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

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices. - Nicola Cannata; Stefano Toppo; Chiara Romualdi; Giorgio Valle (Bioinform., 2002)

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts. - Stefano Toppo; Nicola Cannata; Paolo Fontana; Chiara Romualdi; Paolo Laveder; Emanuela Bertocco; Gerolamo Lanfranchi; Giorgio Valle (Bioinform., 2003)

RAP: a new computer program for de novo identification of repeated sequences in whole genomes. - Davide Campagna; Chiara Romualdi; Nicola Vitulo; Micky Del Favero; Matej Lexa; Nicola Cannata; Giorgio Valle (Bioinform., 2005)

MIDAW: a web tool for statistical analysis of microarray data. - Chiara Romualdi; Nicola Vitulo; Micky Del Favero; Gerolamo Lanfranchi (Nucleic Acids Res., 2005)

A global gene evolution analysis on Vibrionaceae family using phylogenetic profile. - Nicola Vitulo; Alessandro Vezzi; Chiara Romualdi; Stefano Campanaro; Giorgio Valle (BMC Bioinform., 2007)

Morphology and evolution of cortical lesions in multiple sclerosis. A longitudinal MRI study. - Massimiliano Calabrese; Massimo Filippi; Marco Rovaris; Irene Mattisi; Valentina Bernardi; Matteo Atzori; Alice Favaretto; Luigi Barachino; Luciano Rinaldi; Chiara Romualdi; Paola Perini; Paolo Gallo (NeuroImage, 2008)

A modified LOESS normalization applied to microRNA arrays: a comparative evaluation. - Davide Risso; Maria Sofia Massa; Monica Chiogna; Chiara Romualdi (Bioinform., 2009)

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)

A comparison on effects of normalisations in the detection of differentially expressed genes. - Monica Chiogna; Maria Sofia Massa; Davide Risso; Chiara Romualdi (BMC Bioinform., 2009)

Gene set analysis exploiting the topology of a pathway. - Maria Sofia Massa; Monica Chiogna; Chiara Romualdi (BMC Syst. Biol., 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)

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. - Luca Beltrame; Enrica Calura; Razvan R. Popovici; Lisa Rizzetto; Damariz Rivero Guedez; Michele Donato; Chiara Romualdi; Sorin Draghici; Duccio Cavalieri (Bioinform., 2011)

parmigene - a parallel R package for mutual information estimation and gene network reconstruction. - Gabriele Sales; Chiara Romualdi (Bioinform., 2011)

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies. - Paolo G. V. Martini; Davide Risso; Gabriele Sales; Chiara Romualdi; Gerolamo Lanfranchi; Stefano Cagnin (BMC Bioinform., 2011)

graphite - a Bioconductor package to convert pathway topology to gene network. - Gabriele Sales; Enrica Calura; Duccio Cavalieri; Chiara Romualdi (BMC Bioinform., 2012)

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)

Graphite Web: web tool for gene set analysis exploiting pathway topology. - Gabriele Sales; Enrica Calura; Paolo G. V. Martini; Chiara Romualdi (Nucleic Acids Res., 2013)

timeClip: pathway analysis for time course data without replicates. - Paolo G. V. Martini; Gabriele Sales; Enrica Calura; Stefano Cagnin; Monica Chiogna; Chiara Romualdi (BMC Bioinform., 2014)

Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data. - Fabrizio Serra; Chiara Romualdi; Federico Fogolari (J. Comput. Biol., 2016)

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. - Marco Moretto; Paolo Sonego; Nicolas Dierckxsens; Matteo Brilli; Luca Bianco; Daniela Ledezma-Tejeida; Socorro Gama-Castro; Marco Galardini; Chiara Romualdi; Kris Laukens; Julio Collado-Vides; Pieter Meysman; et al. (Nucleic Acids Res., 2016)

Cortical Thickness variability in Multiple Sclerosis: The role of lesion segmentation and filling. - Alessandro Palombit; Marco Castellaro; Massimiliano Calabrese; Chiara Romualdi; Francesca Benedetta Pizzini; Stefania Montemezzi; Enrico Grisan; Alessandra Bertoldo (ISBI, 2017)

simPATHy: a new method for simulating data from perturbed biological PATHways. - Elisa Salviato; Vera Djordjilovic; Monica Chiogna; Chiara Romualdi (Bioinform., 2017)

Searching for the Source of Difference: A Graphical Model Approach. - Vera Djordjilovic; Monica Chiogna; Chiara Romualdi; Elisa Salviato (CIBB, 2018)

metaGraphite-a new layer of pathway annotation to get metabolite networks. - Gabriele Sales; Enrica Calura; Chiara Romualdi (Bioinform., 2019)

SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways. - Elisa Salviato; Vera Djordjilovic; Monica Chiogna; Chiara Romualdi (PLoS Comput. Biol., 2019)

PsiNorm: a scalable normalization for single-cell RNA-seq data. - Matteo Borella; Graziano Martello; Davide Risso; Chiara Romualdi (Bioinform., 2021)

The Power of Alignment-Free Histogram-based Functions: a Comprehensive Genome Scale Experimental Analysis - Version 1. - Giuseppe Cattaneo; Umberto Ferraro Petrillo; Raffaele Giancarlo; Francesco Palini; Chiara Romualdi (CoRR, 2021)

NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data. - Federico Agostinis; Chiara Romualdi; Gabriele Sales; Davide Risso (Bioinform., 2022)

The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis. - Giuseppe Cattaneo; Umberto Ferraro Petrillo; Raffaele Giancarlo; Francesco Palini; Chiara Romualdi (Bioinform., 2022)

benchdamic: benchmarking of differential abundance methods for microbiome data. - Matteo Calgaro; Chiara Romualdi; Davide Risso; Nicola Vitulo (Bioinform., 2023)

A pan-cancer landscape of pathogenic somatic copy number variations. - Tommaso Becchi; Luca Beltrame; Laura Mannarino; Enrica Calura; Sergio Marchini; Chiara Romualdi (J. Biomed. Informatics, 2023)

SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline. - Sara Potente; Diego Boscarino; Dino Paladin; Sergio Marchini; Luca Beltrame; Chiara Romualdi (Briefings Bioinform., 2024)