Publications

Cinzia Pizzi co-authored more than 60 peer-reviewed publications, 30 of which in international journals. She is corresponding (or co-corresponding) author (^*) of more than 20 papers published in international journals as first/senior author. Moreover she has been corresponding author or co-corresponding author of nearly 30 book chapters (Springer Lecture Notes, LIPI, InTech) either as a first, equal or senior contributor.

International Journals

[30] Lorenzo Spina, Cinzia Pizzi^*
XAVAMB: Enhancing Autoencoders-based Metagenomic Binning
In preparation to submit to an international journal

[29] G.Faldani, E.Rossignolo, E.Signor, A.Longo, S.Faggion, L.Bargelloni\ , M. Comin, C.Pizzi ^*
Machine Learning Methods for Phenotype Prediction from High-dimensional, Low Population Aquaculture Data
Submitted to an international journal

[28] L. Gemin, C. Pizzi^*, M.Comin
DuoHash: fast hashing of spaced seeds with application to spaced k-\ mers counting
Submitted to an international Journal

[27] Francesco Tomasella, Cinzia Pizzi^*
MetaComBin: combining abundances and overlaps for binning metagenomics reads
Frontiers in Bioinformatics 2025 Mar 3;5:1504728. doi: 10.3389/fbinf.\ 2025.1504728.Open access

[26] Eleonora Mian, Enrico Petrucci, Cinzia Pizzi^*, Matteo Comin
MISSH: Fast Hashing of Multiple Spaced Seeds
IEEE/ACM Trans Comput Biol Bioinform. Nov.-Dec. 2024, pp. 2330-2339, vol. 21
DOI Bookmark: 10.1109/TCBB.2024.3467368 Online

[25] F.Andreace, C.Pizzi^*, M.Comin
MetaProb 2: Metagenomic Reads Binning based on Assembly using Minimizers and K-mers Statistics
Journal of Computational Biology, 28(11), 1052-1062, 2021
pdf

[24] M. Comin, B. Di Camillo, C. Pizzi, F. Vandin
Comparison of microbiome samples: methods and computational challenges
Briefings in Bioinformatics, Volume 22, Issue 1, January 2021,
https://doi.org/10.1093/bib/bbaa121
online

[23] L.Pellegrina, C.Pizzi, F.Vandin
Fast Approximation of Frequent k-mers and Applications to Metagenomics
Journal of Computational Biology, 27(4), 534-549, 2020
Online online
pdf

[22] E.Petrucci, L.Noe, C. Pizzi^*, M.Comin
Iterative Spaced Seed Hashing: Closing the Gap between Spaced Seed Hashing and k-mer Hashing
Journal of Computational Biology, 27(2), 2020 online
pdf

[21] S.Girotto, M.Comin, C.Pizzi^*
Efficient computation of spaced seed hashing with block indexing
BMC Bioinformatics, 19(15), 2018 open access

[20] S.Girotto, M.Comin, C.Pizzi^*
FSH: Fast Spaced Seed Hashing based on adjacent hashes
BMC Algorithms for Molecular Biology, 13(8), 2018 open access

[19] C.Pizzi^*, M.Ornamenti, S.Spangaro, S.E.Rombo, L.Parida
Efficient Algorithms for Sequence Analysis with Entropic Profiles
IEEE Transaction in Computational Biology and Bioinformatics, 15(1): 117-128, 2018 online

[18] S.Girotto, M.Comin, C.Pizzi^*
Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads
BMC Genomics,18(10):971, 6th December 2017 open access

[17] U. Ferraro-Petrillo, C.Guerra, C.Pizzi^*
A new distributed alignment-free approach to compare whole proteomes
Theoretical Computer Science, 698:100-112, 2017 online

[16] S.Girotto, M.Comin, C.Pizzi^*
Metagenomic reads binning with spaced seeds
Theoretical Computer Science, 698:88-99, 2017 online

[15] S.Girotto, C.Pizzi^*, M. Comin
MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures
Bioinformatics 2016 32 (17): i567-i575 online

[14] A.Apostolico, C.Guerra, G.M.Landau, C.Pizzi^*
Sequence Similarity Measures based on Bounded Hamming distance
Theoretical Computer Science, 638:76-90, 2016 online

[13] C.Pizzi^*
MissMax: alignment-free sequences comparison with mismatches through filtering and heuristics
Algorithms for Molecular Biology, 2016, 11:6 open access

[12] L.Parida, C.Pizzi, S.E.Rombo
Irredundant Tandem Motifs
Theoretical Computer Science, 525:89-102, 2014 online

[11] A.Apostolico, P.L.Erdos, E.Gyory, Z.Liptak, C.Pizzi^*
Efficient Algorithms for the Periodic Subgraphs Mining Problem
Journal of discrete algorithms, 17:24-30, 2012 online

[10] A.Apostolico, C.Pizzi^*, E.Ukkonen
Efficient Algorithms for the Discovery of Gapped Factors
Algorithms for Molecular Biology, 2011, 6:5 online

[9] A.Apostolico, M.Barbares, C.Pizzi^*
Speedup for a Periodic Subgraph Miner
Information Processing Letters, 111: 521-523, 2011 online

[8] C.Pizzi^*, P.Rastas, E.Ukkonen
Finding significant matches of position weight matrices in linear time
IEEE Transaction on Computational Biology and Bioinformatics, 8(1):69-79, 2011 online

[7] J.Korhonen, P.Martinmaki, C.Pizzi, P.Rastas, E.Ukkonen
MOODS: fast search for position weight matrix matches in DNA sequences
Bioinformatics 2009, 25(23):3181-3182; online

[6] C.Pizzi^*
k-difference matching in amortized linear time for all the words in a text
Theoretical Computer Science, 410(8-10): 983--987, 2009 online

[5] A.Apostolico, C.Pizzi^*
Scoring Unusual Words with Varying Mismatch Errors
Mathematics in Computer Science, Special Issue in Combinatorial Algorithms, 1(4):639-653, 2008 online

[4] C.Pizzi^*, E.Ukkonen
Fast Profile Matching Algorithms - a survey
Theoretical Computer Science, 395(2-3), 2008, pp 137--157, Special Issue SAIL: String Algorithms, Information and Learning online
(Note: Profile = Position Specific Scoring Matrices = Position Weight Matrices = Weighted Patterns)

[3] A.Apostolico, C.Pizzi^*
Motif Discovery by Monotone Scores
Discrete Applied Mathematics, vol. 155(6-7), 2007, pp. 695-706, special issue Computational Molecular Biology Series online

[2] C.Pizzi, S.Bortoluzzi, A.Bisognin, A.Coppe, G.A.Danieli
Detecting Seeded Motifs in DNA Sequences
Nucleic Acids Research, 33: e135, 2005 - Selected as Cover Paper open access

[1] S.Bortoluzzi, A.Coppe, A.Bisognin, C.Pizzi, G.A.Danieli
A Multistep Bioinformatic Approach Detects Putative Regulatory Elements in Gene Promoters
BMC Bioinformatics 2005, 6:121 (18 May 2005) open access

Book Chapter

[1] C.Pizzi^*
Motif discovery with compact approaches - design and applications.
In: Ning-Sun Yang (ED). Systems and Computational Biology - Molecular and Cellular Experimental Systems. p. 217-234, Intech 2011 online

International Conferences

[28] Giorgio Gallina, Cinzia Pizzi^*
On kmer-based dissimilarity measures for metagenome samples comparison
Accepted at CIBB2025

[27] Lorenzo Spina, Cinzia Pizzi^*
XAVAMB: Enhancing Autoencoders-based Metagenomic Bi\ nning
Accepted at CIBB2025

[26] I Bušelić Garber, A Longo, S Faggion, R Mukiibi, M Comin, C Pizzi, Enrico Rossignolo, Eleonora Signor, Giovanni Faldani, Massimiliano Babbucci, Paolo Carnier, Diego Robledo, Luca Bargelloni Integration of functional annotation data into genomic prediction models for VNN resistance in European sea bass using bayesian and machine learning approaches
Aquaculture Europe 2025 Book of abstracts, 255-256

[25] G.Faldani, E.Rossignolo, E.Signor, A.Longo, S.Faggion, L.Bargelloni, M. Comin, C.Pizzi^*
Machine Learning Methods for Phenotype Prediction from High-dimensional, Low Population Aquaculture Data
Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2025) - Volume 1, pages 638-646. Online

[24] L. Gemin, C. Pizzi^*, M.Comin
DuoHash: fast hashing of spaced seeds with application to spaced k-mers counting
Proceedings Computational Advances in Bio and Medical Sciences: 13th International Conference, ICCABS 2025, Atlanta, GA, USA, January 12–14, 2025, Revised Selected Papers, Pages 28 - 39 online

[23] F.Tomasella, C.Pizzi^*
On Multi-Phase Metagenomics Reads Binning
In proceedings of Computational Advances in Bio and Medical Sciences. ICCABS 2023. Lecture Notes in Computer Science, vol 14548. Springer Online

[22] E. Mian, E. Petrucci, C. Pizzi^*, M. Comin
Efficient Hashing of Multiple Spaced Seeds with Application
Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2023)-Volume 3: BIOINFORMATICS, 2023

[21]C.Pizzi^*
Efficient counting of k-mers and spaced-seeds to speed-up alignment-free methods
Abstract for the invited talk at CiE special session on Combinatiorial String Matching, in "Beyond the Horizon of Computability" - 16th Conference on Computability in Europe, CiE 2020, June 29-July 3, 2020, Proceedings, LNCS/LNTCS, volume 12098.

[20] F.Andreace, C.Pizzi^*, M.Comin
MetaProb 2: Improving Unsupervised Metagenomic Binning with Efficient Reads Assembly using Minimizers
2020 10th International Conference on Computational Advances in Bio and medical Sciences (ICCABS 2020) Dec. 10-12, 2020. Lecture Notes in Computer Science, vol 12686, pages 15-25. Springer, Cham. online

[19] E.Petrucci, L.Noe, C.Pizzi^*, M.Comin
Iterative spaced seed hashing: Closing the gap between spacedseed hashing and k-mer hashing
15th International Symposium on Bioinformatics Research and Applications - ISBRA 2019, Barcelona 3-6 June 2019

[18] L.Pellegrina, C.Pizzi, F.Vandin
Fast Approximation of Frequent k-mers and Applications to Metagenomics
International Conference on Research in Computational Molecular Biology RECOMB 2019,LNCS, volume 11467, pp 208-226 online

[17] S.Girotto, M.Comin, C.Pizzi^*
Fast Spaced Seed Hashing
17th Workshop on Algorithms in Bioinformatics - WABI 2017 online - open access

[16] 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 online

[15] F.Carbone, A.Cenedese, C.Pizzi^*
Consensus-based Anomaly Detection for Efficient Heating Management
IEEE International Conference on Smart City Innovations (IEEE SCI 2017), San Francisco (CA), USA, August 4-8 2017 online

[14] 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. online

[13] 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 - ICCABS 2016, Atlanta 13-15 Oct. 2016. online Invited for a journal special issue

[12] C.Pizzi^*
A filtering approach for alignment-free biosequences comparison with mismatches
In proceedings of WABI 2015, LNCS 9289, pp 231-242. online

[11] L.Parida, C.Pizzi^*, S.E.Rombo
Entropic profiles, maximal motifs and the discovery of significant repetitions in genomic sequences
In proceedings of WABI 2014, LNCS 8701, pp 148-160 online

[10] A.Apostolico, C.Guerra, C.Pizzi^*
Alignment Free Sequence Similarity with Bounded Hamming Distance
In Proc. of Data Compression Conference (DCC 2014), Snowbird, UT, USA, March 2014, pp 183-192, IEEE 2014, ISBN 978-1-4799-3882-7 online

[9] L.Parida, C.Pizzi^*, S.E.Rombo
Characterization and Extraction of Irredundant Tandem Motifs
In Proc. of 19th Symposium on String Processing and Information Retrieval (SPIRE 2012), Cartagena de Indias, Colombia, Oct 2012, LNCS 7608 pp 385--397. online

[8] C.Pizzi^* and A.Favaretto
Efficient Search of Position Weight Matrices with a Truncated Suffix Tree
3rd International Conference on Bioinformatics and Biomedical Technology, 2011

[7] C.Pizzi^*
Efficient Computation of Statistics for Words with Mismatches
In Structure Discovery in Biology: Motifs, Networks and Phylogenies, Dagsthul Seminar Proceedings, 2010 online

[6] C.Pizzi^*, M.Bianco
Expectation of Strings with Mismatches Under Markov Chain Distribution
In Proc. of 16th Symposium on String Processing and Information Retrieval (SPIRE 2009), Saariselka, Finland, Aug 2009, LNCS 5721 pp 222--233. online

[5] C.Pizzi^*, E.Ukkonen
Efficient Discovery of Significant Co-occurrences with an Application to Dyad Motif Finding(abstract)
In Proc. of the 4th Annual RECOMB Satellite on Regulatory Genomics, BROAD Institute Cambridge(MA), USA , Oct 2007

[4] C.Pizzi^*, P.Rastas, E.Ukkonen
Fast Search Algorithms for Position Specific Scoring Matrices
In Proc. of the 1st Conference on Bioinformatics Research and Development (BIRD 07), Berlin, Germany, March 2007, LNCS/LCBI 4414 pp 239--250. online

[3] A.Apostolico, C.Pizzi^*
On the Monotonicity of the String Correction Factor for Words with Mismatches
In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery, Dagsthul Seminar Proceedings, 2006 online

[2] A.Apostolico, C.Pizzi^*
Monotone Scoring of Pattern with Mismatches
In Proc. of the 4th Workshop on Algorithms in Bioinformatics (WABI 2004), Bergen, Norway, Sept 2004, LNCS/LCBI 3240 pp 87--98. online

[1] A.Apostolico, C.Pizzi^*, G.Satta
Optimal Discovery of Subword Associations in Strings
In Proc. of the 7th International Conference on Dicovery Science (DS 2004), Padova, Italy, Oct 2004, LNCS 3245 pp 270--277. online

Other Manuscripts:

[1] C.Pizzi, Conservative Approaches to the Discovery of Patterns in Biosequences, PhD Thesis, 2004

[2] C.Pizzi, Architettura e Funzionalita' di un Web Search Agent, Laurea Thesis, 2001

[3] C.Pizzi, Ontologies for Bioinformatics, 2002

[4] C.Pizzi, Cluster Analysis, 2002

[5] C.Pizzi, M.Falda, Le Reti Bayesiane, 2003

[6] C.Pizzi, HMM and their Applications to Bioinformatics, 2004

Research Publications ABCLab Software Teaching Contacts