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Luciano Milanesi
Socio Ordinario
Ricercatore
CNR
Contact Information
phone
0226422604
fax
0226422770
RESEARCH AREA
algorithms,biological data integration,biological data modelling,biological ontologies,comparative genomics,knowledge base management,IT-ICT technology,machine learning,network systems,sequence analysis,structural genomics,structure analysis,system biology
RESEARCH ACTIVITY
He contributes in the coordination of the Bioinformatics Research Unit of the Institute of Biomedical Technologies of the National Research Council (CNR-ITB). This division was established in 1986 to work in the framework of the Italian Human Genome Strategic Project coordinated by the Nobel Price Prof. Renato Dulbecco. He carried out research to develop tools for the genome sequence analysis and prediction of gene structure in different organisms and to studying the functions of genes, promoter prediction, gene expression analysis gene network, system biology and to develop data mining tools integrated with sequence analysis tools.
1988 – 1991
Strategic Project: The Human Genome. Coordinated by the Nobel Price Prof. Renato Dulbecco.
Title: Genomic sequence analysis tools and data collection systems for the processing of data generated during the Human Genome Project
1992 – 1996
CNR-ITBA Research Unit for the Italian CNR Genetic Engineering Project
Title: Computerized system for the analysis of human DNA sequences.
1996 – 1999
Scientific Supervisor of the Research Unit for the European TRADAT project. Coordinated by Prof. Edgar Wingender
Title: Transcription Databases and Analysis Tools (TRADAT)
2001 – 2002
Scientific Supervisor of the Research Unit for CNR Molecular Genetics Project. Coordinated by Dr. Glauco Tocchini Valentini.
Title: development of a computerized system for analysis and identification of genes and the regulator regions of Human Genome.
2002 - 2005
Scientific Supervisor of the Research Unit for the Oncology Over Internet (O2I) project coordinated by Ing. Paolo Romano (IST-Genova)
Title: Development and implementation of software for researchers, filtering and searching over internet oncology related information.
2002 – 2004
Scientific Supervisor of the Research Unit for the CNR/MURST research project: Functional Genomics, coordinated by Dr. Glauco Tocchini Valentini.
Title: Research to find new kinases specifically for the brain using an in silico approach combined with experimental trials
2002 – 2004
Scientific Supervisor of the Research Unit for the European project: ORIEL Coordinated by Dr. Les Grivel (EMBO)
Title: ORIEL - Online Research Information Environment for the Life Sciences.
2001 - 2010
Scientific Supervisor of the Bioinformatics Research Unit Centre for the Bio-molecular Interdisciplinary Studies and Industrial Applications (CISI) of the University of Studies of Milan.
2004 – 2006
Project Coordinator of the NATO Science Programme – Cooperative Science Technology Sub-Programme “Collaborative Linkage Grant”.
Title: Gene networks of co-expressed genes: modeling and 5’-UTR sequence analysis.
2003 – 2006
Scientific Supervisor of the Research Unit for developing Bioinformatics applications in the Italian MIUR- FIRB project “GRID.IT”, coordinated by Prof. Vanneschi Marco
Title: enable platforms for high-performance computational grids oriented to scalable virtual organizations (GRID.IT).
2003 –2006
Scientific Supervisor of the Research Unit for the MIUR-FIRB Project: Post-Genomics, Coordinated by Prof.ssa Cecilia Saccone.
Title: Bioinformatics for Genomics and Proteomics
2004 – 2006
Scientific Supervisor of the Research Unit for the International Project Programme INTAS, coordinated by: Dr. Alexander Kel (BIOBASE).
Title: CYCLONET: “Building a comprehensive model of mammalian cell-cycle regulatory network in normal and pathological states to predict potential anticancer pharmacological agents for key target molecules”.
2005 – 2006
Scientific Supervisor of the Research Unit for the European Project Specific Support Action (SYMBIOmatics) in the 6th Framework Programme. Coordinated by: Dr. Graham Cameron - European Bioinformatics Institute – Cambridge UK
Title: Synergies in Medical Informatics and Bioinformatics. (SYMBIOmatics)
2005 – 2010
Scientific Coordinator of the MIUR-FIRB Public-Private Laboratory LITBIO (project in the Bioinformatics area.
Title: Laboratory of Interdisciplinary Technologies in Bioinformatics (LITBIO) (RBLA0332RH).
2006 – 2007
Scientific European coordinator in the 6th Framework European Project Specific Support Action (BIOINFOGRID).
Title: Bioinformatics Grid Application for Life Science (BIOINFOGRID).
http://www.bioinfogrid.eu
2006-2009
Scientific Supervisor of the Research Unit for the International Project INTAS Ref. Nr 05-1000008-8028, coordinated by: Prof. Dmitrij Frishman - Department of Genome-Oriented Bioinformatics - Institute for Bioinformatics - Technische Universitaet Minich. Germany. Starting date June 2006 duration 30 month
Title: Comparative genomics of bacteria: functional annotation, metabolic reconstruction, evolution of metabolic pathways and regulatory systems
2006-2008
Scientific Supervisor of the Research Unit for the project “EGEEII” Ref. Nr. 031688 Commission of the European Communities information society and Media - Research Infrastructures Integrated Infrastructure Initiative. Coordinated by: Prof Bob Jones CERN Genève. Starting date 1 April 2006 duration 24 month.
Title: EGEE-II: Enabling Grids for E-sciencE-II
2007-2010
Scientific partner of the Italian Research Unit in the project “Net2Drug” project contract N° 037590 on the 6th EU call “Specific targeted Research or innovative Project dedicated to SMEs” coordinated by: Dr. Alexander Kel.
Title: From gene regulatory networks to drug prediction.
2007-2010
Scientific coordinator of the Italian Research Unit in the project “Bioinformatics Population Genetics Analysis” MIUR-FIRB international scientific and technological cooperation project between Italy and Canada contact N° RBIN064YAT.
Title: Bioinformatics Population Genetics Analysis
2007-today
Scientific coordinator of the Italian CNR Bioinformatics project “CNR-BIOINFORMATCS”
Title: CNR-BIOINFORMATICS: CNR Interdepartmental coordinating Bioinformatics research activities in 12 different CNR institutes in all Italy. http://www.cnr-bioinformatics.it
2008-2011
Scientific partner of the FP7- “ESFRI” project
Title: BBMRI - Biobanking and Biomolecular Resources Research Infrastructure. http://www.bbmri.eu
2008-2010
Scientific Supervisor of the Research Unit for the project EGEEIII. Commission of the Europen Communities information society and Media - Research Infrastructures Integrated Infrastructure Initiative. Coordinated by: Prof Bob Jones CERN Genève.
Title: EGEE-III - Enabling Grids for E-sciencE-III (INFSO-RI-222667)
http://www.eu-egee.org/
23/01/2007 - 23/01/2013
Scientific Coordination of the MIUR-FIRB Italian Bioinformatics Network “ITALBIONET”
Title: ITALBIONET – Italian Bioinformatics Network (RBPR05ZK2Z)
2008-2010
Scientific subcontractor in the FP7 “EDGeS” project.
Title: EDGeS - Enabling Desktop Grids for e-Science.
This European project with the aim of creating an integrated Grid infrastructure to interconnect the largest European Service Grid infrastructure (EGEE) with existing Desktop Grid (DG) systems in a strong partnership with the EGEE consortium. Service Grids (SG) can be used with a broader variety of applications.
2010-2012
Scientific partners in the Grant “Parents of Galactosemic Children (PGC) USA”.
Title: Computational biology strategy for the development of ligands of GALK enzyme as potential drugs for people with classical galactosemia.
2010-2012
Scientific subcontractor in the FP7 “SHIWA” project.
Title: SHaring Interoperable Workflows for large-scale scientific simulations on Available DCIs. SHIWA is a European project is funded for 2 years to develop solutions for interoperability among grid workflow systems.
2011-2012
Scientific subcontractor in the FP7 “INBIOMEDVision” project
Title: INBIOMEDVision
Promoting and Monitoring Biomedical Informatics in Europe” aims to be a European-wide initiative intended to monitor and address the current challenges of the Biomedical Informatics field by means of an EU-funded Coordination and Support Action (Grant agreement number 270107).
01/12/2011- today
Scientific partner in the Italian Ministry of Health (Grant agreement number GR-2009-1570296).
Title “The relationship among food, mycotoxins, gastrointestinal disorders, and autism: a multidisciplinary approach for the molecular investigation".
01/01/2012-31/12/2017
Title: MIMOmics (Methods for Integrated analysis of Multiple Omics datasets) is a FP7-HEALTH-2012 Innovation project funded by the European Commission.
01/01/2014 – 2018
Title: BBMRI-ERIC Biobanking and BioMolecular Research Infrastructure. Promoted by the European Commission.
01/01/2014 – today
Title: ELIXIR. Bioinformatics Research Infrastructure. Promoted by the European Commission.
01/01/2012-2019
Scientific Director of the MIUR - CNR Italian flagship project “INTEROMICS”
Title: Development of an integrated "Omics" science platform for the definition of diagnostic, predictive and theranostic biomarkers profiles.


SELECTED PUBLICATIONS
- Maccaferri M, Harris NS, Twardziok SO, Milanesi L et al. Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet. 2019;51(5):885‐895.

- Nassa G, Salvati A, Tarallo R, Milanesi L. et al. Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells. Sci Adv. 2019;5(2):eaav5590. Published 2019 Feb 6.

- De Santis B, Raggi ME, Moretti G, Milanesi L. et al. Study on the Association among Mycotoxins and other Variables in Children with Autism. Toxins (Basel). 2017;9(7):203. Published 2017 Jun 29.

- Tarallo R, Giurato G, Bruno G, Milanesi L. et al. The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading. Genome Biol. 2017;18(1):189. Published 2017 Oct 6.

- Spinelli CC, Carrizzo A, Ferrario A, Milanesi L. et al. LAV-BPIFB4 isoform modulates eNOS signalling through Ca2+/PKC-alpha-dependent mechanism. Cardiovasc Res. 2017;113(7):795‐804

- Vecchione C, Villa F, Carrizzo A, Milanesi L. et al. Author Correction: A rare genetic variant of BPIFB4 predisposes to high blood pressure via impairment of nitric oxide signaling. Sci Rep. 2019;9(1):9574. Published 2019 Jun 28.

- Di Nanni N, Bersanelli M, Cupaioli FA, Milanesi L, Mezzelani A, Mosca E. Network-Based Integrative Analysis of Genomics, Epigenomics and Transcriptomics in Autism Spectrum Disorders. Int J Mol Sci. 2019;20(13):3363. Published 2019 Jul 9.

- Mezzelani A, Landini M, Facchiano F, Raggi ME, Villa L, Molteni M, De Santis B, Brera C, Caroli AM, Milanesi L, Marabotti A. Environment, dysbiosis, immunity and sex-specific susceptibility: A translational hypothesis for regressive autism pathogenesis. Nutr Neurosci. 2014 Jan 21. [PubMed PMID: 24621061.

- Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano (2014) A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units. in BMC Bioinformatics 2014, 15(Suppl 1):S10 doi:10.1186/1471-2105-15-S1-S10

- F.Viti, S.Scaglione, A. Orro, L.Milanesi (2014) Guidelines for managing data and processes in bone and cartilage tissue engineering. BMC Bioinformatics 2014, 15(Suppl 1):S14 doi:10.1186/1471-2105-15-S1-S14

- Di Gennaro, P; Zampolli, J; Presti, I; Cappelletti, M; D'Ursi, P; Orro, A; Mezzelani, A; Milanesi, L (2014) Genome Sequence of Rhodococcus opacus Strain R7, a Biodegrader of Mono- and Polycyclic Aromatic Hydrocarbons. Genome Announc. July/August 2014 vol. 2 no. 4 e00827-14. doi: 10.1128/genomeA.00827-14

- Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano (2014) GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads. PloS one: May 19, 2014 doi: 10.1371/journal.pone.0097277

- Bocchio-Chiavetto, Luisella; Maffioletti, Elisabetta; Bettinsoli, Paola; Giovannini, Caterina; Bignotti, Stefano; Tardito, Daniela; Corrada, Dario; Milanesi, Luciano; Gennarelli, Massimo (2013). Blood microRNA changes in depressed patients during antidepressant treatment. European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology. 08/2012;

- Vezzoli, Giuseppe; Terranegra, Annalisa; Aloia, Andrea; Arcidiacono, Teresa; Milanesi, Luciano; Mosca, Ettore; Mingione, Alessandra; Spotti, Donatella; Cusi, Daniele; Hou, Jianghui; Hendy, Geoffrey N.; Soldati, Laura (2013). Decreased Transcriptional Activity of Calcium-sensing receptor Gene Promoter 1 Is Associated With Calcium Nephrolithiasis in The Journal of clinical endocrinology and metabolism. doi: 10.1210/jc.2013-1834

- M Cappelletti, P Di Gennaro, P D'Ursi, A Orro, A Mezzelani, M Landini, S Fedi, D Frascari, A Presentato, D Zannoni, L Milanesi. Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds.Genome announcements 01/2013; 1(5). doi:10.1128/genomeA.00657-13

- Cichero, Elena; D'Ursi, Pasqualina; Moscatelli, Marco; Bruno, Olga; Orro, Alessandro; Rotolo, Chiara; Milanesi, Luciano; Fossa, Paola (2013) Homology Modeling, Docking Studies and Molecular Dynamic Simulations Using Graphical Processing Unit Architecture to Probe the Type-11 Phosphodiesterase Catalytic Site: A Computational Approach for the Rational Design of Selective Inhibitors in Chemical biology & drug design doi: 10.1111/cbdd.12193.

- Mosca, Ettore; Milanesi, Luciano (2013) Network-based analysis of omics with multi-objective optimization. in Molecular BioSystems. 2013,9, 2971-2980 doi: 10.1039/C3MB70327D

- Merelli, Ivan; Lio, Pietro; Milanesi, Luciano (2013) NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotationsi. In PloS one. doi: 10.1371/journal.pone.0075146

- Merelli I., Calabria A., Cozzi P. A., Viti F., Mosca E. and Milanesi L. SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. BMC Bioinfomatics 08/2013; 14(1). doi:10.1186/1471-2105-14-S1-S9.

- Chiappori, Federica; Merelli, Ivan; Milanesi, Luciano; Marabotti, Anna (2013) Static and dynamic interactions between GALK enzyme and known inhibitors: Guidelines to design new drugs for galactosemic patients. in European journal of medicinal chemistry doi: 10.1016/j.ejmech.2013.02.021

- Mosca E., Alfieri R., Maj C., Bevilacqua A., Canti G., Milanesi L. Computational Modelling of the Metabolic States Regulated by the Kinase Akt. Frontiers in Physiology 2012, 3:418 DOI: 10.3389/fphys.2012.00418
OTHER MEMBERSHIPS
- President of the BITS Bioinformatics Italian Association
- Member of AIA Artificial Intelligence Association
- Member of SIB Italian Society in Biophysics
- Member of ISCB International Society for Computational Biology
- Member of AICA Italian
EDITORIAL BOARDS
- Briefings in Bioinformatics (Managing Editor M. J. Bishop), Henry Stewart Publications, London (2000 – 2008)

- IEEE Trans. In NanoBiosciences (Managing Editor C. Ruggero),

- In Silico Biology. An International Journal on Computational Molecular Biolog
MAIN TEACHINGS
- Lecturer in “Fundamental Information Science” in Bioinformatics Degree, at the Milan State University (Milano-Bicocca), for the academic year 2006/2007.

- Lecturer in “Bioinformatics” in the Medical Biotechnology Degree, at the Milan State University for the academic year 2005/2006.

- Lecturer in “Fundamental Information Science” in Bioinformatics Degree, at the Milan State University (Milano-Bicocca), for the academic year 2005/2006.

- Lecturer in “Bioinformatics” in the Medical Biotechnology Degree, at the Milan State University for the academic year 2004/2005.

- Lecturer in “Fundamental Information Science” in Bioinformatics Degree, at the Milan State University (Milano-Bicocca), for the academic year 2004/2005.

- Lecturer for the Post Graduate Programme in Bioinformatics PGBIOINF. “Functional and Comparative Genomics” Istituto Gulbenkian de Ciencia, Lisbon (Portugal), April 11 – 15, 2005

Lecturer in “Bioinformatics” in Medical Biotechnology. Degree, at the Milan State University for the academic year 2003/2004.

- Lecturer in “Fundamental Information Science” in Bioinformatics Degree, at the Milan State University (Milano-Bicocca), year 2003/2004.

- Lecturer in “Bioinformatics” in the Medical Biotechnology Degree, at the Milan State University for the academic year 2002/2003.

OTHER TEACHINGS
He has been involved in the organization and teaching of national and international specialized courses on Bioinformatics:

- Main Organizer and Director of the 3rd BioMedGRID Summer School 2009 10-15 May 2009, Varenna, Italy

- Lecturer in the 2008 BGRS International Summer School for young scientists "Evolution, Systems Biology and High-Performance Computing Bioinformatics" Bioinformatics applications by using the GRID computing technology", Novosibirsk, Russia June 29-July 2, 2008

- Main Organizer and Director of the 2nd BioMedGRID Summer School 2008 12-16 May 2008, Varenna, Italy

- Lecturer in the EUROMISE ISSBI – 1° International Summer School of Biomedical Informatics, Prague, Czech, July 8–11, 2008 (http://www.euromise.org/cbi/issbi.html)

- Lecturer in the XXVI Scuola Annuale “GENOMICA PROTEOMICA COMPUTAZIONALE”, 24 - 28 September 2007 Bressanone, Italy

- Organizer and Lecturer of the BioinfoGRID Symposium 2007, 10-13 December 2007, Segrate, Milan, Italy

- Organizer and Lecturer of the 1st BioMedGRID Summer School 2007 14-19 May 2007, Varenna, Italy

- Lecturer at the Ettore Majorana Foundation and Centre for Scientific Culture “Modelling and simulation in science” 15-22 April 2007, EMFCSC, Erice, Italy

- Lecturer at the International Winter School on “BIOINFORMATICS”, at the University of Hyderabad, India December 8-16, 2006

- Lecturer in the 2006 BGRS International Summer School for young scientists "Evolution, Systems Biology and High-Performance Computing Bioinformatics", Novosibirsk, Russia July 12-15, 2006.

- Main Organizer and Lecturer of the BioinfoGRID Initial training course 08 - 10 March 2006, INFN Bari-Italy

- Lecturer in Practical Course "Bioinformatics: Computer Methods in Molecular Biology", International Centre for Genetic Engineering and Biotechnology -Trieste (I), June 23-30, 2006.

- Lecturer for the Post Graduate Programme in Bioinformatics PGBIOINF. “Proteomics, Transcriptomics, Metabolomics” Istituto Gulbenkian de Ciencia, Lisbon (Portugal), April 4 – 8, 2005.

- Practical Course "Bioinformatics: Computer Methods in Molecular Biology", Trieste (I), June 27-July 4, 2005.

- Practical Course "Bioinformatics: Computer Methods in Molecular Biology", Trieste (I), June 27-July 4, 2004.

- Lecturer in the Post Graduate Programme in Bioinformatics PGBIOINF. “Proteomics, Transcriptomics, Metabolomics” Istituto Gulbenkian de Ciencia, Lisbon (Portugal), June 7 – 9, 2004

- The Post Graduate Programme in Bioinformatics PGBIOINF. “Functional and Comparative Genomics” Istituto Gulbenkian de Ciencia, Lisbon (Portugal), March 22 – 25, 2004

- Practical Course "Bioinformatics: Computer Methods in Molecular Biology", Trieste (I), June 27-July 4, 2003.

- Bioinformatics Course, Master in Bioinformatics BIOGEM, Mariano Irpino (I), February 25-March 4, 2003.

- Bioinformatics EMBnet Course, Agrobios Metapontum Consortium, Metaponto (Hu), March 18-22, 2002.

- Practical Course "Bioinformatics: Computer Methods in Molecular Biology", Trieste (I), June 28-July 5, 2002.

- Practical Course "Bioinformatics: Computer Methods in Molecular Biology", Trieste (I), June 29-July 6, 2001.

- “Mediterranean Summer School on Telemedicine and Medical Informatics”, Palermo (I), June 30-Julay 13, 2002

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Hinxton (UK), May 13-15, 2002. Practical Course Bioinformatics and Medical Informatics: “Computer Methods in Biomedical

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Hinxton (UK), October 28-30, 2001.

- EMBnet Course "Molecular Bioinformatics Gene Identification", Beijing (Cn), November 7-14, 2000.

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Hinxton (UK), June 14-16, 2000.

- Practical Course "Bioinformatics: Computer Methods in Molecular Biology", Trieste (I), June 30-July 7, 2000.

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Hinxton (UK), September 30- October 1, 1999.

- Practical Course "Bioinformatics: Computer Methods in Molecular Biology", Trieste (I), July 9-16, 1999.

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Hinxton (UK), June 10-11, 1999.

- ICGEB course "Molecular Biology Databases and Analysis Tools", Beijing (Cn), April 6-12, 1999.

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Cambridge (UK), September 30- October 1, 1998.

- Course "Bioinformatics: Computer Methods in Molecular Biology", Trieste (I), July 3-11, 1998.

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Cambridge (UK), June 14-16, 1998.

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Cambridge (UK), September 30- October 1, 1997.

- HGMP Training Courses in Bioinformatics "Gene Identification and Protein Functional Analysis", Cambridge (UK), June 14-16, 1997.