Archivio Istituzionale della RicercaPACIELLO, GIULIA
A COMBINED APPROACH TO DETECT RARE FUSION EVENTS IN ACUTE MYELOID LEUKEMIA
2016 A., Padella; G., Simonetti; Paciello, Giulia; A., Ferrari; E., Zago; C., Baldazzi; V., Guadagnuolo; C., Papayannidis; V., Robustelli; E., Imbrogno; N., Testoni; M., Cavo; M., Delledonne; I., Iacobucci; Ct, Storlazzi; Ficarra, Elisa; G., Martinelli
A Molecular Dynamics study of a miRNA:mRNA interaction
2011 Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Deriu, MARCO AGOSTINO; Macii, Enrico
A NOVEL ANALYSIS FLOW FOR FUSED TRANSCRIPTS DISCOVERY FROM PAIRED-END RNA-SEQ DATA
2012 Abate, Francesco; Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Ferrarini, A.; Delledonne, M.; Macii, Enrico
A novel framework for chimeric transcript detection based on accurate gene fusion model
2011 Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; Paciello, Giulia; Macii, Enrico; A., Ferrarini; M., Delledonne; S., Soverini; G., Martinelli
A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer
2014 Paciello, Giulia; Acquaviva, Andrea; Consalvo, Petti; Claudio, Isella; Enzo, Medico; Ficarra, Elisa
A novel pipeline for V(D)J junction identification using RNA-Seq paired-end reads
2013 Paciello, Giulia; Ficarra, Elisa; Alberto, Zamò; Chiara, Pighi; Carmelo, Foti; Abate, Francesco; Macii, Enrico; Acquaviva, Andrea
Bellerophontes: a RNA-seq data analysis framework tor chimeric transcripts discovery base on accurate fusion model
2012 Abate, Francesco; Acquaviva, Andrea; Paciello, Giulia; Foti, Carmelo; Ficarra, Elisa; Ferrarini, A.; Delle donne, M.; Iacobucci, I.; Soverini, S.; Martinelli, G.; Macii, Enrico
Binding free energy calculation via Molecular Dynamics simulations for a miRNA:mRNA interaction
2011 Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Deriu, MARCO AGOSTINO; Macii, Enrico
Bioinformatics methods and tools for identifying disease-associated B-cell populations, miRNA patterns and gene fusions in RNA-Seq data
2017 Paciello, Giulia
Detection of rearranged light chain sequences by RNA-Seq in B-cell lymphomas and reactive lymphadenopathies
2016 Paciello, Giulia; Pighi, C.; Ficarra, Elisa; Zamo', A.
Directly linking non-coding SNPs to changes in epithelial enhancer activity
2016 Jacobs, J.; Christiaens, ; V, .; Potier, ; D, .; Svetlichnyy, ; D, .; Romanelli, ; L, .; Taskiran, Ihsan; I, .; Paciello, Giulia; G, .; Aerts,
Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimisation
2014 Urgese, Gianvito; Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Graziano, Mariagrazia; Zamboni, Maurizio
FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples
2017 Paciello, Giulia; Ficarra, Elisa
geneEX a novel tool to assess differential expression from gene and exon sequencing data
2018 Scicolone, ORAZIO MARIA; Paciello, Giulia; Ficarra, Elisa
isomiR-SEA: An RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation
2016 Urgese, Gianvito; Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa
isomiR-SEA: miRNA and isomiR expression level detection in seven RNA-Seq datasets
2017 Urgese, Gianvito; Paciello, Giulia; Macii, Enrico; Acquaviva, Andrea; Ficarra, Elisa
MDM2 and Aurora Kinase a Contribute to SETD2 Loss of Function in Advanced Systemic Mastocytosis: Implications for Pathogenesis and Treatment
2018 Mancini, Manuela; Monaldi, Cecilia; De Santis, Sara; Papayannidis, Cristina; Rondoni, Michela; Bavaro, Luana; Martelli, Margherita; Maria Chiara, Abbenante; Curti, Antonio; Ficarra, Elisa; Paciello, Giulia; Chiara Fontana, Maria; Zanotti, Roberta; Bonifacio, Massimiliano; Scaffidi, Luigi; Pagano, Livio; Criscuolo, Marianna; Albano, Francesco; Ciceri, Fabio; Elena, Chiara; Tosi, Patrizia; Delledonne, Massimo; Avanzato, Carla; Xumerle, Luciano; Valent, Peter; Martinelli, GIOVANNI ATTILIO; Cavo, Michele; Soverini, Simona
miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction
2014 Urgese, Gianvito; Paciello, Giulia; Isella, C.; Medico, E.; Macii, Enrico; Ficarra, Elisa; Acquaviva, Andrea
Multiscale Modelling of Cellular Actin Filaments: From Atomistic Molecular to Coarse Grained Dynamics
2012 Deriu, MARCO AGOSTINO; Shkurti, Ardita; Paciello, Giulia; Bidone, TAMARA CARLA; Morbiducci, Umberto; Ficarra, Elisa; Audenino, Alberto; Acquaviva, Andrea
Next-Generation Sequencing Analysis Revealed That BCL11B Chromosomal Translocation Cooperates with Point Mutations in the Pathogenesis of Acute Myeloid Leukemia
2014 Antonella, Padella; Giorgia, Simonetti; Viviana, Guadagnuolo; Emanuela, Ottaviani; Anna, Ferrari; Elisa, Zago; Francesca, Griggio; Marianna, Garonzi; Paciello, Giulia; Simona, Bernardi; Carmen, Baldazzi; Cristina, Papayannidis; Maria Chiara, Abbenante; Francesca, Volpato; Raffaele, Calogero; Nicoletta, Testoni; Ficarra, Elisa; Alberto, Ferrarini; Massimo, Delledonne; Ilaria, Iacobucci; Giovanni, Martinelli
| Citazione | Data di pubblicazione | Autori | File |
|---|---|---|---|
| A COMBINED APPROACH TO DETECT RARE FUSION EVENTS IN ACUTE MYELOID LEUKEMIA / A., Padella; G., Simonetti; Paciello, Giulia; A., Ferrari; E., Zago; C., Baldazzi; V., Guadagnuolo; C., Papayannidis; V., Robustelli; E., Imbrogno; N., Testoni; M., Cavo; M., Delledonne; I., Iacobucci; Ct, Storlazzi; Ficarra, Elisa; G., Martinelli. - In: HAEMATOLOGICA. - ISSN 0390-6078. - ELETTRONICO. - 101:(2016), pp. 666-667. (Intervento presentato al convegno 21st Congress Of The European Hematology Association tenutosi a Copenhagen, Denmark nel June 9–12, 2016). | 1-gen-2016 | PACIELLO, GIULIAFICARRA, ELISA + | - |
| A Molecular Dynamics study of a miRNA:mRNA interaction / Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Deriu, MARCO AGOSTINO; Macii, Enrico. - In: JOURNAL OF MOLECULAR MODELING. - ISSN 1610-2940. - STAMPA. - 17:11(2011), pp. 2895-2906. [10.1007/s00894-011-0991-x] | 1-gen-2011 | PACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISADERIU, MARCO AGOSTINOMACII, Enrico | - |
| A NOVEL ANALYSIS FLOW FOR FUSED TRANSCRIPTS DISCOVERY FROM PAIRED-END RNA-SEQ DATA / Abate, Francesco; Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Ferrarini, A.; Delledonne, M.; Macii, Enrico. - STAMPA. - (2012), pp. 331-334. (Intervento presentato al convegno International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2012) tenutosi a Vilamoura, Algarve (Portugal) nel 1-4 February 2012) [10.5220/0003789003310334]. | 1-gen-2012 | ABATE, FRANCESCOPACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISAMACII, Enrico + | - |
| A novel framework for chimeric transcript detection based on accurate gene fusion model / Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; Paciello, Giulia; Macii, Enrico; A., Ferrarini; M., Delledonne; S., Soverini; G., Martinelli. - STAMPA. - (2011), pp. 34-41. (Intervento presentato al convegno IEEE International Conference on Bioinformatics and Biomedicine tenutosi a Atlanta, Georgia (USA) nel 12-15 Nov. 2011) [10.1109/BIBMW.2011.6112352]. | 1-gen-2011 | ABATE, FRANCESCOACQUAVIVA, ANDREAFICARRA, ELISAPACIELLO, GIULIAMACII, Enrico + | 2443775-mod.pdf |
| A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer / Paciello, Giulia; Acquaviva, Andrea; Consalvo, Petti; Claudio, Isella; Enzo, Medico; Ficarra, Elisa. - (2014), pp. 142-148. (Intervento presentato al convegno BIOSTEC 2014 tenutosi a Eseo, Angers, Loire Valley, France nel 3-6 March 2014) [10.5220/0004799401420148]. | 1-gen-2014 | PACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISA + | - |
| A novel pipeline for V(D)J junction identification using RNA-Seq paired-end reads / Paciello, Giulia; Ficarra, Elisa; Alberto, Zamò; Chiara, Pighi; Carmelo, Foti; Abate, Francesco; Macii, Enrico; Acquaviva, Andrea. - STAMPA. - (2013). (Intervento presentato al convegno Bioinformatics 2013, International Conference on Bioinformatics Models, Methods and Algorithms tenutosi a Barcelona, Spain nel 11-14 February 2013). | 1-gen-2013 | PACIELLO, GIULIAFICARRA, ELISAABATE, FRANCESCOMACII, EnricoACQUAVIVA, ANDREA + | Biostec_camera_ready.pdf |
| Bellerophontes: a RNA-seq data analysis framework tor chimeric transcripts discovery base on accurate fusion model / Abate, Francesco; Acquaviva, Andrea; Paciello, Giulia; Foti, Carmelo; Ficarra, Elisa; Ferrarini, A.; Delle donne, M.; Iacobucci, I.; Soverini, S.; Martinelli, G.; Macii, Enrico. - In: BIOINFORMATICS. - ISSN 1367-4803. - STAMPA. - 28:16(2012), pp. 2114-2121. [10.1093/bioinformatics/bts334] | 1-gen-2012 | ABATE, FRANCESCOACQUAVIVA, ANDREAPACIELLO, GIULIAFOTI, CARMELOFICARRA, ELISAMACII, Enrico + | - |
| Binding free energy calculation via Molecular Dynamics simulations for a miRNA:mRNA interaction / Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Deriu, MARCO AGOSTINO; Macii, Enrico. - STAMPA. - (2011), pp. 318-321. (Intervento presentato al convegno Bioinformatics 2011, International Conference on Bioinformatics Models Methods and Algorithms tenutosi a Rome (IT) nel 26 - 29 January 2011). | 1-gen-2011 | PACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISADERIU, MARCO AGOSTINOMACII, Enrico | - |
| Bioinformatics methods and tools for identifying disease-associated B-cell populations, miRNA patterns and gene fusions in RNA-Seq data / Paciello, Giulia. - (2017). | 1-gen-2017 | PACIELLO, GIULIA | - |
| Detection of rearranged light chain sequences by RNA-Seq in B-cell lymphomas and reactive lymphadenopathies / Paciello, Giulia; Pighi, C.; Ficarra, Elisa; Zamo', A.. - (2016). (Intervento presentato al convegno EAHP 2016: 18th Meeting of the European Association for Hemathopathology tenutosi a Basilea nel 3-8 Sept. 2016). | 1-gen-2016 | PACIELLO, GIULIAFICARRA, ELISA + | - |
| Directly linking non-coding SNPs to changes in epithelial enhancer activity / Jacobs, J.; Christiaens, ; V, .; Potier, ; D, .; Svetlichnyy, ; D, .; Romanelli, ; L, .; Taskiran, Ihsan; I, .; Paciello, Giulia; G, .; Aerts,. - (2016). (Intervento presentato al convegno EMBL Transcription and Chromatin, Edition 12 tenutosi a Heidelberg nel 27-30 Aug 2016). | 1-gen-2016 | PACIELLO, GIULIA + | - |
| Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimisation / Urgese, Gianvito; Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Graziano, Mariagrazia; Zamboni, Maurizio. - STAMPA. - 2:(2014), pp. 1347-1358. (Intervento presentato al convegno 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) tenutosi a Granada nel April 7-9 2014). | 1-gen-2014 | URGESE, GIANVITOPACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISAGRAZIANO, MARIAGRAZIAZAMBONI, Maurizio | IWBBIO_2014_paper_143.pdf |
| FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples / Paciello, Giulia; Ficarra, Elisa. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 18:1(2017), pp. 1-12. [10.1186/s12859-016-1450-6] | 1-gen-2017 | PACIELLO, GIULIAFICARRA, ELISA | 12859_2016_Article_1450_FuGePrior.pdf |
| geneEX a novel tool to assess differential expression from gene and exon sequencing data / Scicolone, ORAZIO MARIA; Paciello, Giulia; Ficarra, Elisa. - 3:(2018), pp. 174-181. (Intervento presentato al convegno 9th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2018 - Part of 11th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2018 tenutosi a Funchal - Madeira, Portugal nel 19-21 January, 2018). | 1-gen-2018 | SCICOLONE, ORAZIO MARIAPaciello, GiuliaFicarra, Elisa | geneEX.pdf |
| isomiR-SEA: An RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation / Urgese, Gianvito; Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - ELETTRONICO. - 17:148(2016). [10.1186/s12859-016-0958-0] | 1-gen-2016 | URGESE, GIANVITOPACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISA | s12859-016-0958-0.pdf |
| isomiR-SEA: miRNA and isomiR expression level detection in seven RNA-Seq datasets / Urgese, Gianvito; Paciello, Giulia; Macii, Enrico; Acquaviva, Andrea; Ficarra, Elisa. - ELETTRONICO. - (2017). (Intervento presentato al convegno Joint 25th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 16th European Conference on Computational Biology (ECCB) 2017 tenutosi a Prague nel 21-25 July 2017) [10.7490/f1000research.1114698.1]. | 1-gen-2017 | URGESE, GIANVITOPACIELLO, GIULIAMACII, EnricoACQUAVIVA, ANDREAFICARRA, ELISA | f1000research-173536_post_print.pdf |
| MDM2 and Aurora Kinase a Contribute to SETD2 Loss of Function in Advanced Systemic Mastocytosis: Implications for Pathogenesis and Treatment / Mancini, Manuela; Monaldi, Cecilia; De Santis, Sara; Papayannidis, Cristina; Rondoni, Michela; Bavaro, Luana; Martelli, Margherita; Maria Chiara, Abbenante; Curti, Antonio; Ficarra, Elisa; Paciello, Giulia; Chiara Fontana, Maria; Zanotti, Roberta; Bonifacio, Massimiliano; Scaffidi, Luigi; Pagano, Livio; Criscuolo, Marianna; Albano, Francesco; Ciceri, Fabio; Elena, Chiara; Tosi, Patrizia; Delledonne, Massimo; Avanzato, Carla; Xumerle, Luciano; Valent, Peter; Martinelli, GIOVANNI ATTILIO; Cavo, Michele; Soverini, Simona. - In: BLOOD. - ISSN 0006-4971. - ELETTRONICO. - 132:1(2018), pp. 1779-1779. [10.1182/blood-2018-99-113278] | 1-gen-2018 | Elisa FicarraGiulia PacielloGiovanni Martinelli + | - |
| miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction / Urgese, Gianvito; Paciello, Giulia; Isella, C.; Medico, E.; Macii, Enrico; Ficarra, Elisa; Acquaviva, Andrea. - STAMPA. - 2:(2014), pp. 1015-1026. (Intervento presentato al convegno 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) tenutosi a Granada nel April 7-9 2014). | 1-gen-2014 | URGESE, GIANVITOPACIELLO, GIULIAMACII, EnricoFICARRA, ELISAACQUAVIVA, ANDREA + | IWBBIO_2014_paper_105.pdf |
| Multiscale Modelling of Cellular Actin Filaments: From Atomistic Molecular to Coarse Grained Dynamics / Deriu, MARCO AGOSTINO; Shkurti, Ardita; Paciello, Giulia; Bidone, TAMARA CARLA; Morbiducci, Umberto; Ficarra, Elisa; Audenino, Alberto; Acquaviva, Andrea. - In: PROTEINS. - ISSN 0887-3585. - ELETTRONICO. - 80:6(2012), pp. 1598-1609. [10.1002/prot.24053] | 1-gen-2012 | DERIU, MARCO AGOSTINOSHKURTI, ARDITAPACIELLO, GIULIABIDONE, TAMARA CARLAMORBIDUCCI, UMBERTOFICARRA, ELISAAUDENINO, AlbertoACQUAVIVA, ANDREA | - |
| Next-Generation Sequencing Analysis Revealed That BCL11B Chromosomal Translocation Cooperates with Point Mutations in the Pathogenesis of Acute Myeloid Leukemia / Antonella, Padella; Giorgia, Simonetti; Viviana, Guadagnuolo; Emanuela, Ottaviani; Anna, Ferrari; Elisa, Zago; Francesca, Griggio; Marianna, Garonzi; Paciello, Giulia; Simona, Bernardi; Carmen, Baldazzi; Cristina, Papayannidis; Maria Chiara, Abbenante; Francesca, Volpato; Raffaele, Calogero; Nicoletta, Testoni; Ficarra, Elisa; Alberto, Ferrarini; Massimo, Delledonne; Ilaria, Iacobucci; Giovanni, Martinelli. - In: BLOOD. - ISSN 0006-4971. - ELETTRONICO. - 124:21(2014). | 1-gen-2014 | PACIELLO, GIULIAFICARRA, ELISA + | - |