Consiglio Nazionale delle Ricerche

The CNR-IBBE team has a long-standing experience in molecular biology and bioinformatics approaches applied to several topics of basic and applied Life Sciences as Genomics, mitochondrial biogenesis and function analysis, Molecular Biodiversity and Evolution, characterization of specific molecular processes in aging, neurodegenerative diseases and tumors and identification of specific biomarkers of the pathological condition and its progression.

In particular, the IBBE research activity in “omic” fields is based on multidisciplinary expertise, integration of the most advanced biomolecular and computational analysis resources for the production and the interpretation of data and support of major European research infrastructures such as ELIXIR (Bioinformatics) and LIFEWATCH (Molecular Biodiversity) to which CNR-IBBE contribute by developing and hosting the Italian MoBiLab (Molecular Biodiversity Laboratory). MoBiLab includes high-throughput sequencing (HTS) facilities for Genomics and Metagenomics, computational platforms providing bioinformatic tools and workflows for Phylogenetics, DNA barcoding and Metagenomics and Molecular Biodiversity databases. The main research activities of IBBE include the development of bioinformatics methodologies and specialized databases for taxonomic analysis and functional characterization of "omics" data aimed at assembly and annotation of viral, prokaryotic and eukaryotic genomes, at characterization of metagenomes, at survey of transcriptomes, alternative splicing, RNA editing and epigenetic features. In particular, taxonomic and functional characterization of the microbiome in environmental, clinical and food samples, based on metagenomic approaches through HTS technologies and advanced bioinformatics tools, currently represents a major interest for CNR-IBBE. Identification and characterization of new microbial strains and gene products are included in this activity with the aim of developing innovative processes for biotechnological applications in medical, nutritional and environmental fields.

Relevant previous projects or activities

  • PO-FESR 2007-2013, PONa3_000325 “BIOforIU”, for the construction of an advanced infrastructure for Molecular Biodiversity (Coordinator)
  • EU-FP7 - CReATIVE-B, Coordination of Research e-Infrastructures Activities Toward an International Virtual Environment for Biodiversity (2011-2014, GA N. 284441) (PI)
  • EU-FP7 INFRASTRUCTURES-2011, BioVel - Biodiversity Virtual e-laboratory (2011-2014, GA N. 283359) (PI); 4) FAIR-CT98-4239, Novel PI Crops (PI).
  • LIFEWATCH E-Science European Infrastructure for Biodiversity and Ecosystem Research - FP7-INFRASTRUCTURES-2007-1

Project Members

Francesca de Leo

Dr. Francesca De Leo (female) is a researcher at the Institute of Biomembranes and Bioenergetics of the CNR.  PhD in Biochemistry and Molecular Biology, since 2005 she is also involved in activities focused on exploitation of research results. She participates in the FP7 Biodiversity Virtual e-Laboratory (BioVeL) project and in the CReATIVE-B project. Currently, she mainly works in the project PO-FESR 2007-2013, PONa3_000325 “BIOforIU”, with the aim to construct an advanced infrastructure for Molecular Biodiversity directly linked to the LifeWatch infrastructure.

Monica Santamaria

Dr. Monica Santamaria (female) is a researcher at the Institute of Biomembranes and Bioenergetics of the CNR. She has a substantial background in Molecular Biodiversity and Bioinformatics and her research activity is mainly focused on DNA Barcoding and Metagenomic analysis of prokaryotic and eukaryotic communities residing in several natural, food and clinical environment by means of high-throughput sequencing and advanced bioinformatic approaches. She is primarily involved in the activities of Italian e-Biodiversity Research Institute of “Lifewatch” Research Infrastructure, in the JPI HDHL ENPADASI project and in PONa3_000325 “BIOforIU” project.

Graziano Pesole

Graziano Pesole is full professor of Molecular Biology in the University of Bari and Director of the Institute of Biomembranes and Bioenergetics of the National Research Council. His prevalent research interests are in the fields of bioinformatics, comparative genomics and molecular biodiversity. He has developed several specialised database (UTRdb/UTRsite, ASPidDB, SpliceAidF) and developed widely used analysis software and algorithms which are available through the web. He coordinated research units in several research project funded by national (MIUR, CNR, Telethon, AIRC, AISM) and international (EU, NIH) agencies, and has filed two international patents. He is a member of the editorial Board of international journals (BMC Bioinformatics, BMC Genomics, Computational Biology and Chemistry, Briefings in Bioinformatics; Comparative and Functional Genomics; International Journal of evolutionary Biology), author of over 200 papers published in international journals (>12000 citations, h-index ISI=47) and co-author of books on Bioinformatics, Genomics and Molecular Biology published by italian (Zanichelli, Ambrosiana, Gnocchi) and international (Wiley) editors. For further information see http://pesolelab.ibbe.cnr.it/

 

Recent publications

  • Kissling, W.D., Hardisty, A., García, E.A., Santamaria, M., De Leo, F., Pesole, G., Freyhof, J., Manset, D., Wissel, S., Konijn, J. & Los, W. (2015): Towards global interoperability for supporting biodiversity research on Essential Biodiversity Variables (EBVs). Biodiversity in press.
  • Fosso B., Santamaria M., Marzano M.,  Alonso-Alemany D., Valiente G., Donvito G., Monaco A., Notarangelo P., and Pesole P. (2015) BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC Bioinformatics. in press
  • Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G. (2012) Reference databases for taxonomic assignment in metagenomics Brief Bioinform. Nov;13(6):682-95. doi: 10.1093/bib/bbs036.