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omiXcore: a web server for prediction of protein interactions with large RNA.
Armaos A, Cirillo D, Gaetano Tartaglia G. Armaos A, et al. Among authors: cirillo d. Bioinformatics. 2017 Oct 1;33(19):3104-3106. doi: 10.1093/bioinformatics/btx361. Bioinformatics. 2017. PMID: 28637296 Free PMC article.
A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression.
Bolognesi B, Lorenzo Gotor N, Dhar R, Cirillo D, Baldrighi M, Tartaglia GG, Lehner B. Bolognesi B, et al. Among authors: cirillo d. Cell Rep. 2016 Jun 28;16(1):222-231. doi: 10.1016/j.celrep.2016.05.076. Epub 2016 Jun 16. Cell Rep. 2016. PMID: 27320918 Free PMC article.
Quantitative predictions of protein interactions with long noncoding RNAs.
Cirillo D, Blanco M, Armaos A, Buness A, Avner P, Guttman M, Cerase A, Tartaglia GG. Cirillo D, et al. Nat Methods. 2016 Dec 29;14(1):5-6. doi: 10.1038/nmeth.4100. Nat Methods. 2016. PMID: 28032625 No abstract available.
By the company they keep: interaction networks define the binding ability of transcription factors.
Cirillo D, Botta-Orfila T, Tartaglia GG. Cirillo D, et al. Nucleic Acids Res. 2015 Oct 30;43(19):e125. doi: 10.1093/nar/gkv607. Epub 2015 Jun 18. Nucleic Acids Res. 2015. PMID: 26089389 Free PMC article.
SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences.
Agostini F, Cirillo D, Ponti RD, Tartaglia GG. Agostini F, et al. Among authors: cirillo d. BMC Genomics. 2014 Oct 23;15(1):925. doi: 10.1186/1471-2164-15-925. BMC Genomics. 2014. PMID: 25341390 Free PMC article.
Discovery of protein-RNA networks.
Cirillo D, Livi CM, Agostini F, Tartaglia GG. Cirillo D, et al. Mol Biosyst. 2014 Jul;10(7):1632-42. doi: 10.1039/c4mb00099d. Epub 2014 Apr 23. Mol Biosyst. 2014. PMID: 24756571 Review.
ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli.
Agostini F, Cirillo D, Livi CM, Delli Ponti R, Tartaglia GG. Agostini F, et al. Among authors: cirillo d. Bioinformatics. 2014 Oct 15;30(20):2975-7. doi: 10.1093/bioinformatics/btu420. Epub 2014 Jul 1. Bioinformatics. 2014. PMID: 24990610 Free PMC article.
Discovering the 3' UTR-mediated regulation of alpha-synuclein.
Marchese D, Botta-Orfila T, Cirillo D, Rodriguez JA, Livi CM, Fernández-Santiago R, Ezquerra M, Martí MJ, Bechara E, Tartaglia GG; Catalan MSA Registry (CMSAR). Marchese D, et al. Among authors: cirillo d. Nucleic Acids Res. 2017 Dec 15;45(22):12888-12903. doi: 10.1093/nar/gkx1048. Nucleic Acids Res. 2017. PMID: 29149290 Free PMC article.
catRAPID omics: a web server for large-scale prediction of protein-RNA interactions.
Agostini F, Zanzoni A, Klus P, Marchese D, Cirillo D, Tartaglia GG. Agostini F, et al. Among authors: cirillo d. Bioinformatics. 2013 Nov 15;29(22):2928-30. doi: 10.1093/bioinformatics/btt495. Epub 2013 Aug 23. Bioinformatics. 2013. PMID: 23975767 Free PMC article.
Neurodegenerative diseases: quantitative predictions of protein-RNA interactions.
Cirillo D, Agostini F, Klus P, Marchese D, Rodriguez S, Bolognesi B, Tartaglia GG. Cirillo D, et al. RNA. 2013 Feb;19(2):129-40. doi: 10.1261/rna.034777.112. Epub 2012 Dec 21. RNA. 2013. PMID: 23264567 Free PMC article.
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