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).
Curriculum (pdf)
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)
[JP56] G. Fiscon, F. Conte, L. Farina and P. Paci, Network-based approaches to explore complex biological
systems towards network medicine, Genes
9:437 (2018)
[JP57] L. Farina and P. Paci, A feature-based
integrated scoring scheme for cell cycle-regulated genes prioritization, Journal of theoretical Biology 450:101-141 (2018)
Other topics
- 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)
- F. Guarascio, L.
Farina, Topological analysis of migration flows (the case of political
refugees), Int. J. of
Computational Economics and Econometrics 7(4) (2017)