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Data-Driven Genomic Computing

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Publications

CamurWeb: a classification software and a large knowledge base for gene expression data of cancer

Author(s): Emanuel Weitschek, Silvia Di Lauro, Eleonora Cappelli, Paola Bertolazzi, Giovanni Felici
Published in: BMC Bioinformatics, 19/S10, 2018, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-018-2299-7

Association rule mining to identify transcription factor interactions in genomic regions

Author(s): Gaia Ceddia, Liuba Nausicaa Martino, Alice Parodi, Piercesare Secchi, Stefano Campaner, Marco Masseroli
Published in: Bioinformatics, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz687

Investigating Italian disinformation spreading on Twitter in the context of 2019 European elections

Author(s): Francesco Pierri, Alessandro Artoni, Stefano Ceri
Published in: PLOS ONE, 15/1, 2020, Page(s) e0227821, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0227821

OpenGDC: Unifying, Modeling, Integrating Cancer Genomic Data and Clinical Metadata

Author(s): Eleonora Cappelli, Fabio Cumbo, Anna Bernasconi, Arif Canakoglu, Stefano Ceri, Marco Masseroli, Emanuel Weitschek
Published in: Applied Sciences, 10/18, 2020, Page(s) 6367, ISSN 2076-3417
Publisher: mdpi
DOI: 10.3390/app10186367

How Schools Affected the COVID-19 Pandemic in Italy: Data Analysis for Lombardy Region, Campania Region, and Emilia Region

Author(s): Davide Tosi, Alessandro Siro Campi
Published in: Future Internet, 13/5, 2021, Page(s) 109, ISSN 1999-5903
Publisher: MDPI
DOI: 10.3390/fi13050109

Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries

Author(s): Luca Nanni, Stefano Ceri, Colin Logie
Published in: Genome Biology, 21/1, 2020, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-020-02108-x

GenoSurf: metadata driven semantic search system for integrated genomic datasets

Author(s): Arif Canakoglu, Anna Bernasconi, Andrea Colombo, Marco Masseroli, Stefano Ceri
Published in: Database, 2019, 2019, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baz132

The road towards data integration in human genomics: players, steps and interactions

Author(s): Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Stefano Ceri
Published in: Briefings in Bioinformatics, 2020, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa080

Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks

Author(s): Arnaud Ceol, Piero Montanari, Ilaria Bartolini, Stefano Ceri, Paolo Ciaccia, Marco Patella, Marco Masseroli
Published in: BMC Bioinformatics, 21/1, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-03781-2

ViruSurf: an integrated database to investigate viral sequences

Author(s): Arif Canakoglu, Pietro Pinoli, Anna Bernasconi, Tommaso Alfonsi, Damianos P Melidis, Stefano Ceri
Published in: Nucleic Acids Research, 49/D1, 2020, Page(s) D817-D824, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa846

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

Author(s): Stefano Ceri, Pietro Pinoli
Published in: SN Computer Science, 1/1, 2020, ISSN 2662-995X
Publisher: Springer
DOI: 10.1007/s42979-019-0005-0

META-BASE: a Novel Architecture for Large-Scale Genomic Metadata Integration

Author(s): Anna Bernasconi, ARIF CANAKOGLU, Marco Masseroli, Stefano Ceri
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, Page(s) 1-1, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2020.2998954

Matrix Factorization-based Technique for Drug Repurposing Predictions

Author(s): G. Ceddia, P. Pinoli, S. Ceri, M. Masseroli
Published in: IEEE Journal of Biomedical and Health Informatics, 24/11, 2020, Page(s) 3162-3172, ISSN 2168-2194
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/jbhi.2020.2991763

A review on viral data sources and search systems for perspective mitigation of COVID-19

Author(s): Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Pietro Pinoli, Stefano Ceri
Published in: Briefings in Bioinformatics, 2020, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa359

Federated sharing and processing of genomic datasets for tertiary data analysis

Author(s): Arif Canakoglu, Pietro Pinoli, Andrea Gulino, Luca Nanni, Marco Masseroli, Stefano Ceri
Published in: Briefings in Bioinformatics, 2020, ISSN 1477-4054
Publisher: Oxford Acedemics
DOI: 10.1093/bib/bbaa091

Explorative visual analytics on interval-based genomic data and their metadata

Author(s): Vahid Jalili, Matteo Matteucci, Marco Masseroli, Stefano Ceri
Published in: BMC Bioinformatics, 18/1, 2017, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-017-1945-9

Framework for Supporting Genomic Operations

Author(s): Abdulrahman Kaitoua, Pietro Pinoli, Michele Bertoni, Stefano Ceri
Published in: IEEE Transactions on Computers, 66/3, 2017, Page(s) 443-457, ISSN 0018-9340
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/TC.2016.2603980

Indexing Next-Generation Sequencing data

Author(s): Vahid Jalili, Matteo Matteucci, Marco Masseroli, Stefano Ceri
Published in: Information Sciences, 384, 2017, Page(s) 90-109, ISSN 0020-0255
Publisher: Elsevier BV
DOI: 10.1016/j.ins.2016.08.085

TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas

Author(s): Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, Emanuel Weitschek
Published in: BMC Bioinformatics, 18/1, 2017, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-016-1419-5

Classification of Large DNA Methylation Datasets for Identifying Cancer Drivers

Author(s): Fabrizio Celli, Fabio Cumbo, Emanuel Weitschek
Published in: Big Data Research, 2018, ISSN 2214-5796
Publisher: Elsevier Inc.
DOI: 10.1016/j.bdr.2018.02.005

Data Management for Heterogeneous Genomic Datasets

Author(s): Stefano Ceri, Abdulrahman Kaitoua, Marco Masseroli, Pietro Pinoli, Francesco Venco
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14/6, 2017, Page(s) 1251-1264, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/TCBB.2016.2576447

MuSERA: Multiple Sample Enriched Region Assessment

Author(s): Vahid Jalili, Matteo Matteucci, Marco J. Morelli, Marco Masseroli
Published in: Briefings in Bioinformatics, 18 (3), 2017, Page(s) bbw029, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbw029

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

Author(s): Marco Masseroli, Arif Canakoglu, Pietro Pinoli, Abdulrahman Kaitoua, Andrea Gulino, Olha Horlova, Luca Nanni, Anna Bernasconi, Stefano Perna, Eirini Stamoulakatou, Stefano Ceri
Published in: Bioinformatics, 2018, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty688

Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration

Author(s): Alice Cambiaghi, Manuela Ferrario, Marco Masseroli
Published in: Briefings in Bioinformatics, 2017, Page(s) bbw031, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbw031

Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages

Author(s): Cheng Wang, Luca Nanni, Boris Novakovic, Wout Megchelenbrink, Tatyana Kuznetsova, Hendrik G. Stunnenberg, Stefano Ceri, Colin Logie
Published in: Scientific Reports, 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-39395-9

Optimal Binning for Genomics

Author(s): Andrea Gulino, Abdulrahman Kaitoua, Stefano Ceri
Published in: IEEE Transactions on Computers, 68/1, 2019, Page(s) 125-138, ISSN 0018-9340
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tc.2018.2854880

TICA: Transcriptional Interaction and Coregulation Analyzer

Author(s): Stefano Perna, Pietro Pinoli, Stefano Ceri, Limsoon Wong
Published in: Genomics, Proteomics & Bioinformatics, 16/5, 2018, Page(s) 342-353, ISSN 1672-0229
Publisher: Kexue Chubaneshe/Science Press
DOI: 10.1016/j.gpb.2018.05.004

Metadata management for scientific databases

Author(s): Pietro Pinoli, Stefano Ceri, Davide Martinenghi, Luca Nanni
Published in: Information Systems, 81, 2019, Page(s) 1-20, ISSN 0306-4379
Publisher: Elsevier Science & Technology
DOI: 10.1016/j.is.2018.10.002

Next Generation Indexing for Genomic Intervals

Author(s): Vahid Jalili, Matteo Matteucci, Jeremy Goecks, Yashar Deldjoo, Stefano Ceri
Published in: IEEE Transactions on Knowledge and Data Engineering, 2018, Page(s) 1-1, ISSN 1041-4347
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tkde.2018.2871031

Exploring chromatin conformation and gene co-expression through graph embedding

Author(s): Marco Varrone, Luca Nanni, Giovanni Ciriello, Stefano Ceri
Published in: Bioinformatics, 36/Supplement_2, 2020, Page(s) i700-i708, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa803

VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants

Author(s): Anna Bernasconi, Andrea Gulino, Tommaso Alfonsi, Arif Canakoglu, Pietro Pinoli, Anna Sandionigi, Stefano Ceri
Published in: Nucleic Acids Research, 49/15, 2021, Page(s) e90-e90, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab478

Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction

Author(s): Eleonora Cappelli, Giovanni Felici, Emanuel Weitschek
Published in: BioData Mining, 11/1, 2018, ISSN 1756-0381
Publisher: BioMed Central
DOI: 10.1186/s13040-018-0184-6

Data quality-aware genomic data integration

Author(s): Anna Bernasconi
Published in: Computer Methods and Programs in Biomedicine Update, 1, 2021, Page(s) 100009, ISSN 2666-9900
Publisher: Elsevier
DOI: 10.1016/j.cmpbup.2021.100009

How Data Analytics and Big Data Can Help Scientists in Managing COVID-19 Diffusion: Modeling Study to Predict the COVID-19 Diffusion in Italy and the Lombardy Region

Author(s): Davide Tosi, Alessandro Campi
Published in: Journal of Medical Internet Research, 22/10, 2020, Page(s) e21081, ISSN 1438-8871
Publisher: Journal of medical Internet Research
DOI: 10.2196/21081

Exploiting Conceptual Modeling for Searching Genomic Metadata: A Quantitative and Qualitative Empirical Study

Author(s): Anna Bernasconi, Arif Canakoglu, Stefano Ceri
Published in: Advances in Conceptual Modeling - ER 2019 Workshops FAIR, MREBA, EmpER, MoBiD, OntoCom, and ER Doctoral Symposium Papers, Salvador, Brazil, November 4–7, 2019, Proceedings, 11787, 2019, Page(s) 83-94, ISBN 978-3-030-34145-9
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-34146-6_8

From a Conceptual Model to a Knowledge Graph for Genomic Datasets

Author(s): Anna Bernasconi, Arif Canakoglu, Stefano Ceri
Published in: Conceptual Modeling - 38th International Conference, ER 2019, Salvador, Brazil, November 4–7, 2019, Proceedings, 11788, 2019, Page(s) 352-360, ISBN 978-3-030-33222-8
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-33223-5_29

Empowering Virus Sequence Research Through Conceptual Modeling

Author(s): Anna Bernasconi, Arif Canakoglu, Pietro Pinoli, Stefano Ceri
Published in: Conceptual Modeling - 39th International Conference, ER 2020, Vienna, Austria, November 3–6, 2020, Proceedings, 12400, 2020, Page(s) 388-402, ISBN 978-3-030-62521-4
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-62522-1_29

Network Modeling and Analysis of Normal and Cancer Gene Expression Data

Author(s): Gaia Ceddia, Sara Pidò, Marco Masseroli
Published in: Computational Intelligence Methods for Bioinformatics and Biostatistics - 16th International Meeting, CIBB 2019, Bergamo, Italy, September 4–6, 2019, Revised Selected Papers, 12313, 2020, Page(s) 257-270, ISBN 978-3-030-63060-7
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-63061-4_23

Automated Integration of Genomic Metadata with Sequence-to-Sequence Models

Author(s): Giuseppe Cannizzaro, Michele Leone, Anna Bernasconi, Arif Canakoglu, Mark J. Carman
Published in: Machine Learning and Knowledge Discovery in Databases. Applied Data Science and Demo Track - European Conference, ECML PKDD 2020, Ghent, Belgium, September 14–18, 2020, Proceedings, Part V, 12461, 2021, Page(s) 187-203, ISBN 978-3-030-67669-8
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-67670-4_12

Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language

Author(s): Stefano Perna, Arif Canakoglu, Pietro Pinoli, Stefano Ceri, Limsoon Wong
Published in: Data Mining for Systems Biology - Methods and Protocols, 1807, 2018, Page(s) 63-81, ISBN 978-1-4939-8560-9
Publisher: Springer New York
DOI: 10.1007/978-1-4939-8561-6_6

Exploiting Ladder Networks for Gene Expression Classification

Author(s): Guray Golcuk, Mustafa Anil Tuncel, Arif Canakoglu
Published in: Bioinformatics and Biomedical Engineering, 10813, 2018, Page(s) 270-278, ISBN 978-3-319-78722-0
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-78723-7_23

Designing and Evaluating Deep Learning Models for Cancer Detection on Gene Expression Data

Author(s): Arif Canakoglu, Luca Nanni, Artur Sokolovsky, Stefano Ceri
Published in: Computational Intelligence Methods for Bioinformatics and Biostatistics - 15th International Meeting, CIBB 2018, Caparica, Portugal, September 6–8, 2018, Revised Selected Papers, 11925, 2020, Page(s) 249-261, ISBN 978-3-030-34584-6
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-34585-3_22

CoV2K: A Knowledge Base of SARS-CoV-2 Variant Impacts

Author(s): Ruba Al Khalaf, Tommaso Alfonsi, Stefano Ceri, Anna Bernasconi
Published in: Research Challenges in Information Science - 15th International Conference, RCIS 2021, Limassol, Cyprus, May 11–14, 2021, Proceedings, 415, 2021, Page(s) 274-282, ISBN 978-3-030-75017-6
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-75018-3_18

Modeling Gene Transcriptional Regulation by Means of Hyperplanes Genetic Clustering

Author(s): Fabrizio Frasca, Matteo Matteucci, Marco Masseroli, Marco Morelli
Published in: 2018 International Joint Conference on Neural Networks (IJCNN), 2018, Page(s) 1-8, ISBN 978-1-5090-6014-6
Publisher: IEEE
DOI: 10.1109/ijcnn.2018.8489054

Performance Prediction for Data-driven Workflows on Apache Spark

Author(s): Andrea Gulino, Arif Canakoglu, Stefano Ceri, Danilo Ardagna
Published in: 2020 28th International Symposium on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS), 2020, Page(s) 1-8, ISBN 978-1-7281-9238-3
Publisher: IEEE
DOI: 10.1109/mascots50786.2020.9285944

Conceptual modeling for genomics: Building an integrated repository of open data

Author(s): Anna Bernasconi, Stefano Ceri, Alessandro Campi, Marco Masseroli
Published in: 36th International Conference on Conceptual Modeling, ER 2017, 2017, Page(s) 325-339, ISBN 9783-319699035
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-69904-2_26

Scalable Genomic Data Management System on the Cloud

Author(s): Abdulrahman Kaitoua, Andrea Gulino, Marco Masseroli, Pietro Pinoli, Stefano Ceri
Published in: 2017 International Conference on High Performance Computing & Simulation (HPCS), 2017, Page(s) 58-63, ISBN 978-1-5386-3250-5
Publisher: IEEE
DOI: 10.1109/HPCS.2017.19

Evaluating Big Data Genomic Applications on SciDB and Spark

Author(s): Simone Cattani, Stefano Ceri, Abdulrahman Kaitoua, Pietro Pinoli
Published in: Web Engineering. ICWE 2017, 10360, 2017, Page(s) 482-493, ISBN 9783-319601304
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-60131-1_34

Bi-Dimensional Binning for Big Genomic Datasets

Author(s): Simone Cattani, Stefano Ceri, Abdulrahman Kaitoua, Pietro Pinoli
Published in: Proceedings of the 4th Algorithms and Systems on MapReduce and Beyond - BeyondMR'17, 2017, Page(s) 1-4, ISBN 9781-450350198
Publisher: ACM Press
DOI: 10.1145/3070607.3070615

Overview of GeCo: A Project for Exploring and Integrating Signals from the Genome

Author(s): Stefano Ceri, Anna Bernasconi, Arif Canakoglu, Andrea Gulino, Abdulrahman Kaitoua, Marco Masseroli, Luca Nanni, Pietro Pinoli
Published in: Data Analytics and Management in Data Intensive Domains. DAMDID/RCDL 2017, 822, 2018, Page(s) 46-57, ISBN 978-3-319-96552-9
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-96553-6_4

Drug Repositioning Predictions by Non-Negative Matrix Tri-Factorization of Integrated Association Data

Author(s): Gaëtan Dissez, Gaia Ceddia, Pietro Pinoli, Stefano Ceri, Marco Masseroli
Published in: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '19, 2019, Page(s) 25-33, ISBN 9781-450366663
Publisher: ACM Press
DOI: 10.1145/3307339.3342154

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

Author(s): Gaia Ceddia, Pietro Pinoli, Stefano Ceri, Marco Masseroli
Published in: 2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2019, Page(s) 1-7, ISBN 978-1-7281-1462-0
Publisher: IEEE
DOI: 10.1109/cibcb.2019.8791474

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

Author(s): Pietro Pinoli, Eirini Stamoulakatou, An-Phi Nguyen, María Rodríguez Martínez, Stefano Ceri
Published in: PLOS ONE, 15/1, 2020, Page(s) e0227180, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0227180

Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes

Author(s): Yuanlong Liu, Luca Nanni, Stephanie Sungalee, Marie Zufferey, Daniele Tavernari, Marco Mina, Stefano Ceri, Elisa Oricchio, Giovanni Ciriello
Published in: Nature Communications, 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22666-3

Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response

Author(s): Pietro Pinoli, Sriganesh Srihari, Limsoon Wong, Stefano Ceri
Published in: BMC Bioinformatics, 22/1, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04168-7

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

Author(s): Stefano Perna, Pietro Pinoli, Stefano Ceri, Limsoon Wong
Published in: Biology Direct, 15/1, 2020, ISSN 1745-6150
Publisher: BioMed Central
DOI: 10.1186/s13062-020-00268-1

Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization

Author(s): Pietro Pinoli, Gaia Ceddia, Stefano Ceri, Marco Masseroli
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021, Page(s) 1-1, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2021.3091814