the Markowetz lab

Integrative Cancer Biology @ Cancer Research UK Cambridge Institute

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Federico M. Giorgi

I am a research scientist with experimental molecular biology education and nine years of experience in the Bioinformatics field. My main interest is unraveling the mechanisms of cellular regulation through the analysis of transcriptomic and genomic data. Specifically, I’ve worked for four years on studying the mechanisms of plant cell wall synthesis and response to hypoxia, and my current main project involves identifying early markers of tumorigenesis through the integration of gene expression and mutational data. To achieve my research goals I favor an integrative theoretical/experimental approach.

Publications

(Personal contributions in brackets)

1. Rambaldi D, Giorgi FM, Capuani F, Ciliberto A, Ciccarelli FD. “Low duplicability and network fragility of cancer genes”, Trends in Genetics 2008. (Analysis of the local network properties of specific cancer genes and development of a web interface for data mining).
2. 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 Environment 2009. (Study on the influence of data normalization procedures on gene coexpression networks).
3. Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S. “Transcriptional wiring of cell wall-related genes in Arabidopsis”, Molecular Plant 2009. (Protein family association and statistical analysis).
4. 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 Physiology 2010. (Microarray datasets quality controls and program debugging).
5. 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. (Remote homology analysis, protein domain characterization and detailed structure folding prediction).
6. Giorgi FM, Bolger AM, Lohse M and Usadel B. “Algorithm-driven Artifacts in median polish summarization of Microarray data”, BMC Bioinformatics 2010. (Conceived the study and carried out the statistical experiments).
7. Licausi F, Giorgi FM, Zenoni S, Osti F, Pezzotti M and Perata P. “Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera”, BMC Genomics 2010. (Cross-species gene prediction through domain scan of the grapevine genome, statistical analysis of expression).
8. Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z and Persson S. “PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species”, The Plant Cell 2011. (Analysis of relationships between protein domains and expression across species).
9. Giorgi FM, Licausi F, Schmaelzlin E, Usadel B, Perata P, van Dongen J and 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 Physiology 2011. (Conceived the coexpression analysis).
10. Ryngajllo M, Childs L, Lohse M, Giorgi FM, Lude A, Selbig J and Usadel B. "SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data". Frontiers in Plant Science 2011. (Developed the web server and conducted cross-species assessment of subcellular localization).
11. 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. (Analysis of the genomic spectrum of oxygen sensing transcription factors and phylogenetic analysis).
12. 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”. Molecular Biosystems 2012. (Design of the in silico and in vivo novel gene discovery pipeline).
13. 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 Physiology 2012. (Phylogenetic and expression analysis).
14. 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 Horticulturae 2012. (Gene Expression and Pathway differential analysis).
15. Giorgi FM, Del Fabbro C, Licausi F. ”Comparative study of RNA-seq- and Microarray- derived coexpression networks in Arabidopsis thaliana”. Bioinformatics 2013. (Corresponding author).
16. 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”. Briefings in Bioinformatics 2013 (Curated the RNA-Seq and bisulphite-based methylation parts).
17. 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. (Designed and performed the computational elements of the study).
18. 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. Doi: 10.1371/journal.pone.0085024. (Corresponding author).
19. Tosetti R, Tardelli F, Tardiello F, Zaffalon V, Giorgi FM, Guidi L, Trainotti L, Bonghi C and Tonutti P. “Molecular and biochemical responses to wounding in mesocarp of peach (Prunus persica L. Batsch) ripe fruits”. Postharvest Biology and Technology 2014. (Carried out the Transcriptomics analyses).
20. Giorgi FM, Lopez G, Woo JH, Califano, A Bansal M. “Inferring protein modulation from gene expression data using Conditional Mutual Information”. PLOS ONE 2014. (Performed the comparative analysis).
21. Hughes JM, Salvatori B, Giorgi FM, Bozzoni I, Fatica A. “CEBPA-regulated lncRNAs, new players in the study of acute myeloid leukemia.” J Hematol Oncol 2014. (Performed the sequence analysis).
22. Sepulveda JL, Gutierrez-Pajares JL, Luna A, Yao Y, Tobias JW, Thomas S, Woo Y, Giorgi FM, Komissarova EV, Califano A, Wang TC, Sepulveda AR. “High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing.” Modern Pathology 2016. (Performed the TCGA data collection and algorithm development).
23. Giorgi FM, Lachmann A, Alvarez MJ, Califano A. “Detection and removal of spatial bias in multi-well assays”. Bioinformatics 2016, DOI: 10.1093/bioinformatics/btw092. (Wrote the manuscript, designed the experiments).
24. Giorgi FM, Lachmann A, Garcia GL, Califano A. ARACNe-AP: “Gene Network Reverse Engineering through Adaptive Partitioning inference of Mutual Information”. Bioinformatics 2016, 10.1093/bioinformatics/btw216. (Wrote the manuscript, developed the new implementation of the algorithm).
25. Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A. “Dissecting the mutational landscape of cancer by integrative inference and analysis of protein activity”. Nature Genetics 2016. (Organization and analysis of the TCGA data).
26. Giorgi FM, Aytes A, Torre D, Alvarez MJ, Abate-Shen C, Califano A. “Regulatory network-based discovery of Pan-cancer drivers of tumor initiation and progression”. Nature Genetics, in preparation. (Designed the study and performed the experiments).

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