Pubblications



Journal Papers

S. Girotto, C. Pizzi, M. Comin
"Metagenomic reads binning with spaced seeds"
To appear in Theoretical Computer Science 2017. Pdf

M.Comin, M. Schimd
"Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values"
BMC Medical Genomics 2016, 9(Suppl 1):36 Open Access
(impact factor 2.72)

M. Comin, M. Antonello
"On the comparison of regulatory sequences with multiple resolution Entropic Profiles"
BMC Bioinformatics 2016, 17:130 Pdf
(impact factor 2.58)

M. Comin, A. Leoni, M. Schimd
"Clustering of reads with alignment-free measures and quality values",
In BMC Algorithms for Molecular Biology 2015, 10:4 Pdf
(impact factor 1.61)

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, 2014, Vol. 11, No. 3, pp. 500-509 Pdf
(impact factor 1.7)

M. Comin, M. Farreras
"Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes"
Journal of Computational Biology 2014, Vol. 21, No. 4, pp. 330-344. Pdf
(impact factor 1.67)

M. Comin, D. Verzotto,
"Filtering Degenerate Motifs with Application to Protein Sequence Analysis",
Algorithms 2013, Vol. 6, No. 2, pp. 352-370. Pdf

A. Apostolico, M. Comin, A. Dress, L. Parida,
"Ultrametric Networks: A New Tool For Phylogenetic Analysis",
In BMC Algorithms for Molecular Biology 2013, 8:7 Pdf
(impact factor 1.61)

M. Comin, D. Verzotto,
"Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords",
In BMC Algorithms for Molecular Biology 2012, 7:34. Pdf
(impact factor 1.61)

M. Comin, D. Verzotto,
"The Irredundant Class Method for Remote Homology Detection of Protein Sequences",
Journal of Computational Biology. December 2011, Vol. 18, No.12, pp. 1819-1829. doi Pdf
(2011 impact factor 1.86)

A. Apostolico, M. Comin, L. Parida,
"VARUN: Discovering Extensible Motifs under Saturation Constraints"
IEEE/ACM Transactions on Computational Biology and Bioinformatics, October-December 2010, Vol. 7, No. 4, pp. 752-762. Pdf
(2010 impact factor 2.1)

M. Comin, F. Dellaert, C. Guerra,
"Binding Balls: Fast detection of Binding Sites using a property of Spherical Fourier Transform"
Journal of Computational Biology 2009, Vol. 16 No. 11, pp. 1577-1591. Pdf
(2009 impact factor 1.7)

M. Comin, C. Guerra, G. Zanotti,
"Mining Over-Represented 3DPatterns of Secondary Structures in Proteins"
Journal of Bioinformatics and Computational Biology 2008, Vol. 6, No. 06, pp. 1067 - 1087. Pdf Supplemental Material
(2008 impact factor 1.3)

G. Ciriello, M. Comin, C. Guerra,
"Algorithmic Re-Structuring and Data Replication for Protein Structure Comparison on a GRID"
Future Generation Computer System 2006, Special Issue on Life Science Grids for Biomedicine and Bioinformatics, Vol. 23, pp. 391-397. Pdf
(impact factor 1.86)

A. Apostolico, M. Comin and L. Parida,
"Mining, compressing and classifying with extensible motifs"
Algorithms for Molecular Biology 2006, 1:4. Pdf doi pmid
(impact factor 1.61)

A. Apostolico, M. Comin, L. Parida,
"Bridging lossy and lossless compression by motif pattern discovery", (extended abstract)
Electronic Notes in Discrete Mathematics, Volume 21, 1 August 2005, pp. 219-225 Pdf

M. Comin, C. Guerra and G. Zanotti,
"PROuST: a comparison method of three-dimensional structures of proteins using indexing techniques"
in Journal of Computational Biology 2004, Vol. 11, No. 6, pp 1061-1072. Pdf doi pmid
(2004 impact factor 3.78)

M. Comin, C. Ferrari, C. Guerra,
"Grid deployment of bioinformatics applications: a case study in protein similarity determination"
in Parallel Processing Letters 2004, World Scientific Publishing Company, Vol. 14 No. 2, pp 163-176. Pdf

Book chapters and invited contributions

M. Comin, D. Verzotto,
"Alignment-Free Measures for Whole-Genome Comparison",
in ``Pattern Recognition in Computational Molecular Biology: Techniques and Approaches'',
Edited by M. Elloumi, C. S. Iliopoulos, J.T.L. Wang and A.Y. Zomaya
Wiley, 2014.

M. Comin, D. Verzotto,
"Comparing ranking and filtering motifs with character classes: application to biological sequence analysis",
in ``Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data'',
Edited by M. Elloumi and A. Y. Zomaya
Wiley, 2013/14.

M. Comin, C. Guerra,
"Protein Structure Comparison, High Performance Computing",
in ``Encyclopedia of System Biology''
Edited by W. Dubitzky, O. Wolkenhauer, K.H. Cho and H. Yokota. Springer, 2013.

M. Comin, D. Verzotto,
"Remote Homology Detection of Protein Sequences",
in Dagstuhl Proceedings 10231 "Structure Discovery in Biology: Motifs, Networks and Phylogenies", 2010: 2741.

M. Comin, C. Guerra, G. Zanotti,
"Invariant geometric properties of secondary structure elements in proteins",
in ``Biological Data Mining'', Chapter 2, pp. 27-49.
Edited by J. Chen and S. Lonardi,
Chapman & Hall/CRC, 2009.

M. Comin, L. Parida,
"Detection of Subtle Variations as Consensus Motifs"
in "SAIL: String Algorithms, Information and Learning" edited by R. Giancarlo and S. Lonardi
Special Issue of Theoretical Computer Science, Vol. 395 No. 2-3, pp. 158-170, 2008. doi Pdf

A. Apostolico, M. Comin, L. Parida,
"Bridging Lossy and Lossless Compression by Motif Pattern Discovery"
General Theory of Information Transfer and Combinatorics, Lecture Notes in Computer Science, Vol. 4123, pp. 793-813, 2006. Pdf

M. Cannataro, M. Comin, C. Ferrari, C. Guerra, A. Guzzo, and P. Veltri,
"Modelling a Protein Structure Comparison Application on the Grid using PROTEUS"
SAG 2004, Lecture Notes in Computer Science Vol. 3458, pp: 75-85, 2005. Pdf

Conference Paper

S. Girotto, C. Pizzi, M. Comin
"Fast Spaced Seed Hashing"
Accepted at the 17th The Workshop on Algorithms in Bioinformatics (WABI) 2017.

S. Girotto, C. Pizzi, M. Comin
"Binning metagenomic reads with probabilistic sequence signatures based on spaced seeds"
Accepted at the IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2017).

D. Marchiori, M. Comin
"SKraken: Fast and Sensitive Classification of Short Metagenomic Reads based on Filtering Uninformative k-mers".
In Proceedings of the 10th International Conference on Bioinformatics Models, Methods and Algorithms (Bioinformatics 2017), pp. 59-67. Pdf

S. Girotto, C. Pizzi, M. Comin
"MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures"
In Proceedings of 15th European Conference on Computational Biology 2016
Bioinformatics (2016) 32 (17): i567-i575. Pdf
(impact factor 5.76)

S. Girotto, M. Comin, C. Pizzi
"Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads"
In Proceedings of the IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) 2016 Pdf

M. Comin, M. Antonello
"Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles".
In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (Bioinformatics 2015), pp. 171-177. Pdf

M.Comin, A. Leoni, M. Schimd
"QCluster: Extending Alignment-free Measures with Quality Values for Reads Clustering",
Proceedings of the 14th Workshop on Algorithms in Bioinformatics (WABI) 2014.
Lecture Notes in BIoinformatics (LNBI) 2014, 8701, pp. 1-13.

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 2014, Vol. 15, No. 9, S1. Open Access (impact factor 2.67)

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, 2014, Vol. 11, No. 4, pp. 628-637 Pdf
(impact factor 1.7)

M.Comin, M. Farreras,
"Efficient Parallel Construction of Suffix Trees for Genomes Larger than Main Memory''
Proceedings of the 20th European MPI 2013, pp. 211-216. Pdf

M.Comin, D. Verzotto,
"Reducing the space of degenerate patterns in protein remote homology detection"
Proceedings of 24rd International Workshop on Database and Expert Systems Applications, BIOKDD 2013
pp.76-80. Pdf

M. Antonello, M. Comin,
"Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes",
Proceedings of Pattern Recognition in Bioinformatics 2013,
Lecture Notes in BIoinformatics (LNBI) 2013, 7986, pp. 277--288. Pdf
(accepted 39%)

M.Comin, D. Verzotto,
"Whole-Genome Phylogeny by Virtue of Unic Subwords"
Proceedings of 23rd International Workshop on Database and Expert Systems Applications, BIOKDD 2012.
pp. 190-194. IEEE Explore Pdf

M.Comin, D. Verzotto,
"Classification of Protein Sequences by means of Irredundant Patterns"
Proceedings of Asia-Pacific Bioinformatics Conference, 2010.
BMC Bioinformatics 2010, 11(Suppl 1):S16. Open Access
(accepted 28%, impact factor 3.02)

M. Comin, C. Guerra and G. Zanotti,
"Mining Over-Represented 3D Patterns of Secondary Structures in Proteins"
Proceedings of 7th International Workshop on Data Mining in Bioinformatics (BIOKDD '07). Pdf
(accepted 25%)

M. Comin, L. Parida,
"Subtle motif discovery for the detection of DNA regulatory sites"
Series on Advances in Bioinformatics and Computational Biology,
Proceedings of Asia Pacific Bioinformatics Conference (APBC2007), vol 5, Hong Kong, pp. 27-36 Pdf
(accepted 17%)

G.Ciriello, M.Comin, C.Guerra,
"Application Re-Structuring and Data Management on a GRID Environment: a Case Study for Bioinformatics"
Proceedings of IEEE International Workshop on High Performance Computational Biology, 2006:9. Pdf doi

G. Ciriello and M. Comin,
"High-Performance Protein Structure Comparison", (abstract)
In Proceedings of RECOMB 2006.

A. Apostolico, M. Comin, L. Parida,
"Conservative Extraction of Over-represented Extensible Motifs"
Proceeding of the 13th Annual International conference on Intelligent Systems for Molecular Biology (ISMB 2005)
Supplement of Bioinformatics 2005: pp. 9-18. Pdf doi pmid
(accepted 13%, impact factor 6.02)

A. Apostolico, M. Comin, L. Parida,
"Off-line Compression by Extensible Motifs"
Proceedings of IEEE DCC Data Compression Conference, Computer Society Press, pp. 450, (2005). doi

A. Apostolico, M. Comin, L. Parida,
"Motifs in Ziv-Lempel-Welch Clef"
Proceedings of IEEE DCC Data Compression Conference, Computer Society Press, pp. 72-81, (2004). Pdf doi
(accepted 20%)

Patents

Inventor of the following IBM patents :
- "Method and structure for lossy compression of continuous data with extensible motifs",
US Patent 7259701, 2007.
- "Methods and systems for conservative extraction of over-represented extensible motifs",
US Patent 7865313, 2011.
- "Method and apparatus for detection consensus motifs in data sequences",
United States Patent Application 20080167850, filed.



Thus my Erdos Number is : 3



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