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Results: 1 to 20 of 59

1.

Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalis.

Racioppi C, Kamal AK, Razy-Krajka F, Gambardella G, Zanetti L, di Bernardo D, Sanges R, Christiaen LA, Ristoratore F.

Nat Commun. 2014 Sep 5;5:4830. doi: 10.1038/ncomms5830.

PMID:
25189217
[PubMed - in process]
2.

A network-based approach to dissect the cilia/centrosome complex interactome.

Amato R, Morleo M, Giaquinto L, di Bernardo D, Franco B.

BMC Genomics. 2014 Aug 7;15:658. doi: 10.1186/1471-2164-15-658.

PMID:
25102769
[PubMed - in process]
Free PMC Article
3.

A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders.

Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, di Bernardo D.

BMC Genomics. 2014;15 Suppl 3:S5. doi: 10.1186/1471-2164-15-S3-S5. Epub 2014 May 6.

PMID:
25078076
[PubMed - in process]
Free PMC Article
4.

In-vivo real-time control of protein expression from endogenous and synthetic gene networks.

Menolascina F, Fiore G, Orabona E, De Stefano L, Ferry M, Hasty J, di Bernardo M, di Bernardo D.

PLoS Comput Biol. 2014 May 15;10(5):e1003625. doi: 10.1371/journal.pcbi.1003625. eCollection 2014 May.

PMID:
24831205
[PubMed - in process]
Free PMC Article
5.

The phytoestrogen genistein modulates lysosomal metabolism and transcription factor EB (TFEB) activation.

Moskot M, Montefusco S, Jakóbkiewicz-Banecka J, Mozolewski P, Węgrzyn A, Di Bernardo D, Węgrzyn G, Medina DL, Ballabio A, Gabig-Cimińska M.

J Biol Chem. 2014 Jun 13;289(24):17054-69. doi: 10.1074/jbc.M114.555300. Epub 2014 Apr 25.

PMID:
24770416
[PubMed - in process]
6.

Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis.

Carrella D, Napolitano F, Rispoli R, Miglietta M, Carissimo A, Cutillo L, Sirci F, Gregoretti F, Di Bernardo D.

Bioinformatics. 2014 Jun 15;30(12):1787-8. doi: 10.1093/bioinformatics/btu058. Epub 2014 Feb 20.

PMID:
24558125
[PubMed - in process]
7.

Network based elucidation of drug response: from modulators to targets.

Iorio F, Saez-Rodriguez J, di Bernardo D.

BMC Syst Biol. 2013 Dec 13;7:139. doi: 10.1186/1752-0509-7-139. Review.

PMID:
24330611
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Reverse engineering transcriptional gene networks.

Belcastro V, di Bernardo D.

Methods Mol Biol. 2014;1101:179-96. doi: 10.1007/978-1-62703-721-1_10.

PMID:
24233783
[PubMed - indexed for MEDLINE]
9.

MiRNAs confer phenotypic robustness to gene networks by suppressing biological noise.

Siciliano V, Garzilli I, Fracassi C, Criscuolo S, Ventre S, di Bernardo D.

Nat Commun. 2013;4:2364. doi: 10.1038/ncomms3364.

PMID:
24077216
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

An experimental approach to identify dynamical models of transcriptional regulation in living cells.

Fiore G, Menolascina F, di Bernardo M, di Bernardo D.

Chaos. 2013 Jun;23(2):025106. doi: 10.1063/1.4808247.

PMID:
23822504
[PubMed - indexed for MEDLINE]
11.

Differential network analysis for the identification of condition-specific pathway activity and regulation.

Gambardella G, Moretti MN, de Cegli R, Cardone L, Peron A, di Bernardo D.

Bioinformatics. 2013 Jul 15;29(14):1776-85. doi: 10.1093/bioinformatics/btt290. Epub 2013 Jun 6.

PMID:
23749957
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop.

Settembre C, De Cegli R, Mansueto G, Saha PK, Vetrini F, Visvikis O, Huynh T, Carissimo A, Palmer D, Klisch TJ, Wollenberg AC, Di Bernardo D, Chan L, Irazoqui JE, Ballabio A.

Nat Cell Biol. 2013 Jun;15(6):647-58. doi: 10.1038/ncb2718. Epub 2013 Apr 21. Erratum in: Nat Cell Biol. 2013 Aug;15(8):1016.

PMID:
23604321
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19.

Di Stefano M, Rosa A, Belcastro V, di Bernardo D, Micheletti C.

PLoS Comput Biol. 2013;9(3):e1003019. doi: 10.1371/journal.pcbi.1003019. Epub 2013 Mar 28.

PMID:
23555238
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient.

Pagliarini R, di Bernardo D.

J Comput Biol. 2013 May;20(5):383-97. doi: 10.1089/cmb.2012.0276. Epub 2013 Mar 6.

PMID:
23464878
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation.

De Cegli R, Iacobacci S, Flore G, Gambardella G, Mao L, Cutillo L, Lauria M, Klose J, Illingworth E, Banfi S, di Bernardo D.

Nucleic Acids Res. 2013 Jan;41(2):711-26. doi: 10.1093/nar/gks1136. Epub 2012 Nov 23.

PMID:
23180766
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Engineering and control of biological systems: A new way to tackle complex diseases.

Menolascina F, Siciliano V, di Bernardo D.

FEBS Lett. 2012 Jul 16;586(15):2122-8. doi: 10.1016/j.febslet.2012.04.050. Epub 2012 May 10. Review.

PMID:
22580058
[PubMed - indexed for MEDLINE]
Free Article
17.

Id proteins synchronize stemness and anchorage to the niche of neural stem cells.

Niola F, Zhao X, Singh D, Castano A, Sullivan R, Lauria M, Nam HS, Zhuang Y, Benezra R, Di Bernardo D, Iavarone A, Lasorella A.

Nat Cell Biol. 2012 Apr 22;14(5):477-87. doi: 10.1038/ncb2490.

PMID:
22522171
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Predicting synthetic gene networks.

di Bernardo D, Marucci L, Menolascina F, Siciliano V.

Methods Mol Biol. 2012;813:57-81. doi: 10.1007/978-1-61779-412-4_4.

PMID:
22083736
[PubMed - indexed for MEDLINE]
19.

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function.

Belcastro V, Siciliano V, Gregoretti F, Mithbaokar P, Dharmalingam G, Berlingieri S, Iorio F, Oliva G, Polishchuck R, Brunetti-Pierri N, di Bernardo D.

Nucleic Acids Res. 2011 Nov 1;39(20):8677-88. doi: 10.1093/nar/gkr593. Epub 2011 Jul 23.

PMID:
21785136
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Construction and modelling of an inducible positive feedback loop stably integrated in a mammalian cell-line.

Siciliano V, Menolascina F, Marucci L, Fracassi C, Garzilli I, Moretti MN, di Bernardo D.

PLoS Comput Biol. 2011 Jun;7(6):e1002074. doi: 10.1371/journal.pcbi.1002074. Epub 2011 Jun 30.

PMID:
21765813
[PubMed - indexed for MEDLINE]
Free PMC Article

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