Data-Driven Genomic Computing

Project Information

GeCo

Grant agreement ID: 693174

DOI

10.3030/693174

Project closed

EC signature date 18 July 2016

Start date 1 September 2016

End date 31 August 2021

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

POLITECNICO DI MILANO
Italy

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (34)

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 22/10, 2020, Page(s) e21081, ISSN 1438-8871
Publisher: Journal of medical Internet Research
DOI: 10.2196/21081

Book chapters (9)

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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

Conference proceedings (9)

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, Issue 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, Issue 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 9781450366663
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

Non-peer reviewed articles (5)

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, Issue 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, Issue 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, Issue 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, Issue 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