Publications Francesco Ferrari

Federica Lucini, Cristiano Petrini, Elisa Salviato, Koustav Pal, Valentina Rosti, Francesca Gorini, Philina Santarelli, Roberto Quadri, Giovanni Lembo, Giulia Graziano, Emanuele Di Patrizio Soldateschi, Ilario Tagliaferri, Eva Pinatel, Endre Sebestyén, Luca Rotta, Francesco Gentile, Valentina Vaira, Chiara Lanzuolo*, Francesco Ferrari*.
Biochemical properties of chromatin domains define genome compartmentalization
Nucleic Acids Research 2024 - IN PRESS
(* co-corresponding/co-last authors)

Judith Mary Hariprakash, Elisa Salviato, Federica La Mastra, Endre Sebestyén, Ilario Tagliaferri, Raquel Sofia Silva, Federica Lucini, Lorenzo Farina, Mario Cinquanta, Ilaria Rancati, Mirko Riboni, Simone Minardi, Luca Roz, Francesca Gorini, Chiara Lanzuolo, Stefano Casola, Francesco Ferrari.
Leveraging tissue-specific enhancer-target gene regulatory networks identifies enhancer somatic mutations that functionally impact lung cancer.
Cancer Research 2024 Jan 2;84(1):133-153.

Salviato E*, Djordjilović V, Hariprakash JM, Tagliaferri I, Pal K, Ferrari F*.
Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.
Nucleic Acids Research 2021 Sep 27;49(17):e97.
(* co-corresponding authors)

Pal K* and Ferrari F*.
Visualising and annotating Hi-C data. Book chapter for "Hi-C data analysis: methods and protocols" volume of the Methods in Molecular Biology book series by Springer.
2021
(* co-corresponding authors)

Sebestyén E, Marullo F, Lucini F, Petrini C, Bianchi A, Valsoni S, Olivieri I, Antonelli L, Gregoretti F, Oliva G, Ferrari F*, Lanzuolo C*.
SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome.
Nature Communications 2020 Dec 8;11(1):6274.
(* co-corresponding/co-last authors)

Hariprakash JM, Ferrari F.
Computational biology solutions to identify enhancers-target gene pairs.
Comput Struct Biotechnol J. 2019 Jun 14;17:821-831.

Pal K, Forcato M, Jost D, Sexton T, Vaillant C, Salviato E, Mazza EMC, Lugli E, Cavalli G, Ferrari F.
Global chromatin conformation differences in the Drosophila dosage compensated chromosome X.
Nature Communications 2019 Nov 25;10(1):5355.

Pal K, Tagliaferri I, Livi CM,Ferrari F..
HiCBricks: building blocks for efficient handling of large Hi-C datasets.
Bioinformatics. 2019 Nov 7. pii: btz808.

Puccio S, Grillo G, Liciulli F, Severgnini M, Liuni S, Bicciato S, De Bellis G, Ferrari F.*, Peano C*.
WoPPER: Webserver for Position Related data analysis of gene Expression in Prokaryotes.
Nucleic Acids Res., 2017 July 3; 45(W1):W109-115. Epub 2017 Apr 29 (* co-corresponding/co-last authors)

Forcato M, Nicoletti C, Pal K, Livi CM, Ferrari F.*, Bicciato S*.
Comparison of computational methods for the analysis of Hi-C data.
Nature Methods, 2017 Jul; 14(7):679-685. (* co-corresponding/co-last authors)

Frittoli E, Palamidessi A, Iannelli F, Zanardi F, Villa S, Barzaghi L, Abdo H, Cancila V, Beznoussenko GV, Della Chiara G, Pagani M, Malinverno C, Bhattacharya D, Pisati F, Yu W, Galimberti V, Bonizzi G, Martini E, Mironov AA, Gioia U, Ascione F, Li Q, Havas K, Magni S, Lavagnino Z, Pennacchio FA, Maiuri P, Caponi S, Mattarelli M, Martino S, d'Adda di Fagagna F, Rossi C, Lucioni M, Tancredi R, Pedrazzoli P, Vecchione A, Petrini C, Ferrari F. Lanzuolo C, Bertalot G, Nader G, Foiani M, Piel M, Cerbino R, Giavazzi F, Tripodo C, Scita G.
Tissue fluidification promotes a cGAS-STING cytosolic DNA response in invasive breast cancer.
Nat Mater. 2023 May;22(5):644-655.

Kerschbamer E, Arnoldi M, Tripathi T, Pellegrini M, Maturi S, Erdin S, Salviato E, Di Leva F, Sebestyén E, Dassi E, Zarantonello G, Benelli M, Campos E, Basson MA, Gusella JF, Gustincich S, Piazza S, Demichelis F, Talkowski ME, Ferrari F., Biagioli M.
CHD8 suppression impacts on histone H3 lysine 36 trimethylation and alters RNA alternative splicing.
Nucleic Acids Res. 2022 Dec 9;50(22):12809-12828.

Van Beek JJP, Puccio S, Roberto A, De Paoli F, Graziano G, Salviato E, Alvisi G, Zanon V, Scarpa A, Zaghi E, Calvi M, Di Vito C, Mineri R, Sarina B, De Philippis C, Santoro A, Mariotti J, Bramanti S, Ferrari F., Castagna L, Mavilio D, Lugli E.
C Single-cell profiling reveals the dynamics of cytomegalovirus-specific T cells in haploidentical hematopoietic stem cell transplantation.
Haematologica. 2021 Oct 1;106(10):2768-2773. PMID: 34233445.

Morello G, Cancila V, La Rosa M, Germano G, Lecis D, Amodio V, Zanardi F, Iannelli F, Greco D, La Paglia L, Fiannaca A, Urso AM, Graziano G, Ferrari F, Pupa SM, Sangaletti S, Chiodoni C, Pruneri G, Bardelli A, Colombo MP, Tripodo C.
T Cells Expressing Receptor Recombination/Revision Machinery Are Detected in the Tumor Microenvironment and Expanded in Genomically Over-unstable Models.
Cancer Immunol Res. 2021 May 3. PMID: 33941587

Arnone CM, Polito VA, Mastronuzzi A, Carai A, Diomedi FC, Antonucci L, Petrelli LL, Vinci M, Ferrari F, Salviato E, Scarsella M, De Stefanis C, Weber G, Quintarelli C, De Angelis B, Brenner MK, Gottschalk S, Hoyos V, Locatelli F, Caruana I, Del Bufalo F.
Oncolytic adenovirus and gene therapy with EphA2-BiTE for the treatment of pediatric high-grade gliomas.
J Immunother Cancer. 2021 May;9(5):e001930. PMID: 33963009

Atashpaz S, Samadi Shams S, Martin Gonzalez J, Sebestyén E, Minardi S, Allievi E, Arghavanifard N, Gnocchi A, Albers E, Falco G, Fernandez-Capetillo O, Ferrari F., López-Contreras AJ, Costanzo V.
ATR expands embryonic stem cell fate potential in response to replication stress.
Elife. 2020 Mar 12;9:e54756

Bianchi A, Mozzetta C, Pegoli G, Lucini F, Valsoni S, Rosti V, Petrini C, Cortesi A, Gregoretti F, Antonelli L, Oliva G, De Bardi M, Rizzi R, Bodega B, Pasini D, Ferrari F., Bearzi C, Lanzuolo C.
Dysfunctional polycomb transcriptional repression contributes to Lamin A/C dependent muscular dystrophy.
J Clin Invest. 2020 May 1;130(5):2408-2421.

De Simone G, Mazza EMC, Cassotta A, Davydov AN, Kuka M, Zanon V, De Paoli F, Scamardella E, Metsger M, Roberto A, Pilipow K, Colombo FS, Tenedini E, Tagliafico E, Gattinoni L, Mavilio D, Peano C, Price DA, Singh SP, Farber JM, Serra V, Cucca F, Ferrari F., Orrù V, Fiorillo E, Iannacone M, Chudakov DM, Sallusto F, Lugli E.
CXCR3 Identifies Human Naive CD8(+) T Cells with Enhanced Effector Differentiation Potential.
J Immunol. 2019 Dec 15;203(12):3179-3189.

Brummelman J, Mazza EMC, Alvisi G, Colombo FS, Grilli A, Mikulak J, Mavilio D, Alloisio M, Ferrari F., Lopci E, Novellis P, Veronesi G, Lugli E.
High-dimensional single cell analysis identifies stem-like cytotoxic CD8(+) T cells infiltrating human tumors.
J Exp Med. 2018 Oct 1;215(10):2520-2535.

Uptade: May 2024