King's College London

Research portal

Dr Francesca Ciccarelli

  1. Stratifying cancer therapies by molecular interactions and imaging

    Galazi, M., Weitsman, G., Monypenny, J., Coban, O., Milewicz, H., Gomez, V., Ciccarelli, F. & Ng, T. 23 May 2017 Mechanisms of Molecular Carcinogenesis. Springer International Publishing Switzerland, Vol. 2, p. 315-358 44 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

  2. Synthetic lethal interaction between the tumour suppressor STAG2 and its paralog STAG1.

    Ciccarelli, F. D., Benedetti, L. G., Cereda, M., Monteverde, L. & Desai, N. H. 5 Apr 2017 In : Oncotarget. 8, 23, p. 37619-37632 14 p.

    Research output: Contribution to journalArticle

  3. MEGA-V: detection of variant gene sets in patient cohorts

    Gambardella, G., Cereda, M., Benedetti, L. & Ciccarelli, F. D. 2017 In : BIOINFORMATICS. 33, 8, p. 1248-1249 2 p.

    Research output: Contribution to journalArticle

  4. Patients with genetically heterogeneous synchronous colorectal cancer carry rare damaging germline mutations in immune-related genes

    Cereda, M., Gambardella, G., Benedetti, L. G., Iannelli, F., Patel, D., Basso, G., Guerra, R., Mourikis, T. P., Puccio, I., Sinha, S., Laghi, L., Spencer, J., Rodriguez-Justo, M. & Ciccarelli, F. D. 5 Jul 2016 In : Nature Communications.

    Research output: Contribution to journalArticle

  5. NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings

    An, O., Dall'Olio, G. M., Mourikis, T. P. & Ciccarelli, F. 29 Oct 2015 In : Nucleic Acids Research.

    Research output: Contribution to journalArticle

  6. Corrigendum to "Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency"

    Iannelli, F., Collino, A., Sinha, S., Radaelli, E., Nicoli, P., D'Antiga, L., Sonzogni, A., Faivre, J., Buendia, M. A., Sturm, E., Thompson, R. J., Knisely, A. S., Natoli, G., Ghisletti, S. & Ciccarelli, F. D. 2 Jul 2015 In : Nature Communications. 6, 7456

    Research output: Contribution to journalArticle

  7. Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas

    De Grassi, A., Iannelli, F., Cereda, M., Volorio, S., Melocchi, V., Viel, A., Basso, G., Laghi, L., Caselle, M. & Ciccarelli, F. D. 30 Aug 2014 In : GENOME BIOLOGY. 15, 8, p. 437

    Research output: Contribution to journalArticle

  8. Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency

    Iannelli, F., Collino, A., Sinha, S., Radaelli, E., Nicoli, P., D'Antiga, L., Sonzogni, A., Faivre, J., Annick Buendia, M., Sturm, E., Thompson, R. J., Knisely, A. S., Natoli, G., Ghisletti, S. & Ciccarelli, F. D. 13 May 2014 In : Nature Communications. 5, 11 p., 3850

    Research output: Contribution to journalArticle

  9. NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes

    An, O., Pendino, V., D'Antonio, M., Ratti, E., Gentilini, M. & Ciccarelli, F. 2014 In : DATABASE. 2014, 10 p.

    Research output: Contribution to journalArticle

  10. Recessive cancer genes engage in negative genetic interactions with their functional paralogs

    D'Antonio, M., Guerra, R. F., Cereda, M., Marchesi, S., Montani, F., Nicassio, F., Di Fiore, P. P. & Ciccarelli, F. D. 26 Dec 2013 In : Cell reports. 5, 6, p. 1519-1526 8 p., N/A

    Research output: Contribution to journalArticle

  11. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma

    Shukla, R. , Upton, K. R. , Muñoz-Lopez, M. , Gerhardt, D. J. , Fisher, M. E. , Nguyen, T. , Brennan, P. M. , Baillie, J. K. , Collino, A. , Ghisletti, S. , Sinha, S. , Iannelli, F. , Radaelli, E. , Dos Santos, A. , Rapoud, D. , Guettier, C. , Samuel, D. , Natoli, G. , Carninci, P. , Ciccarelli, F. D. & 3 others Garcia-Perez, J. L., Faivre, J. & Faulkner, G. J. 28 Mar 2013 In : Cell. 153, 1, p. 101-11 11 p.

    Research output: Contribution to journalArticle

  12. Integrated analysis of recurrent properties of cancer genes to identify novel drivers

    D'Antonio, M. & Ciccarelli, F. D. 2013 In : GENOME BIOLOGY. 14, 5, 17 p., R52

    Research output: Contribution to journalArticle

  13. Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes

    D'Antonio, M., Pendino, V., Sihna, S. & Ciccarelli, F. Jan 2012 In : Nucleic Acids Research. 40, D1, p. D978-D983 6 p., N/A

    Research output: Contribution to journalArticle

  14. Modification of gene duplicability during the evolution of protein interaction network

    D'Antonio, M. & Ciccarelli, F. D. Apr 2011 In : PL o S Computational Biology. 7, 4, e1002029

    Research output: Contribution to journalArticle

  15. RECOMB Comparative Genomics 2009: Preface

    I, M. & Ciccarelli, F. Sep 2010 In : Journal of Computational Biology. 17, 9, p. 1095-1096 2 p., N/A

    Research output: Contribution to journalArticle

  16. The (r)evolution of cancer genetics

    Ciccarelli, F. 11 Jun 2010 In : BMC BIOLOGY. 8, 4 p., 74

    Research output: Contribution to journalEditorial

  17. Structural Analysis of the RZZ Complex Reveals Common Ancestry with Multisubunit Vesicle Tethering Machinery

    Civril, F., Wehenkel, A., Giorgi, F. M., Santaguida, S., Di Fonzo, A., Grigorean, G., Ciccarelli, F. D. & Musacchio, A. 12 May 2010 In : Structure. 18, 5, p. 616-626 11 p., N/A

    Research output: Contribution to journalArticle

  18. Global repression of cancer gene expression in a zebrafish model of melanoma is linked to epigenetic regulation.

    Anelli, V., Santoriello, C., Distel, M., Köster, R. W., Ciccarelli, F. D. & Mione, M. 4 Jan 2010 In : Zebrafish. 6, 4, p. 417-424 8 p., N/A

    Research output: Contribution to journalArticle

  19. Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes

    Syed, A. S., D'Antonio, M. & Ciccarelli, F. D. Jan 2010 In : Nucl. Acids Res.. 38, s1, p. D670-675 6 p., N/A

    Research output: Contribution to journalArticle

  20. Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability

    De Grassi, A., Segala, C., Iannelli, F., Volorio, S., Bertario, L., Radice, P., Bernard, L. & Ciccarelli, F. D. Jan 2010 In : PL o S Biology. 8, 1, e1000275

    Research output: Contribution to journalArticle

  21. Tandem repeats modify the structure of human genes hosted in segmental duplications

    De Grassi, A. & Ciccarelli, F. 2 Dec 2009 In : GENOME BIOLOGY. 10, 12, p. N/A 12 p., R137

    Research output: Contribution to journalArticle

  22. FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci

    Rambaldi, D. & Ciccarelli, F. D. 1 Sep 2009 In : BIOINFORMATICS. 25, 17, p. 2281-2282 2 p., N/A

    Research output: Contribution to journalArticle

  23. Low duplicability and network fragility of cancer genes

    Rambaldi, D., Giorgi, F. M., Capuani, F., Ciliberto, A. & Ciccarelli, F. D. Sep 2008 In : Trends in Genetics. 24, 9, p. 427-430 4 p., N/A

    Research output: Contribution to journalArticle

  24. Non-random retention of protein-coding overlapping genes in Metazoa

    Soldà, G., Suyama, M., Pelucchi, P., Boi, S., Guffanti, A., Rizzi, E., Bork, P., Tenchini, M. L. & Ciccarelli, F. D. 16 Apr 2008 In : BMC Genomics. 9, N/A, p. N/A 12 p., 174

    Research output: Contribution to journalArticle

  25. Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates

    Fumasoni, I., Meani, N., Rambaldi, D., Scafetta, G., Alcalay, M. & Ciccarelli, F. 4 Oct 2007 In : Bmc Evolutionary Biology. 7, N/A, p. N/A 11 p., 187

    Research output: Contribution to journalArticle

  26. Toward automatic reconstruction of a highly resolved tree of life

    Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B. & Bork, P. 3 Mar 2006 In : Science. 311, 5765, p. 1283-1287 5 p., N/A

    Research output: Contribution to journalArticle

  27. Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases

    Mees, A., Rock, R., Ciccarelli, F. D., Leberfinger, C. B., Borawski, J. M., Bork, P., Wiese, S., Gessler, M. & Kerkhoff, E. Dec 2005 In : Gene Expression Patterns. 6, 1, p. 79-85 7 p., N/A

    Research output: Contribution to journalArticle

  28. The WHy domain mediates the response to desiccation in plants and bacteria

    Ciccarelli, F. D. & Bork, P. 15 Apr 2005 In : BIOINFORMATICS. 21, 8, p. 1304-1307 4 p., N/A

    Research output: Contribution to journalArticle

  29. Generation and annotation of the DNA sequences of human chromosomes 2 and 4

    Hillier, L. W. , Graves, T. A. , Fulton, R. S. , Fulton, L. A. , Pepin, K. H. , Minx, P. , Wagner-McPherson, C. , Layman, D. , Wylie, K. , Sekhon, M. , Becker, M. C. , Fewell, G. A. , Delehaunty, K. D. , Miner, T. L. , Nash, W. E. , Kremitzki, C. , Oddy, L. , Du, H. , Sun, H. , Bradshaw-Cordum, H. & 102 others Ali, J., Carter, J., Cordes, M., Harris, A., Isak, A., van Brunt, A., Nguyen, C., Du, F., Courtney, L., Kalicki, J., Ozersky, P., Abbott, S., Armstrong, J., Belter, E. A., Caruso, L., Cedroni, M., Cotton, M., Davidson, T., Desai, A., Elliott, G., Erb, T., Fronick, C., Gaige, T., Haakenson, W., Haglund, K., Holmes, A., Harkins, R., Kim, K., Kruchowski, S. S., Strong, C. M., Grewal, N., Goyea, E., Hou, S., Levy, A., Martinka, S., Mead, K., McLellan, M. D., Meyer, R., Randall-Maher, J., Tomlinson, C., Dauphin-Kohlberg, S., Kozlowicz-Reilly, A., Shah, N., Swearengen-Shahid, S., Snider, J., Strong, J. T., Thompson, J., Yoakum, M., Leonard, S., Pearman, C., Trani, L., Radionenko, M., Waligorski, J. E., Wang, C., Rock, S. M., Tin-Wollam, A-M., Maupin, R., Latreille, P., Wendl, M. C., Yang, S-P., Pohl, C., Wallis, J. W., Spieth, J., Bieri, T. A., Berkowicz, N., Nelson, J. O., Osborne, J., Ding, L., Meyer, R., Sabo, A., Shotland, Y., Sinha, P., Wohldmann, P. E., Cook, L. L., Hickenbotham, M. T., Eldred, J., Williams, D., Jones, T. A., She, X., Ciccarelli, F. D., Izaurralde, E., Taylor, J., Schmutz, J., Myers, R. M., Cox, D. R., Huang, X., McPherson, J. D., Mardis, E. R., Clifton, S. W., Warren, W. C., Chinwalla, A. T., Eddy, S. R., Marra, M. A., Ovcharenko, I., Furey, T. S., Miller, W., Eichler, E. E., Bork, P., Suyama, M., Torrents, D., Waterston, R. H. & Wilson, R. K. 7 Apr 2005 In : NATURE. 434, 7034, p. 724-731 8 p., N/A

    Research output: Contribution to journalArticle

  30. Complex genomic rearrangements lead to novel primate gene function

    Ciccarelli, F. D., von Mering, C., Suyama, M., Harrington, E. D., Izaurralde, E. & Bork, P. Mar 2005 In : Genome Research. 15, 3, p. 343-351 9 p., N/A

    Research output: Contribution to journalArticle

  31. Genome-wide analysis of mRNAs regulated by the THO complex in Drosophila melanogaster

    Rehwinkel, J., Herold, A., Gari, K., Kocher, T., Rode, M., Ciccarelli, F. L., Wilm, M. & Izaurralde, E. Jun 2004 In : NATURE STRUCTURAL AND MOLECULAR BIOLOGY. 11, 6, p. 558-566 9 p., N/A

    Research output: Contribution to journalArticle

  32. RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export

    Forler, D., Rabut, G., Ciccarelli, F. D., Herold, A., Kocher, T., Niggeweg, R., Bork, P., Ellenberg, J. & Izaurralde, E. Feb 2004 In : Molecular and Cellular Biology. 24, 3, p. 1155-1167 13 p., N/A

    Research output: Contribution to journalArticle

  33. SMART 4.0: towards genomic data integration

    Letunic, I., Copley, R. R., Schmidt, S., Ciccarelli, F. D., Doerks, T., Schultz, J., Ponting, C. P. & Bork, P. 1 Jan 2004 In : Nucleic Acids Res. 32 , s1, p. D142-144 3 p., N/A

    Research output: Contribution to journalArticle

  34. Genome evolution reveals biochemical networks and functional modules

    von Mering, C., Zdobnov, E. M., Tsoka, S., Ciccarelli, F., Pereira-Leal, J. B., Ouzounis, C. A. & Bork, P. 23 Dec 2003 In : Proceedings of the National Academy of Sciences of the United States of America. 100, 26, p. 15428 - 15433 6 p.

    Research output: Contribution to journalArticle

  35. The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold

    Ciccarelli, F. D., Izaurralde, E. & Bork, P. 19 Dec 2003 In : BMC Bioinformatics. 4, N/A, p. N/A 5 p., 64

    Research output: Contribution to journalArticle

  36. Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways

    Gatfield, D., Unterholzner, L., Ciccarelli, F. D., Bork, P. & Izaurralde, E. 1 Aug 2003 In : The EMBO journal. 22, 15, p. 3960-3970 11 p., N/A

    Research output: Contribution to journalArticle

  37. The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold

    Ciccarelli, F. D., Bork, P. & Kerkhoff, E. 1 Jul 2003 In : TRENDS IN BIOCHEMICAL SCIENCES. 28, 7, p. 349-352 4 p., N/A

    Research output: Contribution to journalArticle

  38. The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia

    Ciccarelli, F. D., Proukakis, C., Patel, H., Cross, H., Azam, S., Patton, M. A., Bork, P. & Crosby, A. H. Apr 2003 In : Genomics. 81, 4, p. 437-441 5 p., N/A

    Research output: Contribution to journalArticle

  39. A protocol for the update of references to scientific literature in biological databases

    Perez-Iratxeta, C., Astola, N., Ciccarelli, F. D., Sha, P. K., Bork, P. & Andrade, M. A. 2003 In : Appl Bioinformatics. 2, 3, p. 189-191 3 p., N/A

    Research output: Contribution to journalArticle

  40. Recent improvements to the SMART domain-based sequence annotation resource

    Letunic, I., Goodstadt, L., Dickens, N. J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R. R., Ponting, C. P. & Bork, P. 1 Oct 2002 In : Nucleic Acids Res. 30, 1, p. 242-244 3 p., N/A

    Research output: Contribution to journalArticle

  41. NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria

    Andrade, M. A., Ciccarelli, F. D., Perez-Iratxeta, C. & Bork, P. 15 Aug 2002 In : GENOME BIOLOGY. 3, 9, p. N/A 5 p., RESEARCH0047

    Research output: Contribution to journalArticle

  42. SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia

    Patel, H., Cross, H., Proukakis, C., Hershberger, R., Bork, P., Ciccarelli, F. D., Patton, M. A., McKusick, V. A. & Crosby, A. H. Aug 2002 In : Nature Genetics. 31, 4, p. 347-348 2 p., N/A

    Research output: Contribution to journalArticle

  43. A complex prediction: three-dimensional model of the yeast exosome

    Aloy, P., Ciccarelli, F. D., Leutwein, C., Gavin, A. C., Superti-Furga, G., Bork, P., Bottcher, B. & Russell, R. B. Jul 2002 In : EMBO REPORTS. 3, 7, p. 628-635 8 p., N/A

    Research output: Contribution to journalArticle

  44. AMOP, a protein module alternatively spliced in cancer cells

    Ciccarelli, F. D., Doerks, T. & Bork, P. 1 Mar 2002 In : TRENDS IN BIOCHEMICAL SCIENCES. 27, 3, p. 113-115 3 p., N/A

    Research output: Contribution to journalArticle

  45. CASH--a beta-helix domain widespread among carbohydrate-binding proteins

    Ciccarelli, F. D., Copley, R. R., Doerks, T., Russell, R. B. & Bork, P. 1 Feb 2002 In : TRENDS IN BIOCHEMICAL SCIENCES. 27, 2, p. 59-62 4 p., N/A

    Research output: Contribution to journalArticle

  46. Large and diverse numbers of human diseases with HIKE mutations

    Ciccarelli, F. D., Acciarito, A. & Alberti, S. 1 Mar 2000 In : Human Molecular Genetics. 9, 6, p. 1001-1007 7 p., N/A

    Research output: Contribution to journalArticle

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