Federico M. Giorgi
Titles
Research Scientist, CRUK, Cambridge University
Lab
A pharmaceutical biotechnologist by training, I am a postdoctoral research scientist in the Califano Lab working to develop and use bioinformatics tools to detect key alteration points in tumor tissues. My current research is focused on understanding gene networks in cancer using genomics and transcriptomics data, with the final goal of developing personalized therapies.
My Bachelor's thesis (Amsterdam Free University, the Netherlands, 2004) focused on the molecular biology of EGFR mutations in non-small cell lung cancer. My Master's thesis (Bologna University, Italy, 2008) analyzed the graph properties of cancer proteins in protein-protein interaction networks. My PhD thesis (Max Planck Institute, Potsdam, Germany, 2011) focused on the reverse engineering of plant transcriptional networks, specifically on the mechanisms of secondary cell wall formation in Arabidopsis and applications for biofuel production, the hypoxia detection pathways, and the mechanisms of cold resistance in plants.
PhD, Max Planck Institute, Potsdam, Germany
Molecular Plant Physiology
MSc, Bologna University, Italy
Pharmaceutical Biotechnology
BSc, Amsterdam Free University, The Netherlands
Biotechnology
Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet. 2016 Jun 20.
Sepulveda JL, Gutierrez-Pajares JL, Luna A, Yao Y, Tobias JW, Thomas S, Woo Y, Giorgi F, Komissarova EV, Califano A, Wang TC, Sepulveda AR. High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing. Mod Pathol. 2016 Feb;29(2):182-93.
Giorgi FM, Lopez G, Woo JH, Bisikirska B, Califano A, Bansal M. Inferring protein modulation from gene expression data using conditional mutual information. PLoS One. 2014 Oct 14;9(10):e109569.
Del Fabbro C, Scalabrin S, Morgante M and Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One. 2013 Dec 23;8(12):e85024.
Lee YP, Giorgi FM, Lohse M, Usadel B, Klages S, Reinhardt R, Hincha DK. Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea. BMC Genomics. 2013 Nov 14;14:793.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Brief Bioinform. 2013 Sep;14(5):548-55.
Giorgi FM, Del Fabbro C, Licausi F. Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana. Bioinformatics. 2013 Mar 15;29(6):717-24.
Santaniello A, Giorgi FM, Di Tommaso D, Di Tommaso G, Piaggesi A, Perata P. Genomic approaches to unveil the physiological pathways activated in Arabidopsis treated with plant-derived raw extracts. Acta Hort. (ISHS) 1009:161-174.
Paparelli E, Gonzali S, Parlanti S, Novi G, Giorgi FM, Licausi F, Kosmacz M, Feil R, Lunn J, Brust H, van Dongen J, Steup M, Perata P. Misexpression of a chloroplast aspartyl protease leads to severe growth defects and alters carbohydrate metabolism in Arabidopsis. Plant Physiol. 2012 Nov;160(3):1237-50.
Giorgi FM, Vasilevski A, Bertinetti L, Usadel B. LASSO modeling of the Arabidopsis thaliana seed/seedling Transcriptome: a model case for detection of novel mucilage and pectin metabolism genes. Mol Biosyst. 2012 Oct;8(10):2566-74.
Licausi F, Kosmacz M, Weits DA, Giuntoli B, Giorgi FM, Voesenek LACJ, Perata P, Van Dongen JT. Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature. 2011 Oct 23;479(7373):419-22.
Ryngajllo M, Childs L, Lohse M, Giorgi FM, Lude A, Selbig J, Usadel B. SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data. Front Plant Sci. 2011 Sep 12;2:43.
Giorgi FM, Licausi F, Schmaelzlin E, Usadel B, Perata P, van Dongen J, Geigenberger P. HRE-Type genes are regulated by growth-related changes in Internal oxygen concentrations during the normal development of potato (Solanum tuberosum) tubers. Plant Cell Physiol. 2011 Nov;52(11):1957-72.
Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S. PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell. 2011 Mar;23(3):895-910.
Licausi F, Giorgi FM, Zenoni S, Osti F, Pezzotti M, Perata P. Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. BMC Genomics. 2010 Dec 20;11:719.
Giorgi FM, Bolger AM, Lohse M, Usadel B. Algorithm-driven artifacts in median Polish summarization of microarray data. BMC Bioinformatics. 2010 Nov 11;11:553.
Civril F, Wehenkel A, Giorgi FM, Santaguida S, Di Fonzo A, Grigorean G, Ciccarelli FD, Musacchio A. Structural analysis of the RZZ complex reveals common ancestry with multisubunit vesicle tethering machinery. Structure. 2010 May 12;18(5):616-26.
Lohse M, Nunes-Nesi A, Krüger P, Nagel A, Hannemann J, Giorgi FM, Childs L, Osorio S, Walther D, Selbig J, Sreenivasulu N, Stitt M, Fernie AR, Usadel B. Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiol. 2010 Jun;153(2):642-51.
Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S. Transcriptional wiring of cell wall-related genes in Arabidopsis. Mol Plant. 2009 Sep;2(5):1015-24.
Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ. Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 2009 Dec;32(12):1633-51.
Rambaldi D, Giorgi FM, Capuani F, Ciliberto A, Ciccarelli FD. Low duplicability and network fragility of cancer genes. Trends Genet. 2008 Sep;24(9):427-30.
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