Biographical Notes: I received the 'Laurea' degree (5 years) in Electronics Engineering (summa cum laude) from the University of Rome 'La Sapienza' and the PhD in Systems Engineering at the same University. I am currently Associate Professor of Bioengineering (ING-INF/06). I teach Computational Methods for Molecular Biology and Bioinformatics at the Faculty of Information Engineering, Informatics and Statistics, of the University of Rome, 'La Sapienza'. In 2014 I obtained the full professor habilitation (ING-INF/04).

 

Selected publications

Books

[B1] L. Farina and S. Rinaldi, Positive Linear Systems: Theory and Applications, Pure and Applied Mathematics: A Wiley-Interscience Series of Text, Monographs, and Tracts, John Wiley & Sons, New York, 2000
[B2] L. Benvenuti, A. De Santis and L. Farina (Eds.), Positive Systems. Proceedings of the First Multidisciplinary Symposium on Positive Systems (POSTA 2003).
Lecture Notes on Control and Information Sciences, v. 294, Springer-Verlag, Heidelberg
[B3] L. Benvenuti, A. De Santis, L. Farina, Sistemi dinamici: modellistica, analisi e controllo.
McGraw Hill, Milano, 2008
[B4] F. Cacace, L. Farina, R. Setola and A. Germani (Eds.), Positive Systems. Proceedings of the Fifth International Symposium on Positive Systems (POSTA 2016). Lecture Notes on Control and Information Sciences, v. 471, Springer-Verlag, Heidelberg (2017)

 

Journal Papers

       Systems and Control (1994-2006)

[JP1] L.Farina, A note on discrete-time positive realizations, Systems & Control Letters 22 (1994) 467-469
[JP2] L. Farina, Necessary conditions for positive realizability of continuous-time linear systems, Systems & Control Letters 25 (1995) 121-124
[JP3] L. Farina and L. Benvenuti, Positive realizations of linear systems, Systems & Control Letters 26 (1996) 1-9
[JP4] B.D.O. Anderson, M. Deistler, L. Farina and L. Benvenuti, Nonnegative realization of a linear system with nonnegative impulse response, IEEE Transactions on Circuits and Systems-I: Fundamental Theory and Applications 43 (1996) 134-142
[JP5] L. Benvenuti and L. Farina, Discrete-time filtering via charge routing networks, Signal Processing 49 (1996) 207-215
[JP6] L. Farina, Minimal order realizations for a class of positive linear systems, Journal of the Franklin Institute 333B (1996) 893-900
[JP7] L. Farina, On the existence of a positive realization, Systems & Control Letters 28 (1996) 219-226
[JP8] L. Farina and L. Benvenuti, Invariant polytopes of linear systems, IMA Journal of Mathematical Control and Information, 15 (1998) 233-240
[JP9] L. Benvenuti and L. Farina, On the class of linear filters attainable with charge routing networks, IEEE Transactions on Circuits and Systems-II: Analog and Digital Signal Processing 43 (1996) 618-622
[JP10] L. Benvenuti and L. Farina, Constrained control for uncertain discrete-time systems, International Journal on Robust and Nonlinear Control, 8 (1998) 555-565
[JP11] L. Farina and L. Benvenuti, Polyhedral reachable set with positive controls, Mathematics of Control, Signals and Systems 10 (1997) 364-380
[JP12] L. Benvenuti and L. Farina, A note on minimality of positive realizations, IEEE Transactions on Circuits and Systems-I: Fundamental Theory and Applications, 45 (1998) 676-678
[JP13] L. Benvenuti and L. Farina, An Example of how positivity may force realizations of ‘large’ dimension, Systems & Control Letters 36 (1999) 261-266
[JP14] L. Benvenuti, L. Farina and B.D.O. Anderson, Filtering through combination of positive filters,  IEEE Transactions on Circuits and Systems-I: Fundamental Theory and Applications, 46 (1999) 1431-1440 This paper has received the 2001 IEEE CAS Guillemin-Cauer Award
[JP15] M.E. Valcher and L. Farina, An algebraic approach to the construction of polyhedral invariant cones, SIAM J. Matrix Analysis Appl, 22 (2000) 453-471
[JP16] L. Benvenuti, L. Farina, B.D.O. Anderson and F. De Bruyne, Minimal discrete-time positive realizations of transfer functions with positive real poles, IEEE Transactions on Circuits and Systems-I: Fundamental Theory and Applications, 47 (2000) 1370-1377
[JP17] A. De Santis and L. Farina, Identification of positive linear systems with Poisson output transformation,  Automatica  (2002) 38 861-868
[JP18] L. Benvenuti and L. Farina,Invariance and feedback control with state and input constraints,  Int. J. Systems Science, 33 (2002) 45-53
[JP19] L. Benvenuti and L. Farina, The design of fiber-optic filters, Journal of Lightwave Technology, 19 (2001) 1366-1375
[JP20] L. Benvenuti and L. Farina, Positive and compartmental systems,  IEEE Transactions on Automatic Control 47 (2002) 370-373
[JP21] L. Benvenuti, L. Farina and B.D.O. Anderson, The positive side of filters, IEEE Circuits and Systems Magazine, 1, (Third Quarter 2001) 32-36, (invited paper)
[JP22] L. Benvenuti, A. De Santis  and L. Farina, On model consistency in compartmental systems identification, Automatica (2002) 38 1969-1976
[JP23] L. Benvenuti and L. Farina, Minimal positive realizations: a survey of recent results and open problems, Kybernetika (2003) 38 217-228 (Special issue on Max-Puls algebra)
[JP24] L. Benvenuti and L. Farina, Eigenvalue regions for positive systems, Systems & Control Letters (2004) 51 325-330
[JP25] L. Benvenuti and L. Farina, A tutorial on the positive realization problem, IEEE Transactions on Automatic Control, (2004) 49 651-664
[JP26]  L. Benvenuti and L. Farina, The geometry of the reachability set for linear discrete-time systems with positive controls, SIAM J. Matrix Analysis, (2006)  28 306-325
[JP27] L. Benvenuti and L. Farina, Nonnegative matrices in signal processing, Signal Processing (2006) 86 2388-2392
[JP28] L. Farina, Discussion on: "Representation of a Class of MIMO Systems via Internally Positive Realization'', European Journal of Control, (2010)  16(3):305-306
[JP29] F. Cacace, L. Farina, A. Germani, C. Manes, Internally positive representation of a class of continuous time systems, IEEE Transactions on Automatic Control, (2012) 57(12):3158-3163
[JP30] L. Benvenuti, L. Farina, Revisiting the linear recursion with nonnegative coefficients problem, Linear Algebra and its Applications, (2017) 535:191-194

 

        Computational Molecular Biology and Bioinformatics (from 2005)

[JP31] M.C. Palumbo, A. Colosimo, A. Giuliani and L. Farina, Functional essentiality from topology features in metabolic networks: a case study in yeast, FEBS Letters (2005) 579 4642-4646
[JP32] Maria Concetta Palumbo, Lorenzo Farina, Alfredo Colosimo, Kyaw Tun, Pawan K. Dhar and Alessandro Giuliani, Networks everywhere? Some general implications of en emergent metaphor, Current Bioinformatics (2006) 1 219-234
[JP33] L. Farina, A. De Santis, G. Morelli and I. Ruberti, Dynamic measure of genes co-regulation, IET Systems Biology (2007) 1 10-17
[JP34] A. Giuliani, M. Tsuchiya, Y. Zhen; A. Colosimo, M.C.Palumbo, L. Farina, M. Crescenzi, A. Mazzola, R. Negri, M. Bianchi, Gene expression waves: cell cycle independent collective dynamics in cultured cells, FEBS Journal (2007)  274 2878-2886 (link)
[JP35]  M.C. Palumbo, A. Colosimo, A. Giuliani and L. Farina, Essentiality is an emergent property of metabolic network wiring, FEBS Letters (2007) 581 2485-2489
[JP36] M.C. Palumbo, L. Farina, A. De Santis, A. Giuliani, A. Colosimo, G. Morelli and I. Ruberti, Collective Behaviour in Gene Regulation: Post-transcriptional Regulation and the Temporal Compartmentalization of Cellular cycles, FEBS Journal  (2008) 275:2364-71. (link)
[JP37] L. Farina, A. De Santis, S. Salvucci, G. Morelli and I. Ruberti, Embedding mRNA stability in correlation analysis of time-series gene expression data, PLoS Computational Biology  (2008) 4(8): e1000141. doi:10.1371/journal.pcbi.1000141 (link)
[JP38] N. Soranzo, M. Zampieri, L. Farina and C. Altafini, mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle, BMC Systems Biology  (2009) 3(18) (link)
[JP39] M.C. Palumbo, L. Farina, A. Colosimo and A. Giuliani,  Metabolic Networks. In: Handbook on Biological Networks, World Scientific Publishing Company, ISBN/ISSN: 9812838791 (2009)
[JP40] P. Palumbo, G. Mavelli, L. Farina and L. Alberghina, Networks and Circuits in Cell Regulation, Biochemical and Biophysical Research Communications (2010) 396(4):881-6
[JP41] P. Palumbo, G. Mavelli, L. Farina and A. Germani, Identification of regulatory network motifs from gene expression data,  Journal of Mathematical Modelling and Algorithms, Volume 9, Number 3, 233-245 (2010)
[JP42] G. Romagnoli, E. Cundari, R. Negri, M. Crescenzi, L. Farina, A. Giuliani and M. Bianchi, Synchronous protein cycling in batch cultures of the yeast Saccharomyces cerevisiae at log growth phase, Experimental Cell Research 317 (2011) 2958-2968, http://dx.doi.org/10.1016/j.yexcr.2011.09.007
[JP43] M. Fasoli, S. Dal Santo, S. Zenoni, G.B. Tornielli, L. Farina, A. Zamboni, A. Porceddu, L. Venturini, M. Bicego, V. Murino, A. Ferrarini, M. Delledonne and M. Pezzotti, The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program, Plant Cell, Sep 4 (2012)
[JP44] S. Camiolo, L. Farina and A. Porceddu, The relation of codon bias to tissue specific gene expression in Arabidopsis thaliana, Genetics, Aug 5 (2012)
[JP45] F. Cacace, P. Paci, V. Cusimano, A. Germani and L. Farina, Stochastic modeling of  expression kinetics identifies messenger half-lives and reveals sequential waves of co-ordinated transcription and decay, PLoS Computational Biology, vol.8, (2012)
[JP46] S. Dal Santo, G.B. Tonielli, S. Zenoni, L. Farina, M. Fasoli, F. Guzzo, M. Delledonne and M. Pezzotti, The plasticity of the grapevine berry transcriptome, Genome Biology, 14:r54 (2013)
[JP47] M. De Santis, F. Rinaldi, E. Falcone, S. Lucidi, G. Piaggio, A. Gurtner and L. Farina, Combining optimization and machine learning tecniques for genome wide prediction of human cell cycle-regulated genes, Bioinformatics, 30(2):228-233 (2014)
[JP48] P. Paci, T. Colombo and L. Farina, Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in breast cancer, BMC Systems Biology (2014), 8:832
[JP49] M.C. Palumbo, S. Zenoni, M. Fasoli, M. Massonet,  L. Farina, F. Castiglione, M. Pezzotti and P. Paci, Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development, Plant Cell (2014), 26(12):4617-35
[JP50] M.C. Palumbo, L. Farina and P. Paci, Kinetic effects and modeling of mRNA turnover, WIREs RNA (2015),
6(3):327-336
[JP51] T. Colombo, L. Farina, G. Macino and P. Paci, PVT1: a rising star among oncogenic long non-coding RNAs,  BioMed Research International (2015),
2015:304208. doi:10.1155/2015/304208.
[JP52]  J.B. Kullan, D.L. Paim Pinto, E. Bertolini, M. Fasoli, S. Zenoni , G.B. Tornielli, M. Pezzotti, B. Meyers, L.Farina, M.E. Pè, E. Mica, miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing, BMC Genomics (2015), 16:393,
DOI: 10.1186/s12864-015-1610-5
[JP53] …, L. Farina, … Gut Microbiota Meta-omics Charts Supporting CF Patients' Laboratory and Clinical Management, Journal of clinical gastroenterology (2016), 50 p. S222
[JP54] F. Conte, G. Fiscon, M. Chiara, T. Colombo, L. Farina and P. Paci, Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer, PLoS ONE 12(2):e0171661 (2017)
[JP55] P. Paci, T. Colombo, G. Fiscon, A. Gurtner, G. Pavesi  and L. Farina, SWIM: a computational tool to unveiling crucial nodes in complex biological networks, Scientific Reports – Nature 7:44797 (2017)

        Other topics

[JP55] Modonesi C, Farina L, Licata I, Germano R, Zbilut JP, Giuliani A., A contemporary pathology of science, Ann Ist Super Sanita. 44(3):211-3 (2008)
[JP56]
F. Guarascio, L. Farina, Topological analysis of migration flows (the case of political refugees), Int. J. of Computational Economics and Econometrics 7(4) (2017)