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Other IDs

Scopus Author ID: 56373576900
SciProfiles: 778991
Loop profile: 1754072

Keywords

Bioinformatics, Computational Biology, Metagenomics, Computer Science, Machine Learning, Microbiome, Vector-Symbolic Architectures

Countries

Italy, United States

Activities

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Employment (5)

Cleveland Clinic: Cleveland, OH, US

2022-03 to present | Postdoctoral Researcher (Genomic Medicine Institute, Lerner Research Institute)
Employment
Source: Self-asserted source
Fabio Cumbo

University of Trento: Povo, IT

2018-11 to 2021-12 | Postdoctoral Researcher (Department of Cellular, Computational and Integrative Biology (CIBIO))
Employment
Source: Self-asserted source
Fabio Cumbo

Consiglio Nazionale delle Ricerche: Rome, IT

2015-11 to 2020-01 | Research Associate (Institute for Systems Analysis and Computer Science "Antonio Ruberti")
Employment
Source: Self-asserted source
Fabio Cumbo

University of Roma Tre: Rome, IT

2015-11 to 2018-10 | PhD Candidate (Department of Engineering)
Employment
Source: Self-asserted source
Fabio Cumbo

The Pennsylvania State University: University Park, PA, US

2017-03 to 2018-03 | Research Lab Assistant (Department of Biochemistry and Molecular Biology)
Employment
Source: Self-asserted source
Fabio Cumbo

Education and qualifications (2)

Università degli Studi Roma Tre: Roma, Lazio, IT

2015-11-01 to 2018-10-31 | Ph.D. in Computer Science and Automation Engineering (Department of Engineering)
Education
Source: Self-asserted source
Fabio Cumbo

Università degli Studi Roma Tre: Roma, Lazio, IT

2014-07-27 | Master of Science Degree in Software Engineer (Department of Engineering)
Education
Source: Self-asserted source
Fabio Cumbo

Works (36)

The Microbiology Galaxy Lab: A community-driven gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data

2024-12-27 | Preprint
DOI: 10.1101/2024.12.23.629682
Contributors: Engy Nasr; Pierre Amato; Matthias Bernt; Anshu Bhardwaj; Daniel Blankenberg; Daniela Brites; Fabio Cumbo; Katherine Do; Emanuele Ferrari; Timothy J. Griffin et al.
Source: check_circle
Crossref

Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer

2024-11-20 | Preprint
DOI: 10.1101/2024.11.18.624180
Contributors: Fabio Cumbo; Simone Truglia; Emanuel Weitschek; Daniel Blankenberg
Source: check_circle
Crossref

Characterizing and evaluating cell specialization through Gini index of gene expression: TCGA normal vs tumor case study

2024-06-23 | Preprint
DOI: 10.1101/2024.06.19.599717
Contributors: Fabio Cumbo; Daniele Santoni
Source: check_circle
Crossref

Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m6A site accessibility

Nature Communications
2024-05-20 | Journal article
DOI: 10.1038/s41467-024-48549-x
Contributors: Debjit Khan; Iyappan Ramachandiran; Kommireddy Vasu; Arnab China; Krishnendu Khan; Fabio Cumbo; Dalia Halawani; Fulvia Terenzi; Isaac Zin; Briana Long et al.
Source: check_circle
Crossref

Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding

eBioMedicine
2024-01 | Journal article
DOI: 10.1016/j.ebiom.2023.104917
Contributors: Mireia Valles-Colomer; Paolo Manghi; Fabio Cumbo; Giulia Masetti; Federica Armanini; Francesco Asnicar; Aitor Blanco-Miguez; Federica Pinto; Michal Punčochář; Alberto Garaventa et al.
Source: check_circle
Crossref

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Nature Biotechnology
2023-11 | Journal article
DOI: 10.1038/s41587-023-01688-w
Contributors: Aitor Blanco-Míguez; Francesco Beghini; Fabio Cumbo; Lauren J. McIver; Kelsey N. Thompson; Moreno Zolfo; Paolo Manghi; Leonard Dubois; Kun D. Huang; Andrew Maltez Thomas et al.
Source: check_circle
Crossref

hdlib: A Python library for designing Vector-Symbolic Architectures

Journal of Open Source Software
2023-09-11 | Journal article
DOI: 10.21105/joss.05704
Contributors: Fabio Cumbo; Emanuel Weitschek; Daniel Blankenberg
Source: check_circle
Crossref

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

PLOS Computational Biology
2023-07-06 | Journal article
DOI: 10.1371/journal.pcbi.1011224
Contributors: Davide Chicco; Francis Ouellette; Fabio Cumbo; Claudio Angione
Source: check_circle
Crossref

Population-level impacts of antibiotic usage on the human gut microbiome

Nature Communications
2023-03-02 | Journal article
DOI: 10.1038/s41467-023-36633-7
Contributors: Kihyun Lee; Sebastien Raguideau; Kimmo Sirén; Francesco Asnicar; Fabio Cumbo; Falk Hildebrand; Nicola Segata; Chang-Jun Cha; Christopher Quince
Source: check_circle
Crossref

Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks

Bioinformatics
2023-01-01 | Journal article
DOI: 10.1093/bioinformatics/btac763
Contributors: Nicola Apollonio; Daniel Blankenberg; Fabio Cumbo; Paolo Giulio Franciosa; Daniele Santoni
Source: check_circle
Crossref

Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

2022-08-22 | Preprint
DOI: 10.1101/2022.08.22.504593
Contributors: Aitor Blanco-Miguez; Francesco Beghini; Fabio Cumbo; Lauren J. McIver; Kelsey N. Thompson; Moreno Zolfo; Paolo Manghi; Leonard Dubois; Kun D. Huang; Andrew Maltez Thomas et al.
Source: check_circle
Crossref

Commensal <i>Bifidobacterium</i> Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines

Vaccines
2021-11 | Journal article | Author
DOI: 10.3390/vaccines9111356
Contributors: Michele Tomasi; Mattia Dalsass; Francesco Beghini; Ilaria Zanella; ELENA CAPRONI; Laura Fantappiè; ASSUNTA GAGLIARDI; Carmela Irene; Enrico König; Luca Frattini et al.
Source: check_circle
Multidisciplinary Digital Publishing Institute

An In-Memory Cognitive-Based Hyperdimensional Approach to Accurately Classify DNA-Methylation Data of Cancer

2020 | Book chapter
DOI: 10.1007/978-3-030-59028-4_1
Contributors: Fabio Cumbo; Emanuel Weitschek
Source: check_circle
Crossref

Extending Knowledge on Genomic Data and Metadata of Cancer by Exploiting Taxonomy-Based Relaxed Queries on Domain-Specific Ontologies

2020 | Book chapter
DOI: 10.1007/978-3-030-63061-4_4
Contributors: Eleonora Cappelli; Emanuel Weitschek; Fabio Cumbo
Source: check_circle
Crossref

A Brain-Inspired Hyperdimensional Computing Approach for Classifying Massive DNA Methylation Data of Cancer

Algorithms
2020-09-17 | Journal article
DOI: 10.3390/a13090233
Contributors: Fabio Cumbo; Eleonora Cappelli; Emanuel Weitschek
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

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

Applied Sciences
2020-09-12 | Journal article
DOI: 10.3390/app10186367
Contributors: Eleonora Cappelli; Fabio Cumbo; Anna Bernasconi; Arif Canakoglu; Stefano Ceri; Marco Masseroli; Emanuel Weitschek
Source: check_circle
Crossref
grade
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Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

Nature Communications
2020-05-25 | Journal article
DOI: 10.1038/s41467-020-16438-8
Contributors: Edoardo Pasolli; Francesca De Filippis; Italia E. Mauriello; Fabio Cumbo; Aaron M. Walsh; John Leech; Paul D. Cotter; Nicola Segata; Danilo Ercolini
Source: check_circle
Crossref

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Nature Communications
2020-05-19 | Journal article
DOI: 10.1038/s41467-020-16366-7
Contributors: Francesco Asnicar; Andrew Maltez Thomas; Francesco Beghini; Claudia Mengoni; Serena Manara; Paolo Manghi; Qiyun Zhu; Mattia Bolzan; Fabio Cumbo; Uyen May et al.
Source: check_circle
Crossref

An ontology-based approach to improve data querying and organization of Alzheimer's Disease data

Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
2019 | Conference paper
DOI: 10.1109/BIBM.2018.8621524
EID:

2-s2.0-85062569481
Contributors: Arisi, I.; Bertolazzi, P.; Cappelli, E.; Conte, F.; Cumbo, F.; Fiscon, G.; Sonnessa, M.; Taglino, F.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

GMS – Gammadiae Management System: Cataloguing and interpretation project of the socalled gammadiae starting from the iconographic evidences in the Roman catacombs

Conservar Patrimonio
2019 | Journal article
DOI: 10.14568/cp2018015
EID:

2-s2.0-85067824737
Contributors: Cumbo, C.; Cumbo, F.A.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier
grade
Preferred source (of 2)‎

Smart Persistence and Accessibility of Genomic and Clinical Data

2019 | Book chapter
DOI: 10.1007/978-3-030-27684-3_2
Contributors: Eleonora Cappelli; Emanuel Weitschek; Fabio Cumbo
Source: check_circle
Crossref

Bioconda: Sustainable and comprehensive software distribution for the life sciences

Nature Methods
2018 | Journal article
DOI: 10.1038/s41592-018-0046-7
EID:

2-s2.0-85049501214
Contributors: Dale, R.; Grüning, B.; Sjödin, A.; Rowe, J.; Chapman, B.A.; Tomkins-Tinch, C.H.; Valieris, R.; Batut, B.; Caprez, A.; Cokelaer, T. et al.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

Classification of Large DNA Methylation Datasets for Identifying Cancer Drivers

Big Data Research
2018 | Journal article
DOI: 10.1016/j.bdr.2018.02.005
EID:

2-s2.0-85044256269
Contributors: Celli, F.; Cumbo, F.; Weitschek, E.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

Classifying Big DNA Methylation Data: A Gene-Oriented Approach

2018 | Book chapter
DOI: 10.1007/978-3-319-99133-7_11
Contributors: Emanuel Weitschek; Fabio Cumbo; Eleonora Cappelli; Giovanni Felici; Paola Bertolazzi
Source: check_circle
Crossref
grade
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Investigating transcription factor synergism in humans

DNA Research
2018 | Journal article
DOI: 10.1093/dnares/dsx041
EID:

2-s2.0-85042628370
Contributors: Cumbo, F.; Vergni, D.; Santoni, D.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

IWTomics: Testing high-resolution sequence-based 'Omics' data at multiple locations and scales

Bioinformatics
2018 | Journal article
DOI: 10.1093/bioinformatics/bty090
EID:

2-s2.0-85050817224
Contributors: Cremona, M.A.; Pini, A.; Cumbo, F.; Makova, K.D.; Chiaromonte, F.; Vantini, S.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

COSYS: A Computational Infrastructure for Systems Biology

2017 | Book chapter
DOI: 10.1007/978-3-319-67834-4_7
Contributors: Fabio Cumbo; Marco S. Nobile; Chiara Damiani; Riccardo Colombo; Giancarlo Mauri; Paolo Cazzaniga
Source: check_circle
Crossref
grade
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Genomic Data Integration: A Case Study on Next Generation Sequencing of Cancer

Proceedings - International Workshop on Database and Expert Systems Applications, DEXA
2017 | Conference paper
DOI: 10.1109/DEXA.2016.025
EID:

2-s2.0-85012050308
Contributors: Weitschek, E.; Cumbo, F.; Cappelli, E.; Felici, G.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

IRIS-TCGA: An Information Retrieval and Integration System for Genomic Data of Cancer

2017 | Book chapter
DOI: 10.1007/978-3-319-67834-4_13
Contributors: Fabio Cumbo; Emanuel Weitschek; Paola Bertolazzi; Giovanni Felici
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

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

BMC Bioinformatics
2017 | Journal article
DOI: 10.1186/s12859-016-1419-5
EID:

2-s2.0-85008177178
Contributors: Cumbo, F.; Fiscon, G.; Ceri, S.; Masseroli, M.; Weitschek, E.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

TCGA2BED and CAMUR for cancer NGS data processing

F1000RESEARCH
2016 | Journal article
Source: Self-asserted source
Fabio Cumbo

TCGA2BED: converting and querying The Cancer Genome Atlas.

BITS 2016: 13th Annual Meeting of the Bioinformatics Italian Society
2016 | Conference paper
Source: Self-asserted source
Fabio Cumbo

The Cancer Genome Atlas data querying tool

BITS 2015: 12th Annual Meeting of the Bioinformatics Italian Society
2015 | Conference paper
Source: Self-asserted source
Fabio Cumbo

Time dynamics of protein complexes in the AD11 transgenic mouse model for Alzheimer's disease like pathology

BMC Neuroscience
2015 | Journal article
DOI: 10.1186/s12868-015-0155-5
EID:

2-s2.0-84929440972
Contributors: Arisi, I.; D'Onofrio, M.; Brandi, R.; Cattaneo, A.; Bertolazzi, P.; Cumbo, F.; Felici, G.; Guerra, C.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

GIANT: A cytoscape plugin for modular networks

PLoS ONE
2014 | Journal article
DOI: 10.1371/journal.pone.0105001
EID:

2-s2.0-84907487776
Contributors: Cumbo, F.; Paci, P.; Santoni, D.; Di Paola, L.; Giuliani, A.
Source: Self-asserted source
Fabio Cumbo via Scopus - Elsevier

Selecting relevant nodes and structures in biological networks. BiNAT: a new plugin for Cytoscape

F1000Research
2014 | Journal article
Source: Self-asserted source
Fabio Cumbo
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