Applications to Metagenomics. - Leonardo Pellegrina; Cinzia Pizzi; Fabio Vandin (J. Comput. Biol., 2020)

Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing. - Enrico Petrucci; Laurent Noé; Cinzia Pizzi; Matteo Comin (J. Comput. Biol., 2020)

Comparison of microbiome samples: methods and computational challenges. - Matteo Comin; Barbara Di Camillo; Cinzia Pizzi; Fabio Vandin (Briefings Bioinform., 2021)

MetaProb 2: Metagenomic Reads Binning Based on Assembly Using Minimizers and K-Mers Statistics. - Francesco Andreace; Cinzia Pizzi; Matteo Comin (J. Comput. Biol., 2021)

Efficient Hashing of Multiple Spaced Seeds with Application. - Eleonora Mian; Enrico Petrucci; Cinzia Pizzi; Matteo Comin (BIOINFORMATICS, 2023)

On Multi-phase Metagenomics Reads Binning. - Francesco Tomasella; Cinzia Pizzi (ICCABS, 2023)

MISSH: Fast Hashing of Multiple Spaced Seeds. - Eleonora Mian; Enrico Petrucci; Cinzia Pizzi; Matteo Comin (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Machine Learning Methods for Phenotype Prediction from High-Dimensional, Low Population Aquaculture Data. - Giovanni Faldani; Enrico Rossignolo; Eleonora Signor; Alessio Longo; Sara Faggion; Luca Bargelloni; Matteo Comin; Cinzia Pizzi (BIOSTEC (1), 2025)

MetaComBin: combining abundances and overlaps for binning metagenomics reads. - Francesco Tomasella; Cinzia Pizzi (Frontiers Bioinform., 2025)