Publications

Google Scholar metrics:
  • Total number of citations:2435
  • h-index: 21
PEER REVIEWED PUBLICATIONS
  • 29. Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. “A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development”. Cell Stem Cell 2018.
  • 28.Giuntoli B, Shukla V, Maggiorelli F, Giorgi FM, Lombardi L, Perata P, Licausi F. “Age-dependent regulation of ERF-VII transcription factor activity in Arabidopsis thaliana”Plant Cell Environ 2017.
  • 27. Sibout S, Proost S, Hansen BO, Vaid N, Giorgi FM, …, Persson S, Mutwil M. “Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon”. New Phytologist 2017.
  • 26. Ginzberg P, Giorgi FM, Califano A. “Searching for Gene Sets with Mutually Exclusive Mutations”. arXiv:1609.05564 2016.
  • 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.
  • 24. Giorgi FM, Lachmann A, Garcia GL, Califano A. ARACNe-AP: “Gene Network Reverse Engineering through Adaptive Partitioning inference of Mutual Information”. Bioinformatics 2016.
  • 23. Giorgi FM, Lachmann A, Alvarez MJ, Califano A. “Detection and removal of spatial bias in multi-well assays”. Bioinformatics 2016.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 15. Giorgi FM, Del Fabbro C, Licausi F. ”Comparative study of RNA-seq- and Microarray- derived coexpression networks in Arabidopsis thaliana”. Bioinformatics 2013.
  • 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.
  • 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.
  • 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 Biosystems2012.
  • 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”. Nature2011.
  • 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.
  • 09. 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.
  • 08. 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.
  • 07. 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.
  • 06. Giorgi FM, Bolger AM, Lohse M and Usadel B. “Algorithm-driven Artifacts in median polish summarization of Microarray data”, BMC Bioinformatics 2010.
  • 05. 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”, Structure2010.
  • 04. 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.
  • 03. Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S. “Transcriptional wiring of cell wall-related genes in Arabidopsis”, Molecular Plant 2009.
  • 02. 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.
  • 01. Rambaldi D, Giorgi FM, Capuani F, Ciliberto A, Ciccarelli FD. “Low duplicability and network fragility of cancer genes”, Trends in Genetics 2008.
BOOKS
  • Giorgi FM. “Expression-based reverse engineering of plant transcriptional networks: A practical study on the interpretation of Next Generation Sequencing and Microarray data in plants”. Lambert Academic Publishing, 2012. ISBN 978-3846584644.
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