Pagina web di Michele Caselle

[Universita' di Torino]	[Facolta' di Scienze M.F.N.]	[Corso di Laurea in Fisica]
[Dip.to di Fisica Teorica]	[I.N.F.N. Sez. di Torino]	[I.N.F.N. TO - Gruppo teorico]

Michele Caselle

Dipartimento di Fisica Teorica
Via P. Giuria 1 -10125 Torino
Tel. 011-670.7205 Fax 011-670.7214
E-mail: caselle@to.infn.it
Ubicazione ufficio: EN-E7

Recent papers in Computational Biology

Cantini L, Caselle M.
"Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data."
Sci Rep. 2019 Jan 23;9(1):337.

Cantini L, Bertoli G, Cava C, Dubois T, Zinovyev A, Caselle M, Castiglioni I, Barillot E, Martignetti L.
"Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer.."
Nucleic Acids Res. 2019 Jan 18.

Furlan M, Galeota E, de Pretis S, Caselle M, Pelizzola M.
"m6A-Dependent RNA Dynamics in T Cell Differentiation."
Genes (Basel). 2019 Jan 8;10(1).

Cora' D, Caselle M.
"The Epithelial-Mesenchymal Transition, as Hacked by a microRNA Combinatorial Code."
Cell Syst. 2018 Jul 25;7(1):3-4.

Andrea Mazzolini, Alberto Colliva, Michele Caselle, Matteo Osella
"Heaps' law, statistics of shared components and temporal patterns from a sample-space-reducing process ."
Phys. Rev. E 98, 052139 (2018).

Andrea Mazzolini, Marco Gherardi, Michele Caselle, Marco Cosentino Lagomarsino, Matteo Osella.
"Statistics of shared components in complex component systems ."
Phys. Rev. X 8, 021023 (2018)

Rosanova A, Colliva A, Osella M, Caselle M.
"Modelling the evolution of transcription factor binding preferences in complex eukaryotes."
Sci Rep. 2017 Aug 8;7(1):7596.

Cora' D, Re A, Caselle M, Bussolino F.
"MicroRNA-mediated regulatory circuits: outlook and perspectives."
Phys Biol. 2017 Jun 6;14(4):045001.

Cantini L, Caselle M, Forget A, Zinovyev A, Barillot E, Martignetti L.
"A review of computational approaches detecting microRNAs involved in cancer."
Front Biosci (Landmark Ed). 2017 Jun 1;22:1774-1791. Review.

Dal Co A, Lagomarsino MC, Caselle M, Osella M.
"Stochastic timing in gene expression for simple regulatory strategies."
Nucleic Acids Res. 2016 Dec 9.

Orso F, Quirico L, Virga F, Penna E, Dettori D, Cimino D, Coppo R, Grassi E, Elia AR, Brusa D, Deaglio S, Brizzi MF, Stadler MB, Provero P, Caselle M, Taverna D.
"miR-214 and miR-148b Targeting Inhibits Dissemination of Melanoma and Breast Cancer."
Cancer Res. 2016 Sep 1;76(17):5151-62.

Cantini L, Medico E, Fortunato S and Caselle M.
"Detection of gene communities in multi-networks reveals cancer drivers"
Scientific Reports (2015) Volume: 5 Article Number: 17386

Laura Cantini, Claudio Isella, Consalvo Petti, Gabriele Picco, Simone Chiola, Elisa Ficarra, Michele Caselle & Enzo Medico
"MicroRNA-mRNA interactions underlying colorectal cancer molecular subtypes"
Nature Communications (2015) Volume: 6 Article Number: 8878 .

Colliva, A.; Pellegrini, R.; Testori, A., Caselle M.
"Ising-model description of long-range correlations in DNA sequences"
Physical Review E Volume: 91 (2015) Issue: 5 Article Number: 052703.

Osella M, Riba A, Testori A, Corà D, Caselle M.
"Interplay of microRNA and epigenetic regulation in the human regulatory network."
Front Genet. 2014 Oct 6;5:345.

De Grassi A, Iannelli F, Cereda M, Volorio S, Melocchi V, Viel A, Basso G, Laghi L, Caselle M, Ciccarelli FD.
"Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas."
Genome Biol. 2014 Aug 30;15(8):437.

Giancaspero TA, Dipalo E, Miccolis A, Boles E, Caselle M, Barile M.
"Alteration of ROS homeostasis and decreased lifespan in S. cerevisiae elicited by deletion of the mitochondrial translocator FLX1."
Biomed Res Int. 2014;2014:101286.

Caizzi L, Ferrero G, Cutrupi S, Cordero F, Ballaré C, Miano V, Reineri S, Ricci L, Friard O, Testori A, Corà D, Caselle M, Di Croce L, De Bortoli M.
"Genome-wide activity of unliganded estrogen receptor-alpha in breast cancer cells."
Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4892-7.

Riba A, Bosia C, El Baroudi M, Ollino L, Caselle M.
"A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes."
PLoS Comput Biol. 2014 Feb 27;10(2):e1003490

Carla Bosia, Matteo Osella, Mariama El Baroudi, Davide Corá, Michele Caselle
"Gene autoregulation via intronic microRNAs and its functions."
BMC Syst Biol. 2012 Oct 10;6:131.

Testori A, Caizzi L, Cutrupi S, Friard O, De Bortoli M, Cora' D, Caselle M.
"The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors."
BMC Genomics. 2012 Aug 16;13:400.

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.
Preprint available here

Grassi L, Caselle M, Lercher MJ, Lagomarsino MC.
"Horizontal gene transfers as metagenomic gene duplications."
Mol Biosyst. 2012 Jan 4, Vol. 8, 790-795

Matteo Osella, Carla Bosia, Davide Corá, Michele Caselle
"The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering"
PLoS Comput Biol 2011 Mar 8; 7(3): e1001101

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

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.

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

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.

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.

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.
Preprint available here
Supplementary Material

C. Bosia, M. Caselle, D. Corá
"Nucleation dynamics in two-dimensional cylindrical Ising models and chemotaxis"
Physical Review E 81 (2), 021907 (2010)
Preprint available here

M.Osella and M.Caselle
"Entropic contribution to the splicing process."
Phys. Biol. 6 (2009) 046018
Preprint available here

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.

Re A, Corá D, Taverna D, Caselle M
"Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human."
Mol Biosyst. 2009 Aug;5(8):854-67.

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

A. Re, I. Molineris and M. 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

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

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.

Martignetti L, Caselle M.
" Universal power law behaviors in genomic sequences and evolutionary models"
Phys. Rev. E 76, 021902 (2007)
Preprint available here

D. Cora' , F. Di Cunto , M. Caselle and P. Provero
"Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions"
BMC Bioinformatics 2007, 8:174

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

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 genomic"
BMC Bioinformatics 2005, 6:110

D. Cora', F. Di Cunto, P. Provero, L. Silengo and M. Caselle
"Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs"
BMC Bioinformatics 2004, 5:57

M. Caselle, F. Di Cunto and P. Provero
"Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes"
BMC Bioinformatics 2002, 3:7