Michele Caselle

Michele Caselle

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Michele Caselle

Michele Caselle

Publications by authors named "Michele Caselle"

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Identification of altered biological processes in heterogeneous RNA-sequencing data by discretization of expression profiles.

Nucleic Acids Res 2020 02;48(4):1730-1747

IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy.

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http://dx.doi.org/10.1093/nar/gkz1208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038995PMC
February 2020

Investigating the epi-miRNome: identification of epi-miRNAs using transfection experiments.

Epigenomics 2019 11 6;11(14):1581-1599. Epub 2019 Nov 6.

Department of Physics & INFN, University of Torino, 10125, Torino, Italy.

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http://dx.doi.org/10.2217/epi-2019-0050DOI Listing
November 2019

BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics.

BMC Bioinformatics 2019 Nov 22;20(Suppl 9):562. Epub 2019 Nov 22.

Department of Physics, University of Turin, Via Pietro Giuria 1, 10126, Torino, Italy.

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http://dx.doi.org/10.1186/s12859-019-3175-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873652PMC
November 2019

m6A-Dependent RNA Dynamics in T Cell Differentiation.

Genes (Basel) 2019 01 8;10(1). Epub 2019 Jan 8.

Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy.

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http://www.mdpi.com/2073-4425/10/1/28
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http://dx.doi.org/10.3390/genes10010028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356486PMC
January 2019

Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data.

Sci Rep 2019 01 23;9(1):337. Epub 2019 Jan 23.

Universitá degli Studi di Torino, Department of Physics and INFN, via P. Giuria 1, I-10125, Turin, Italy.

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http://dx.doi.org/10.1038/s41598-018-36744-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344502PMC
January 2019

The Epithelial-Mesenchymal Transition, as Hacked by a microRNA Combinatorial Code.

Cell Syst 2018 07;7(1):3-4

Deparment of Physics, University of Torino and INFN, Via P. Giuria 1, I-10125 Torino, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.07.003DOI Listing
July 2018

Modelling the evolution of transcription factor binding preferences in complex eukaryotes.

Sci Rep 2017 08 8;7(1):7596. Epub 2017 Aug 8.

Department of Physics and INFN, Università degli Studi di Torino, via P.Giuria 1, I-10125, Turin, Italy.

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http://dx.doi.org/10.1038/s41598-017-07761-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548724PMC
August 2017

A review of computational approaches detecting microRNAs involved in cancer.

Front Biosci (Landmark Ed) 2017 06 1;22:1774-1791. Epub 2017 Jun 1.

Institut Curie, INSERM U900, PSL Research University, Mines ParisTech, 26, rue d'Ulm, F-75248 Paris, France.

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http://dx.doi.org/10.2741/4571DOI Listing
June 2017

MicroRNA-mediated regulatory circuits: outlook and perspectives.

Phys Biol 2017 06 6;14(4):045001. Epub 2017 Jun 6.

Department of Oncology, University of Torino, Str. Prov. 142 Km 3.95, I-10060 Candiolo, Italy. Candiolo Cancer Institute-FPO, IRCCS, Str. Prov. 142 Km 3.95, I-10060 Candiolo, Italy. Center for Molecular Systems Biology, University of Torino, Regione Gonzole 10, I-10043 Orbassano, Italy. Current address: Department of Translational Medicine, Piemonte Orientale University 'Amedeo Avogadro', Via Solaroli 17, I-28100 Novara, Italy.

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http://dx.doi.org/10.1088/1478-3975/aa6f21DOI Listing
June 2017

Stochastic timing in gene expression for simple regulatory strategies.

Nucleic Acids Res 2017 02;45(3):1069-1078

Department of Physics and INFN, Università degli Studi di Torino, via P. Giuria 1, Turin, Italy.

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http://dx.doi.org/10.1093/nar/gkw1235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388427PMC
February 2017

miR-214 and miR-148b Targeting Inhibits Dissemination of Melanoma and Breast Cancer.

Cancer Res 2016 09 21;76(17):5151-62. Epub 2016 Jun 21.

Molecular Biotechnology Center (MBC), University of Torino, Torino, Italy. Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy. Center for Complex Systems in Molecular Biology and Medicine, University of Torino, Torino, Italy.

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-15-1322DOI Listing
September 2016

Detection of gene communities in multi-networks reveals cancer drivers.

Sci Rep 2015 Dec 7;5:17386. Epub 2015 Dec 7.

Università di Torino, Department of Physics and INFN, Torino, Italy.

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http://dx.doi.org/10.1038/srep17386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671005PMC
December 2015

MicroRNA-mRNA interactions underlying colorectal cancer molecular subtypes.

Nat Commun 2015 11 17;6:8878. Epub 2015 Nov 17.

Department of Oncology, Università degli Studi di Torino, S.P. 142, km 3, 95-10060 Candiolo, Italy.

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http://dx.doi.org/10.1038/ncomms9878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4660217PMC
November 2015

Alteration of ROS homeostasis and decreased lifespan in S. cerevisiae elicited by deletion of the mitochondrial translocator FLX1.

Biomed Res Int 2014 8;2014:101286. Epub 2014 May 8.

Istituto di Biomembrane e Bioenergetica, CNR, Via Amendola 165/A, 70126 Bari, Italy ; Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari "A. Moro", Via Orabona 4, 70126 Bari, Italy.

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http://dx.doi.org/10.1155/2014/101286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033422PMC
January 2015

Interplay of microRNA and epigenetic regulation in the human regulatory network.

Front Genet 2014 6;5:345. Epub 2014 Oct 6.

Dipartimento di Fisica, Istituto Nazionale di Fisica Nucleare, Università di Torino Torino, Italy.

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http://dx.doi.org/10.3389/fgene.2014.00345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4186481PMC
October 2014

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. Epub 2014 Feb 27.

Department of Physics and INFN, University of Torino, Torino, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1003490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937125PMC
February 2014

Molecular and morphologic characterization of superficial- and deep-subcutaneous adipose tissue subdivisions in human obesity.

Obesity (Silver Spring) 2013 Dec 11;21(12):2562-70. Epub 2013 Jun 11.

Laboratory of Molecular Biology, Istituto Auxologico Italiano, IRCCS, Milan, Italy.

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http://dx.doi.org/10.1002/oby.20417DOI Listing
December 2013

Gene autoregulation via intronic microRNAs and its functions.

BMC Syst Biol 2012 Oct 10;6:131. Epub 2012 Oct 10.

Human Genetics Foudation, V Nizza 52, Torino I-10126, Italy.

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http://dx.doi.org/10.1186/1752-0509-6-131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534558PMC
October 2012

The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors.

BMC Genomics 2012 Aug 16;13:400. Epub 2012 Aug 16.

Center for Molecular Systems Biology, University of Turin, Turin, Candiolo I-10060, Italy.

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http://dx.doi.org/10.1186/1471-2164-13-400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478180PMC
August 2012

Horizontal gene transfers as metagenomic gene duplications.

Mol Biosyst 2012 Mar 4;8(3):790-5. Epub 2012 Jan 4.

Università degli Studi di Torino, Dipartimento di Fisica Teorica, Torino, Italy.

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http://dx.doi.org/10.1039/c2mb05330fDOI Listing
March 2012

Dynamic modeling of miRNA-mediated feed-forward loops.

J Comput Biol 2012 Feb;19(2):188-99

Department of Information Engineering, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1089/cmb.2011.0274DOI Listing
February 2012

A curated database of miRNA mediated feed-forward loops involving MYC as master regulator.

PLoS One 2011 Mar 3;6(3):e14742. Epub 2011 Mar 3.

Department of Theoretical Physics, University of Turin and National Institute for Nuclear Physics, Turin, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014742PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048388PMC
March 2011

The role of incoherent microRNA-mediated feedforward loops in noise buffering.

PLoS Comput Biol 2011 Mar 10;7(3):e1001101. Epub 2011 Mar 10.

Dipartimento di Fisica Teorica and INFN University of Torino, Torino, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1001101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053320PMC
March 2011

Identity and divergence of protein domain architectures after the yeast whole-genome duplication event.

Mol Biosyst 2010 Nov 26;6(11):2305-15. Epub 2010 Aug 26.

Università degli Studi di Torino, Dip. Fisica Teorica-Via Giuria 1, 10125 Torino, Italy.

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http://dx.doi.org/10.1039/c003507fDOI Listing
November 2010

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. Epub 2010 Nov 24.

Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy.

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http://dx.doi.org/10.1186/1472-6807-10-42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002361PMC
November 2010

Ordered structure of the transcription network inherited from the yeast whole-genome duplication.

BMC Syst Biol 2010 Jun 3;4:77. Epub 2010 Jun 3.

Università degli Studi di Milano, Dip, Fisica, Via Celoria 16, 20133 Milano, Italy.

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http://dx.doi.org/10.1186/1752-0509-4-77DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900227PMC
June 2010

Entropic contributions to the splicing process.

Phys Biol 2009 Nov 24;6(4):046018. Epub 2009 Nov 24.

Dipartimento di Fisica Teorica and INFN, Università degli Studi di Torino, v. Pietro Giuria 1, 10125 Torino, Italy.

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http://stacks.iop.org/1478-3975/6/i=4/a=046018?key=crossref.
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http://dx.doi.org/10.1088/1478-3975/6/4/046018DOI Listing
November 2009

Molecular models for intrastrand DNA G-quadruplexes.

BMC Struct Biol 2009 Oct 7;9:64. Epub 2009 Oct 7.

Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Piazzale Kolbe 4 - 33100 Udine, Italy.

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http://dx.doi.org/10.1186/1472-6807-9-64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768733PMC
October 2009

Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human.

Mol Biosyst 2009 Aug 19;5(8):854-67. Epub 2009 Jun 19.

CIBIO-Centre for Integrative Biology, University of Trento, I-38100 Trento, Italy.

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http://dx.doi.org/10.1039/b900177hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898627PMC
August 2009

A new computational approach to analyze human protein complexes and predict novel protein interactions.

Genome Biol 2007 ;8(12):R256

Department of Oncological Sciences and Division of Molecular Angiogenesis, Institute for Cancer Research and Treatment (IRCC), University of Torino Medical School, Strada Provinciale, I-10060 Candiolo (Turin), Italy.

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http://dx.doi.org/10.1186/gb-2007-8-12-r256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246258PMC
March 2008

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. Epub 2007 Sep 27.

Dipartimento di Fisica Teorica, Universià di Torino and INFN, Via P, Giuria 1, 10125 Torino, Italy.

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http://dx.doi.org/10.1186/1472-6807-7-61DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2194778PMC
September 2007

Universal power law behaviors in genomic sequences and evolutionary models.

Phys Rev E Stat Nonlin Soft Matter Phys 2007 Aug 2;76(2 Pt 1):021902. Epub 2007 Aug 2.

Dipartimento di Fisica Teoric, Università di Torino and INFN, Via Pietro Giuria 1, I-10125 Torino, Italy.

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http://dx.doi.org/10.1103/PhysRevE.76.021902DOI Listing
August 2007

Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions.

BMC Bioinformatics 2007 May 24;8:174. Epub 2007 May 24.

Dept of Theoretical Physics, University of Turin and INFN, Turin, Italy.

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http://dx.doi.org/10.1186/1471-2105-8-174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904458PMC
May 2007

Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis.

BMC Bioinformatics 2006 Sep 18;7:413. Epub 2006 Sep 18.

Dipartimento di Fisica Teorica dell'Università degli Studi di Torino e INFN, Via P, Giuria 1--I 10125 Torino, Italy.

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http://dx.doi.org/10.1186/1471-2105-7-413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1601973PMC
September 2006

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.

BMC Bioinformatics 2002 14;3. Epub 2002 Feb 14.

Dipartimento di Fisica Teorica, Università di Torino, and INFN, Sezione di Torino, Torino, Italy.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC77394PMC
http://dx.doi.org/10.1186/1471-2105-3-7DOI Listing
November 2003