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Paolo Marcatili

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Paolo Marcatili 
Curriculum Vitae



Personal information




Paolo Marcatili




Date of birth

October 29, 1977





Education and training




February 2006 - March 2009


PhD (Biophysics)

Principal subjects

Protein biophysics and structural bioinformatics


“Sapienza” University of Rome




May-June 2006


PhD course

Principal subjects

Immunological Bioinformatics


CBS, Denmark




December 2003


MSc Engineering (Information Technology area), cum laude

Principal subjects

Systems theory, Robotics, Control Theory, Informatics


“Sapienza” University of Rome



Work experience




November 2009 to date


Fixed-term assistant professor at  “Sapienza” University of Rome, Physics Dept.

Research Field

Immunoglobulin sequence, structure and function analysis

Group Leader

Prof. Anna Tramontano




May 2008 - October 2009


Research Fellow at the University of Rome “Tor Vergata”

Research Field

Development of methods and algorithms for the analysis of protein structural motifs

Group Leader

Prof. Manuela Helmer Citterich




May 2006 - April 2008


Research fellows at the Department of Experimental Evolutionistic Biology of “Alma Mater Studiorum” University of Bologna

Research Field

Development of methods and algorithms for the analysis of protein interaction networks

Group Leader

Prof. Rita Casadio




February 2006 - April 2006


Research Fellow at Pasteur Institute - Cenci Bolognetti foundation

Research Field

Development of methods and algorithms for the analysis of protein interaction networks

Group Leader

Prof. Anna Tramontano




August 2005 - October 2005


 Project contract position at CNR-IBPM (National Research Council)

Research Field

Development of methods and algorithms for the analysis of the effect of mRNA stability on gene expression

Group Leader

Dr. Ida Ruberti




June 2004 - July 2005


Project contract position at INRAN

Research Field

Development of methods and algorithms for the analysis of gene networks

Group Leader

Prof. Giorgio Morelli




Teaching experience




January 2007 to date


Supervision of Bachelor, Master and PhD students




June 2008 to date


Programming and Machine Learning, “Sapienza” postgraduate course in Bioinformatics




October 2009


“Structural Bioinformatics”, “Gulbenkian Institute” of Oeiras, PhD course




December 2004 – December 2005


Assistant for the “Systems Theory” course, “Sapienza” Engineering faculty



Other   experiences




“Sapienza progetti” grant 2011/2012


Member of the “ECCB08” Organizing Committee


Referee for Proteins, PLoS ONE, Bioinformatics, FEBS



Personal skills and competences



Mother tongue


Other languages

English (Advanced), Spanish (Basic), Russian (beginner)

Social skills

Positive team spirit, excellent ability to adapt to different and multicultural environments. Excellent communication skills.

Organisational skills

Good organization and motivation skills, acquired in the working and personal context.

Technical skills

Small-Medium networks system admin


Computer skills

Programming languages: Java, C/C++, Perl, Python, MySQL, R, Matlab, jQuery

Most bioinformatics tools (blast, psi-blast, hmmer, hhpred, t-coffee, rosetta, modeller,  MEME, SCWRL, SPDBV, etc.),  MS Office, Photoshop





(in bold if first or last author)


Olimpieri, P. P., Chailyan, A., Tramontano, A., Marcatili, P. Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server, submitted



Marcatili, P., Ghiotto, F., Tenca, C., … Manlio Ferrarini, M., Chiorazzi, N., Tramontano, A., Fais, F. Immunoglobulins expressed by chronic lymphocytic leukemia B cells show limited binding site structure variability. J Immunol., in press



Zingaretti, C., Arigò, M., Cardaci, A.,, …  Marcatili, P., … Pagani, M., Muratori, L., Abrignani, S.,Bombaci M. Identification of new autoantigens by protein array indicates a role for IL4 neutralization in Autoimmune Hepatitis., Mol Cell Proteomics. 2012, doi:10.1074/mcp.M112.018713



Chailyan, A., Tramontano, A., Marcatili, P.  A database of immunoglobulins with integrated tools: DIGIT, Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr806



Ko W.Y., Kaercher K.A.,Giombini E., Marcatili P. et al. Effects of Natural Selection and Gene Conversion on the Evolution of Human Glycophorins Coding for MNS Blood Polymorphisms in Malaria-Endemic African Populations, AJHG 88 (2011)



Chailyan, A., Marcatili, P., Tramontano, A. The association of heavy and light chain variable domains in antibodies: implications for antigen specificity, FEBS journal, in press (2011)



Ghiotto, F., Marcatili, P. et al. Mutation pattern of paired immunoglobulin heavy and
light variable domains in chronic lymphocytic leukemia B-cells, Mol. Med., in press (2011)



Floris, M., Raimondo, D., Leoni, G., Orsini, M., Marcatili, P. and Tramontano, A. MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics btr198v1-btr198. (2011)



Chailyan, A., Marcatili, P., Cirillo, D. and Tramontano, A. Structural repertoire of immunoglobulin λ light chains. Proteins, DOI: 10.1002/prot.22979 (2011)



Chinappi M, Via A, Marcatili P, Tramontano A, 2010 On the Mechanism of Chloroquine Resistance in Plasmodium falciparum. PLoS ONE 5(11): e14064. doi:10.1371/journal.pone.001406 (2010)



Le Pera, L., Marcatili, P., Tramontano, A. Picmi: mapping point mutations on genomes, Bioinformatics, 26(22): 2904-2905 (2010)



Zibellini,S. ,  Capello, D.,  Forconi, F.,  Marcatili, P.,  … , Paulli, M.,  Gaidano, G., and  Arcaini, L. Stereotyped patterns of B-cell receptor in splenic marginal zone lymphoma (2010) Haematologica



Marcatili, P., Rosi, A. and Tramontano, A. PIGS: Automatic prediction of antibody structures (2008) Bioinformatics, 24(17):1953-1954.



Ausiello, G., Gherardini, P.F., Marcatili, P., Tramontano, A., Via, A., Helmer-Citterich, M. FunClust: A web server for the identification of structural motifs in a set of non-homologous proteins. (2008) BMC Bioinformatics, 9:S2



Marcatili, P., Bussotti, G., Tramontano, A. The MoVin server (2008) BMC Bioinformatics, 9:S11





Marcatili , P., Chailyan, A., Cirillo, D. and Tramontano, A. Modeling of Antibody Structures (in press) in “Encyclopedia of Biophysics”, DOI 10.1007/978-3-642-16712-6


Marcatili P, Tramontano A: “Network Cleansing: Reliable interaction networks” in  “Biological Data Mining in Protein Interaction Networks” di Xiao-Li Li, See-Kiong Ng  Idea Group Inc (IGI), 2009, ISBN 1605663980, 9781605663982




Posters and Invited Talks




Hierarchical Clustering of B-Cell Receptor Structures in Splenic Marginal Zone Lymphoma”, ASH conference, Atlanta, GA, 2012

Invited Talk

EBI Industry workshop on “Antibody informatics”, July 2012

Invited Talk

“Antibody: From sequence to Structure to Function”, INGM, Milan

Oral Presentation

“MoVIN: Motif Validation of Interaction Networks”, BITS 2008, Naples




Last Updated ( Monday, 20 May 2013 17:06 )