Archivio Istituzionale della RicercaSfoglia per Autore
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 Molecular Dynamics study of a miRNA:mRNA interaction
2011 Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Deriu, MARCO AGOSTINO; 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
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
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
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
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
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
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
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
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
VDJSeq-Solver: In Silico V(D)J Recombination Detection tool
2015 Paciello, Giulia; Acquaviva, Andrea; Chiara, Pighi; Alberto, Ferrarini; Macii, Enrico; Alberto, Zamò; Ficarra, Elisa
On the relevance of a complete characterisation of miRNAs, isomiRs and miRNA-mRNA interaction sites through miRNA-specific alignment tools
2015 Urgese, Gianvito; Paciello, Giulia; Ficarra, Elisa; Macii, Enrico; Acquaviva, Andrea
RNA Sequencing Reveals Novel and Rare Fusion Transcripts in Acute Myeloid Leukemia
2015 Padella, A.; Simonetti, G.; Paciello, Giulia; Ferrari, A.; Zago, E.; Baldazzi, C.; Guadagnuolo, V.; Papayannidis, C.; Robustelli, V.; Imbrogno, E.; Testoni, N.; Musuraca, G.; Soverini, S.; Delledonne, M.; Iacobucci, I.; Storlazzi, C. T.; Ficarra, Elisa; Martinelli, G.
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,
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.
Novel fusion transcripts identified by RNAseq cooperate with somatic mutations in the pathogenesis of acute myeloid leukemia
2016 Antonella, Padella; Giorgia, Simonetti; Anna, Ferrari; Paciello, Giulia; Elisa, Zago; Carmen, Baldazzi; Viviana, Guadagnuolo; Cristina, Papayannidis; Valentina, Robustelli; Enrica, Imbrogno; Nicoletta, Testoni; Massimo, Delledonne; Ilaria, Iacobucci; Tiziana Clelia, Storlazzi; Ficarra, Elisa; Pier Luigi, Lollini; Giovanni, Martinelli
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
The Genomic and Transcriptomic Landscape of Systemic Mastocytosis
2016 Simona, Soverini; Caterina De, Benedittis; Michela, Rondoni; Cristina, Papayannidis; Ficarra, Elisa; Paciello, Giulia; Marco, Manfrini; Manuela, Mancini; Roberta, Zanotti; Luigi, Scaffidi; Giorgina, Specchia; Francesco, Albano; Serena, Merante; Chiara, Elena; Livio, Pagano; Domenica, Gangemi; Patrizia, Tosi; Luana, Bavaro
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
| Citazione | Data di pubblicazione | Autori | File |
|---|---|---|---|
| A novel framework for chimeric transcript detection based on accurate gene fusion model / Abate, F., Acquaviva, A., Ficarra, E., Paciello, G., Macii, E., A., F., M., D., S., S., G., M.. - STAMPA. - (2011), pp. 34-41. (IEEE International Conference on Bioinformatics and Biomedicine Atlanta, Georgia (USA) 12-15 Nov. 2011) [10.1109/BIBMW.2011.6112352]. | 1-gen-2011 | ABATE, FRANCESCOACQUAVIVA, ANDREAFICARRA, ELISAPACIELLO, GIULIAMACII, Enrico + | 2443775-mod.pdf |
| A Molecular Dynamics study of a miRNA:mRNA interaction / Paciello, G., Acquaviva, A., Ficarra, E., Deriu, M.A., Macii, E.. - 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 | - |
| Binding free energy calculation via Molecular Dynamics simulations for a miRNA:mRNA interaction / Paciello, G., Acquaviva, A., Ficarra, E., Deriu, M.A., Macii, E.. - STAMPA. - (2011), pp. 318-321. (Bioinformatics 2011, International Conference on Bioinformatics Models Methods and Algorithms Rome (IT) 26 - 29 January 2011). | 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, F., Paciello, G., Acquaviva, A., Ficarra, E., Ferrarini, A., Delledonne, M., Macii, E.. - STAMPA. - (2012), pp. 331-334. (International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2012) Vilamoura, Algarve (Portugal) 1-4 February 2012) [10.5220/0003789003310334]. | 1-gen-2012 | ABATE, FRANCESCOPACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISAMACII, Enrico + | - |
| Bellerophontes: a RNA-seq data analysis framework tor chimeric transcripts discovery base on accurate fusion model / Abate, F., Acquaviva, A., Paciello, G., Foti, C., Ficarra, E., Ferrarini, A., Delle donne, M., Iacobucci, I., Soverini, S., Martinelli, G., Macii, E.. - 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 + | - |
| Multiscale Modelling of Cellular Actin Filaments: From Atomistic Molecular to Coarse Grained Dynamics / Deriu, M.A., Shkurti, A., Paciello, G., Bidone, T.C., Morbiducci, U., Ficarra, E., Audenino, A., Acquaviva, A.. - 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 | - |
| A novel pipeline for V(D)J junction identification using RNA-Seq paired-end reads / Paciello, G., Ficarra, E., Alberto, Z., Chiara, P., Carmelo, F., Abate, F., Macii, E., Acquaviva, A.. - STAMPA. - (2013). (Bioinformatics 2013, International Conference on Bioinformatics Models, Methods and Algorithms Barcelona, Spain 11-14 February 2013). | 1-gen-2013 | PACIELLO, GIULIAFICARRA, ELISAABATE, FRANCESCOMACII, EnricoACQUAVIVA, ANDREA + | Biostec_camera_ready.pdf |
| Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimisation / Urgese, G., Paciello, G., Acquaviva, A., Ficarra, E., Graziano, M., Zamboni, M.. - STAMPA. - 2:(2014), pp. 1347-1358. (2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) Granada April 7-9 2014). | 1-gen-2014 | URGESE, GIANVITOPACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISAGRAZIANO, MARIAGRAZIAZAMBONI, Maurizio | IWBBIO_2014_paper_143.pdf |
| A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer / Paciello, G., Acquaviva, A., Consalvo, P., Claudio, I., Enzo, M., Ficarra, E.. - (2014), pp. 142-148. (BIOSTEC 2014 Eseo, Angers, Loire Valley, France 3-6 March 2014) [10.5220/0004799401420148]. | 1-gen-2014 | PACIELLO, GIULIAACQUAVIVA, ANDREAFICARRA, ELISA + | - |
| miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction / Urgese, G., Paciello, G., Isella, C., Medico, E., Macii, E., Ficarra, E., Acquaviva, A.. - STAMPA. - 2:(2014), pp. 1015-1026. (2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) Granada April 7-9 2014). | 1-gen-2014 | URGESE, GIANVITOPACIELLO, GIULIAMACII, EnricoFICARRA, ELISAACQUAVIVA, ANDREA + | IWBBIO_2014_paper_105.pdf |
| Next-Generation Sequencing Analysis Revealed That BCL11B Chromosomal Translocation Cooperates with Point Mutations in the Pathogenesis of Acute Myeloid Leukemia / Antonella, P., Giorgia, S., Viviana, G., Emanuela, O., Anna, F., Elisa, Z., Francesca, G., Marianna, G., Paciello, G., Simona, B., Carmen, B., Cristina, P., Maria Chiara, A., Francesca, V., Raffaele, C., Nicoletta, T., Ficarra, E., Alberto, F., Massimo, D., Ilaria, I., et al.. - In: BLOOD. - ISSN 0006-4971. - ELETTRONICO. - 124:21(2014). | 1-gen-2014 | PACIELLO, GIULIAFICARRA, ELISA + | - |
| VDJSeq-Solver: In Silico V(D)J Recombination Detection tool / Paciello, G., Acquaviva, A., Chiara, P., Alberto, F., Macii, E., Alberto, Z., Ficarra, E.. - In: PLOS ONE. - ISSN 1932-6203. - ELETTRONICO. - 10:3(2015), pp. 1-26. [10.1371/journal.pone.0118192] | 1-gen-2015 | PACIELLO, GIULIAACQUAVIVA, ANDREAMACII, EnricoFICARRA, ELISA + | VDJSeq-Solver.pdf |
| On the relevance of a complete characterisation of miRNAs, isomiRs and miRNA-mRNA interaction sites through miRNA-specific alignment tools / Urgese, G., Paciello, G., Ficarra, E., Macii, E., Acquaviva, A.. - ELETTRONICO. - (2015). (RNAi 2015: Short & Long Non-coding RNAs, 10th International Conference & Exhibition Oxford (UK) 24-26 March 2015). | 1-gen-2015 | URGESE, GIANVITOPACIELLO, GIULIAFICARRA, ELISAMACII, EnricoACQUAVIVA, ANDREA | Urgese-RNAi15_2.pdf |
| RNA Sequencing Reveals Novel and Rare Fusion Transcripts in Acute Myeloid Leukemia / Padella, A., Simonetti, G., Paciello, G., Ferrari, A., Zago, E., Baldazzi, C., Guadagnuolo, V., Papayannidis, C., Robustelli, V., Imbrogno, E., Testoni, N., Musuraca, G., Soverini, S., Delledonne, M., Iacobucci, I., Storlazzi, C.T., Ficarra, E., Martinelli, G.. - In: BLOOD. - ISSN 0006-4971. - 126:(2015), pp. 3627-3627. | 1-gen-2015 | 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, I., I, ., Paciello, G., G, ., Aerts,. - (2016). (EMBL Transcription and Chromatin, Edition 12 Heidelberg 27-30 Aug 2016). | 1-gen-2016 | PACIELLO, GIULIA + | - |
| Detection of rearranged light chain sequences by RNA-Seq in B-cell lymphomas and reactive lymphadenopathies / Paciello, G., Pighi, C., Ficarra, E., Zamo', A.. - (2016). (EAHP 2016: 18th Meeting of the European Association for Hemathopathology Basilea 3-8 Sept. 2016). | 1-gen-2016 | PACIELLO, GIULIAFICARRA, ELISA + | - |
| Novel fusion transcripts identified by RNAseq cooperate with somatic mutations in the pathogenesis of acute myeloid leukemia / Antonella, P., Giorgia, S., Anna, F., Paciello, G., Elisa, Z., Carmen, B., Viviana, G., Cristina, P., Valentina, R., Enrica, I., Nicoletta, T., Massimo, D., Ilaria, I., Tiziana Clelia, S., Ficarra, E., Pier Luigi, L., Giovanni, M.. - In: CANCER RESEARCH. - ISSN 1538-7445. - 76:14(2016), pp. 113-113. [10.1158/1538-7445.AM2016-113] | 1-gen-2016 | PACIELLO, GIULIAFICARRA, ELISA + | - |
| A COMBINED APPROACH TO DETECT RARE FUSION EVENTS IN ACUTE MYELOID LEUKEMIA / A., P., G., S., Paciello, G., A., F., E., Z., C., B., V., G., C., P., V., R., E., I., N., T., M., C., M., D., I., I., Ct, S., Ficarra, E., G., M.. - In: HAEMATOLOGICA. - ISSN 0390-6078. - ELETTRONICO. - 101:(2016), pp. 666-667. (21st Congress Of The European Hematology Association Copenhagen, Denmark June 9–12, 2016). | 1-gen-2016 | PACIELLO, GIULIAFICARRA, ELISA + | - |
| The Genomic and Transcriptomic Landscape of Systemic Mastocytosis / Simona, S., Caterina De, B., Michela, R., Cristina, P., Ficarra, E., Paciello, G., Marco, M., Manuela, M., Roberta, Z., Luigi, S., Giorgina, S., Francesco, A., Serena, M., Chiara, E., Livio, P., Domenica, G., Patrizia, T., Luana, B.. - In: BLOOD. - ISSN 0006-4971. - 128:22(2016). [10.1182/blood.V128.22.3136.3136] | 1-gen-2016 | FICARRA, ELISAPACIELLO, GIULIA + | - |
| isomiR-SEA: An RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation / Urgese, G., Paciello, G., Acquaviva, A., Ficarra, E.. - 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 |
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