Motifs in Ziv-Lempel-Welch Clef. - Alberto Apostolico; Matteo Comin; Laxmi Parida (Data Compression Conference, 2004)

Modelling a Protein Structure Comparison Application on the Grid Using PROTEUS. - Mario Cannataro; Matteo Comin; Carlo Ferrari; Concettina Guerra; Antonella Guzzo; Pierangelo Veltri (SAG, 2004)

PROuST: A Comparison Method of Three-Dimensional Structures of Proteins Using Indexing Techniques. - Matteo Comin; Concettina Guerra; Giuseppe Zanotti (J. Comput. Biol., 2004)

Grid Deployment Of Bioinformatics Applications: A Case Study In Protein Similarity Determination. - Matteo Comin; Carlo Ferrari; Concettina Guerra (Parallel Process. Lett., 2004)

Off-Line Compression by Extensible Motifs. - Alberto Apostolico; Matteo Comin; Laxmi Parida (DCC, 2005)

Conservative extraction of over-represented extensible motifs. - Alberto Apostolico; Matteo Comin; Laxmi Parida (ISMB (Supplement of Bioinformatics), 2005)

Bridging Lossy and Lossless Compression by Motif Pattern Discovery. - Alberto Apostolico; Matteo Comin; Laxmi Parida (Electron. Notes Discret. Math., 2005)

Application re-structuring and data management on a grid environment: a case study for bioinformatics. - Giovanni Ciriello; Matteo Comin; Concettina Guerra (IPDPS, 2006)

Mining, compressing and classifying with extensible motifs. - Alberto Apostolico; Matteo Comin; Laxmi Parida (Algorithms Mol. Biol., 2006)

Subtle Motif Discovery for Detection of DNA Regulatory Sites. - Matteo Comin; Laxmi Parida (APBC, 2007)

Algorithmic re-structuring and data replication for protein structure comparison on a GRID. - Giovanni Ciriello; Matteo Comin; Concettina Guerra (Future Gener. Comput. Syst., 2007)

Mining Overrepresented 3D Patterns of Secondary Structures in proteins. - Matteo Comin; Concettina Guerra; Giuseppe Zanotti (J. Bioinform. Comput. Biol., 2008)

Detection of subtle variations as consensus motifs. - Matteo Comin; Laxmi Parida (Theor. Comput. Sci., 2008)

Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform. - Matteo Comin; Concettina Guerra; Frank Dellaert (J. Comput. Biol., 2009)

Remote Homology Detection of Protein Sequences. - Matteo Comin; Davide Verzotto (Structure Discovery in Biology: Motifs, Networks & Phylogenies, 2010)

Classification of protein sequences by means of irredundant patterns. - Matteo Comin; Davide Verzotto (BMC Bioinform., 2010)

VARUN: Discovering Extensible Motifs under Saturation Constraints. - Alberto Apostolico; Matteo Comin; Laxmi Parida (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

The Irredundant Class Method for Remote Homology Detection of Protein Sequences. - Matteo Comin; Davide Verzotto (J. Comput. Biol., 2011)

Whole-Genome Phylogeny by Virtue of Unic Subwords. - Matteo Comin; Davide Verzotto (DEXA Workshops, 2012)

Alignment-free phylogeny of whole genomes using underlying subwords. - Matteo Comin; Davide Verzotto (Algorithms Mol. Biol., 2012)

Reducing the Space of Degenerate Patterns in Protein Remote Homology Detection. - Matteo Comin; Davide Verzotto (DEXA Workshops, 2013)

Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes. - Matteo Comin; Morris Antonello (PRIB, 2013)

Efficient parallel construction of suffix trees for genomes larger than main memory. - Matteo Comin; Montse Farreras (EuroMPI, 2013)

Filtering Degenerate Patterns with Application to Protein Sequence Analysis. - Matteo Comin; Davide Verzotto (Algorithms, 2013)

Ultrametric networks: a new tool for phylogenetic analysis. - Alberto Apostolico; Matteo Comin; Andreas W. M. Dress; Laxmi Parida (Algorithms Mol. Biol., 2013)

QCluster: Extending Alignment-Free Measures with Quality Values for Reads Clustering. - Matteo Comin; Andrea Leoni; Michele Schimd (WABI, 2014)

Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns. - Matteo Comin; Michele Schimd (BMC Bioinform., 2014)

Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes. - Matteo Comin; Montse Farreras (J. Comput. Biol., 2014)

Fast Entropic Profiler: An InformationTheoretic Approach for the Discovery ofPatterns in Genomes. - Matteo Comin; Morris Antonello (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison. - Matteo Comin; Davide Verzotto (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles. - Matteo Comin; Morris Antonelli (BIOINFORMATICS, 2015)

Clustering of reads with alignment-free measures and quality values. - Matteo Comin; Andrea Leoni; Michele Schimd (Algorithms Mol. Biol., 2015)

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

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

On the comparison of regulatory sequences with multiple resolution Entropic Profiles. - Matteo Comin; Morris Antonello (BMC Bioinform., 2016)

Assembly-Free Techniques for NGS Data. - Matteo Comin; Michele Schimd (Algorithms for Next-Generation Sequencing Data, 2017)

SKraken: Fast and Sensitive Classification of Short Metagenomic Reads based on Filtering Uninformative k-mers. - Davide Marchiori; Matteo Comin (BIOINFORMATICS, 2017)

Fast and Sensitive Classification of Short Metagenomic Reads with SKraken. - Jia Qian; Davide Marchiori; Matteo Comin (BIOSTEC (Selected Papers), 2017)

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

Data-Driven Smart Bike-Sharing System by Implementing Machine Learning Algorithms. - Jia Qian; Matteo Comin; Livio Pianura (ES, 2018)

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

MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage. - Jia Qian; Matteo Comin (BMC Bioinform., 2019)

Better quality score compression through sequence-based quality smoothing. - Yoshihiro Shibuya; Matteo Comin (BMC Bioinform., 2019)

Indexing k-mers in linear space for quality value compression. - Yoshihiro Shibuya; Matteo Comin (J. Bioinform. Comput. Biol., 2019)

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

Improving Metagenomic Classification Using Discriminative k-mers from Sequencing Data. - Davide Storato; Matteo Comin (ISBRA, 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)

Boosting Metagenomic Classification with Reads Overlap Graphs. - Margherita Cavattoni; Matteo Comin (ISBRA, 2021)

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)

Special Issue of the 1st International Applied Bioinformatics Conference (iABC'21). - Jens Allmer; Mourad Elloumi; Matteo Comin; Ralf Hofestädt (J. Integr. Bioinform., 2021)

Fast alignment of reads to a variation graph with application to SNP detection. - Maurilio Monsu; Matteo Comin (J. Integr. Bioinform., 2021)

Efficient k-mer Indexing with Application to Mapping-free SNP Genotyping. - Mattia Marcolin; Francesco Andreace; Matteo Comin (BIOINFORMATICS, 2022)

SPRISS: approximating frequent k-mers by sampling reads, and applications. - Diego Santoro; Leonardo Pellegrina; Matteo Comin; Fabio Vandin (Bioinform., 2022)

K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification. - Davide Storato; Matteo Comin (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

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

USTAR: Improved Compression of k-mer Sets with Counters Using de Bruijn Graphs. - Enrico Rossignolo; Matteo Comin (ISBRA, 2023)

ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs. - Margherita Cavattoni; Matteo Comin (J. Comput. Biol., 2023)

USTAR2: Fast and Succinct Representation of k-mer Sets Using De Bruijn Graphs. - Enrico Rossignolo; Matteo Comin (BIOSTEC (1), 2024)

Enhanced Compression of k-Mer Sets with Counters via de Bruijn Graphs. - Enrico Rossignolo; Matteo Comin (J. Comput. Biol., 2024)

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)