Bioinformatics and Evolutionary Genomics of Cancer

Selected publications

• Ciccarelli FD
  The (r)evolution of cancer genetics
  BMC Biology BMC Biology 8: 74 Invited commentary (2010)
• Çivril 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 18:616-626 (2010)
• De Grassi A, Segala C, Volorio S, Bertario L, Radice P, Bernard L, Ciccarelli FD
  Ultra-deep Sequencing of a Human Ultraconserved Region Reveals Somatic and Constitutional Genomic Instability
  PLoS Biology 8: e1000275 (2010)
• Anelli V, Santoriello C, Distel M, Köster RW, Ciccarelli FD, Mione M
  Global repression of cancer gene expression in a zebrafish model of melanoma is linked to epigenetic regulation
  Zebrafish 6:174-186 (2010)
• Syed A, D´Antonio M, Ciccarelli FD
  Network of Cancer Genes: a Web Resource to Analyze Duplicability, Orthology and Network Properties of Cancer Genes
  Nucleic Acids Res 38:D670 (2010)
• De Grassi A, Ciccarelli FD
  Tandem repeats modify the structure of primate-specific genes expanding in the human population
  Genome Biol 10:R137 (2009)
• Rambaldi D, Ciccarelli FD
  FancyGene: interactive visualization of gene structures and protein domain architectures on genomic loci
  Bioinformatics 25:2281 (2009)
• Rambaldi D, Giorgi FM, Capuani F, Ciliberto A, Ciccarelli FD.
  Low duplicability and network fragility of cancer genes.
  Trends Genet. 24:427-30 9,729 1 (2008)
• Solda´ G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD
  Non-random retention of protein-coding overlapping genes in Metazoa.
  BMC Genomics 9:174-186 4,180 (2008)
• Fumasoni I, Meani N, Rambaldi D, Scafetta G, Alcalay M, Ciccarelli FD
  Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates.
  BMC Evol Biol 7:187-199 4,091 4 (2007)
• Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, and Bork P.
  Toward automatic reconstruction of a highly resolved tree of life.
  Science 311:1283-87 26,372 165 (2006)
• Ciccarelli FD, von Mering C, Suyama M, Harrington ED, Izaurralde E. and Bork P.
  Complex genomic rearrangements lead to novel primate gene function.
  Genome Res 15:343-351 11,224 30 (2005)
• The Chromosomes 2 and 4 Consortium
  Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
  Nature 434:724-731. 28,751 14 (2005)
• Mees A, Rock R, Ciccarelli FD, Leberfinger CB, Borawski JM, et al.
  Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases.
  Gene Expression Patterns 6:79-85 2,238 3 (2005)
• Ciccarelli FD, Bork P
  The WHy domain mediates the response to desiccation in plants and bacteria.
  Bioinformatics 21:1304-1307 5,039 4 (2005)
• Forler D, Rabut G, Ciccarelli FD, Herold A, Kocher T, et al.
  RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export.
  Mol Cell Biol 24:1155-1167 6,420 19 (2004)
• Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, et al.
  SMART 4.0: towards genomic data integration.
  Nucleic Acids Res 32 Database issue: D142-144. 6,954 324 (2004)
• Rehwinkel J, Herold A, Gari K, Kocher T, Rode M, et al.
  Genome-wide analysis of mRNAs regulated by the THO complex in Drosophila melanogaster.
  Nat Struct Mol Biol 11:558-566 11,085 47 (2004)
• Ciccarelli FD, Bork P, Kerkhoff E
  The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold.
  Trends Biochem Sci 28:349-352 14,994 16 (2003)
• Ciccarelli FD, Izaurralde E, Bork P
  The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
  BMC Bioinformatics 4: 64. 3,493 5 (2003)
• Gatfield D, Unterholzner L, Ciccarelli FD, Bork P, Izaurralde E
  Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways.
  EMBO J 22: 3960-3970. 8,662 103 (2003)
• Perez-Iratxeta C, Astola N, Ciccarelli FD, Sha PK, Bork P, et al.
  A protocol for the update of references to scientific literature in biological databases.
  Appl Bioinformatics 2: 189-191. (2003)
• von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, et al.
  Genome evolution reveals biochemical networks and functional modules.
  PNAS 100: 15428-15433. 9,598 66 (2003)
• Ciccarelli F.D., Proukakis C., Patel H., Cross H., Azam S., Patton M.A., Bork P., and Crosby A.H.
  The identification of a conserved domain in both spartin and spastin, genes mutated in hereditary spastic paraplegia.
  Genomics 81:437-41. 3,613 52 (2003)
• Andrade M.A., Ciccarelli F.D., Perex-Iratxeta C., and Bork P.
  NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter for Gram-positive pathogenic bacteria.
  Genome Biol 3:RESEARCH0047. 6,589 2 (2002)
• Patel H., Cross H., Proukakis C., Hershberger R., Bork P., Ciccarelli F.D., King T., Brown N., Patton M.A., McKusick V.A., and Crosby A.H.
  SPG20 is mutated in Troyer syndrome, a hereditary spastic paraplegia.
  Nat. Genet 31:347-8. 25,556 74 (2002)
• Aloy P., Ciccarelli F.D., Leutwein C., Gavin A.C., Superti-Furga G., Bork P., Bottcher B., and Russell R.B.
  A complex prediction: three-dimensional model of the yeast exosome.
  EMBO Rep 3:628-35. 7,450 65 (2002)
• Ciccarelli F.D., Doerks T. and Bork P.
  AMOP, a protein module alternatively spliced in cancer cells.
  Trends Biochem. Sci 27:113-5. 14,994 12 (2002)
• Ciccarelli F.D., Copley R.R., Doerks T., Russell R.B., and Bork P.
  CASH – a beta-helix domain widespread among carbohydrate-binding proteins.
  Trends Biochem. Sci 27:59-62. 14,994 14 (2002)
• Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., Ciccarelli F.D., Copley R.R., Ponting C.P., and Bork P.
  Recent improvements to the SMART domain-based sequence annotation resource.
  Nucleic Acids Res 30:242-244. 6,954 450 (2002)
• Ciccarelli F.D., Acciarito A. and Alberti S.
  Large and diverse numbers of human diseases with HIKE mutations.
  Hum Mol Genet 9:1001-1007. Review. 7,806 9 (2000)