Publications

 

International Journals


  1. 1.S. Lane, P. Di Lena, K. Tormanen, P. Baldi, H. Liu

    Function and regulation of Cph2 in Candida albicans.

    Eukaryot Cell, 2015. In press.

  1. 2.P. Di Lena, P.L. Martelli, P. Fariselli, R. Casadio.

    NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases.

    BMC Genomics,16(8):S6, 2015.

  1. 3.J.E. Dent, V. Devescovi, H. Li, P. Di Lena, Y. Lu, Y. Liu, C. Nardini.

    Mechanotransduction map: Simulation model,molecular pathway,gene set.

    Bioinformatics, 31(7), 1053-1059, 2015.

  1. 4.P. Di Lena, L. Margara.

    Nondeterministic Cellular Automata.

    Information Sciences, 287, 13-25, 2014.

  1. 5.P. Di Lena, G. Wu, P.L. Martelli, R. Casadio, C. Nardini.

    MIMO: an efficient tool for molecular interaction maps overlap.

    BMC Bioinformatics, 14:159, 2013.

  1. 6.A. Dennunzio, P. Di Lena, E. Formenti, L. Margara.

    Periodic Orbits and Dynamical Complexity in Cellular Automata.

    Fundamenta Informaticae, 126(2-3), 183-199, 2013.

  1. 7.P. Di Lena, K. Nagata, P. Baldi

    Deep architectures for protein contact map prediction

    Bioinformatics, 28 (19), 2449-457, 2012.

  1. 8.P. Di Lena, L. Margara

    On the Undecidability of Attractor Properties for Cellular Automata

    Fundamenta Informaticae, 115 (1), 75-85, 2012.

  1. 9.B. Tang, P. Di Lena, L. Schaffer, S.R. Head, P. Baldi, E.A. Thomas

    Genome-Wide Identification of Bcl11b Gene Targets Reveals Role in Brain-Derived Neurotrophic Factor Signaling

    PLoS ONE, 6 (9), e23691, 2011

  1. 10.M. Vassura, P. Di Lena, L. Margara, M. Mirto, G. Aloisio, P. Fariselli, R. Casadio

    Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure

    BioData Mining, 4 (1), 1-15, 2011

  1. 11.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, 8 (4), 1017-1028, 2011

  1. 12.P. Di Lena, P. Fariselli, L. Margara, M. Vassura, R. Casadio

    Fast overlapping of protein contact maps by alignment of eigenvectors

    Bioinformatics, 26 (18), 2250-2258, 2010

  1. 13.P. Di Lena, L. Margara

    Optimal global alignment of signals by maximization of Pearson correlation

    Information Processing Letters, 110 (16), 679–686, 2010.

  1. 14.P. Di Lena, L. Margara

    On the undecidability of the limit behavior of Cellular Automata

    Theoretical Computer Science, 411 (7-9), 1075–1084, 2010

  1. 15.A. Dennunzio, P. Di Lena, E. Formenti, L. Margara

    On the directional dynamics of additive cellular automata

    Theoretical Computer Science, 410 (47-49), 4823–4833, 2009

16. P. Di Lena, M. Vassura, L. Margara, P. Fariselli, R. Casadio

    On the reconstruction of three-dimensional protein structures from contact maps

    Algorithms, 2 (1), 76–92, 2009.

17. P. Di Lena, L. Margara

    Computational complexity of dynamical systems: the case of cellular automata

    Information and Computation, 206 (9-10), 1104–1116, 2008

18 M. Vassura, L. Margara, P. Di Lena, F. Medri, P. Fariselli, R. Casadio

    FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps

    Bioinformatics, 24 (10), 1313–1315, 2008

19. M. Vassura, L. Margara, P. Di Lena, F. Medri, P. Fariselli, R. Casadio

    Reconstruction of 3D Structures From Protein Contact Maps

    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5 (3) pp. 357–367, 2008

20. P. Di Lena

    On Computing the Topological Entropy of one-sided Cellular Automata

    Journal of Cellular Automata, 2 (2), pp. 121–130, 2007

21. P. Di Lena, L. Margara

    Row Subshifts and Topological Entropy of Cellular Automata

    Journal of Cellular Automata, 2 (2), pp. 131–140, 2007

  1. 1.P. Di Lena, K. Nagata, P. Baldi

    Deep Architectures and Deep Learning for Protein Structure Prediction (Extended Abstract)

    Machine Learning in Computational Biology (MLCB) 2012, December 7, 2012, Lake Tahoe, Nevada, United States

  1. 2.P. Di Lena, K. Nagata, P. Baldi

    Deep Spatio-Temporal Architectures and Learning for Protein Structure Prediction

    Neural Information Processing Systems (NIPS 2012), December 3-6, 2012, Lake Tahoe, Nevada, United States.

  1. 3.A. Dennunzio, P. Di Lena, L. Margara

    Strictly Periodic Points in Cellular Automata

    In Proceedings of 18th International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA 2012), September 19-21, La Marana, Corsica

  1. 4.P. Di Lena, P. Fariselli, L. Margara, M. Vassura, R. 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 Proceedings of the 9th International Workshop on Algorithms in Bioinformatics, WABI 2009,

    Philadelphia, PA, USA, September 12-13, 2009.

    Lecture Notes in Computer Science, 5724, pp. 62-72, 2009

  1. 5.D. Piovesan, P. Di Lena, M. Vassura

    Unconventional Training for Neural Network Predictions of Inter-Residue Contacts

    In Proceedings of the 1st ACM workshop on Breaking frontiers of computational biology, CompBio 2009,    

    18-20 May 2009, Ischia, Italy, pp. 19–26, 2009

  1. 6.P. Di Lena, L. Margara

    Undecidable properties of limit set dynamics of cellular automata

    In Proceedings of the 26th International Symposium on Theoretical Aspects of Computer Science,

    STACS 2009, February 26-28 2009, Freiburg, Germany, pp. 337–348, 2009

  1. 7.P. Di Lena, L. Margara, M. Vassura, P. Fariselli, R. Casadio

    A new protein representation based on fragment contacts: towards an improvement of contact maps

    prediction

    In Proceedings of the 5th international meeting on Computational Intelligence methods for Bioinformatics

    and Biostatistics, CIBB 2008, 3-4 October 2008 IIASS - Vietri sul Mare, Salerno, Italy. Lecture Notes in    

    Computer Science, 5488, pp. 210–220, 2008

  1. 8.A. Dennunzio, P. Di Lena, E. Formenti, L. Margara

    Classification of directional dynamics for Additive Cellular Automata

    In Proceedings of the 1st International Symposium on Cellular Automata, Journées Automates Cellulaires,

    JAC 2008, 21-25 April 2008, Uzès, France, pp. 40–53, 2008

  1. 9.M. Vassura, L. Margara, P. Di Lena, F. Medri, P. Fariselli, R. Casadio

    Fault tolerance for large scale protein 3D reconstruction from contact maps

    In Proceedings of the 7th International Workshop, WABI 2007, Philadelphia, PA, USA, Sep 8-9, 2007.    

    Lecture Notes in Computer Science, 4645, pp. 25–37, 2007

  1. 10.M. Vassura, L. Margara, F. Medri, P. Di Lena, P. Fariselli, R. Casadio

    Reconstruction of 3D structures from protein contact maps

    In Proceedings of the 3rd International Symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007.

    Lecture Notes in Computer Science, 4463, pp. 578–589, 2007

  1. 11.P. Di Lena, L. Margara

    Computational Complexity of Dynamical Systems: the case of Cellular Automata

    In Pre-proceedings of the 1st International Conference on Languages and Automata Theory and

    Application, LATA 2007, March 29 - April 4 2007, Tarragona, Spain, pp. 211–222, 2007

  1. 12.P. Di Lena

    Decidable properties for Regular Cellular Automata

    In Proceedings of the IFIP 19th Worm Computer Congress, TC-1, Foundations of Computer Science,

    IFIP/TCS 2006, August 23-24 2006, Santiago, Chile. IFIP international Federation for Information

    Processing, 209, pp. 185-196, 2006

BOOK CHAPTERS

  1. 1.P. Di Lena, P. Fariselli, L. Margara, M. Vassura, R. Casadio

    Divide & Conquer strategies for protein structure prediction

    Contribute chapter for Mathematical Approaches to Polymer Sequence Analysis. Editor: Renato Bruni,    

    University of Rome Sapienza, Italy. Publisher: Springer, New York, NY. Accepted for publication.

  1. 2.M. Mirto et al.

    The LIBI Grid Platform for Bioinformatics

    In Mario Cannataro (Ed.), Handbook of Research on Computational Grid Technologies for Life Sciences,

    Biomedicine and Healthcare, vol II, pp. 577–613. IGI Global, 2009

PROCEEDINGS OF INTERNATIONAL CONFERENCES