Engineering a synthetic gene circuit for high-performance inducible expression in mammalian systems. De Carluccio G, Fusco V and di Bernardo D. Nature Commun.15, Article number: 3311 (2024) https://doi.org/10.1038/s41467-024-47592-y

Computational drug prediction in hepatoblastoma by integrating pan-cancer transcriptomics with pharmacological response. Failli M, Demir S, Del Río-Álvarez Á, Carrillo-Reixach J, Royo L, Domingo-Sàbat M, Childs M, Maibach R, Alaggio R, Czauderna P, Morland B, Branchereau S, Cairo S, Kappler R, Armengol C, di Bernardo D. Hepatology. 2023 Sep 20. doi: 10.1097/HEP.0000000000000601. Online ahead of print. PMID: 37729391

The VersaLive platform enables microfluidic mammalian cell culture for versatile applications. Nocera GM, Viscido G, Criscuolo S, Brillante S, Carbone F, Staiano L, Carrella S, di Bernardo D. Commun Biol. 2022 Sep 29;5(1):1034. doi: 10.1038/s42003-022-03976-8. PMID: 36175545 Free PMC article.

A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response. Gambardella G, Viscido G, Tumaini B, Isacchi A, Bosotti R, di Bernardo D. Nature Commun. 2022 Mar 31;13(1):1714. doi: 10.1038/s41467-022-29358-6. PMID: 35361816 Free PMC article.

Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control. Perrino G, Napolitano S, Galdi F, La Regina A, Fiore D, Giuliano T, di Bernardo M, di Bernardo D. Nature Commun. 2021 Apr 27;12(1):2452. doi: 10.1038/s41467-021-22689-w. PMID: 33907191 

Automatic identification of small molecules that promote cell conversion and reprogramming. Napolitano F, Rapakoulia T, Annunziata P, Hasegawa A, Cardon M, Napolitano S, Vaccaro L, Iuliano A, Wanderlingh LG, Kasukawa T, Medina DL, Cacchiarelli D*, Gao X*, di Bernardo D*, Arner E*. Stem Cell Reports. 2021 May 11;16(5):1381-1390. doi: 10.1016/j.stemcr.2021.03.028. Epub 2021 Apr 22. PMID: 33891873 Free PMC article. *co-last

Drug Repurposing in Rare Diseases: An Integrative Study of Drug Screening and Transcriptomic Analysis in Nephropathic Cystinosis. Bellomo F, De Leo E, Taranta A, Giaquinto L, Di Giovamberardino G, Montefusco S, Rega LR, Pastore A, Medina DL, Di Bernardo D, De Matteis MA, Emma F. Int J Mol Sci. 2021 Nov 27;22(23):12829. doi: 10.3390/ijms222312829.

PMID: 34884638 Free PMC article.

Fat Induces Glucose Metabolism in Nontransformed Liver Cells and Promotes Liver Tumorigenesis. Broadfield LA, Duarte JAG, Schmieder R, Broekaert D, Veys K, Planque M, Vriens K, Karasawa Y, Napolitano F, Fujita S, Fujii M, Eto M, Holvoet B, Vangoitsenhoven R, Fernandez-Garcia J, Van Elsen J, Dehairs J, Zeng J, Dooley J, Rubio RA, van Pelt J, Grünewald TGP, Liston A, Mathieu C, Deroose CM, Swinnen JV, Lambrechts D, di Bernardo D, Kuroda S, De Bock K, Fendt SM. Cancer Res. 2021 Apr 15;81(8):1988-2001. doi: 10.1158/0008-5472.CAN-20-1954. Epub 2021 Mar 9.

PMID: 33687947 Free PMC article.

GADD34 is a modulator of autophagy during starvation.

Gambardella G, Staiano L, Moretti MN, De Cegli R, Fagnocchi L, Di Tullio G, Polletti S, Braccia C, Armirotti A, Zippo A, Ballabio A, De Matteis MA, di Bernardo D. Science Adv. 2020 Sep 25;6(39):eabb0205. doi: 10.1126/sciadv.abb0205. Print 2020 Sep. PMID: 32978159 Free PMC article. 

A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data. Messa GM, Napolitano F, Elsea SH, di Bernardo D, Gao X. Bioinformatics. 2020 Dec 30;36(Suppl_2):i787-i794. doi: 10.1093/bioinformatics/btaa841.

PMID: 33381827

Pharmacoproteomics pinpoints HSP70 interaction for correction of the most frequent Wilson disease-causing mutant of ATP7B.

Concilli M, Petruzzelli R, Parisi S, Catalano F, Sirci F, Napolitano F, Renda M, Galietta LJV, Di Bernardo D, Polishchuk RS.

Proc Natl Acad Sci U S A. 2020 Dec 22;117(51):32453-32463. doi: 10.1073/pnas.2006648117. Epub 2020 Dec 7.

PMID: 33288711 Free PMC article.

Impaired mitophagy links mitochondrial disease to epithelial stress in methylmalonyl-CoA mutase deficiency. Luciani A, Schumann A, Berquez M, Chen Z, Nieri D, Failli M, Debaix H, Festa BP, Tokonami N, Raimondi A, Cremonesi A, Carrella D, Forny P, Kölker S, Diomedi Camassei F, Diaz F, Moraes CT, Di Bernardo D, Baumgartner MR, Devuyst O. Nat Commun. 2020 Feb 20;11(1):970. doi: 10.1038/s41467-020-14729-8. PMID: 32080200 Free PMC article.

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.

PMID: 30995486 Free PMC article.

gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.

Napolitano F, Carrella D, Gao X, di Bernardo D.

Bioinformatics. 2019 Oct 24;36(6):1944-5. doi: 10.1093/bioinformatics/btz803. Online ahead of print.

PMID: 31647521 Free PMC article.

A Tool for Visualization and Analysis of Single-Cell RNA-Seq Data Based on Text Mining. Gambardella G, di Bernardo D. Front Genet. 2019 Aug 9;10:734. doi: 10.3389/fgene.2019.00734. eCollection 2019. PMID: 31447887 Free PMC article

A transcriptomic study of Williams-Beuren syndrome associated genes in mouse embryonic stem cells. De Cegli R, Iacobacci S, Fedele A, Ballabio A, di Bernardo D. Sci Data. 2019 Nov 6;6(1):262. doi: 10.1038/s41597-019-0281-5. PMID: 31695049 Free PMC article.

TRPV4 and purinergic receptor signalling pathways are separately linked in airway epithelia to CFTR and TMEM16A chloride channels.

Genovese M, Borrelli A, Venturini A, Guidone D, Caci E, Viscido G, Gambardella G, di Bernardo D, Scudieri P, Galietta LJV. J Physiol. 2019 Dec;597(24):5859-5878. doi: 10.1113/JP278784. Epub 2019 Nov 12. PMID: 31622498 Free article.

A tunable dual-input system for on-demand dynamic gene expression regulation. Pedone E, Postiglione L, Aulicino F, Rocca DL, Montes-Olivas S, Khazim M, di Bernardo D, Pia Cosma M, Marucci L. Nature Commun. 2019 Oct 2;10(1):4481. doi: 10.1038/s41467-019-12329-9.

PMID: 31578371 Free PMC article.

Predictive Signatures Inform the Effective Repurposing of Decitabine to Treat KRAS-Dependent Pancreatic Ductal Adenocarcinoma.

Mottini C, Tomihara H, Carrella D, Lamolinara A, Iezzi M, Huang JK, Amoreo CA, Buglioni S, Manni I, Robinson FS, Minelli R, Kang Y, Fleming JB, Kim MP, Bristow CA, Trisciuoglio D, Iuliano A, Del Bufalo D, Di Bernardo D, Melisi D, Draetta GF, Ciliberto G, Carugo A, Cardone L.

Cancer Res. 2019 Nov 1;79(21):5612-5625. doi: 10.1158/0008-5472.CAN-19-0187. Epub 2019 Sep 5.

PMID: 31492820

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. PMID: 31014245 Free PMC article. 

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.

PMID: 30862866 Free PMC article.