Differential expression of genes coding for ribosomal proteins in different human tissues. - Stefania Bortoluzzi; Fabio d'Alessi; Chiara Romualdi; Gian Antonio Danieli (Bioinform., 2001)

Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma. - Andrea Bisognin; Stefania Bortoluzzi; Gian Antonio Danieli (BMC Bioinform., 2004)

A multistep bioinformatic approach detects putative regulatory elements in gene promoters. - Stefania Bortoluzzi; Alessandro Coppe; Andrea Bisognin; Cinzia Pizzi; Gian Antonio Danieli (BMC Bioinform., 2005)

REEF: searching REgionally Enriched Features in genomes. - Alessandro Coppe; Gian Antonio Danieli; Stefania Bortoluzzi (BMC Bioinform., 2006)

Novel definition files for human GeneChips based on GeneAnnot. - Francesco Ferrari; Stefania Bortoluzzi; Alessandro Coppe; Alexandra Sirota; Marilyn Safran; Michael Shmoish; Sergio Ferrari; Doron Lancet; Gian Antonio Danieli; Silvio Bicciato (BMC Bioinform., 2007)

A-MADMAN: Annotation-based microarray data meta-analysis tool. - Andrea Bisognin; Alessandro Coppe; Francesco Ferrari; Davide Risso; Chiara Romualdi; Silvio Bicciato; Stefania Bortoluzzi (BMC Bioinform., 2009)

Critical Analysis of Transcriptional and Post-Transcriptional Regulatory Networks in Multiple Myeloma. - Marta Biasiolo; Mattia Forcato; Lino Possamai; Francesco Ferrari; Luca Agnelli; Marta Lionetti; Katia Todoerti; Antonino Neri; Massimo Marchiori; Stefania Bortoluzzi; Silvio Bicciato (Pacific Symposium on Biocomputing, 2010)

MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. - Gabriele Sales; Alessandro Coppe; Andrea Bisognin; Marta Biasiolo; Stefania Bortoluzzi; Chiara Romualdi (Nucleic Acids Res., 2010)

MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). - Andrea Bisognin; Gabriele Sales; Alessandro Coppe; Stefania Bortoluzzi; Chiara Romualdi (Nucleic Acids Res., 2012)

A survey of software tools for microRNA discovery and characterization using RNA-seq. - Michele Bortolomeazzi; Enrico Gaffo; Stefania Bortoluzzi (Briefings Bioinform., 2019)

iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data. - Andrea Binatti; Silvia Bresolin; Stefania Bortoluzzi; Alessandro Coppe (Briefings Bioinform., 2021)

Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2. - Enrico Gaffo; Alessia Buratin; Anna Dal Molin; Stefania Bortoluzzi (Briefings Bioinform., 2022)

CRAFT: a bioinformatics software for custom prediction of circular RNA functions. - Anna Dal Molin; Enrico Gaffo; Valeria Difilippo; Alessia Buratin; Caterina Tretti Parenzan; Silvia Bresolin; Stefania Bortoluzzi (Briefings Bioinform., 2022)

Correction to: CRAFT a bioinformatics software for custom prediction of circular RNA functions. - Anna Dal Molin; Enrico Gaffo; Valeria Difilippo; Alessia Buratin; Caterina Tretti Parenzan; Silvia Bresolin; Stefania Bortoluzzi (Briefings Bioinform., 2022)

Systematic benchmarking of statistical methods to assess differential expression of circular RNAs. - Alessia Buratin; Stefania Bortoluzzi; Enrico Gaffo (Briefings Bioinform., 2023)

Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion. - Anna Dal Molin; Caterina Tretti Parenzan; Enrico Gaffo; Cristina Borin; Elena Boldrin; Lueder H. Meyer; Geertruij te Kronnie; Silvia Bresolin; Stefania Bortoluzzi (Briefings Bioinform., 2023)