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Transcriptional profiles in melanocytes from clinically unaffected skin distinguish the neoplastic growth pattern in patients with melanoma.

Br J Dermatol 2007; 62-71. doi: 10.1111/j.1365-2133.2006.07564.x

Ferrari F, Bortoluzzi S, Coppe A, Basso D, Bicciato S, Zini R, Gemelli C, Danieli GA, Ferrari S

Genomic expression during human myelopoiesis.

BMC Genomics 2007; 264. doi: 10.1186/1471-2164-8-264

Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S

Novel definition files for human GeneChips based on GeneAnnot.

BMC Bioinformatics 2007; 446. doi: 10.1186/1471-2105-8-446

Peano C, Bicciato S, Corti G, Ferrari F, Rizzi E, Bonnal RJ, Bordoni R, Albertini A, Bernardi LR, Donadio S, De Bellis G

Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays.

Microb Cell Fact 2007; 37. doi: 10.1186/1475-2859-6-37

Gemelli C, Orlandi C, Zanocco Marani T, Martello A, Vignudelli T, Ferrari F, Montanari M, Parenti S, Testa A, Grande A, Ferrari S

The vitamin D3/Hox-A10 pathway supports MafB function during the monocyte differentiation of human CD34+ hemopoietic progenitors.

J Immunol 2008; 5660-72. doi: 10.4049/jimmunol.181.8.5660

Lymboussaki A, Gemelli C, Testa A, Facchini G, Ferrari F, Mavilio F, Grande A

PPARdelta is a ligand-dependent negative regulator of vitamin D3-induced monocyte differentiation.

Carcinogenesis 2009; 230-7. doi: 10.1093/carcin/bgn272

Coppe A, Ferrari F, Bisognin A, Danieli GA, Ferrari S, Bicciato S, Bortoluzzi S

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

Nucleic Acids Res 2009; 533-49. doi: 10.1093/nar/gkn948

Bicciato S, Spinelli R, Zampieri M, Mangano E, Ferrari F, Beltrame L, Cifola I, Peano C, Solari A, Battaglia C

A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets.

Nucleic Acids Res 2009; 5057-70. doi: 10.1093/nar/gkp520

Aprile A, Mastrangelo AM, De Leonardis AM, Galiba G, Roncaglia E, Ferrari F, De Bellis L, Turchi L, Giuliano G, Cattivelli L

Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome.

BMC Genomics 2009; 279. doi: 10.1186/1471-2164-10-279

Bisognin A, Coppe A, Ferrari F, Risso D, Romualdi C, Bicciato S, Bortoluzzi S

A-MADMAN: annotation-based microarray data meta-analysis tool.

BMC Bioinformatics 2009; 201. doi: 10.1186/1471-2105-10-201

Hedegaard J, Arce C, Bicciato S, Bonnet A, Buitenhuis B, Collado-Romero M, Conley LN, SanCristobal M, Ferrari F, Garrido JJ, Groenen MA, Hornshøj H, Hulsegge I, Jiang L, Jiménez-Marín Á, Kommadath A, Lagarrigue S, Leunissen JA, Liaubet L, Neerincx PB, Nie H, Poel JV, Prickett D, Ramirez-Boo M, Rebel JM, Robert-Granié C, Skarman A, Smits MA, Sørensen P, Tosser-Klopp G, Watson M

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment.

BMC Proc 2009; S5. doi: 10.1186/1753-6561-3-s4-s5

Nie H, Neerincx PB, van der Poel J, Ferrari F, Bicciato S, Leunissen JA, Groenen MA

Microarray data mining using Bioconductor packages.

BMC Proc 2009; S9. doi: 10.1186/1753-6561-3-S4-S9

Biasiolo M, Forcato M, Possamai L, Ferrari F, Agnelli L, Lionetti M, Todoerti K, Neri A, Marchiori M, Bortoluzzi S, Bicciato S

Critical analysis of transcriptional and post-transcriptional regulatory networks in multiple myeloma.

Pac Symp Biocomput 2010; 397-408. doi: 10.1142/9789814295291_0042

Mosca L, Fabris S, Lionetti M, Todoerti K, Agnelli L, Morabito F, Cutrona G, Andronache A, Matis S, Ferrari F, Gentile M, Spriano M, Callea V, Festini G, Molica S, Deliliers GL, Bicciato S, Ferrarini M, Neri A

Integrative genomics analyses reveal molecularly distinct subgroups of B-cell chronic lymphocytic leukemia patients with 13q14 deletion.

Clin Cancer Res 2010; 5641-53. doi: 10.1158/1078-0432.CCR-10-0151

Agnelli L, Forcato M, Ferrari F, Tuana G, Todoerti K, Walker BA, Morgan GJ, Lombardi L, Bicciato S, Neri A

The reconstruction of transcriptional networks reveals critical genes with implications for clinical outcome of multiple myeloma.

Clin Cancer Res 2011; 7402-12. doi: 10.1158/1078-0432.CCR-11-0596

Benatti C, Valensisi C, Blom JM, Alboni S, Montanari C, Ferrari F, Tagliafico E, Mendlewicz J, Brunello N, Tascedda F

Transcriptional profiles underlying vulnerability and resilience in rats exposed to an acute unavoidable stress.

J Neurosci Res 2012; 2103-15. doi: 10.1002/jnr.23100

Zini R, Norfo R, Ferrari F, Bianchi E, Salati S, Pennucci V, Sacchi G, Carboni C, Ceccherelli GB, Tagliafico E, Ferrari S, Manfredini R

Valproic acid triggers erythro/megakaryocyte lineage decision through induction of GFI1B and MLLT3 expression.

Exp Hematol 2012; 1043-1054.e6. doi: 10.1016/j.exphem.2012.08.003

Puccio S, Grillo G, Licciulli F, Severgnini M, Liuni S, Bicciato S, De Bellis G, Ferrari F, Peano C

WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes.

Nucleic Acids Res 2017; W109-W115. doi: 10.1093/nar/gkx329

Forcato M, Nicoletti C, Pal K, Livi CM, Ferrari F, Bicciato S

Comparison of computational methods for Hi-C data analysis.

Nat Methods 2017; 679-685. doi: 10.1038/nmeth.4325

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; 2520-2535. doi: 10.1084/jem.20180684

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; 3179-3189. doi: 10.4049/jimmunol.1901072

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.

Nat Commun 2019; 5355. doi: 10.1038/s41467-019-13350-8

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; 2408-2421. doi: 10.1172/JCI128161

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.

Nat Commun 2020; 6274. doi: 10.1038/s41467-020-20048-9

Arnone CM, Polito VA, Mastronuzzi A, Carai A, Diomedi FC, Antonucci L, Petrilli 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; . doi: 10.1136/jitc-2020-001930

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

Single-cell profiling reveals the dynamics of cytomegalovirus-specific T cells in haploidentical hematopoietic stem cell transplantation.

Haematologica 2021; 2768-2773. doi: 10.3324/haematol.2020.276352

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; 12809-12828. doi: 10.1093/nar/gkac1134

Lucini F, Petrini C, Salviato E, Pal K, Rosti V, Gorini F, Santarelli P, Quadri R, Lembo G, Graziano G, Di Patrizio Soldateschi E, Tagliaferri I, Pinatel E, Sebestyén E, Rotta L, Gentile F, Vaira V, Lanzuolo C, Ferrari F

Biochemical properties of chromatin domains define genome compartmentalization.

Nucleic Acids Res 2024; e54. doi: 10.1093/nar/gkae454

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Chromatin remodeling restrains oncogenic functions in prostate cancer.

Nat Commun 2025; 9174. doi: 10.1038/s41467-025-64213-4

Del Sal G, Storici P, Schneider C, Romeo D, Zanetti M

cDNA cloning of the neutrophil bactericidal peptide indolicidin.

Biochem Biophys Res Commun 1992; 467-72. doi: 10.1016/s0006-291x(05)81517-7

Manfioletti G, Ruaro ME, Del Sal G, Philipson L, Schneider C

A growth arrest-specific (gas) gene codes for a membrane protein.

Mol Cell Biol 1990; 2924-30. doi: 10.1128/mcb.10.6.2924-2930.1990

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A fast method for high-quality genomic DNA extraction from whole human blood.

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Carninci P, Gustincich S, Bottega S, Patrosso C, Del Sal G, Manfioletti G, Schneider C

A simple discontinuous buffer system for increased resolution and speed in gel electrophoretic analysis of DNA sequence.

Nucleic Acids Res 1990; 204. doi: 10.1093/nar/18.1.204

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Role of the ubiquitin-proteasome pathway in regulating abundance of the cyclin-dependent kinase inhibitor p27.

Science 1995; 682-5. doi: 10.1126/science.7624798

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Structure, function, and chromosome mapping of the growth-suppressing human homologue of the murine gas1 gene.

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