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Data-Driven Genomic Computing

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Publications

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
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
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
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
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
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
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
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
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
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
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
DOI: 10.1109/tc.2018.2854880

TICA: Transcriptional Interaction and Coregulation Analyzer


Published in: ISSN 1672-0229
DOI: 10.1016/j.gpb.2018.05.004

Metadata management for scientific databases


Published in: ISSN 0306-4379
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
DOI: 10.1109/tkde.2018.2871031

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
DOI: 10.1007/978-3-319-69904-2_26

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
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
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
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
DOI: 10.1145/3307339.3342154

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
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
DOI: 10.1007/978-3-319-78723-7_23