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Visiting scientist

Center

CGS@SEMM Milano

Contacts

IIT@SEMM c/o IFOM-IEO-CAMPUS Via Adamello 16

About

11/2010 - present        Head of Computational Research (IIT@SEMM Milan)

01/2002 – 2010           Group Leader Applied Bioinformatics

                                  (European Institute of Oncology Milan)

03/2000-12/2001        Head of Affymetrix expression microarray facility

                                  at Pharmacia&Upjohn Nerviano (Italy)

11/1995- 02/2000       postdoctoral studies at the European Institute of Oncology in

                                  Milan (supervisor Prof. Kristian Helin)

EDUCATION AND TRAINING

09/1990 – 10/1995      Ph.D. studies on cell cycle regulation

                                  Max Delbrück Center Berlin and

                                  Danish Cancer Society Copenhagen

                                  Supervisors: Prof. Michael Strauss, Prof. Jiri Bartek

                                                         Thesis title: “Cell Cycle and Cancer: The Tumor  

                                  Suppressor pRB Stimulates the Expression of

                                  Proto-oncogene Cyclin D1”

06/1990                      Masters thesis in Biophysics

                                  Thesis: “Studies on gene transfer and homologous

                                  recombination in lymphoid cells via electroporation and

                                  lipofection”

                                  Supervisor: Dr. Ralf Glaser (Maximum honors)

09/1987 – 06/1990      Humboldt   University Berlin (Biophysics)

09/1983 – 06/1987      Second Medical Institute Moscow (Biomedicine/Biophysics)

07/1983                      Maturity (average mark 1.0, maximum honors)

Projects

1. Streamlining NGS data analysis pipelines.

2. Identification of tumor driver mutations by meta-analysis of resequencing studies.

3. Statistics of association in bipartite graph models.

4. Enumeration of 0-1 matrices with arbitrary marginal sums.

Selected Publications

PEER REVIEWED PUBLICATIONS

 

Oncogene. 2011 Aug 22. doi: 10.1038/onc.2011.359

Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts.

Perna D,Fagà G,Verrecchia A,Gorski, MM,Barozzi I,Narang V,Khng J,Lim KC,Sung WK,Sanges R,Stupka E,Oskarsson T,Trumpp A,Wei CL,Müller H,Amati B

Google scholar citations: 1

 

PLoS Biol 2010 May 11 8 e100038

A large fraction of extragenic RNA pol II transcription sites overlap enhancers.

De Santa F,Barozzi I,Mietton F,Ghisletti S,Polletti S,Tusi BK,Muller H,Ragoussis J,Wei CL,Natoli G

Google scholar citations: 52

 

Cell Cycle 2010 Dec 1 9 4622-6

TGFß-dependent gene expression shows that senescence correlates with abortive differentiation along several lineages in Myc-induced lymphomas

Müller J,Samans B,van Riggelen J,Fagà G,Peh K N R,Wei CL,Müller H,Amati B,Felsher D,Eilers M

Google scholar citations: 3

 

Plos One, 2008, Vol. 3 (9), e3178

Identification and analysis of co-occurrence networks with NetCutter

Heiko Muller and Francesco Mancuso

Google scholar citations: 6

 

Bioinformatics and Biology Insights, 2008, 2, 203–213

Topological properties of co-occurrence networks in published gene expression signatures

Heiko Muller and Francesco Acquati

 

Nucleic Acids Research, 2007, 35(7), 2343-2355

Identification of cancer signaling pathways from published gene expression signatures using PubLiME.

Giacomo Finocchiaro, Francesco Mattia Mancuso, Heiko Muller

Google scholar citations: 13 (857 downloads)

 

Nucleic Acids Research, 2007, 35 (5), 1488-1500

Localizing hotspots of antisense transcription

Giacomo Finocchiaro, Maria Stella Carro, Stephanie Francois, Paola Parise, Valentina DiNinni, Heiko Muller

Google scholar citations: 15 (1179 downloads)

 

Cell Cycle, 2006, Vol. 5, (12), 1331-1341

Lap2a Expression is Controlled by E2F and Deregulated in Various Human Tumors.

Parise, P., G. Finocchiaro, B. Masciadri, M. Quarto, S. Francois, F. Mancuso, and H. Muller.

Google scholar citations: 14

 

Cell Cycle, 2006, Vol. 5, (11), 1202-1207

DEK Expression is Controlled by E2F and Deregulated in Diverse Tumor Types.

Carro, M.S., F.M. Spiga, M. Quarto, V. Di Ninni, S. Volorio, M. Alcalay, and H. Muller.

Google scholar citations: 45

 

BMC Bioinformatics, 2005, Vol. 6, Suppl. 4, S14

Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control

Finocchiaro G., Mancuso, F., Muller H.

Google scholar citations: 17

 

Oncogene, 2005, Vol. 24 (20),  3358-3368

Molecular Signature of Retinoic Acid Treatment in Acute Promyleocytic Leukemia

Meani, N., Minardi, S., Licciulli, S., Gelmetti, V., Lo Coco, F., Nervi, C., Pelicci, P.G., Muller, H., Alcalay, M.

Google scholar citations: 28

 

Bioinformatics, 2004, Vol. 20 (18), 3670-3672

GenePicker: replicate analysis of Affymetrix gene expression microarrays

Finocchiaro G., Parise P., Minardi S. P., Alcalay M., Muller H.

Google scholar citations: 19

 

Applied Bioinformatics, 2003, Vol. 2 (4), 245-9

Automated DNA chip annotation tables at IFOM: the importance of sequence databases synchronization and cross-references

Guffanti A, Finocchiaro G, Reid JF, Luzi L, Alcalay M, Confalonieri S, Muller H

Google scholar citations: 4

 

J. Clin Invest, 2003, Vol 112 (11), 1751-61

Acute Myeloid Leukemia fusion proteins deregulate genes involved in stem cell maintenance and DNA repair

Alcalay M, Meani N, Gelmetti V, Fantozzi A, Fagioli M, Orleth A, Riganelli D, Sebastani C, Cappelli E, Casciari C, Sciurpi MT, Mariano AR, Minardi SP, Luzi L, Muller H, Di Fiore PP, Frosina G and Pelicci PG

Google scholar citations: 131

 

J Biol Chem 2003 Vol. 278, 46124-37

Identification of Target Genes of the p16INK4A-pRB-E2F Pathway

Vernell R, Helin K, Muller H.

Google scholar citations: 74

 

Eur J Biochem 2001 Sep;268(18):4969-4978

E2F1-mediated transcriptional inhibition of the plasminogen activator inhibitor type 1 gene.

Koziczak M, Muller H, Helin K, Nagamine Y.

Google scholar citations: 23

 

Nature Cell Biology 2001 Jun;3(6):552-8 IF:12.0

APAF1 is a transcriptional target for E2F and p53

M. Cristina Moroni, Emma S. Hickman, Eros Lazzerini Denchi, Greta Caprara, Elena Colli, Francesco Cecconi, Heiko Müller & Kristian Helin

Google scholar citations: 469

 

Genes Dev. 2001 Feb 1;15(3):267-85.

E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis.

Muller H, Bracken AP, Vernell R, Moroni MC, Christians F, Grassilli E, Prosperini E, Vigo E, Oliner JD, Helin K.

Google scholar citations: 554

 

Mol. Cell Biol. 1999; 19(9): 6379 - 6395

CDC25A phosphatase is a target of E2F and is required for efficient E2F induced S phase

Vigo E, Muller H, Prosperini E, Hateboer G, Cartwright P, Moroni C, Helin K

Google scholar citations: 277

 

Oncogene 1999 Mar 11;18(10):1845-53

The cyclin B2 promoter depends on NF-Y, a trimer whose CCAAT-binding activity is cell-cycle regulated.

Bolognese F, Wasner M, Dohna CL, Gurtner A, Ronchi A, Muller H, Manni I, Mossner J, Piaggio G, Mantovani R, Engeland K

Google scholar citations: 100

 

Oncogene 1998 Aug 6;17(5):611-623

E2F-6: a novel member of the E2F family is an inhibitor of E2F-dependent transcription.

Cartwright P, Muller H, Wagener C, Holm K, Helin K

Google scholar citations: 148

 

Mol Cell Biol 1997 Sep;17(9):5508-5520

Induction of S-phase entry by E2F transcription factors depends on their nuclear localization.

Muller H, Moroni MC, Vigo E, Petersen BO, Bartek J, Helin K

Google scholar citations: 154

 

Methods Enzymol 1995;254:304-321

Analysis of altered gene expression by differential display.

Liang P, Bauer D, Averboukh L, Warthoe P, Rohrwild M, Muller H, Strauss M, Pardee AB

Google scholar citations: 148

 

Cancer Res 1995 Feb 15;55(4):949-956

Abnormal patterns of D-type cyclin expression and G1 regulation in human head and neck cancer.

Bartkova J, Lukas J, Muller H, Strauss M, Gusterson B, Bartek J

Google scholar citations: 214

 

J Cell Biol 1994 May;125(3):625-638

DNA tumor virus oncoproteins and retinoblastoma gene mutations share the ability to relieve the cell's requirement for cyclin D1 function in G1.

Lukas J, Muller H, Bartkova J, Spitkovsky D, Kjerulff AA, Jansen-Durr P, Strauss M, Bartek J

Google scholar citations: 234

 

Int J Cancer 1994 May 1;57(3):353-361

Cyclin D1 protein expression and function in human breast cancer.

Bartkova J, Lukas J, Muller H, Lutzhoft D, Strauss M, Bartek J

Google scholar citations: 436

 

Proc Natl Acad Sci U S A 1994 Apr 12;91(8):2945-2949

Cyclin D1 expression is regulated by the retinoblastoma protein.

Muller H, Lukas J, Schneider A, Warthoe P, Bartek J, Eilers M, Strauss M

Google scholar citations: 216

 

Nucleic Acids Res 1993 Sep 11;21(18):4272-4280

Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR).

Bauer D, Muller H, Reich J, Riedel H, Ahrenkiel V, Warthoe P, Strauss M

Google scholar citations: 609

 

 

BOOK CHAPTERS AND REVIEWS

 

Artificial Intelligence and Heuristic Methods in Bioinformatics

Edited by Paolo Frasconi and Ron Shamir

NATO Science Series

2003, IOS Press, pp 208-223

Near Genome Wide Expression Screening of Tumor Suppressor Pathways using Model Cell Lines with Inducible Transcription Factors - Data Acquisition and Analysis

Heiko Mueller & Myriam Alcalay

 

Microarrays And Cancer Research,

Edited by Janet A. Warrington, Randy Todd, and David Wong

Biotechniques Press 2002, pp 45-60

Tumor Cell Biology, Cell Lines: Identification of Statistically Robust Gene Expression Patterns in Model Cell Lines and Their Use in Functional Expression Data Mining

Heiko Müllerand Myriam Alcalay

 

Biochim Biophys Acta. 2000 Feb 14;1470(1):M1-12. Review.

The E2F transcription factors: Key regulators of cell proliferation

Heiko Mueller and Kristian Helin

Google scholar citations: 171

 

Total Google scholar citations: 3664

 

 

POSTER PRESENTATIONS

 

2012    poster BITS 2012: Bioinformatic Italian Society annual meeting

02-04 May, Catania

AnnotateGenomicRegions: A web application

Heiko Muller, Bucci Gabriele, Luca Zammataro

 

2012    poster BITS 2012: Bioinformatic Italian Society annual meeting

02-04 May, Catania

Integrated Analysis of Epigenetic and Transcriptional Circuits in Gliomagenesis

Gabriele Bucci, Elena Signaroldi, Pasquale Laise, Pierre-Luc Germain, Luca Zammataro, Heiko Muller, Giuseppe Testa

 

2011    poster BITS 2011: Bioinformatic Italian Society annual meeting

20-22 June, Pisa

Digital Signal Processing of Quantitative Genomic Data.

Cittaro Davide, Bucci Gabriele, Muller Heiko

 

2011    poster BITS 2011: Bioinformatic Italian Society annual meeting

20-22 June, Pisa

UsingSugarCRM in Streamlining a NGS data-analysis pipeline

Heiko Muller, Gabriele Bucci, Davide Cittaro

 

2011    poster HITSEQ 2011: Conference on High Throughput Sequencing Analysis and Algorithms, special interest group of

ISMB (Intelligent System for Molecular Biology)

14-16 July, Vienna

Digital Signal Processing of Quantitative Genomic Data.

Cittaro Davide, Bucci Gabriele, Muller Heiko

 

2007    oral, best poster award

Annual meeting of the Italian Bioinformatics Society (BITS), April 26-28

Naples, Aula Magna Partenope, Via Partenope 36, Italy

“Identification of cancer signaling pathways from published gene expession signatures using PubLiME”

Muller, H.; Mancuso, F.M.; Cittaro, D.; Finocchiaro, G.

 

2006    oral

Genetics meets Systems Biology: Theory and Practice, November 13-15

Paris, Institut Curie, Amphithéatre Constant Burg, 12 rue Lhomond, France

“Graph-based identification of cancer signaling pathways from published gene expression signatures”

Muller, H.; Mancuso, F.M.; Cittaro, D.; Finocchiaro, G.

 

2006    poster

Annual meeting of the Italian Bioinformatics Society (BITS), April, 28-29

Bologna, Salone Bolognini, Piazza San Domenico 13, Italy

“Publime: a new tool for meta-analysis of cancer-related microarray experiments”

Finocchiaro, G.; Mancuso, F.M.; Muller, H.

 

2006    oral

Annual meeting of the Italian Bioinformatics Society (BITS), April 28-29

Bologna, Salone Bolognini, Piazza San Domenico 13, Italy

“Intragenic antisense transcription correlates with long UTRs”

Muller, H.; Parise, P.; Di Ninni, V.; Francois, S.; Carro, M.S.; Finocchiaro, G.

 

2005    oral by G.F.

Gene Signature Symposia 05

            April 13, Aula Magna Univ. of Milan, Milan, Italy

“Mining published lists of cancer related microarray experiments: Identification of a gene signature having a critical role in cell-cycle control.”

Finocchiaro, G.; Mancuso, F.M.; Muller, H.

 

2005    oral by G.F.

Annual meeting of the Italian Bioinformatics Society (BITS), March 17-19

Milan, Leonardo Da Vinci Congress Center, Via Senigallia 6, Italy

“Mining published lists of cancer related microarray experiments: Identification of a gene signature having a critical role in cell-cycle control.”

Finocchiaro, G.; Mancuso, F.M.; Muller, H.

 

2004    poster

CNIO Symposium: The Molecular Taxonomy of Cancer, February 3-6

Madrid, Hospital Clínico San Carlos,Spain

“Identification of Target Genes of the p16INK4A-pRB-E2F Pathway”

Richard Vernell, Giacomo Finocchiaro, Kristian Helin, and Heiko Muller

 

2000    oral

October Workshop on Functional Genomics, Expression Array Technologies and Methods of Analysis, Oct 11-15

Los Angeles, UCLA, Institute for Pure and Applied Mathematics, USA

“Statistically Robust E2F Induced Gene Expression Patterns in Functional Gene Expression Data Mining (Target Gene Bias Analysis)”

Muller, H.; Helin, K.

 

1998    poster

CSHL Symposium: The Cell Cycle, May 20-24

Cold Spring Harbor Laboratories, Cold Spring Harbor, USA

Identification of direct targets of E2F family members

Vigo, E.; Muller, H.; Cartwright, P.; Helin, K.

 

1998    poster

Giovanni Armenise – Harvard Foundation 2nd Annual Symposium, June 22-23,

Cape Cod, Chatham   Bars Inn, USA

“Analysis of E2F4 phosphorylation”

Muller, H.; Helin, K.

 

1997    oral

11th European Cell Cycle Conference, April 23-26

Gardone Riviera, Villa Alba, Italy

“Induction of S-phase entry by E2F transcription factors depends on their nuclear localization”

Muller, H.; Moroni, M. C.; Vigo, E.; Petersen, B. O.; Bartek, J.; Helin, K.

 

1994    oral

CSHL Symposium: The Cell Cycle, May 18-22,

Cold Spring Harbor Laboratories, Cold Spring Harbor, USA

“Cyclin D1 expression is regulated by the retinoblastoma protein”

Muller, H.; Lukas, J.; Schneider, A.; Warthoe, P.; Bartek, J.; Eilers, M.; Strauss, M.

 

1994    poster

EMBL Conference Oncogenes and Growth Control, April 18-21,

EMBL, Heidelberg, Germany

“Cyclin D1 expression is regulated by the retinoblastoma protein”

Muller, H.; Lukas, J.; Schneider, A.; Warthoe, P.; Bartek, J.; Eilers, M.; Strauss, M.

 

 

INVITED PRESENTATIONS

2009    14th January, Norwegian University of Science and Technology, Trondheim, NO

            “Decoding the non-coding: Emerging roles of non-coding RNA”

 

2008    invited seminar

            July 18th, The Institute of Cancer Research, London, UK

            Meta-analysis of genomic data: Pathway identification using Poisson-binomial

            statistics and network partitioning

 

2007    invited seminar

            May 20, Linz, Johannes Kepler University, Institute of Biophysics, Austria

            “Identification of cancer signaling pathways by meta-analysis of genomic data”

 

2006    invited seminar

            April 21, Berlin, Humboldt Univ., Inst. Theor. Biol., Invalidenstr. 43, Germany

           “Meta-analysis of microarray data: Sense and antisense of mammalian

            gene expression”

 

2005    invited seminar

           April 4, Nerviano, Nerviano Medical Sciences, Italy

           “Meta-analysis of gene expression microarray data - identification of cancer

           genes using Systems Biology and Comparative Genomics approaches”

 

2005    invited seminar

            January 11, University of Warwick, Mathematics Institute, Coventry, UK

           “Meta-analysis of gene expression microarray data - identification of cancer

            genes using Systems Biology and Comparative Genomics approaches”

 

2004    invited speaker

            Silicon Genetics European Users Conference

            September 16-17, Royal Library, London, UK

            “Meta-analysis of gene expression microarray data - identification of cancer

            genes using Systems Biology and Comparative Genomics approaches”

 

2004    invited speaker

            3rd Arrays Symposium in Research and Diagnosis,

            October 29-30, Aarhus University Hospital, Brendstrupgaardvej 100, Denmark

            “Meta-analysis of gene expression microarray data - identification of cancer

            genes using Systems Biology and Comparative Genomics approaches”

 

2004    invited seminar

           February 12, Institute Mario Negri, Milan, Via La Masa 19, Italy

          “From co-regulated genes to cis-regulatory elements in mammalian promoters”

 

2003    invited seminar

           November 18, Brescia, University of Brescia, Dept. Biomedical Sciences

           & Biotechnology, viale Europa 11, Italy,

           “From co-regulated genes to cis-regulatory motifs in the p16-pRB-E2F

           pathway”

 

2002    invited speaker:

           Molecular Genetics of ageing and neoplastic transformation

           March 22-28, Alba, Italy,

           “High-throughput approaches in biology”

 

2002    invited speaker:

           The Proteomics Congress, May 14-15, London, Café Royal, UK,

          “Near genome wide expression screening of the pRB tumor suppressor

           pathway”

 

2002    invited speaker and session chair on pathway informatics:

           CHI Symposium on Integrated Bioinformatics: High-throughput interpretation

           or Pathways and Biology

           January 16-18, Zurich, Swissotel, Switzerland,

           “Expression analysis of the pRB tumor suppressor pathway”

 

2002    invited speaker:

           Affymetrix European Seminar Tour

           November 4, Rome, Hilton Airport Hotel, Italy

           “From co-regulated genes to cis-regulatory motifs in the p16-pRB-E2F

           pathway”

 

2002    invited speaker

           Belgian Bioinformatics Conference

           April 12, Namur, University of Namur, rue de Bruxelles 61, Namur, Belgium

          “Near genome wide expression screening of the pRB tumor suppressor

           pathway”

 

2001    invited speaker

           NATO Symposium:

           Artificial Intelligence and Heuristic Methods for Bioinformatics

           October 1-11, San   Miniato, Italy

           “Near genome wide expression pattern analysis of the pRB tumor suppressor

           pathway”

Awards

Lessing medal, 1983

“Research Student” fellowship at Humboldt University, 1990

Marie Curie Fellowship, European Community, 1996

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I numeri di IIT

L’Istituto Italiano di Tecnologia (IIT) è una fondazione di diritto privato - cfr. determinazione Corte dei Conti 23/2015 “IIT è una fondazione da inquadrare fra gli organismi di diritto pubblico con la scelta di un modello di organizzazione di diritto privato per rispondere all’esigenza di assicurare procedure più snelle nella selezione non solo nell’ambito nazionale dei collaboratori, scienziati e ricercatori ”.

IIT è sotto la vigilanza del Ministero dell'Istruzione, dell'Università e della Ricerca e del Ministero dell'Economia e delle Finanze ed è stato istituito con la Legge 326/2003. La Fondazione ha l'obiettivo di promuovere l'eccellenza nella ricerca di base e in quella applicata e di favorire lo sviluppo del sistema economico nazionale. La costruzione dei laboratori iniziata nel 2006 si è conclusa nel 2009.

Lo staff complessivo di IIT conta circa 1440 persone. L’area scientifica è rappresentata da circa l’85% del personale. Il 45% dei ricercatori proviene dall’estero: di questi, il 29% è costituito da stranieri provenienti da oltre 50 Paesi e il 16% da italiani rientrati. Oggi il personale scientifico è composto da circa 60 principal investigators, circa 110 ricercatori e tecnologi di staff, circa 350 post doc, circa 500 studenti di dottorato e borsisti, circa 130 tecnici. Oltre 330 posti su 1400 creati su fondi esterni. Età media 34 anni. 41% donne / 59 % uomini.

Nel 2015 IIT ha ricevuto finanziamenti pubblici per circa 96 milioni di euro (80% del budget), conseguendo fondi esterni per 22 milioni di euro (20% budget) provenienti da 18 progetti europei17 finanziamenti da istituzioni nazionali e internazionali, circa 60 progetti industriali

La produzione di IIT ad oggi vanta circa 6990 pubblicazioni, oltre 130 finanziamenti Europei e 11 ERC, più di 350 domande di brevetto attive, oltre 12 start up costituite e altrettante in fase di lancio. Dal 2009 l’attività scientifica è stata ulteriormente rafforzata con la creazione di dieci centri di ricerca nel territorio nazionale (a Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) e internazionale (MIT ed Harvard negli USA) che, unitamente al Laboratorio Centrale di Genova, sviluppano i programmi di ricerca del piano scientifico 2015-2017.

IIT: the numbers

Istituto Italiano di Tecnologia (IIT) is a public research institute that adopts the organizational model of a private law foundation. IIT is overseen by Ministero dell'Istruzione, dell'Università e della Ricerca and Ministero dell'Economia e delle Finanze (the Italian Ministries of Education, Economy and Finance).  The Institute was set up according to Italian law 326/2003 with the objective of promoting excellence in basic and applied research andfostering Italy’s economic development. Construction of the Laboratories started in 2006 and finished in 2009.

IIT has an overall staff of about 1,440 people. The scientific staff covers about 85% of the total. Out of 45% of researchers coming from abroad 29% are foreigners coming from more than 50 countries and 16% are returned Italians. The scientific staff currently consists of approximately 60 Principal Investigators110 researchers and technologists350 post-docs and 500 PhD students and grant holders and 130 technicians. External funding has allowed the creation of more than 330 positions . The average age is 34 and the gender balance proportion  is 41% female against 59% male.

In 2015 IIT received 96 million euros in public funding (accounting for 80% of its budget) and obtained 22 million euros in external funding (accounting for 20% of its budget). External funding comes from 18 European Projects, other 17 national and international competitive projects and approximately 60 industrial projects.

So far IIT accounts for: about 6990 publications, more than 130 European grants and 11 ERC grants, more than 350 patents or patent applications12 up start-ups and as many  which are about to be launched. The Institute’s scientific activity has been further strengthened since 2009 with the establishment of 11 research nodes throughout Italy (Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) and abroad (MIT and Harvard University, USA), which, along with the Genoa-based Central Lab, implement the research programs included in the 2015-2017 Strategic Plan.