About me

Fabio Cumbo

I'm a Software Engineer with a Ph.D. in Computer Science and Automation Engineering, currently Postdoctoral Researcher at the Computational Metagenomics Laboratory - Segata Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO) of the University of Trento, Italy.

Click here to download my updated Curriculum Vitae

Affiliations

November 2018 - ongoing: Postdoctoral Researcher at the Computational Metagenomics Laboratory - Segata Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO) of the University of Trento, Via Sommarive 9, 38121 Povo (Trento), Italy
References: Prof. Nicola Segata

April 2018 - September 2018: Ph.D. Fellow at the Galaxy Lab, Institut für Informatik, Albert-Ludwigs-Universität Freiburg, Georges-Koehler-Allee, Geb 106, D-79110 Freiburg im Breisgau, Germany
References: Prof. Dr. Rolf Backofen and Dr. rer. nat. Björn Grüning

March 2017 - March 2018: Research Lab Assistant at the Galaxy Lab, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Wartik Building, University Park, 16802 PA, USA
References: Prof. Anton Nekrutenko and Prof. Francesca Chiaromonte

October 2016 - October 2018: Teaching Assistant at the Department of Engineering, International Telematic University of Uninettuno, Corso Vittorio Emanuele II 39, 00186 RM, Rome, Italy
References: Prof. Emanuel Weitschek

November 2015 - October 2018: Research Associate at SYSBIO.IT - Centre of Systems Biology, Piazza della Scienza 2, 20126 MI, Milan, Italy
References: Prof. Lilia Alberghina and Prof. Giancarlo Mauri

November 2015 - October 2018: Ph.D. Candidate at the Department of Engineering, University of Roma Tre, Via della Vasca Navale 79/81, 00146 RM, Rome, Italy
References: Prof. Maurizio Patrignani

November 2015 - January 2020: Research Associate at the Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Via dei Taurini 19, 00185 RM, Rome, Italy
References: Dr. Paola Bertolazzi and Dr. Giovanni Felici

Experiences

Work Experiences

Research Associate February 2019 - February 2020

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Rome, Italy

Postdoctoral Researcher November 2018 - ongoing

Computational Metagenomics Laboratory - Segata Lab, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Italy

Development of new software tools for the characterization of bacterial species
EU-ERC (MetaPG-716575)

Professional Collaborator March 2018 - December 2018

ACTOR (Analytics, Control Technologies and Operations Research) S.R.L., Rome, Italy

  • Development of a technological platform to establish an early and non-invasive diagnosis of neurodegenerative diseases;
  • Extraction and standardization of data from the IDA (Image and Data Archive) database powered by LONI (Laboratory of Neuro Imaging) funded by NIH and NIBIB;
  • Creation of an ontology in order to better understand how these data are organized and to create an easy access service to the data themselves.

Collaborations

  • EBRI (European Brain Research Insititute) - Rita Levi Montalcini Foundation, Rome, Italy
  • Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Rome, Italy

Keywords: Bioinformatics, Ontologies, Machine Learning, Alzheimer and Parkinson's disease, Diagnostics

Ph.D. Fellow April 2018 - September 2018

Institut für Informatik of the Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Baden-Württemberg, Germany

Development of bioinformatics tools for the Galaxy platform

Research Lab Assistant September 2017 - March 2018

Wartik Laboratory – Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park Campus, 16802 PA, Pennsylvania, USA

Development of a portal which allows to fast query massive sequence datasets using the Sequence Bloom Trees

Collaborations

  • Galaxy Lab, Nekrutenko Lab
  • Medvedev Lab

Keywords: Bioinformatics, Galaxy, Information Retrieval, Sequence Bloom Tree

Intern March 2017 - September 2017

Wartik Laboratory – Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park Campus, 16802 PA, Pennsylvania, USA

  • Collaboration with the team of the Galaxy project to extend and implement new features for the Galaxy platform;
  • Development of new statistical analysis and algorithms, and contribute to the development of Galaxy, Conda, and Bioconda projects.

Collaborations

  • Galaxy Lab, Nekrutenko Lab
  • Medvedev Lab

Keywords: Bioinformatics, Galaxy, Functional Data Analysis, Information Retrieval

Professional Collaborator February 2017 - November 2018

Department of Engineering, International Telematic University of Uninettuno, Rome, Italy

  • Development of a software to automatically extract, extend, and standardize clinical and genomic data from the Genomic Data Commons Portal;
  • This project is part of the Data-Driven Genomic Computing (GeCo), focusing on tertiary analysis for genomic data integration, and funded with an ERC Advanced Grant (September 2016 – August 2021)

Collaborations

  • Department of Electronics, Information and Bioengineering of the Polytechnic University of Milan
  • Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy

Keywords: Bioinformatics, ERC, GeCo, TCGA2BED

Teaching Assistant September 2016 - November 2018

Department of Engineering, International Telematic University of Uninettuno, Rome, Italy

  • Proposal of a training plan for the new Master’s Degree courses in Software Engineering (Big Data branch): (i) "Introduction to Big Data" and (ii) "Big Data Analytics and Visualization";
  • Teaching assistant and Lecturer for both the "Introduction to Big Data" and "Big Data Analytics and Visualization" courses;
  • Proposed theses:
    • "Analysis and implementation of a web platform for the management and querying of genomic Big Data" (Bachelor's Degree): Candidate "Lorenzo Di Nardo", Supervisor "Prof. Emanuel Weitschek", Co-supervisor "Fabio Cumbo";
    • "The structure of the Bloom Filters for the management and querying of Big Data" (Master's Degree): Candidate "Antonio Tranchida", Supervisor "Prof. Emanuel Weitschek", Co-supervisor "Fabio Cumbo";
    • "Probabilistic data structures for the reference-free alignment of sequences" (Master's Degree): Candidate "Federico Ferranti", Supervisor "Prof. Emanuel Weitschek", Co-supervisor "Fabio Cumbo";
    • "Hyperdimensional Computing for the Supervised Machine Learning" (Master's Degree): Candidate "Simone Truglia", Supervisor "Prof. Emanuel Weitschek", Co-supervisor "Fabio Cumbo"

Keywords: Hadoop, Spark, MapReduce, Machine Learning, D3.js, Data Visualization

Professional Collaborator September 2016 - March 2017

Marine Technology Research Institute (INSEAN-CNR), National Research Council of Italy, Rome, Italy

Development of a database containing data about military and merchant ships in which were used amiantus as a thermal insulator and data about officers and machinists affected by mesothelioma

Keywords: Amiantus, Database, Mesothelioma, Military and Merchant Ships

Ph.D. Candidate October 2015 - November 2018

Department of Engineering, University of Roma Tre, Rome, Italy

  • Development of an innovative platform for the acquisition, storage, management, integration, and analysis of heterogeneous biomedical data;
  • Proposed theses:
    • "Analysis and development of a web service for the computation, visualization, and comparison of gene co-expression networks" (Bechelor's Degree): Candidate "Dalila Rosati", Supervisor "Prof. Maurizio Patrignani", Co-supervisor "Fabio Cumbo";
    • "TCGAinBED Web: Managing and querying genomic Big Data" (Bachelor's Degree): Candidate "Luca Wissel", Supervisor "Prof. Maurizio Patrignani", Co-supervisor "Fabio Cumbo"

Collaborations

  • Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy
  • SYSBIO.IT - Center for Systems Biology, Milan, Italy

Professional Collaborator March 2015 - September 2015

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Rome, Italy

Analysis and development of toolkits for bioinformatics analysis in addition to the extraction, storage, and management of genomic data from TCGA

Keywords: Bioinformatics, The Cancer Genome Atlas, Data Extraction

Professional Collaborator December 2014 - November 2018

SYSBIO.IT - Center for Systems Biology, Milan, Italy

  • Development of COSYS, a platform for the interoperability of different software tools for a Systems Biology oriented analysis;
  • The platform guarantees the data sharing between researchers of different European research centers;
  • Part of ISBE (Infrastructure for Systems Biology – Europe), a large-scale European research infrastructure project on the European Strategy Forum on Research Infrastructures (ESFRI) Roadmap

Collaborations

  • Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy
  • Department of Informatics, Systems and Communication (DISCo), University of Milano-Bicocca

Keywords: Systems Biology, COSYS, ISBE

Professional Collaborator September 2014 - March 2015

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Rome, Italy

Design and implementation of a software for the storage, management, and querying of genomic and clinical data. Application of the software to The Cancer Genome Atlas

Keywords: Bioinformatics, The Cancer Genome Atlas, Data Extraction

Professional Collaborator February 2014 - February 2016

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Rome, Italy

  • Development of a data extraction and analysis tool of genomic data from The Cancer Genome Atlas;
  • Part of the Data-Centric Genomic Computing (GenData 2020) project funded by the Ministry of Education, University, and Research of Italy under the PRIN program

Collaborations

  • Department of Electronics, Information and Bioengineering of the Polytechnic University of Milan

Keywords: Bioinformatics, The Cancer Genome Atlas, Data Extraction

Professional Collaborator February 2013 - August 2014

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Rome, Italy

  • Software development for the analysis of Protein-Protein Interaction Networks (PPI);
  • Analysis of significant changes in the structure of protein complexes starting from temporal gene expression microarray data for the transgenic Mouse organism affected by Alzheimer's disease

Collaborations

  • EBRI (European Brain Research Institute), Rita Levi Montalcini Foundation, Rome, Italy

Keywords: Bioinformatics, AD11 Mouse Model, Alzheimer's Disease, Microarray, Time Dynalics, Protein Complexes, CORUM, PPI

Intern September 2011 - November 2012

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Rome, Italy

Design and development of algorithms for the computation of characteristical parameters in biological networks

Keywords: Bioinformatics, PPI, Cytoscape, Network Theory

Publications
Google Scholar

2020

Fabio Cumbo, Eleonora Cappelli, and Emanuel Weitschek
A brain-inspired hyperdimensional computing approach for classifying massive DNA methylation data of cancer
Algorithms 2020, 13, 233.

Eleonora Cappelli, Fabio Cumbo, Anna Bernasconi, Arif Canakoglu, Stefano Ceri, Marco Masseroli, and Emanuel Weitschek
OpenGDC: unifying, modeling, integrating cancer genomic data and clinical metadata
Appl. Sci. 2020, 10, 6367
Zenodo resources: https://zenodo.org/record/4000250

Fabio Cumbo and Emanuel Weitschek
An in-memory cognitive-based hyperdimensional approach to accurately classify DNA-Methylation data of cancer
The 11th International Workshop on Biological Knowledge Discovery from Big Data (BIOKDD'20), Communications in Computer and Information Science, vol 1285. Springer, Cham, 2020

Edoardo Pasolli, Francesca De Filippis, Ilia Mauriello, Fabio Cumbo, Aaron Walsh, John Leech, Paul Cotter, Nicola Segata, and Danilo Ercolini
Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome
Nature Communications, 2020

Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi, Qiyun Zhu, Mattia Bolzan, Fabio Cumbo, Uyen May, Jon G. Sanders, Moreno Zolfo, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower, and Nicola Segata
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Nature Communications, 2020

Eleonora Cappelli, Emanuel Weitschek, and Fabio Cumbo
Extending knowledge on genomic data and metadata of cancer by exploiting taxonomy-based relaxed queries on domain-specific ontologies
Accepted at The 16th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2019), in press on the conference post-proceedings, Lecture Notes in Bioinformatics (LNBI) by Springer

2019

Serena Manara, Francesco Asnicar, Francesco Beghini, Davide Bazzani, Fabio Cumbo, Moreno Zolfo, Eleonora Nigro, Nicolai Karcher, Paolo Manghi, Marisa Isabell Metzger, Edoardo Pasolli, and Nicola Segata
Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
BMC Genome Biology volume 20, Article number: 299 (2019)

Eleonora Cappelli, Emanuel Weitschek, and Fabio Cumbo
Smart persistence and accessibility of genomic and clinical data
The 10th International Workshop on Biological Knowledge Discovery from Big Data (BIOKDD'19), Communications in Computer and Information Science, vol 1062. Springer, Cham, 2019

Lorenza Fiumi, Fabio Cumbo, Cinzia Crenca, Dario Gallo, and Carlo Meoni
The AMINAVI database: Know the presence of asbestos on board ships, in the past and in the present
Epidemiologia & Prevenzione, 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

Ivan Arisi, Paola Bertolazzi, Eleonora Cappelli, Federica Conte, Fabio Cumbo, Giulia Fiscon, Michele Sonnessa, Francesco Taglino
An ontology-based approach to improve data querying and organization of Alzheimer's Disease data
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Proceedings, Volume 1, pg 2732-2734, 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
Zenodo resources: https://zenodo.org/deposit/1288391

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

Presentations

Time dynamics of protein complexes in a transgenic mouse model for Alzheimer's disease - Master's Degree - Final discussion - Department of Engineering, University of Roma Tre, Rome, Italy

IRIS-TCGA: an information retrieval and integration system for genomic data of cancer - 13th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics 2016 - Computer Science Division, University of Stirling, Stirling, Scotland, United Kingdom

COSYS: a computational infrastructure for Systems Biology - 1st SYSBIO.IT School on Computational Systems Biology - An introduction to dynamic modeling, simulation, and analysis of biological systems - Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy

Self Introduction - Computation, Bioinformatics, and Statistics (CBIOS) Practicum 2017/2018 - The Pennsylvania State University, University Park, Pennsylvania, United States of America

Rapid querying of massive sequence datasets - v0.2 - April 26, 2018 - Institut für Informatik, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany

Rapid querying of massive sequence datasets - v0.1 - YES@IASI - Young Experts Seminars at IASI - March 09, 2018 - Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Rome, Italy

Alignment-free approaches to rapidly query massive sequence datasets exploiting NoSQL technologies - Proposals - Internal meeting - May 28, 2018

Modeling short reads experiments for reference-free applications - Proposals - Internal meeting - June 04, 2018

Data and Models Integration in Biomedical Information Systems - PhD Defense Seminar - October 30, 2018

An in-memory cognitive-based hyperdimensional approach to accurately classify DNA-Methylation data of cancer - The 11th International Workshop on Biological Knowledge Discovery from Big Data (BIOKDD'20) - Virtual Conference - September 15, 2020

Posters

Eleonora Cappelli, Federica Conte, Fabio Cumbo, Giulia Fiscon
Combining knowledge-base approach with logical data mining techniques to improve data querying and analysis on Alzheimer's disease data
Artificial Intelligence and Health - [Exposed on December 14, 2018, Rome, Italy]

Ivan Arisi, Paola Bertolazzi, Eleonora Cappelli, Federica Conte, Fabio Cumbo, Giulia Fiscon, Michele Sonnessa, and Francesco Taglino
An ontology-based approach to improve data querying and organization of Alzheimer's Disease data
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018) - [Exposed on December 3-6, 2018, Madrid, Spain]

Eleonora Cappelli, Fabio Cumbo, Anna Bernasconi, Marco Masseroli, and Emanuel Weitschek
OpenGDC: standardizing, extending, and integrating genomics data of cancer
European Student Council Symposium 2018 - [Exposed on September 8-12, 2018, Stavros Niarchos Foundation Cultural Center, Athens, Greece]

Fabio Cumbo, Anton Nekrutenko, and Giovanni Felici
GDCWebApp: filtering, extracting, and converting genomic and clinical data from the Genomic Data Commons portal
Cold Spring Harbor meeting: Genome Informatics - [Exposed on November 1-4, 2017, Cold Spring Harbor, NY, USA]

Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, and Emanuel Weitschek
The Cancer Genome Atlas Data Querying Tool
BITS 2015 Conference - 12th Annual Meeting of the Bioinformatics Italian Society - [Exposed on June 3-5, 2015, Milan, Italy]

Others

AMINAVI: SULLE TRACCE DI UN KILLER SILENZIOSO published on GARR NEWS on December 19, 2019