PUBLICATIONS


GOOGLE SCHOLAR PERSONAL PAGE


Work in progress

Eleonora Cappelli, Emanuel Weitschek, and Fabio Cumbo
Extending knowledge on genomic data and metadata of cancer with domain-specific ontologies and taxonomy-based relaxed queries

Eleonora Cappelli, Emanuel Weitschek, and Fabio Cumbo
Omica: a unified access point to standardised omics data of multiple sources

Eleonora Cappelli, Emanuel Weitschek, and Fabio Cumbo
Smart persistence and accessibility of genomic and clinical data

Eleonora Cappelli, Fabio Cumbo*, Anna Bernasconi, Arif Canakoglu, Stefano Ceri, Marco Masseroli and Emanuel Weitschek
OpenGDC: promoting data standardization in the Life Sciences. A concrete effort toward the harmonization of clinical and genomic cancer data
*Co-first Author

Fabio Cumbo, Robert S. Harris, Paul Medvedev, and Anton Nekrutenko
Fast querying of massive sequence datasets

2019

Cristina Cumbo, Fabio Cumbo
GMS – Gammadiae Management System: cataloguing and interpretation project of the so-called gammadiae starting from the iconographic evidences in the Roman catacombs
Conservar Património, January, 2019

2018

Emanuel Weitschek, Fabio Cumbo, Eleonora Cappelli, Giovanni Felici, and Paola Bertolazzi
Classifying big DNA methylation data: a gene-oriented approach
Communications in Computer and Information Science vol. 903, DEXA-BIOKDD 2018, 9th International Workshop on Biological Knowledge Discovery from Data, Springer, October, 2018

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, The Bioconda Team, and Johannes Köster
Bioconda: A sustainable and comprehensive software distribution for the life sciences
Nature Methods, volume 15, pages 475–476 (2018)
The Bioconda Team: Consortium author list

Fabrizio Celli, Fabio Cumbo, and Emanuel Weitschek
Classification of large DNA methylation data sets for identifying cancer drivers: BIGBIOCL
Big Data Research 2018

Marzia A. Cremona, Alessia Pini, Fabio Cumbo, Kateryna D. Makova, Francesca Chiaromonte, and Simone Vantini
IWTomics: testing high-resolution "Omics" data at multiple locations and scales
Bioinformatics 2018

Fabio Cumbo, Davide Vergni, and Daniele Santoni
Investigating transcription factor synergism in humans
DNA Research, Volume 25, Issue 1, Pages 103–112 (2018)

2017

Fabio Cumbo, Marco S. Nobile, Chiara Damiani, Riccardo Colombo, Giancarlo Mauri, and Paolo Cazzaniga
COSYS: A Computational Infrastructure for Systems Biology
Lecture Notes in Bioinformatics vol. 10477, Computational Intelligence Methods for Bioinformatics and Biostatistics, Springer, October, 2017

Fabio Cumbo, Emanuel Weitschek, Paola Bertolazzi, and Giovanni Felici
IRIS-TCGA: an information retrieval and integration system for genomic data of cancer
Lecture Notes in Bioinformatics vol. 10477, Computational Intelligence Methods for Bioinformatics and Biostatistics, Springer, October, 2017

Fabio Cumbo, Giulia Fiscon, Marco Masseroli, Stefano Ceri, and Emanuel Weitschek
TCGA2BED: Extracting, Extending, Integrating, and Querying The Cancer Genome Atlas
BMC Bioinformatics 2016

2016

Emanuel Weitschek, Fabio Cumbo, Eleonora Cappelli, and Giovanni Felici
Genomic Data Integration: A case study on next generation sequencing of cancer
27th International Workshop on Database and Expert Systems Applications (DEXA) 2016

Emanuel Weitschek, Fabio Cumbo, Giulia Fiscon, Valerio Cestarelli, Stefano Ceri, and Marco Masseroli
TCGA2BED and CAMUR for cancer NGS data processing
F1000Research, 1899-1899 (2016)

Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, and Emanuel Weitschek
TCGA2BED: converting and querying The Cancer Genome Atlas
BITS 2016: 13th Annual Meeting of the Bioinformatics Italian Society, 28-29 (2016)

2015

Ivan Arisi, Mara D'Onofrio, Rossella Brandi, Antonio Cattaneo, Paola Bertolazzi, Fabio Cumbo, Giovanni Felici, and Concettina Guerra
Time Dynamics Of Protein Complexes In The AD11 Transgenic Mouse Model For Alzheimer's Disease Like Pathology
BMC Neuroscience 16, no.1 (2015): 28

Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, and Emanuel Weitschek
The Cancer Genome Atlas data querying tool
BITS 2015: 12th Annual Meeting of the Bioinformatics Italian Society, 120-121 (2015)

2014

Fabio Cumbo, Giovanni Felici, and Paola Bertolazzi
Selecting Relevant Nodes And Structures In Biological Networks. BiNAT: A New Plugin For Cytoscape
F1000Research 2014, 3:287 (doi:10.12688/f1000research.5753.1)

Fabio Cumbo, Paola Paci, Daniele Santoni, Luisa Di Paola, and Alessandro Giuliani
GIANT: A Cytoscape Plugin For Modular Networks
PLOS ONE 9, no. 10 (2014): e105001