USMI Bioinformatics Lab home page

Bioinformatics Laboratory - Proteomics and Mass Spectrometry Unit
IRCCS Ospedale Policlinico San Martino - Genova

Contact: paolo.dm.romano@gmail.com - https://proteomics.hsanmartino.it/promano/ -

Research interests

Biomedical data management and integration.
Network standards, technologies, tools and applications in bioinformatics.
Mass Spectrometry data analysis.

Current projects

The Microbial Resource Research Infrastructure (MIRRI) is a European Research Infrastructure aiming at improving the adoption of quality microbial resources with great potential in many application domains

Microbial Resource Research Infrastructure (MIRRI)
The Joint Research Unit MIRRI-IT is a partnership towards the creation of the Italian node of MIRRI, the Microbial Resource Research Infrastructure

Joint Research Unit MIRRI-IT

EOSC-Life

IS_MIRRI21

BY-COVID: Beyond Covid
The MicroBioDiverSar project for 'Conservation, protection and valorization of Microbial AgroBiodiversity of Sardinia'

The MicroBioDiverSar project for 'Conservation, protection and valorization of Microbial AgroBiodiversity of Sardinia'

MicroBioDiverSar (MBDS)

Data analysis tools

Geena 2

GeenaR

SeraDeg

MultiTargetScan (discontinued)

Network Tools

biowep

IBWS is a suite of Web Services allowing programmatic access to CABRI, TP53 by SRS, and SWS (SRS by Web Services).

IST Bioinformatics Web Services
A Galaxy implementation meant to demonstrate integration of microbial domain Biological Resource Centers (mBRCs) catalogues in the bioinformatics data integration environment.

A Galaxy implementation meant to demonstrate integration of microbial domain Biological Resource Centers (mBRCs) catalogues in the bioinformatics data integration environment.

Galaxy USMI Demonstrator (discontinued)

Databases

CLIMA 2

CABRI

HyperCLDB

The Molecular Probe Data Base (MPDB) contains information on synthetic oligonucleotides with a sequence of up to 100 nucleotides. Data are mainly taken from the literature and are encoded on the basis of controlled vocabularies.

Molecular Probe Data Base (MPDB)
An SRS based implementation of the IARC TP53 Mutation database.

IARC TP53 Mutation Database on SRS
The BITS Meetings' Virtual Library includes abstracts from Italian Bioinformatics Meetings since 1999...

BITS Library
PROTEIN-LIGAND Interaction is a database that describes the interactions that a small molecules (identified by a Het_Id code) perform with target proteins, as observed in PDB complexes.

PROTEIN-LIGAND Interaction is a database that describes the interactions that a small molecules (identified by a Het_Id code) perform with target proteins, as observed in PDB complexes.

PLI: Protein-Ligand Interaction

Bioinformatics Events (BIECR, discontinued)

European Collection for Biomedical Research (ECBR, discontinued)

Web sites

The web site of the Interlab Cell Line Collection of Human and animal cell lines

ICLC Cell Bank Web site
The catalogue of the Interlab Cell Line Collection of Human and animal cell lines. Query cell lines by name, code and properties.

The catalogue of the Interlab Cell Line Collection of Human and animal cell lines. Query cell lines by name, code and properties.

ICLC Cell Bank Catalogue Search
The web site of the Joint Research Unit MIRRI-IT, Italian node of the European Research Infrastructure MIRRI (Microbial Resource Research Infrastructure)

MIRRI-IT

The web site of the MicroBioDiverSar (MBDS) project

MicroBioDiverSar (MBDS)
BITS 2009 - Sixth Annual Meeting of the Bioinformatics Italian Society, March 18 - 20, 2009, Genoa

BITS 2009

European Biological Resource Centers Network (EBRCN, discontinued)

Hormone Responsive Breast Cancer Network (HRBC, discontinued)

Selected publications

Daga E, Budroni M, Multineddu C, Cosentino S, Deplano M, Romano P, Comunian R. The MicroBioDiverSar project: exploring the microbial biodiversity in ex situ collections of Sardinia. Sustainability 2021, 13(15):8494. DOI: 10.3390/su13158494

Del Prete E, Facchiano A, Profumo A, Angelini C, Romano P. GeenaR: a web tool for reproducible MALDI-TOF analysis. Frontiers in Genetics. 29 March 2021. 12:635814. DOI: 10.3389/fgene.2021.635814 PMID: 33854526

Romano P, Profumo A, Facchiano A. Pre-processing MALDI/TOF mass spectra by using Geena 2. Current Protocols in Bioinformatics 2018, 64(1):e59. DOI: 10.1002/cpbi.59 PMID: 30422396

Romano P, Beitia San Vicente M, Profumo A. A mass spectrometry based method and a software tool to assess degradation status of serum samples to be used in proteomics for biomarker discovery. Journal of Proteomics 2018, 173: 99-106. DOI: 10.1371/10.1016/j.jprot.2017.12.004 PMID: 29242081

Romano P, Profumo A, Rocco M, Mangerini R, Ferri F, Facchiano A. Geena 2, improved automated analysis of MALDI/TOF mass spectra. BMC Bioinformatics 2016, 17(Suppl 4):61 DOI: 10.1186/s12859-016-0911-2 PMID: 26961516

Zappa A, Splendiani A, Romano P. Towards linked open gene mutations data. BMC Bioinformatics 2012, 13(Suppl 4):S7 DOI: 10.1186/1471-2105-13-S4-S7 PMID: 22536974

Zappa A, Miele M, Romano P. IBWS: IST Bioinformatics Web Services. Nucleic Acids Research (2010) 38 (suppl 2): W712-W718. DOI: 10.1093/nar/gkq416 PMID: 20484374

Romano P, Manniello A, Aresu O, Armento M, Cesaro M, Parodi B. Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines, Nucleic Acids Research 2009 37(Database issue):D925-D932 DOI: 10.1093/nar/gkn730 PMID: 18927105

Romano P, Marra D. SWS: accessing SRS sites contents through Web Services, BMC Bioinformatics, 2008 9(Suppl 2):S15 DOI: 10.1186/1471-2105-9-S2-S15 PMID: 18387203

Romano P. Automation of in-silico data analysis processes through workflow management systems, Briefings in Bioinformatics, 2008 9(1):57-68 DOI: 10.1093/bib/bbm056 PMID: 18056132

Bioinformatics Laboratory - Proteomics and Mass Spectrometry UnitIRCCS Ospedale Policlinico San Martino - Genova

Bioinformatics Laboratory - Proteomics and Mass Spectrometry Unit
IRCCS Ospedale Policlinico San Martino - Genova