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Paolo Marcatili

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Paolo Marcatili 
Curriculum Vitae
marcatili

 

 

Personal information

 

 

Name

Paolo Marcatili

E-mail

paolo.marcatili@gmail.com

Nationality

Italian

Date of birth

October 29, 1977

Gender

Male

 

 

Education and training

 

 

 

February 2006 - March 2009

Qualification

PhD (Biophysics)

Principal subjects

Protein biophysics and structural bioinformatics

University

“Sapienza” University of Rome

 

 

 

May-June 2006

Qualification

PhD course

Principal subjects

Immunological Bioinformatics

University

CBS, Denmark

 

 

 

December 2003

Qualification

MSc Engineering (Information Technology area), cum laude

Principal subjects

Systems theory, Robotics, Control Theory, Informatics

University

“Sapienza” University of Rome

 

 

Work experience

 

 

 

November 2009 to date

Position

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

Position

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

Position

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

Position

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

Position

 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

Position

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

Role

Supervision of Bachelor, Master and PhD students

 

 

 

June 2008 to date

Course

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

 

 

 

October 2009

Course

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

 

 

 

December 2004 – December 2005

Course

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

 

 

Other   experiences

 

 

Grant

“Sapienza progetti” grant 2011/2012

Organization

Member of the “ECCB08” Organizing Committee

Referee

Referee for Proteins, PLoS ONE, Bioinformatics, FEBS

 

 

Personal skills and competences

 

 

Mother tongue

Italian

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

Papers:

 

 

 

(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

Chapters

 

 

 

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

 

 

Poster

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 )