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Scopus Author ID: 55338424700
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Systematic analysis of SARS-CoV-2 Omicron subvariants’ impact on B and T cell epitopes

PLOS ONE
2024-09-19 | Journal article
DOI: 10.1371/journal.pone.0307873
Contributors: Ruba Al Khalaf; Nagarajan Raju; Anna Bernasconi; Pietro Pinoli
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Non-Negative Matrix Tri-Factorization for Representation Learning in Multi-Omics Datasets with Applications to Drug Repurposing and Selection

International Journal of Molecular Sciences
2024-09-04 | Journal article
DOI: 10.3390/ijms25179576
Contributors: Letizia Messa; Carolina Testa; Stephana Carelli; Federica Rey; Emanuela Jacchetti; Cristina Cereda; Manuela Teresa Raimondi; Stefano Ceri; Pietro Pinoli
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Exploring Federated Learning for Emotion Recognition on Brain-Computer Interfaces

2024-06-27 | Conference paper
DOI: 10.1145/3631700.3665194
Contributors: Sofia Mongardi; Pietro Pinoli
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The molecular basis of the anticancer effect of statins

2024-02-08 | Preprint
DOI: 10.1101/2024.02.05.578869
Contributors: Giovanni Buccioli; Carolina Testa; Emanuela Jacchetti; Pietro Pinoli; Stephana Carelli; Stefano Ceri; Manuela T. Raimondi
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Ask Your Data—Supporting Data Science Processes by Combining AutoML and Conversational Interfaces

IEEE Access
2023 | Journal article
DOI: 10.1109/ACCESS.2023.3272503
Contributors: Sara Pidó; Pietro Pinoli; Pietro Crovari; Francesca Ieva; Franca Garzotto; Stefano Ceri
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Leveraging Non-negative Matrix Tri-Factorization and Knowledge-Based Embeddings for Drug Repurposing: an Application to Parkinson's Disease

2023-11-09 | Conference paper
DOI: 10.1145/3637732.3637783
Contributors: Letizia Messa; Carolina Testa; Stephana Carelli; Federica Rey; Cristina Cereda; Manuela Teresa Raimondi; Stefano Ceri; Pietro Pinoli
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VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants

Database
2023-07-06 | Journal article
DOI: 10.1093/database/baad044
Contributors: Pietro Pinoli; Arif Canakoglu; Stefano Ceri; Matteo Chiara; Erika Ferrandi; Luca Minotti; Anna Bernasconi
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Inference of Synthetically Lethal Pairs of Genes Involved in Metastatic Processes via Non-Negative Matrix Tri-Factorization

2023-05-26 | Conference paper
DOI: 10.1145/3608164.3608171
Contributors: Carolina Testa; Sara Pidò; Emanuela Jacchetti; Manuela Teresa Raimondi; Stefano Ceri; Pietro Pinoli
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SARS-CoV-2 viremia and COVID-19 mortality: A prospective observational study

PLOS ONE
2023-04-28 | Journal article
DOI: 10.1371/journal.pone.0281052
Contributors: Andrea Giacomelli; Mohammad-Reza Malekpour; Elena Righini; Valeria Micheli; Pietro Pinoli; Anna Bernasconi; Alberto Rizzo; Letizia Oreni; Anna Lisa Ridolfo; Spinello Antinori et al.
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A Non-Negative Matrix Tri-Factorization Based Method for Predicting Antitumor Drug Sensitivity

2022 | Book chapter
DOI: 10.1007/978-3-031-20837-9_8
Contributors: Carolina Testa; Sara Pidò; Pietro Pinoli
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Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2

Computational and Structural Biotechnology Journal
2022 | Journal article
DOI: 10.1016/j.csbj.2022.07.051
Contributors: Ruba Al Khalaf; Anna Bernasconi; Pietro Pinoli; Stefano Ceri
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Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2022-07-01 | Journal article
DOI: 10.1109/TCBB.2021.3091814
Contributors: Pietro Pinoli; Gaia Ceddia; Stefano Ceri; Marco Masseroli
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ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time

Bioinformatics
2022-03-28 | Journal article
DOI: 10.1093/bioinformatics/btac030
Contributors: Luca Cilibrasi; Pietro Pinoli; Anna Bernasconi; Arif Canakoglu; Matteo Chiara; Stefano Ceri; Jonathan Wren
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High Performance Integration Pipeline for Viral and Epitope Sequences

BioTech
2022-03-21 | Journal article
DOI: 10.3390/biotech11010007
Contributors: Tommaso Alfonsi; Pietro Pinoli; Arif Canakoglu
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Investigating Deep Learning Based Breast Cancer Subtyping Using Pan-Cancer and Multi-Omic Data

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2022-01-01 | Journal article
DOI: 10.1109/TCBB.2020.3042309
Contributors: Francisco Cristovao; Silvia Cascianelli; Arif Canakoglu; Mark Carman; Luca Nanni; Pietro Pinoli; Marco Masseroli
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VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis

BioTech
2021-11-06 | Journal article
DOI: 10.3390/biotech10040027
Contributors: Pietro Pinoli; Anna Bernasconi; Anna Sandionigi; Stefano Ceri
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EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species

Database
2021-09-29 | Journal article
DOI: 10.1093/database/baab059
Contributors: Anna Bernasconi; Luca Cilibrasi; Ruba Al Khalaf; Tommaso Alfonsi; Stefano Ceri; Pietro Pinoli; Arif Canakoglu
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VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants

Nucleic Acids Research
2021-09-07 | Journal article
DOI: 10.1093/nar/gkab478
Contributors: Anna Bernasconi; Andrea Gulino; Tommaso Alfonsi; Arif Canakoglu; Pietro Pinoli; Anna Sandionigi; Stefano Ceri
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ViruSurf: an integrated database to investigate viral sequences

Nucleic Acids Research
2021-01-08 | Journal article
DOI: 10.1093/nar/gkaa846
Contributors: Arif Canakoglu; Pietro Pinoli; Anna Bernasconi; Tommaso Alfonsi; Damianos P Melidis; Stefano Ceri
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Empowering Virus Sequence Research Through Conceptual Modeling

2020 | Book chapter
DOI: 10.1007/978-3-030-62522-1_29
Contributors: Anna Bernasconi; Arif Canakoglu; Pietro Pinoli; Stefano Ceri
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Impact of mutational signatures on microRNA and their response elements

Pacific Symposium on Biocomputing
2020 | Journal article
EID:

2-s2.0-85075985466

Part of ISBN:

23356936 23356928
Contributors: Stamoulakatou, E.; Pinoli, P.; Ceri, S.; Piro, R.M.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

NAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information

Biology Direct
2020-12 | Journal article
DOI: 10.1186/s13062-020-00268-1
Contributors: Stefano Perna; Pietro Pinoli; Stefano Ceri; Limsoon Wong
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ViruSurf: an integrated database to investigate viral sequences

2020-08-11 | Preprint
DOI: 10.1101/2020.08.10.244624
Contributors: Arif Canakoglu; Pietro Pinoli; Anna Bernasconi; Tommaso Alfonsi; Damianos P. Melidis; Stefano Ceri
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Empowering Virus Sequences Research through Conceptual Modeling

2020-04-30 | Preprint
DOI: 10.1101/2020.04.29.067637
Contributors: Anna Bernasconi; Arif Canakoglu; Pietro Pinoli; Stefano Ceri
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Crossref

Data Science for Genomic Data Management: Challenges, Resources, Experiences

SN Computer Science
2020-01 | Journal article
DOI: 10.1007/s42979-019-0005-0
Contributors: Stefano Ceri; Pietro Pinoli
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Crossref

Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries

PLOS ONE
2020-01-16 | Journal article
DOI: 10.1371/journal.pone.0227180
Contributors: Pietro Pinoli; Miltiadis Paliouras; Eirini Stamoulakatou; An-Phi Nguyen; María Rodríguez Martínez; Stefano Ceri
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Analysis and Visualization of Mutation Enrichments for Selected Genomic Regions and Cancer Types

Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019
2019 | Conference paper
DOI: 10.1109/BIBM47256.2019.8983196
EID:

2-s2.0-85084341732
Contributors: Gulino, A.; Stamoulakatou, E.; Canakoglu, A.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Deleterious impact of mutational processes on transcription factor binding sites in human cancer

Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019
2019 | Conference paper
DOI: 10.1109/BIBE.2019.00041
EID:

2-s2.0-85078576558
Contributors: Pinoli, P.; Stamoulakatou, E.; Ceri, S.; Piro, R.M.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

DLA: A Distributed, Location-based and Apriori-based Algorithm for Biological Sequence Pattern Mining

Proceedings - 2018 IEEE International Conference on Big Data, Big Data 2018
2019 | Conference paper
DOI: 10.1109/BigData.2018.8622007
EID:

2-s2.0-85062594468
Contributors: Stamoulakatou, E.; Gulino, A.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Drug repositioning predictions by non-negative matrix tri-factorization of integrated association data

ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics
2019 | Conference paper
DOI: 10.1145/3307339.3342154
EID:

2-s2.0-85073157601
Contributors: Dissez, G.; Ceddia, G.; Pinoli, P.; Ceri, S.; Masseroli, M.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Non-negative Matrix Tri-Factorization for Data Integration and Network-based Drug Repositioning

2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2019
2019 | Conference paper
DOI: 10.1109/CIBCB.2019.8791474
EID:

2-s2.0-85071467576
Contributors: Ceddia, G.; Pinoli, P.; Ceri, S.; Masseroli, M.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Processing of big heterogeneous genomic datasets for tertiary analysis of Next Generation Sequencing data

Bioinformatics
2019 | Journal article
DOI: 10.1093/bioinformatics/bty688
EID:

2-s2.0-85062286334

Part of ISBN:

14602059 13674803
Contributors: Masseroli, M.; Canakoglu, A.; Pinoli, P.; Kaitoua, A.; Gulino, A.; Horlova, O.; Nanni, L.; Bernasconi, A.; Perna, S.; Stamoulakatou, E. et al.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets

BMC Bioinformatics
2019 | Journal article
DOI: 10.1186/s12859-019-3159-9
EID:

2-s2.0-85074686066

Part of ISBN:

14712105
Contributors: Nanni, L.; Pinoli, P.; Canakoglu, A.; Ceri, S.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Metadata management for scientific databases

Information Systems
2019-03 | Journal article
DOI: 10.1016/j.is.2018.10.002
Contributors: Pietro Pinoli; Stefano Ceri; Davide Martinenghi; Luca Nanni
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Demonstration of genometric query language

International Conference on Information and Knowledge Management, Proceedings
2018 | Conference paper
DOI: 10.1145/3269206.3269217
EID:

2-s2.0-85058025073
Contributors: Ceri, S.; Canakoglu, A.; Gulino, A.; Kaitoua, A.; Masseroli, M.; Nanni, L.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Experiences in the development of a data management system for genomics

Communications in Computer and Information Science
2018 | Book
DOI: 10.1007/978-3-319-94809-6_10
EID:

2-s2.0-85049673999

Part of ISBN:

18650929
Contributors: Ceri, S.; Canakoglu, A.; Kaitoua, A.; Masseroli, M.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Exploring genomic datasets: From batch to interactive and back

Proceedings of the ACM SIGMOD International Conference on Management of Data
2018 | Conference paper
DOI: 10.1145/3214708.3214710
EID:

2-s2.0-85065130988

Part of ISBN:

07308078
Contributors: Nanni, L.; Pinoli, P.; Canakoglu, A.; Ceri, S.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Implementing a transcription factor interaction prediction system using the genometric query language

Methods in Molecular Biology
2018 | Book chapter
DOI: 10.1007/978-1-4939-8561-6_6
EID:

2-s2.0-85051189882

Part of ISBN:

10643745
Contributors: Perna, S.; Canakoglu, A.; Pinoli, P.; Ceri, S.; Wong, L.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Overview of GeCo: A project for exploring and integrating signals from the genome

Communications in Computer and Information Science
2018 | Book
DOI: 10.1007/978-3-319-96553-6_4
EID:

2-s2.0-85050409917

Part of ISBN:

18650929
Contributors: Ceri, S.; Bernasconi, A.; Canakoglu, A.; Gulino, A.; Kaitoua, A.; Masseroli, M.; Nanni, L.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

TICA: Transcriptional Interaction and Coregulation Analyzer

Genomics, Proteomics & Bioinformatics
2018-10 | Journal article
DOI: 10.1016/j.gpb.2018.05.004
Contributors: Stefano Perna; Pietro Pinoli; Stefano Ceri; Limsoon Wong
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Bi-dimensional binning for big genomic datasets

Proceedings of the 4th ACM SIGMOD Workshop on Algorithms and Systems for MapReduce and Beyond, BeyondMR 2017
2017 | Conference paper
DOI: 10.1145/3070607.3070615
EID:

2-s2.0-85021409362
Contributors: Cattani, S.; Ceri, S.; Kaitoua, A.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Data Management for Heterogeneous Genomic Datasets

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2017 | Journal article
DOI: 10.1109/TCBB.2016.2576447
EID:

2-s2.0-85042637184

Part of ISBN:

15455963
Contributors: Ceri, S.; Kaitoua, A.; Masseroli, M.; Pinoli, P.; Venco, F.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Data-driven genomic computing: Making sense of signals from the genome

CEUR Workshop Proceedings
2017 | Conference paper
EID:

2-s2.0-85040700199

Part of ISBN:

16130073
Contributors: Ceri, S.; Canakoglu, A.; Kaitoua, A.; Masseroli, M.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Evaluating genomic big data operations on SciDB and spark

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2017 | Book
DOI: 10.1007/978-3-319-60131-1_34
EID:

2-s2.0-85020497177

Part of ISBN:

16113349 03029743
Contributors: Cattani, S.; Ceri, S.; Kaitoua, A.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Framework for Supporting Genomic Operations

IEEE Transactions on Computers
2017 | Journal article
DOI: 10.1109/TC.2016.2603980
EID:

2-s2.0-85021218017

Part of ISBN:

00189340
Contributors: Kaitoua, A.; Pinoli, P.; Bertoni, M.; Ceri, S.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Scalable genomic data management system on the cloud

Proceedings - 2017 International Conference on High Performance Computing and Simulation, HPCS 2017
2017 | Conference paper
DOI: 10.1109/HPCS.2017.19
EID:

2-s2.0-85032392940
Contributors: Kaitoua, A.; Gulino, A.; Masseroli, M.; Pinoli, P.; Ceri, S.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Cross-organism learning method to discover new gene functionalities

Computer Methods and Programs in Biomedicine
2016 | Journal article
DOI: 10.1016/j.cmpb.2015.12.002
EID:

2-s2.0-84960104134

Part of ISBN:

18727565 01692607
Contributors: Domeniconi, G.; Masseroli, M.; Moro, G.; Pinoli, P.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Data management for next generation genomic computing

Advances in Database Technology - EDBT
2016 | Conference paper
DOI: 10.5441/002/edbt.2016.46
EID:

2-s2.0-85020545999

Part of ISBN:

23672005
Contributors: Ceri, S.; Kaitoua, A.; Masseroli, M.; Pinoli, P.; Venco, F.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Modeling and interoperability of heterogeneous genomic big data for integrative processing and querying

Methods
2016 | Journal article
DOI: 10.1016/j.ymeth.2016.09.002
EID:

2-s2.0-84999089927

Part of ISBN:

10959130 10462023
Contributors: Masseroli, M.; Kaitoua, A.; Pinoli, P.; Ceri, S.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier

Computational algorithms to predict Gene Ontology annotations

BMC Bioinformatics
2015 | Journal article
DOI: 10.1186/1471-2105-16-S6-S4
EID:

2-s2.0-84964654330

Part of ISBN:

14712105
Contributors: Pinoli, P.; Chicco, D.; Masseroli, M.
Source: Self-asserted source
PIETRO PINOLI via Scopus - Elsevier
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Peer review (8 reviews for 6 publications/grants)

Review activity for Data & knowledge engineering. (1)
Review activity for Entropy : (1)
Review activity for Microorganisms. (1)
Review activity for Oncogene. (1)
Review activity for SN computer science. (3)
Review activity for Soft computing. (1)
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