Journal articles


Pietro Di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
Fast overlapping of protein contact maps by alignment of eigenvectors.
Bioinformatics, in press.

Pietro Di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
Is there an optimal substitution matrix for contact prediction with correlated mutations?
IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.

Pietro Di Lena, Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
On the reconstruction of three-dimensional protein structures from contact maps.
Algorithms. 2009; 2(1):76-92.

Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
A Graph Theoretic Approach to Protein Structure Selection.
Artif Intell Med , 45 (2009), pp. 229-237. DOI information:10.1016/j.artmed.2008.07.016

Marco Vassura, Luciano Margara, Pietro Di Lena, Filippo Medri, Piero Fariselli, Rita Casadio
Reconstruction of 3D Structures From Protein Contact Maps.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 3, July-September 2008.

Marco Vassura, Luciano Margara, Pietro Di Lena, Filippo Medri, Piero Fariselli, Rita Casadio
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps.
Bioinformatics , 2008 ; doi: 10.1093/bioinformatics/btn115.
FT-COMAR.

Proceedings and Lecture Notes in Computer Science


Pietro Di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
On the upper bound of the prediction accuracy of residue contacts in proteins with correlated mutations: the case study of the similarity matrices.
In Proc. of the 9th International Workshop on Algorithms in Bioinformatics (WABI2009), Pennsylvania 2009. Lecture Notes in Computer Science, Publisher Springer Berlin / Heidelberg, ISSN 0302-9743 (Print) 1611-3349 (Online), Vol. 5724/2009, DOI10.1007/978-3-642-04241-6, Copyright2009, ISBN978-3-642-04240-9, Pages 62-72, 2009.

Damiano Piovesan, Pietro Di Lena, Marco Vassura
Unconventional Training for Neural Network Predictions of Inter-Residue Contacts.
In Proceedings of the 1st ACM workshop on Breaking frontiers of computational biology 2009, Ischia, Italy, May 18-20, 2009, 19-25.

Pietro Di Lena, Luciano Margara, Marco Vassura, Piero Fariselli, Rita Casadio
A new protein representation based on fragment contacts: towards an improvement of contact maps predictions.
Proceedings of the fifth international meeting on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB08), 2008. Springer Verlag Lecture Notes in Computer Science 5488, 210-221, 2008.

Marco Vassura, Luciano Margara, Pietro Di Lena, Filippo Medri, Piero Fariselli, Rita Casadio
Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps.
Seventh International Workshop on Algorithms in Bioinformatics (WABI 2007), Pennsylvania 2007. Springer Verlag Lecture Notes in Bioinformatics 4645,25-37,August 2007.
Technical report.

Luciano Margara, Marco Vassura, Pietro Di Lena, Filippo Medri, Piero Fariselli, Rita Casadio
Reconstruction of 3D Structures From Protein Contact Maps.
International Symposium on Bioinformatics Research and Applications (ISBRA 2007), Atlanta, Springer Verlag Lecture Notes in Bioinformatics 4463,578-589, may 2007.
Technical report.

Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
A Graph Theoretic Approach to Protein Structure Selection.
Fourth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 07), Springer Verlag Lecture Notes in Artificial Intelligence 4578 pp. 497-504,August 2007.
Technical report.

Book chapters


Pietro Di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
Divide and Conquer strategies for protein structure prediction
in
Mathematical Approaches to Polymer Sequence Analysis.
Editor Renato Bruni, Ph.D., University of Rome "Sapienza", Italy. Publisher: Springer, New York, NY. In press.

Rita Casadio, Luciano Margara, Piero Fariselli, Marco Vassura
The Graph Theory and the Protein Universe: selecting the close-to-the-native structures within a model decoy set.
in
BIOCOMPLEXITY AT THE CUTTING EDGE OF PHYSICS, SYSTEMS BIOLOGY AND HUMANITIES
Edited by Gastone Castellani, Elena Lamberti, Vita Fortunati and Claudio Franceschi Published by Bononia University Press 2008.

M. Mirto, I. Epicoco, et al.
The LIBI Grid Platform for Bioinformatics.
in
Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare.
Mario Cannataro editore, edizioni IGI Global, pp. 577-613, May 2009 Hard Cover ISBN: 9781605663746, DOI: 10.4018/9781605663746.