Michele Caselle
Michele Caselle
affiliation: Università di Torino
research area(s): Computational Biology, Genetics And Genomics
Course: Complex Systems for Life Sciences
University/Istitution: Università di Torino

Ph. D in Physics, Turin University (1983-1987)


1985-2000 I.N.F.N. researcher
2000-2005 Associate professor at the department of Theoretical Physics of the Turin University
2006 - Full professor at the department of Theoretical Physics of the Turin University (now renamed as department of Physics)

Research Areas:

-Statistical Mechanics,
-Phase Transitions and Critical Phenomena
-Lattice Gauge Theories
-Random Matrix Theories
-Montecarlo simulations of Complex Systems

-Systems Biology,
-Gene regulation,

Scientific Profile.

My research interests are of interdisciplinary nature. I started as a particle physicist,
working on the field theoretical description of Quantum Chromodynamics (QCD).
In this context I was one of the first to use and develop numerical montecarlo methods
for the study of lattice QCD in theoretical physics.
Then I moved to statistical mechanics and to the related problems of theoretical
study of complex and/or critical systems.
In the last 10 years I started also to work in molecular biology (with a
particular attention to gene regulation) with bioinformatic tools.
In this last part of my scientific career I tried to apply in a biological
context the techniques and ideas which I had developed in previous years as a physicist.
In particular the use of sophisticated simulation tools to address biological
problems and the use of advanced methods in network theory to identify
the relevant degrees of freedom of complex systems.

In this framework , with a few collaborators from other departments of the Turin University we started in 2002
a PhD program named ``Complex Systems for Post-genomic Biology''
with the aim to combine together wet biology expertise and theoretical tools to address complex biological problems.

I published more than 100 papers on peer reviewed ISI journals on topics ranging from Quantum Field Theory to Computational Biology.

I serve as referee for several journals both in high energy theoretical physics:
JHEP, JSTAT, Nuclear Physics B, Physical Review Letters...
and in computational Biology:
PloS Comp. Biol., PloS ONE, BMC Bioinformatics, BMC Genomics...

My research activity is mainly devoted to the study of gene regulation.
In particular I am interested in the combination of the transcriptional and post-transcriptional layers of regulation. I address this issue both from the bioinformatic side, trying to reconstruct the network from sequence data, evolutionary conservation constraints and expression data, and from the modeling side, using deterministic and stochastic equations to study the properties of network motifs within the network. More recently I also started to study evolutionary models in yeast. In particular the role of the horizontal gene transfer in shaping the gene distribution and the role of the whole genome duplication event in organizing the regulatory network.
1) Davide Cora', Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo and
Michele Caselle
Computational identification of transcription factor binding sites by functional analysis of sets of
genes sharing overrepresented upstream motifs
BMC Bioinformatics 2004, 5:57

2) D.Cora', C. Herrmann, P.Provero, C. Dieterich, F. DiCunto and M.Caselle
Ab initio identification of putative human transcription factor binding
sites by comparative genomics
BMC Bioinformatics 2005, 6:110

3) A. Re, D. Cora, A. M. Puliti, M. Caselle, I. Sbrana
Correlated fragile site expression allows the identification
of candidate fragile genes involved in immunity and associated with carcinogenesis
BMC Bioinformatics 2006, 7:413

4) Davide Cora' , Ferdinando Di Cunto , Michele Caselle and Paolo Provero
Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of
oligonucleotide distributions
BMC Bioinformatics 2007, 8:174

5) Moroni E, Caselle M, Fogolari F.
Identification of DNA-binding protein target sequences by physical effective energy functions:
free energy analysis of lambda repressor-DNA complexes.
BMC Struct Biol. 2007 Sep 27;7:61.

6) Martignetti L, Caselle M.
Universal power law behaviors in genomic sequences and evolutionary models.
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Aug;76(2 Pt 1):021902. Epub 2007 Aug 2.

7) Zanivan S, Cascone I, Peyron C, Molineris I, Marchio S, Caselle M, Bussolino F.
A new computational approach to analyze human protein complexes and predict novel protein interactions.
Genome Biol. 2007 Dec 4;8(12):R256

8) Zanivan S, Cora D, Caselle M, Bussolino F.
VRG: A database of vascular dysfunctions related genes.
Computers & Mathematics with Applications (2008) Volume 55, Pages 1068-1073

9) Angela Re, Ivan Molineris and Michele Caselle
Graph theory analysis of genomics problems: Community analysis of fragile sites correlations
and of pseudogenes alignments
Computers & Mathematics with Applications (2008) Volume 55, Pages 1034-1043

10) A. Re, D. Cora, D.Taverna and M. Caselle.
Genome-wide survey of microRNA-transcription factor
feed-forward regulatory circuits in human
Mol. BioSyst., 2009, 5, 854 - 867,

11) Fogolari F, Haridas H, Corazza A, Viglino P, Cora' D, Caselle M, Esposito G, Xodo LE.
"Molecular models for intrastrand DNA G-quadruplexes."
BMC Struct Biol. 2009 Oct 7;9(1):64.

12) M.Osella, M.Caselle
Entropic contributions to the splicing process
Phys. Biol. 6 (2009) 046018

13) I. Molineris, G. Sales, F. Bianchi, F. di Cunto and M. Caselle
"A New Approach for the Identification of Processed Pseudogenes"
J Comput Biol. 2010 May;17(5):755-65.

14) Carla Bosia, Michele Caselle, Davide Corá
Nucleation dynamics in 2d cylindrical Ising models and chemotaxis
Physical Review E 81 (2), 021907 (2010)

15) D. Fusco, L. Grassi, M. Caselle, B. Bassetti and M. C. Lagomarsino
"Ordered structure of the transcription network inherited from the yeast whole-genome duplication."
BMC Systems Biology 2010, 4:77.

16) F. Orso, D. Cora', B. Ubezio, P. Provero, M. Caselle and D. Taverna
"Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes "
BMC Genomics 2010, 11:355.

17) Grassi L, Fusco D, Sellerio A, Corà D, Bassetti B, Caselle M, Lagomarsino MC.
"Identity and divergence of protein domain architectures after the yeast
whole-genome duplication event."
Mol Biosyst. 2010 Nov 1;6(11):2305-15. Epub 2010 Aug 26.

18) Torella R, Moroni E, Caselle M, Morra G, Colombo G.
"Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes."
BMC Struct Biol. 2010 Nov 24;10:42.

19) Osella M, Bosia C, Corá D, Caselle M.
The role of incoherent microRNA-mediated feedforward loops in noise buffering.
PLoS Comput Biol. 2011 Mar;7(3):e1001101. Epub 2011 Mar 10.

20) El Baroudi M, Corà D, Bosia C, Osella M, Caselle M.
A curated database of miRNA mediated feed-forward loops involving MYC as master regulator.
PLoS One. 2011 Mar 3;6(3):e14742.

21) Grassi L, Caselle M, Lercher J.M. and Lagomarsino MC.
"Horizontal gene transfers as metagenomic gene duplications."
Mol Biosyst. 2012.

22) Eduati F, di Camillo B, Karbiener M, Scheideler M, Corà D, Caselle M, Toffolo G.
"Dynamic Modeling of miRNA-mediated Feed-Forward Loops."
J Comput Biol. 2012 Feb;19(2):188-99.
Project Title:
Role of Transposable elements in shaping the gene regulatory network in human

Project Title:
Sponge effects in the human regulatory network