Gabriele Ausiello
e-mail: gabriele.ausiello AT uniroma2.it
affiliation: Università di Roma Tor Vergata
research area(s): Computational Biology
Course:
Cell and Molecular Biology
University/Istitution: Università di Roma Tor Vergata
University/Istitution: Università di Roma Tor Vergata
2008 - Researcher BIO/11 in the Department of Biology of the University of Rome "Tor Vergata"
2007-2008 Postdoc researcher in Bioinformatics, University of Rome "La sapienza"
2005-2007 Postdoc researcher in Bioinformatics, University of Bologna
2002-2005 PhD in Cellular and Molecular Biology, University of Rome "Tor Vergata"
2001- 2002 Telethon graduate fellow in Bioinformatics, University of Rome "Tor Vergata"
1996-1998 Graduate fellow under Prof. M. Helmer-Citterich, University of Rome "Tor Vergata"
2007-2008 Postdoc researcher in Bioinformatics, University of Rome "La sapienza"
2005-2007 Postdoc researcher in Bioinformatics, University of Bologna
2002-2005 PhD in Cellular and Molecular Biology, University of Rome "Tor Vergata"
2001- 2002 Telethon graduate fellow in Bioinformatics, University of Rome "Tor Vergata"
1996-1998 Graduate fellow under Prof. M. Helmer-Citterich, University of Rome "Tor Vergata"
Development of computational methods for the analysis of protein structure and the inference of protein interaction and interaction specificity
Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G (2010). Phosphate binding-sites identification in protein structures. Nucl. Acids Res., 4:1231-1242.
Gherardini, PF, Ausiello, A, Helmer-Citterich, M. (2010). Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One, 5(8): e11988.
Gherardini, PF, Ausiello, G, Russell, RB, Helmer-Citterich, M (2010). Modular architecture of nucleotide binding pockets. Nucl. Acids Res., 38: 3809-3816.
Ausiello G, Gherardini PF, Gatti E, Incani, O., Helmer-Citterich, M. (2009). Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics, 10:182.
Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M (2008). FunClust: A web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics, 9,(Suppl. 2): S1.
Gherardini, PF, Ausiello, A, Helmer-Citterich, M. (2010). Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One, 5(8): e11988.
Gherardini, PF, Ausiello, G, Russell, RB, Helmer-Citterich, M (2010). Modular architecture of nucleotide binding pockets. Nucl. Acids Res., 38: 3809-3816.
Ausiello G, Gherardini PF, Gatti E, Incani, O., Helmer-Citterich, M. (2009). Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics, 10:182.
Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M (2008). FunClust: A web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics, 9,(Suppl. 2): S1.
Project Title:
Plant post-genomics: computational tools and analysis.
The proposed project is related to the development of specific computational tools for the annotation of plant genomes. While some genomic annotation pipelines have
been published, we propose two fundamental differences.
(1) The present effort focuses on plants, taking into account several specific aspects and exploiting their differences. With the main focus on alternative splicing and
its effects on environmental plant adaptation and individual differences at the molecular level.
(2) The protein structure level will be brought into play in order to better explain the effects of phenotypic differences at the molecular level. Reliable models will be
built for each gene transcript identified and the models will be used to better define the function of each protein.
The project is devised as a pipeline, progressing from analysis of the DNA sequence to the elucidation of proteins at increasing complexity from the sequence,
structure, function levels towards interactions and systems. The whole pipeline will be tested on well annotated plant genomes like Arabidopsis and rice.
Subsequently, the developed tools will be applied to other plants to improve the available annotations. Of special relevance will be the application of the pipeline to
two genomes of outstanding applicative interest: "Vitis Vinifera" and "Malus domestica". All the annotation data gathered during the project will be made available
via a highly integrated and usable database and web-server interface.
been published, we propose two fundamental differences.
(1) The present effort focuses on plants, taking into account several specific aspects and exploiting their differences. With the main focus on alternative splicing and
its effects on environmental plant adaptation and individual differences at the molecular level.
(2) The protein structure level will be brought into play in order to better explain the effects of phenotypic differences at the molecular level. Reliable models will be
built for each gene transcript identified and the models will be used to better define the function of each protein.
The project is devised as a pipeline, progressing from analysis of the DNA sequence to the elucidation of proteins at increasing complexity from the sequence,
structure, function levels towards interactions and systems. The whole pipeline will be tested on well annotated plant genomes like Arabidopsis and rice.
Subsequently, the developed tools will be applied to other plants to improve the available annotations. Of special relevance will be the application of the pipeline to
two genomes of outstanding applicative interest: "Vitis Vinifera" and "Malus domestica". All the annotation data gathered during the project will be made available
via a highly integrated and usable database and web-server interface.