Matteo Comin

Orcid: 0000-0001-8545-4359

According to our database1, Matteo Comin authored at least 62 papers between 2004 and 2024.

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Bibliography

2024
Enhanced Compression of <i>k</i>-Mer Sets with Counters via de Bruijn Graphs.
J. Comput. Biol., 2024

USTAR2: Fast and Succinct Representation of k-mer Sets Using De Bruijn Graphs.
Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies, 2024

2023
ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs.
J. Comput. Biol., May, 2023

USTAR: Improved Compression of k-mer Sets with Counters Using de Bruijn Graphs.
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

Efficient Hashing of Multiple Spaced Seeds with Application.
Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies, 2023

2022
K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

SPRISS: approximating frequent <i>k</i>-mers by sampling reads, and applications.
Bioinform., 2022

Efficient k-mer Indexing with Application to Mapping-free SNP Genotyping.
Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies, 2022

2021
Fast alignment of reads to a variation graph with application to SNP detection.
J. Integr. Bioinform., 2021

Special Issue of the 1st International Applied Bioinformatics Conference (iABC'21).
J. Integr. Bioinform., 2021

MetaProb 2: Metagenomic Reads Binning Based on Assembly Using Minimizers and K-Mers Statistics.
J. Comput. Biol., 2021

Comparison of microbiome samples: methods and computational challenges.
Briefings Bioinform., 2021

Boosting Metagenomic Classification with Reads Overlap Graphs.
Proceedings of the Bioinformatics Research and Applications - 17th International Symposium, 2021

2020
Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing.
J. Comput. Biol., 2020

Improving Metagenomic Classification Using Discriminative k-mers from Sequencing Data.
Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

MetaProb 2: Improving Unsupervised Metagenomic Binning with Efficient Reads Assembly Using Minimizers.
Proceedings of the Computational Advances in Bio and Medical Sciences, 2020

2019
Indexing k-mers in linear space for quality value compression.
J. Bioinform. Comput. Biol., 2019

Better quality score compression through sequence-based quality smoothing.
BMC Bioinform., 2019

MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage.
BMC Bioinform., 2019

2018
FSH: fast spaced seed hashing exploiting adjacent hashes.
Algorithms Mol. Biol., 2018

Data-Driven Smart Bike-Sharing System by Implementing Machine Learning Algorithms.
Proceedings of the Sixth International Conference on Enterprise Systems, 2018

2017
Metagenomic reads binning with spaced seeds.
Theor. Comput. Sci., 2017

Fast Spaced Seed Hashing.
Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Binning metagenomic reads with probabilistic sequence signatures based on spaced seeds.
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2017

Fast and Sensitive Classification of Short Metagenomic Reads with SKraken.
Proceedings of the Biomedical Engineering Systems and Technologies, 2017

SKraken: Fast and Sensitive Classification of Short Metagenomic Reads based on Filtering Uninformative k-mers.
Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017), 2017

Assembly-Free Techniques for NGS Data.
Proceedings of the Algorithms for Next-Generation Sequencing Data, Techniques, 2017

2016
On the comparison of regulatory sequences with multiple resolution Entropic Profiles.
BMC Bioinform., 2016

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures.
Bioinform., 2016

Higher recall in metagenomic sequence classification exploiting Overlapping Reads.
Proceedings of the 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2016

2015
Clustering of reads with alignment-free measures and quality values.
Algorithms Mol. Biol., 2015

Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles.
Proceedings of the BIOINFORMATICS 2015, 2015

2014
Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Fast Entropic Profiler: An InformationTheoretic Approach for the Discovery ofPatterns in Genomes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes.
J. Comput. Biol., 2014

Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.
BMC Bioinform., 2014

QCluster: Extending Alignment-Free Measures with Quality Values for Reads Clustering.
Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

2013
Ultrametric networks: a new tool for phylogenetic analysis.
Algorithms Mol. Biol., 2013

Filtering Degenerate Patterns with Application to Protein Sequence Analysis.
Algorithms, 2013

Efficient parallel construction of suffix trees for genomes larger than main memory.
Proceedings of the 20th European MPI Users's Group Meeting, 2013

Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes.
Proceedings of the Pattern Recognition in Bioinformatics, 2013

Reducing the Space of Degenerate Patterns in Protein Remote Homology Detection.
Proceedings of the 24th International Workshop on Database and Expert Systems Applications, 2013

2012
Alignment-free phylogeny of whole genomes using underlying subwords.
Algorithms Mol. Biol., 2012

Whole-Genome Phylogeny by Virtue of Unic Subwords.
Proceedings of the 23rd International Workshop on Database and Expert Systems Applications, 2012

2011
The Irredundant Class Method for Remote Homology Detection of Protein Sequences.
J. Comput. Biol., 2011

2010
VARUN: Discovering Extensible Motifs under Saturation Constraints.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Classification of protein sequences by means of irredundant patterns.
BMC Bioinform., 2010

Remote Homology Detection of Protein Sequences.
Proceedings of the Structure Discovery in Biology: Motifs, Networks & Phylogenies, 06.06., 2010

2009
Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform.
J. Comput. Biol., 2009

2008
Detection of subtle variations as consensus motifs.
Theor. Comput. Sci., 2008

Mining Overrepresented 3D Patterns of Secondary Structures in proteins.
J. Bioinform. Comput. Biol., 2008

2007
Algorithmic re-structuring and data replication for protein structure comparison on a GRID.
Future Gener. Comput. Syst., 2007

Subtle Motif Discovery for Detection of DNA Regulatory Sites.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006
Mining, compressing and classifying with extensible motifs.
Algorithms Mol. Biol., 2006

Application re-structuring and data management on a grid environment: a case study for bioinformatics.
Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

2005
Bridging Lossy and Lossless Compression by Motif Pattern Discovery.
Electron. Notes Discret. Math., 2005

Conservative extraction of over-represented extensible motifs.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Off-Line Compression by Extensible Motifs.
Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

2004
Grid Deployment Of Bioinformatics Applications: A Case Study In Protein Similarity Determination.
Parallel Process. Lett., 2004

PROuST: A Comparison Method of Three-Dimensional Structures of Proteins Using Indexing Techniques.
J. Comput. Biol., 2004

Modelling a Protein Structure Comparison Application on the Grid Using PROTEUS.
Proceedings of the Scientific Applications of Grid Computing, First International Workshop, 2004

Motifs in Ziv-Lempel-Welch Clef.
Proceedings of the 2004 Data Compression Conference (DCC 2004), 2004


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