Publications

Journals (first author)

• F. Gori, G. Folino, M. S. M. Jetten, and E. Marchiori. MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. Bioinformatics, 27(2):196-203, 2011a. doi: 10.1093/bioinformatics/btq649. URL http://bioinformatics.oxfordjournals.org/content/27/2/196.abstract
• F. Gori, S. G. Tringe, G. Folino, S. A. F. T. van Hijum, H. J. M. Op den Camp, M. S. M. Jetten, and E. Marchiori. Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes. BMC Genomics, 14:7, 2013. doi: 10.1186/1471-2164-14-7. URL http://www.biomedcentral.com/1471-2164/14/7
• F. Gori, S. G. Tringe, B. Kartal, E. Marchiori, and M. S. M. Jetten. The metagenomic basis of anammox metabolism in Candidatus ‘Brocadia fulgida’. Biochemical Society Transactions, 39:1799 - 1804, 2011c. doi: 10.1042/BST20110707. URL https://portlandpress.com/biochemsoctrans/article-abstract/39/6/1799/66793/The-metagenomic-basis-of-anammox-metabolism-in

Journals (co-first author)

• A. Fuentes-Hernandez, J. Plucain, F. Gori, R. Peña-Miller, G. Jansen, H. Schulenburg, I. Gudelj, and R. Beardmore. Using a sequential regimen to eliminate bacteria at sublethal antibiotic dosages. PLOS Biology, 13(4):e1002104, 04 2015. doi: 10.1371/journal.pbio.1002104. URL http://dx.doi.org/10.1371%2Fjournal.pbio.1002104

Journals (co-author)

• R. E. Beardmore, R. Peña-Miller, F. Gori, and J. Iredell. Antibiotic cycling and antibiotic mixing: which one best mitigates antibiotic resistance? Molecular Biology and Evolution, 2017. doi: 10.1093/molbev/msw292. URL http://mbe.oxfordjournals.org/content/early/2017/01/09/molbev.msw292.abstract
• Carlos Reding-Roman, Mark Hewlett, Sarah Duxbury, Fabio Gori, Ivana Gudelj, and Robert Beardmore. The unconstrained evolution of fast and efficient antibiotic-resistant bacterial genomes. Nature Ecology & Evolution, 1:0050, jan 2017. doi: 10.1038/s41559-016-0050. URL https://doi.org/10.1038%2Fs41559-016-0050

Pre-print (first author)

• Fabio Gori, Dimitrios Mavroeidis, Mike S. M. Jetten, and Elena Marchiori. The importance of Chargaff’s second parity rule for genomic signatures in metagenomics. bioRxiv, 2017. doi: 10.1101/146001. URL http://biorxiv.org/content/early/2017/06/04/146001

Conference Proceedings

• F. Gori, D. Mavroeidis, M. S. M. Jetten, and E. Marchiori. Genomic signatures for metagenomic data analysis: exploiting the reverse complementarity of tetranucleotides. In Proceedings of the 5th IEEE International Conference on Systems Biology (ISB), pages 149 -154, sept. 2011b. doi: 10.1109/ISB.2011.6033147. URL https://ieeexplore.ieee.org/document/6033147 Gori_signature_metagenomics_ISB_2011.pdf
• G. Folino, F. Gori, M. S. M. Jetten, and E. Marchiori. Clustering metagenome short reads using weighted proteins. In Proceedings of the 7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO), number 5483 in LNCS, pages 152-163, 2009b. doi: https://doi.org/10.1007/978-3-642-01184-9_14. URL https://repository.ubn.ru.nl/handle/2066/75322
• G. Folino, F. Gori, M. S. M. Jetten, and E. Marchiori. Evidence-based clustering of reads and taxonomic analysis of metagenomic data. In Proceedings of the 4th IAPR International Conference in Pattern Recognition in Bioinformatics (PRIB), number 5780 in LNBI, pages 102-112, 2009a. doi: https://doi.org/10.1007/978-3-642-04031-3_10. URL https://repository.ubn.ru.nl/bitstream/handle/2066/105783/105783.pdf

Posters

• G. Folino, F. Gori, M. S. M. Jetten, and E. Marchiori. Optimal BLAST-based clustering of metagenome short reads.
  Poster at ISMB/ECCB, 2009

Other Conferences

• Co-author of talk: Quantitative analysis of human equilibrative nucleoside transporter-1, deoxycytidine kinase , 5’-
  nucleotidase, cytidine deaminase and ribonucleotide reductase subunits m1 and m2 in pancreas cancer patients treated
  with gemcitabine. A. La Spina, M. Iannopollo, I. Celi, F. Gori, C. Orlandini, M. Ricasoli, E. Giovannetti, G. Bevilacqua,
  F. Mosca, M. Del Tacca, R. Danesi, S. Ricci. The 11th National Congress of Medical Oncology (“XI Congresso Nazionale
  di Oncologia Medica“), 10-13 October 2009, Milan, Italy.
• Co-author of talk: Medical Databases: difficulties and diagnosis perspectives. G. Fiorentino, A. La Spina, F. Gori, I. Celi.
  The 2nd International Conference on Cancer Risk Assessment (ICCRA 2) - Mathematical, Statistical and Computational
  Methods, May 25-27, 2007, Santorini, Greece.
• Co-author of talk: Database medici: difficolta` e prospettive per la diagnosi. (Italian version of the previous talk) G.
  Fiorentino, A. La Spina, F. Gori, I. Celi. Matematica e Diagnosi medica, January 9, 2007, Pisa, Italy.