Bioinformatics

Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P. The genopolis microarray database. BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S21.

Pelizzola M, Pavelka N, Foti M, Ricciardi-Castagnoli P. AMDA: an R package for the automated microarray data analysis. BMC Bioinformatics. 2006 Jul 6;7:335.

Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P. A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics. 2004 Dec 17;5(1):203 

Functional Genomics

Ivan Zanoni, Renato Ostuni, Giusy Capuano1, Maddalena Collini, Michele Caccia, Antonella Ellena Ronchi,
Marcella Rocchetti, Francesca Mingozzi, Maria Foti, Giuseppe Chirico, Barbara Costa, Antonio Zaza,
Paola Ricciardi-Castagnoli & Francesca Granucci. CD14 regulates the dendritic cell life cycle after LPS
exposure through NFAT activation. Nature. 2009 Jul; (460): 264-268. Epub 2009 June 14.

Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol. 2006 Jul;24(7):832-40. Epub 2006 Jul 2.

Vizzardelli C, Pavelka N, Luchini A, Zanoni I, Bendickson L, Pelizzola M, Beretta O, Foti M, Granucci F, Nilsen-Hamilton M, Ricciardi-Castagnoli P. Effects of dexamethazone on LPS-induced activationand migration of mouse dendritic cells revealed by a genome-wide transcriptional analysis. Eur J Immunol. 2006 Jun;36(6):1504-15.

Foti M, Granucci F, Pelizzola M, Beretta O, Ricciardi-Castagnoli P. Dendritic cells in pathogen recognition and induction of immune responses: a functional genomics approach. J Leukoc Biol. 2006 May;79(5):913-6.

Aebischer T, Bennett CL, Pelizzola M, Vizzardelli C, Pavelka N, Urbano M, Capozzoli M, Luchini A, Ilg T, Granucci F, Blackburn CC, Ricciardi-Castagnoli P. A critical role for lipophosphoglycan in proinflammatory responses of dendritic cells to Leishmania mexicana. Eur J Immunol. 2005 Feb;35(2):476-86

Aidinis V, Carninci P, Armaka M, Witke W, Harokopos V, Pavelka N, Koczan D, Argyropoulos C, Thwin MM, Moller S, Waki K, Gopalakrishnakone P, Ricciardi-Castagnoli P, Thiesen HJ, Hayashizaki Y, Kollias G. Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. PLoS Genet. 2005 Oct;1(4):e48. Epub 2005 Oct 28 . Erratum in: PLoS Genet. 2005 Nov;1(5):e73. Kazunori, Waki [corrected to Waki, Kazunori].

Trottein F, Pavelka N, Vizzardelli C, Angeli V, Zouain CS, Pelizzola M, Capozzoli M, Urbano M, Capron M, Belardelli F, Granucci F, Ricciardi-Castagnoli P. A type I IFN-dependent pathway induced by Schistosoma mansoni eggs in mouse myeloid dendritic cells generates an inflammatory signature. J Immunol. 2004 Mar 1;172(5):3011-7

Ricciardi-Castagnoli P, Granucci F. Interpretation of the complexity of innate immune responses by functional genomics. Nat Rev Immunol. 2002 Nov;2(11):881-9 .

Granucci F, Ricciardi-Castagnoli P. , Rogge L, Sinigaglia F. Gene expression profiling in immune cells using microarray. Int Arch Allergy Immunol. 2001 Dec;126(4):257-66 .

Granucci F, Vizzardelli C, Virzi E, Rescigno M, Ricciardi-Castagnoli P. Transcriptional reprogramming of dendritic cells by differentiation stimuli. Eur J Immunol. 2001 Sep;31(9):2539-46 .

Granucci F, Vizzardelli C, Pavelka N, Feau S, Persico M, Virzi E, Rescigno M, Moro G, Ricciardi-Castagnoli P. Inducible IL-2 production by dendritic cells revealed by global gene expression analysis. Nat Immunol. 2001 Sep;2(9):882-8 .