Welcome!

     I received my Degree in Industrial Biotechnology from the University of Milano-Bicocca in 2001 and my Ph.D. in Immunology from the University of Rome “Tor Vergata” in 2006. I formerly worked as a graduate student in Prof. Paola Ricciardi-Castagnoli's lab at the Department of Biotechnology and Bioscience of the Milano-Bicocca University.  I joined Rong Li’s group as a Postdoctoral Research Associate in May 2006 and currently work in her lab at the Stowers Institute for Medical Research located in Kansas City, Missouri. Here, I also have a joint appointment with the Proteomics Center, headed by Michael Washburn.

     During my Ph.D. studies, my main research focus was in the application of Functional Genomics approaches to study host-pathogen interactions. I therefore acquired a deep expertise in analyzing microarray data to investigate the transcriptional response of cells of the immune system to invading pathogens. In particular, I contributed in developing algorithms and software for the identification of differentially expressed genes in microarray data and I have analyzed the transcriptional modulation of mouse dendritic cells after encounter of various bacteria and parasites.

 

Projects...

In Rong Li’s lab I'm studying how the budding yeast Saccharomyces cerevisiae can adaptively evolve in response to genetic perturbations.

In Mike Washburn's lab, my goal is to transfer my expertise in microarray data analysis to proteomics data analysis.

... and questions:

“Apart from the well-known actomyosin contracile ring, how many alternative pathways can cells evolve to perform cytokinesis?”

“What evolution strategies can eukaryotic cells follow, in order to adapt to a constant internal selective pressure driven by a loss-of-function mutation?”

“If cells are subjected to a high selective pressure for prolonged periods, are there ways for them to enhance their evolvability potential in order to increase the fitness of their progeny?”

“Can proteomics data be analyzed in the same way as we do with microarray data?”

Algorithms, software and databases for the analysis of microarray and proteomics data:

Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP: Statistical Similarities Between Transcriptomics and Quantitative Shotgun Proteomics Data. Mol Cell Proteomics 2008, 7:631-644.

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, 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, 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, 5:203.

Functional Genomics of Host-Pathogen Interactions:

Vizzardelli C, Pavelka N, Luchini A, Zanoni I, Bendickson L, Pelizzola M, Beretta O, Foti M, Granucci F, Nilsen-Hamilton M et al: Effects of dexamethazone on LPS-induced activation and migration of mouse dendritic cells revealed by a genome-wide transcriptional analysis. Eur J Immunol 2006, 36(6):1504-1515.

Foti M, Granucci F, Pelizzola M, Pavelka N, Beretta O, Vizzardelli C, Urbano M, Zanoni I, Capuano G, Mingozzi F et al: Gene Profiling of Dendritic cells during Host-Pathogen Interactions. In: Handbook of Dendritic Cells: Biology, Diseases and Therapies. Edited by Lutz MB, Romani N, Steinkasserer A, vol. 1, 1 edn. Weinheim, Germany: Wiley-VCH; 2006: 175-198.

Foti M, Granucci F, Pelizzola M, Pavelka N, Beretta O, Vizzardelli C, Urbano M, Zanoni I, Capuano G, Mingozzi F et al: Transcriptional profiling of dentritic cells in response to pathogens. In: Immunogenomics and Human Disease. Edited by Falus A, vol. 1, 1 edn. Chichester, England: John Wiley & Sons, Ltd.; 2006: 461-486.

Aebischer T, Bennett CL, Pelizzola M, Vizzardelli C, Pavelka N, Urbano M, Capozzoli M, Luchini A, Ilg T, Granucci F et al: A critical role for lipophosphoglycan in proinflammatory responses of dendritic cells to Leishmania mexicana. Eur J Immunol 2005, 35:476-486.

Trottein F, Pavelka N, Vizzardelli C, Angeli V, Zouain CS, Pelizzola M, Capozzoli M, Urbano M, Capron M, Belardelli F et al: A type I IFN-dependent pathway induced by Schistosoma mansoni eggs in mouse myeloid dendritic cells generates an inflammatory signature. J Immunol 2004, 172:3011-3017.

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, 2:882-888.

Immunobiology of dendritic cells:

Granucci F, Zanoni I, Pavelka N, Van Dommelen SL, Andoniou CE, Belardelli F, Degli Esposti MA, Ricciardi-Castagnoli P: A contribution of mouse dendritic cell-derived IL-2 for NK cell activation. J Exp Med 2004, 200:287-295.

Granucci F, Feau S, Zanoni I, Pavelka N, Vizzardelli C, Raimondi G, Ricciardi-Castagnoli P: The immune response is initiated by dendritic cells via interaction with microorganisms and interleukin-2 production. J Infect Dis 2003, 187 Suppl 2:S346-350.

Other collaborations in Functional Genomics:

Aidinis V, Carninci P, Armaka M, Witke W, Harokopos V, Pavelka N, Koczan D, Argyropoulos C, Thwin MM, Moller S et al: Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. PLoS Genet 2005, 1:e48.