biocomputing.it

Home About us

Daniele Di Marino

Daniele_Di_Marino

Name: Daniele Di marino
Nationality: Italian
Date of Birth: April 09 1982
E-mail:
daniele.dimarino@uniroma1.it
Phone
: +39 06 49914297
Mobile: +39 3334370864
Skype: daniele_molla

Current Position:

February 2012 - up today
Postdoctoral position, Department of Physics - University of Rome "La Sapienza" Italy.
P.le Aldo Moro, 5 - 00185 Rome, Italy.
Prof. Anna Tramontano.

Positions Held:

September 2010 – December2011:
Postdoctoral position, K.U. Leuven, Belgium.
VIB Department of Biology of Deases
Prof. Caludioa Bagni. 

January 2010 – August 2010:
Postdoctoral position, University of Rome "Tor Vergata", Italy.
Faculty of Medicine.
Prof. Maria Giulia Farace.

Education:

November 2006 - Dicember 2009
PhD position in  “ Cellular and Molecular Biology”, University of Rome "Tor Vergata", Italy.
Dept of Biology.
Title of the thesis:
“Molecular dynamics and docking simulations of the ADP/ATP  mitochondrial carrier: structural-dynamical insights for the  inactivation of pathological mutants and detection of potential  ATP binding sites.”
Prof. Alessandro Desideri.

September 2004 – October 2006
Master Degree in Bioinformatics, University of Rome "Tor Vergata", Italy.
Title of the thesis:
“Structural effects of the inhibition of the ADP/ATP mitochondria   carrier revealed through molecular dynamics simulations”.
Prof. Mattia Falconi. 

Semtember 2001 – July 2004
Bachelor Degree in Biotecnology, University of Rome “Tor Vergata”, Italy.
Title of the thesis:
“Homology modeling of the ADP/ATP and GTP/GDP mitochondrial carrier from S. cerevisiae”.
Prof. Mattia Falconi. 

1996– 2001
Liceo scientifico statale “Louis Pasteur” Rome, Italy. 

Languages

Good Knowledge of the English language.

Schools of Specialization

First Biosapiens Permanent School in Bioinformatics. University of Verona (Italy) July 7th - 13th 2004.

Second European School in Bioinformatics. Centre for Molecular and Biomolecular Informatics. Radboud University Nijmegen (Netherlands), Jenuary 22nd – 26th 2005.

Third Biosapiens Permanent European School in Bioinformatica. Biosapiens Network. Univerity of Madrid (Spain), Semtember 19th - 23rd 2005.
Introduction to HPC: Parellel computing. Caspur Rome (Italy), December 3rd - 5th 2007. 

Congresses

BITS Annual Meeting. Bioinformatics Italian Society. Milan (Italy), March 17th-19th2005. Poster presentation.

SimBioMa, Conference on Molecular Simulations in Biosystems and MaterialScience. Konstanz (Germany), April 2nd-5th 2008.
Poster presentation and short communication
.

Conference on Knots and other Entanglements in Biopolymers: Topological andGeometrical Aspects of DNA, RNA and Protein Structures. ICTP Trieste (Italy),September 15th-19th 2008. Poster presentation.

1st Belgian-Dutch Neuroinformatics workshop. University of Antwerp (Belgium), December 10th 2010.

SYMBAD - WP1 Cell-permeable peptides: a tool to study synaptic proteincomplexes in physiology and pathology. University of Milan (Italy), April 18th-21st 2011. Invited speaker. 

Technical experiences:

Knowledge of several OS: Windows, Linux, Mac, Sgi, Solaris.
Knowledge of WORD, EXCEL, POWERPOINT, INDESIGN, ADOBE ACROBAT, ILLUSTRATOR, PHOTOSHOP.
Programming and web site administration: FRONTPAGE, DREAMWEAVER, FLASH, APACHE, MYSQL, PHPMyAdmin, JOOMLA.
Knowledge of biological DataBases: Swissprot, Protein Data Bank, MINT, trEMBL, Entrez, GCG.
Excellent Knowledge of the structural biology softwares: SYBYL, Rasmol, VMD, CHIMERA, SWISS PDB-VIEWER, YASARA, VEGA, PYMOL.
Knowledge of programming languages: C, PHP, PYTHON, and scripting languages.
Installation and usage of computational biology software on different platform: GROMACS, AMBER, CHARMM, AUTODOCK, HEX.
My expertise in the filed of computational biology is mainly in using techniques such as molecular dynamics simulation, coarse grained and martini force field, docking, homology modeling, peptide design and sequence analysis. I started my experience by studying the structural functional relationships of membrane proteins, in particular the ADP/ATP mitochondrial carrier, by means of molecular dynamics and docking. I also performed sequence analysis for the prediction of profile patterns for the cellular localization of mRNAs. Presently I am working in the field of neurosciences, with particular regard to protein-protein recognition and peptide design. 

Didactics Experiences

I was the tutor at the bioinformatics practice exercises during the bioinformatics courses of Prof. Mattia Falconi. I held several structural bioinformatics lessons for the bioinformatics and medical biotechnology courses. 

List of publications

An Impaired Dna Recognition By The Ile304asn Mutation Of The Fragile X Mental Retardation Protein Is At The Basis Of A Severe Manifestation Of The Syndrome.
Di Marino D
, Lacoux C, Falconi M, Bagni C.
Submitted to J.B.S.D.

Molecular and cellular aspects of mental retardation in Fragile X Syndrome: from gene mutation/s to spine dysmorphogenesis.
De Rubeis S*, Fernàndez E*, Buzzi A*, Di Marino D*, Bagni C. *These authors contributed equally.
Adv Exp Med Biol. 2012, 970: 517-571.

BC1-FMRP interaction is modulated by 2’-O Methylation: insights into RNA binding activity of the Tudor domain and translational regulation at synapses.
Lacoux C, Di Marino D, Boyl PP, Zalfa F, Yan B, Falconi M, Urlaub H, Achsel T, Mougin A, Caizergues-Ferrer M, Bagni B.Nucleic Acids Res. 2012 Jan 11. [Epub ahead of print]

Mapping multiple potential ATP binding sites on the matrix side of bovine ADP/ATP carrier by a combined use of MD simulation and docking
.
Di Marino D
, Oteri F, , Morozzo della Rocca B, D’annessa I, Falconi M
J Mol Model. 2011 Oct 12. [Epub ahead of print]

JNK3 as a Therapeutic Target for Neurodegenerative Diseases.
Antoniou X, Falconi M, Di Marino D, Borsello T.
J Alzheimers Dis. 2011;24(4):633-42.

Adp/Atp mitochondrial carrier Md simulations to shed light on the structural-dynamical events that, from a single pathological mutant, generates a functional double mutant.
Di Marino D
, Falconi M, Morozzo della Rocca B, Oteri F, Chillemi G, Palmieri L, Alessandro Desideri A.
J Struct Biol. 2010 Dec;172(3):225-32.

Docking simulation and Competitive experiments validate the interaction between the 2,5-Xylidine inhibitor and Rigidoporus lignosus Laccase.

Maria Teresa Cambria*, Daniele Di Marino*, Mattia Falconi, Silvia Garavaglia, Antonio Cambria
J.B.S.D. 2010 Feb; 27(4):501-510. *These authors contributed equally.

The fragile X syndrome protein represses activity-dependent translation through CYFIP1, a new 4E-BP.

Napoli I, Mercaldo V, Boyl PP, Eleuteri B, Zalfa F, De Rubeis S, Di Marino D, Mohr E, Massimi M, Falconi M, Witke W, Costa-Mattioli M, Sonenberg N, Achsel T, Bagni C.
Cell. 2008 Sep 19;134(6):1042-54.

Screening of EDA1 gene in X-linked anhidrotic ectodermal dysplasia using DHPLC: identification of 14 novel mutations in Italian patients.

Conte C, Gambardella S, Bulli C, Rinaldi F, Di Marino D, Falconi M, Bramanti P, Desideri A, Novelli G.
Genet Test. 2008 Sep;12(3):437-42.

Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies.

Falconi M, Chillemi G, Di Marino D, D'Annessa I, Morozzo della Rocca B, Palmieri L, Desideri A.
Proteins. 2006 Nov 15;65(3):681-9.

 

 

 

 

Last Updated ( Thursday, 23 February 2012 16:54 )