Paolo Romano | IRCCS AOU San Martino-IST Genova (original) (raw)

Papers by Paolo Romano

Zenodo (CERN European Organization for Nuclear Research), Jun 20, 2023

Data Science Journal

The Horizon Europe project ISIDORe is dedicated to pandemic preparedness and responsiveness resea... more The Horizon Europe project ISIDORe is dedicated to pandemic preparedness and responsiveness research. It brings together 17 research infrastructures (RIs) and networks to provide a broad range of services to infectious disease researchers. An efficient and structured treatment of data is central to ISIDORe’s aim to furnish seamless access to its multidisciplinary catalogue of services, and to ensure that users’ results are treated FAIRly. ISIDORe therefore requires a data management plan (DMP) covering both access management and research outputs, applicable over a broad range of disciplines, and compatible with the constraints and existing practices of its diverse partners. Here, we describe how, to achieve that aim, we undertook an iterative, step-by-step, process to build a community-approved living document, identifying good practices and processes, on the basis of use cases, presented as proof of concepts. International fora such as the RDA and EOSC, and primarily the BY-COVID p...

Cancers

To date, the 5-year overall survival rate of 60% for early-stage non-small cell lung cancer (NSCL... more To date, the 5-year overall survival rate of 60% for early-stage non-small cell lung cancer (NSCLC) is still unsatisfactory. Therefore, reliable prognostic factors are needed. Growing evidence shows that cancer progression may depend on an interconnection between cancer cells and the surrounding tumor microenvironment; hence, circulating molecules may represent promising markers of cancer recurrence. In order to identify a prognostic score, we performed in-depth high-throughput analyses of plasma circulating markers, including exosomal microRNAs (Exo-miR) and peptides, in 67 radically resected NSCLCs. The miRnome profile selected the Exo-miR-130a-3p as the most overexpressed in relapsed patients. Peptidome analysis identified four progressively more degraded forms of fibrinopeptide A (FpA), which were depleted in progressing patients. Notably, stepwise Cox regression analysis selected Exo-miR-130a-3p and the greatest FpA (2-16) to build a score predictive of recurrence, where high-r...

Zenodo (CERN European Organization for Nuclear Research), Feb 21, 2022

This deliverable is the blueprint of the Life Science AAI, a common authentication and authorisat... more This deliverable is the blueprint of the Life Science AAI, a common authentication and authorisation service for the European life science research infrastructures. The Life Science AAI provides a way to coordinate the way how user identity and access is managed in research services and data in the (community-specific) federated Infrastructure. The service will be managed by the life sciences community and operated by the e-infrastructures, such as GEANT, EGI and EUDAT. The requirements of the Life Science AAI were initially developed by CORBEL WP5 and piloted with e-infrastructures in the AARC2 project. This deliverable lays the ground for the production deployment with e-infrastructures during the EOSC-Life project. This deliverable and its appendices first introduces the technical and non-technical requirements for the e-infrastructure service offering and further clarifies how that relates to and integrates to the AAI service components operated by the life sciences research inf...

This deliverable addresses WP1's objectives related to publication of data and data resources... more This deliverable addresses WP1's objectives related to publication of data and data resources in cloud repositories by making available resources in EOSC-Life's registries; the implementation of FAIR services and standards, by development of FAIR registries in collaboration with WP6; and evolution of repository infrastructure by making available registry entries deriving from WP3 demonstrators. Use cases for EOSC-Life registries have been defined for general and clinical research data use and the 'EOSC-Life' collection in FAIRsharing has been populated and released comprising more than 100 data resources and standards. A clinical MetaData Repository has also been developed to address challenges of clinical data sharing in Europe. We have engaged with EOSC, sister projects such as FAIRsFAIR and ENVRI to consider the features of registries, cross registry interoperability and use cases which link EOSC projects. We will continue to update the registries as the project p...

Frontiers in Genetics, 2021

Mass spectrometry is a widely applied technology with a strong impact in the proteomics field. MA... more Mass spectrometry is a widely applied technology with a strong impact in the proteomics field. MALDI-TOF is a combined technology in mass spectrometry with many applications in characterizing biological samples from different sources, such as the identification of cancer biomarkers, the detection of food frauds, the identification of doping substances in athletes’ fluids, and so on. The massive quantity of data, in the form of mass spectra, are often biased and altered by different sources of noise. Therefore, extracting the most relevant features that characterize the samples is often challenging and requires combining several computational methods. Here, we present GeenaR, a novel web tool that provides a complete workflow for pre-processing, analyzing, visualizing, and comparing MALDI-TOF mass spectra. GeenaR is user-friendly, provides many different functionalities for the analysis of the mass spectra, and supports reproducible research since it produces a human-readable report ...

Introduction Computational reproducibility refers to the possibility of reconstructing all the st... more Introduction Computational reproducibility refers to the possibility of reconstructing all the steps of a workflow that connects raw data, processed data and results: it is a fundamental issue in the omic studies because of the complex and high-dimensional nature of the involved data. The analysis of omics data needs to exploit multi-step workflows including pre-processing, elaboration, statistical validation, interpretation and presentation. Although some analysis platforms are able to ensure computational reproducibility for different omics studies, they do not provide explicit information about the executed code. The availability of the code increases the quality of research in terms of transparency and knowledge transfer. Moreover, it allows other researchers to reproduce the results in a local system, make a comparison among the results and re-use computer code for analyzing different dataset. Methods Geena 2 is a robust web tool for MALDI-ToF mass spectra pre-processing. Its m...

BMC bioinformatics, 2015

This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014... more This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014.

Semantic Web Applications and Tools for Life Sciences, Dec 7, 2011

BMC Bioinformatics, Jan 25, 2012

As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL ... more As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications. Unsurprisingly, therefore, interest in the SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) activities have remained high, as was evident during the third international SWAT4LS workshop held in Berlin in December 2010. Contributors to this workshop were invited to submit extended versions of their papers, the best of which are now made available in the special supplement of BMC Bioinformatics. The papers reflect the wide range of work in this area, covering the storage and querying of Life Sciences data in RDF triple stores, tools for the development of biomedical ontologies and the semantics-based integration of Life Sciences as well as clinicial data.

BMC bioinformatics, Jan 2, 2016

The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from str... more The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology. The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics, functional proteomics, mass spectrometry, drug discovery, and systems biology.43 scientific contributions were presented at NETTAB 2014, including keynote, special guest and tutorial talks, oral communications, and posters. Full papers from some of the best contributions presented at the workshop were later submitted to a special Call for this Supplement.Here, we provide an overview of the workshop and introduce manuscripts that have been accepted for publication in this Supplement.