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Items: 1 to 50 of 88

1.

Comprehensive kinome NGS targeted expression profiling by KING-REX.

Carapezza G, Cusi C, Rizzo E, Raddrizzani L, Di Bella S, Somaschini A, Leone A, Lupi R, Mutarelli M, Nigro V, di Bernardo D, Magni P, Isacchi A, Bosotti R.

BMC Genomics. 2019 Apr 23;20(1):307. doi: 10.1186/s12864-019-5676-3.

2.

Quantitative Characterization of α-Synuclein Aggregation in Living Cells through Automated Microfluidics Feedback Control.

Perrino G, Wilson C, Santorelli M, di Bernardo D.

Cell Rep. 2019 Apr 16;27(3):916-927.e5. doi: 10.1016/j.celrep.2019.03.081.

3.

Glatiramer Acetate modulates ion channels expression and calcium homeostasis in B cell of patients with relapsing-remitting multiple sclerosis.

Criscuolo C, Cianflone A, Lanzillo R, Carrella D, Carissimo A, Napolitano F, de Cegli R, de Candia P, La Rocca C, Petrozziello T, Matarese G, Boscia F, Secondo A, Di Bernardo D, Brescia Morra V.

Sci Rep. 2019 Mar 12;9(1):4208. doi: 10.1038/s41598-018-38152-8.

4.

The Autophagy Inhibitor Spautin-1 Antagonizes Rescue of Mutant CFTR Through an Autophagy-Independent and USP13-Mediated Mechanism.

Pesce E, Sondo E, Ferrera L, Tomati V, Caci E, Scudieri P, Musante I, Renda M, Baatallah N, Servel N, Hinzpeter A, di Bernardo D, Pedemonte N, Galietta LJV.

Front Pharmacol. 2018 Dec 13;9:1464. doi: 10.3389/fphar.2018.01464. eCollection 2018.

5.

Dissection of metabolic reprogramming in polycystic kidney disease reveals coordinated rewiring of bioenergetic pathways.

Podrini C, Rowe I, Pagliarini R, Costa ASH, Chiaravalli M, Di Meo I, Kim H, Distefano G, Tiranti V, Qian F, di Bernardo D, Frezza C, Boletta A.

Commun Biol. 2018 Nov 16;1:194. doi: 10.1038/s42003-018-0200-x. eCollection 2018.

6.

Regulation of Gene Expression and Signaling Pathway Activity in Mammalian Cells by Automated Microfluidics Feedback Control.

Postiglione L, Napolitano S, Pedone E, Rocca DL, Aulicino F, Santorelli M, Tumaini B, Marucci L, di Bernardo D.

ACS Synth Biol. 2018 Nov 16;7(11):2558-2565. doi: 10.1021/acssynbio.8b00235. Epub 2018 Oct 22.

PMID:
30346742
7.

Induction of Nitric-Oxide Metabolism in Enterocytes Alleviates Colitis and Inflammation-Associated Colon Cancer.

Stettner N, Rosen C, Bernshtein B, Gur-Cohen S, Frug J, Silberman A, Sarver A, Carmel-Neiderman NN, Eilam R, Biton I, Pevsner-Fischer M, Zmora N, Brandis A, Bahar Halpern K, Mazkereth R, di Bernardo D, Brunetti-Pierri N, Premkumar MH, Dank G, Nagamani SCS, Jung S, Harmelin A, Erez A.

Cell Rep. 2018 May 15;23(7):1962-1976. doi: 10.1016/j.celrep.2018.04.053.

8.

Reconstitution of an Ultradian Oscillator in Mammalian Cells by a Synthetic Biology Approach.

Santorelli M, Perna D, Isomura A, Garzilli I, Annunziata F, Postiglione L, Tumaini B, Kageyama R, di Bernardo D.

ACS Synth Biol. 2018 May 18;7(5):1447-1455. doi: 10.1021/acssynbio.8b00083. Epub 2018 May 10.

PMID:
29727574
9.

gene2drug: a computational tool for pathway-based rational drug repositioning.

Napolitano F, Carrella D, Mandriani B, Pisonero-Vaquero S, Sirci F, Medina DL, Brunetti-Pierri N, di Bernardo D.

Bioinformatics. 2018 May 1;34(9):1498-1505. doi: 10.1093/bioinformatics/btx800.

PMID:
29236977
10.

Comparing structural and transcriptional drug networks reveals signatures of drug activity and toxicity in transcriptional responses.

Sirci F, Napolitano F, Pisonero-Vaquero S, Carrella D, Medina DL, di Bernardo D.

NPJ Syst Biol Appl. 2017 Aug 25;3:23. doi: 10.1038/s41540-017-0022-3. eCollection 2017.

11.

The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells.

Gambardella G, Carissimo A, Chen A, Cutillo L, Nowakowski TJ, di Bernardo D, Blelloch R.

Nat Commun. 2017 Jan 19;8:14126. doi: 10.1038/ncomms14126.

12.

PML-RARA-associated cooperating mutations belong to a transcriptional network that is deregulated in myeloid leukemias.

Ronchini C, Brozzi A, Riva L, Luzi L, Gruszka AM, Melloni GEM, Scanziani E, Dharmalingam G, Mutarelli M, Belcastro V, Lavorgna S, Rossi V, Spinelli O, Biondi A, Rambaldi A, Lo-Coco F, di Bernardo D, Pelicci PG.

Leukemia. 2017 Sep;31(9):1975-1986. doi: 10.1038/leu.2016.386. Epub 2016 Dec 27.

PMID:
28025581
13.

Goblet Cell Hyperplasia Requires High Bicarbonate Transport To Support Mucin Release.

Gorrieri G, Scudieri P, Caci E, Schiavon M, Tomati V, Sirci F, Napolitano F, Carrella D, Gianotti A, Musante I, Favia M, Casavola V, Guerra L, Rea F, Ravazzolo R, Di Bernardo D, Galietta LJ.

Sci Rep. 2016 Oct 27;6:36016. doi: 10.1038/srep36016.

14.

Guest Editorial.

di Bernardo D.

IET Syst Biol. 2016 Oct;10(5):167. doi: 10.1049/iet-syb.2016.0038. No abstract available.

PMID:
27762230
15.

Computational drugs repositioning identifies inhibitors of oncogenic PI3K/AKT/P70S6K-dependent pathways among FDA-approved compounds.

Carrella D, Manni I, Tumaini B, Dattilo R, Papaccio F, Mutarelli M, Sirci F, Amoreo CA, Mottolese M, Iezzi M, Ciolli L, Aria V, Bosotti R, Isacchi A, Loreni F, Bardelli A, Avvedimento VE, di Bernardo D, Cardone L.

Oncotarget. 2016 Sep 13;7(37):58743-58758. doi: 10.18632/oncotarget.11318.

16.

Autophagosome-lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL.

De Leo MG, Staiano L, Vicinanza M, Luciani A, Carissimo A, Mutarelli M, Di Campli A, Polishchuk E, Di Tullio G, Morra V, Levtchenko E, Oltrabella F, Starborg T, Santoro M, Di Bernardo D, Devuyst O, Lowe M, Medina DL, Ballabio A, De Matteis MA.

Nat Cell Biol. 2016 Aug;18(8):839-850. doi: 10.1038/ncb3386. Epub 2016 Jul 11.

17.
18.

In Silico Modeling of Liver Metabolism in a Human Disease Reveals a Key Enzyme for Histidine and Histamine Homeostasis.

Pagliarini R, Castello R, Napolitano F, Borzone R, Annunziata P, Mandrile G, De Marchi M, Brunetti-Pierri N, di Bernardo D.

Cell Rep. 2016 Jun 7;15(10):2292-2300. doi: 10.1016/j.celrep.2016.05.014. Epub 2016 May 26.

19.

An atlas of gene expression and gene co-regulation in the human retina.

Pinelli M, Carissimo A, Cutillo L, Lai CH, Mutarelli M, Moretti MN, Singh MV, Karali M, Carrella D, Pizzo M, Russo F, Ferrari S, Ponzin D, Angelini C, Banfi S, di Bernardo D.

Nucleic Acids Res. 2016 Jul 8;44(12):5773-84. doi: 10.1093/nar/gkw486. Epub 2016 May 27.

20.

Evaluation of a systems biology approach to identify pharmacological correctors of the mutant CFTR chloride channel.

Pesce E, Gorrieri G, Sirci F, Napolitano F, Carrella D, Caci E, Tomati V, Zegarra-Moran O, di Bernardo D, Galietta LJ.

J Cyst Fibros. 2016 Jul;15(4):425-35. doi: 10.1016/j.jcf.2016.02.009. Epub 2016 Mar 10.

21.

High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs.

Karali M, Persico M, Mutarelli M, Carissimo A, Pizzo M, Singh Marwah V, Ambrosio C, Pinelli M, Carrella D, Ferrari S, Ponzin D, Nigro V, di Bernardo D, Banfi S.

Nucleic Acids Res. 2016 Feb 29;44(4):1525-40. doi: 10.1093/nar/gkw039. Epub 2016 Jan 26.

22.

Unravelling druggable signalling networks that control F508del-CFTR proteostasis.

Hegde RN, Parashuraman S, Iorio F, Ciciriello F, Capuani F, Carissimo A, Carrella D, Belcastro V, Subramanian A, Bounti L, Persico M, Carlile G, Galietta L, Thomas DY, Di Bernardo D, Luini A.

Elife. 2015 Dec 23;4. pii: e10365. doi: 10.7554/eLife.10365.

23.

In Vivo Real-Time Control of Gene Expression: A Comparative Analysis of Feedback Control Strategies in Yeast.

Fiore G, Perrino G, di Bernardo M, di Bernardo D.

ACS Synth Biol. 2016 Feb 19;5(2):154-62. doi: 10.1021/acssynbio.5b00135. Epub 2015 Dec 4.

PMID:
26554583
24.

Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress.

Tebbi A, Levillayer F, Jouvion G, Fiette L, Soubigou G, Varet H, Boudjadja N, Cairo S, Hashimoto K, Suzuki AM, Carninci P, Carissimo A, di Bernardo D, Wei Y.

Carcinogenesis. 2016 Jan;37(1):39-48. doi: 10.1093/carcin/bgv156. Epub 2015 Nov 5.

25.

Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.

Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S.

BMC Genomics. 2015 Oct 28;16:876. doi: 10.1186/s12864-015-2058-3.

26.

Drug-set enrichment analysis: a novel tool to investigate drug mode of action.

Napolitano F, Sirci F, Carrella D, di Bernardo D.

Bioinformatics. 2016 Jan 15;32(2):235-41. doi: 10.1093/bioinformatics/btv536. Epub 2015 Sep 28.

27.

Automatic Control of Gene Expression in Mammalian Cells.

Fracassi C, Postiglione L, Fiore G, di Bernardo D.

ACS Synth Biol. 2016 Apr 15;5(4):296-302. doi: 10.1021/acssynbio.5b00141. Epub 2015 Oct 6.

PMID:
26414746
28.

A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data.

Gambardella G, Peluso I, Montefusco S, Bansal M, Medina DL, Lawrence N, di Bernardo D.

BMC Bioinformatics. 2015 Sep 3;16:279. doi: 10.1186/s12859-015-0700-3.

29.

Metabolic regulation of the ultradian oscillator Hes1 by reactive oxygen species.

Ventre S, Indrieri A, Fracassi C, Franco B, Conte I, Cardone L, di Bernardo D.

J Mol Biol. 2015 May 22;427(10):1887-902. doi: 10.1016/j.jmb.2015.03.007. Epub 2015 Mar 18.

PMID:
25796437
30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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
36.

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.

37.

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
38.

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.

39.

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
40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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
48.

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.

49.

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.

50.

Reverse engineering and analysis of genome-wide gene regulatory networks from gene expression profiles using high-performance computing.

Belcastro V, Gregoretti F, Siciliano V, Santoro M, D'Angelo G, Oliva G, di Bernardo D.

IEEE/ACM Trans Comput Biol Bioinform. 2012 May-Jun;9(3):668-78. doi: 10.1109/TCBB.2011.60.

PMID:
21464509

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