STRIRED: graphical analysis of string repeats. - Giovanni Iazzetti; Maria Luisa Chiusano; Raffaele A. Calogero (Bioinform., 1998)

VIRTLAB: a virtual molecular biology laboratory. - Giovanni Iazzetti; G. Santini; M. Rau; E. Bucci; Raffaele A. Calogero (Bioinform., 1998)

A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome. - Maria Carmela Accardo; Ennio Giordano; Sara Riccardo; Filomena Anna Digilio; Giovanni Iazzetti; Raffaele A. Calogero; Maria Furia (Bioinform., 2004)

RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets. - Fulvio Lazzarato; Giuliana Franceschinis; Marco Botta; Francesca Cordero; Raffaele A. Calogero (Bioinform., 2004)

An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention. - Federica Cavallo; Annalisa Astolfi; Manuela Iezzi; Francesca Cordero; Pierluigi Lollini; Guido Forni; Raffaele A. Calogero (BMC Bioinform., 2005)

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. - Remo Sanges; Francesca Cordero; Raffaele A. Calogero (Bioinform., 2007)

Cross platform microarray analysis for robust identification of differentially expressed genes. - Roberta Bosotti; Giuseppe Locatelli; Sandra Healy; Emanuela Scacheri; Luca Sartori; Ciro Mercurio; Raffaele A. Calogero; Antonella Isacchi (BMC Bioinform., 2007)

Kohonen neural networks and genetic classification. - Daniela Bianchi; Raffaele A. Calogero; Brunello Tirozzi (Math. Comput. Model., 2007)

Genome-Wide Search for Splicing Defects Associated with Amyotrophic Lateral Sclerosis (ALS). - Silvia C. Lenzken; Silvia Vivarelli; Francesca Zolezzi; Francesca Cordero; Cristina Della Beffa; Raffaele A. Calogero; Silvia Barabino (CISIS, 2009)

Gene Ontology Rewritten for Computing Gene Functional Similarity. - Alessia Visconti; Francesca Cordero; Marco Botta; Raffaele A. Calogero (CISIS, 2010)

Cancer stem cell based adjuvant for oncoantingen-driven vaccination. - Francesca Cordero; Stefania Lanzardo; Maddalena Arigoni; Chiara Fornari; Laura Conti; Gianfranco Balbo; Federica Cavallo; Daniele Manini; Raffaele A. Calogero (BCB, 2011)

Mathematical Approach to Predict the Drug Effects on Cancer Stem Cell Models. - Chiara Fornari; Francesca Cordero; Daniele Manini; Gianfranco Balbo; Raffaele A. Calogero (CS2Bio@DisCoTec, 2011)

Digging in the RNA-seq Garbage: Evaluating the Characteristics of Unmapped RNA-seq Reads in Normal Tissues. - Matteo Carrara; Federica Cavallo; Maddalena Arigoni; Raffaele A. Calogero (CISIS, 2012)

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? - Matteo Carrara; Marco Beccuti; Federica Cavallo; Susanna Donatelli; Fulvio Lazzarato; Francesca Cordero; Raffaele A. Calogero (BMC Bioinform., 2013)

Multi-level model for the investigation of oncoantigen-driven vaccination effect. - Francesca Cordero; Marco Beccuti; Chiara Fornari; Stefania Lanzardo; Laura Conti; Federica Cavallo; Gianfranco Balbo; Raffaele A. Calogero (BMC Bioinform., 2013)

Chimera: a Bioconductor package for secondary analysis of fusion products. - Marco Beccuti; Matteo Carrara; Francesca Cordero; Fulvio Lazzarato; Susanna Donatelli; Francesca Nadalin; Alberto Policriti; Raffaele A. Calogero (Bioinform., 2014)

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. - Matteo Carrara; Josephine Lum; Francesca Cordero; Marco Beccuti; Michael Poidinger; Susanna Donatelli; Raffaele A. Calogero; Francesca Zolezzi (BMC Bioinform., 2015)

A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. - Chiara Fornari; Gianfranco Balbo; Sami M. Halawani; Omar M. Ba-Rukab; Ab Rahman Ahmad; Raffaele A. Calogero; Francesca Cordero; Marco Beccuti (BMC Syst. Biol., 2015)

HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. - Marco Beccuti; Elisa Genuardi; Greta Romano; Luigia Monitillo; Daniela Barbero; Mario Boccadoro; Marco Ladetto; Raffaele A. Calogero; Simone Ferrero; Francesca Cordero (BMC Bioinform., 2017)

ParallelHashClone: A Parallel Implementation of HashClone Suite for Clonality Assessment from NGS Data. - Greta Romano; Elisa Genuardi; Raffaele A. Calogero; Simone Ferrero (PDP, 2018)

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. - Marco Beccuti; Francesca Cordero; Maddalena Arigoni; Riccardo Panero; Elvio Gilberto Amparore; Susanna Donatelli; Raffaele A. Calogero (Bioinform., 2018)

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. - Neha Kulkarni; Luca Alessandrì; Riccardo Panero; Maddalena Arigoni; Martina Olivero; Giulio Ferrero; Francesca Cordero; Marco Beccuti; Raffaele A. Calogero (BMC Bioinform., 2018)

Multiple Sclerosis Disease: A Computational Approach for Investigating Its Drug Interactions. - Simone Pernice; Marco Beccuti; Greta Romano; Marzio Pennisi; Alessandro Maglione; Santina Cutrupi; Francesco Pappalardo 001; Lorenzo Capra; Giuliana Franceschinis; Massimiliano De Pierro; Gianfranco Balbo; Francesca Cordero; et al. (CIBB, 2019)

BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics. - Francesca Cordero; Raffaele A. Calogero; Michele Caselle (BMC Bioinform., 2019)

A computational approach based on the colored Petri net formalism for studying multiple sclerosis. - Simone Pernice; Marzio Pennisi; Greta Romano; Alessandro Maglione; Santina Cutrupi; Francesco Pappalardo 001; Gianfranco Balbo; Marco Beccuti; Francesca Cordero; Raffaele A. Calogero (BMC Bioinform., 2019)

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. - Marco Antonio Tangaro; Pietro Mandreoli; Matteo Chiara; Giacinto Donvito; Marica Antonacci; Antonio Parisi; Angelica Bianco; Angelo Romano; Daniela Manila Bianchi; Davide Cangelosi; Paolo Uva; Ivan Molineris; et al. (BMC Bioinform., 2021)

CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. - Simone Pernice; Roberta Sirovich; Elena Grassi; Marco Viviani 002; Martina Ferri; Francesco Sassi; Luca Alessandrì; Dora Tortarolo; Raffaele A. Calogero; Livio Trusolino; Andrea Bertotti; Marco Beccuti; et al. (Bioinform., 2023)

CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications. - Simone Alessandri; Maria L. Ratto; Sergio Rabellino; Gabriele Piacenti; Sandro Gepiro Contaldo; Simone Pernice; Marco Beccuti; Raffaele A. Calogero; Luca Alessandrì (BMC Bioinform., 2024)