A novel framework for chimeric transcript detection based on accurate gene fusion model. - Francesco Abate; Andrea Acquaviva; Elisa Ficarra; Giulia Paciello; Enrico Macii; Alberto Ferrarini; Massimo Delledonne; Simona Soverini; Giovanni Martinelli (BIBM Workshops, 2011)

Binding Free Energy Calculation via Molecular Dynamics Simulations for a miRNA: mRNA Interaction. - Giulia Paciello; Andrea Acquaviva; Elisa Ficarra; M. A. Deriu; A. Grosso; Enrico Macii (BIOINFORMATICS, 2011)

A Novel Analysis Flow for Fused Transcripts Discovery from Paired-end RNA-Seq Data. - Francesco Abate; Giulia Paciello; Andrea Acquaviva; Elisa Ficarra; Alberto Ferrarini; Massimo Delledonne; Enrico Macii (BIOINFORMATICS, 2012)

Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model. - Francesco Abate; Andrea Acquaviva; Giulia Paciello; Carmelo Foti; Elisa Ficarra; Alberto Ferrarini; Massimo Delledonne; Ilaria Iacobucci; Simona Soverini; Giovanni Martinelli; Enrico Macii (Bioinform., 2012)

A Novel Pipeline for V(D)J Junction Identification using RNA-Seq Paired-end Reads. - Giulia Paciello; Elisa Ficarra; Alberto Zamò; Chiara Pighi; Carmelo Foti; Francesco Abate; Enrico Macii; Andrea Acquaviva (BIOINFORMATICS, 2013)

A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer. - Giulia Paciello; Andrea Acquaviva; Consalvo Petti; Claudio Isella; Enzo Medico; Elisa Ficarra (BIOINFORMATICS, 2014)

Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimization. - Gianvito Urgese; Giulia Paciello; Andrea Acquaviva; Elisa Ficarra; Mariagrazia Graziano; Maurizio Zamboni (IWBBIO, 2014)

miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction. - Gianvito Urgese; Giulia Paciello; Claudio Isella; Enzo Medico; Enrico Macii; Elisa Ficarra; Andrea Acquaviva (IWBBIO, 2014)

isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation. - Gianvito Urgese; Giulia Paciello; Andrea Acquaviva; Elisa Ficarra (BMC Bioinform., 2016)

FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples. - Giulia Paciello; Elisa Ficarra (BMC Bioinform., 2017)

Bioinformatics methods and tools for identifying disease-associated B-cell populations, miRNA patterns and gene fusions in RNA-Seq data. - Giulia Paciello (2017)

geneEx - A Novel Tool to Assess Differential Expression from Gene and Exon Sequencing Data. - Orazio M. Scicolone; Giulia Paciello; Elisa Ficarra (BIOINFORMATICS, 2018)

FUNGI: FUsioN Gene Integration toolset. - Alejandra Cervera; Heidi Rausio; Tiia Kähkönen; Noora Andersson; Gabriele Partel; Ville Rantanen; Giulia Paciello; Elisa Ficarra; Johanna Hynninen; Sakari Hietanen; Olli Carpén; Rainer Lehtonen; et al. (Bioinform., 2021)

Explaining Crash Predictions on Multivariate Time Series Data. - Francesco Spinnato; Riccardo Guidotti; Mirco Nanni; Daniele Maccagnola; Giulia Paciello; Antonio Bencini Farina (DS, 2022)