Chiara Romualdi

发表

timeClip: pathway analysis for time course data without replicates

Paolo G. V. Martini, Gabriele Sales, Enrica Calura, 2014, BMC Bioinformatics.

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices

Stefano Toppo, Giorgio Valle, Chiara Romualdi, 2002, Bioinform..

A modified LOESS normalization applied to microRNA arrays: a comparative evaluation

Monica Chiogna, Chiara Romualdi, Davide Risso, 2009, Bioinform..

Cortical Thickness variability in Multiple Sclerosis: The role of lesion segmentation and filling

Alessandra Bertoldo, Chiara Romualdi, Enrico Grisan, 2017, 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017).

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data

Chiara Romualdi, Davide Risso, Matteo Calgaro, 2020, Genome Biology.

SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways

Monica Chiogna, Chiara Romualdi, Elisa Salviato, 2019, PLoS Comput. Biol..

Along signal paths: an empirical gene set approach exploiting pathway topology

Monica Chiogna, Chiara Romualdi, Paolo Martini, 2012, Nucleic acids research.

simPATHy: a new method for simulating data from perturbed biological PATHways

Monica Chiogna, Chiara Romualdi, Elisa Salviato, 2016, Bioinform..

parmigene - a parallel R package for mutual information estimation and gene network reconstruction

Gabriele Sales, Chiara Romualdi, C. Romualdi, 2011, Bioinform..

metaGraphite–a new layer of pathway annotation to get metabolite networks

Gabriele Sales, Enrica Calura, Chiara Romualdi, 2018, Bioinform..

Graphical modeling for gene set analysis: A critical appraisal

Monica Chiogna, Chiara Romualdi, Vera Djordjilović, 2015, Biometrical journal. Biometrische Zeitschrift.

BIOINFORMATICS ORIGINAL PAPER Sequence analysis RAP: a new computer program for de novo identification of repeated sequences in whole genomes

Giorgio Valle, Chiara Romualdi, Nicola Cannata, 2004 .

Gene set analysis exploiting the topology of a pathway

Monica Chiogna, Chiara Romualdi, Maria Sofia Massa, 2010, BMC Systems Biology.

A comparison on effects of normalisations in the detection of differentially expressed genes

Monica Chiogna, Chiara Romualdi, Davide Risso, 2009, BMC Bioinformatics.

Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data

Chiara Romualdi, Federico Fogolari, Fabrizio Serra, 2016, J. Comput. Biol..

Graphite Web: web tool for gene set analysis exploiting pathway topology

Paolo G. V. Martini, Gabriele Sales, Enrica Calura, 2013, Nucleic Acids Res..

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, Gabriele Sales, Stefano Cagnin, 2011, BMC Bioinformatics.

A global gene evolution analysis on Vibrionaceae family using phylogenetic profile

Giorgio Valle, Chiara Romualdi, Nicola Vitulo, 2007, BMC Bioinformatics.

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses

Chiara Romualdi, Luca Bianco, Julio Collado-Vides, 2015, Nucleic Acids Res..

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts

Paolo Fontana, Stefano Toppo, Giorgio Valle, 2003, Bioinform..

MAGIA2: from miRNA and genes expression data integrative analysis to microRNA–transcription factor mixed regulatory circuits (2012 update)

Gabriele Sales, Chiara Romualdi, Andrea Bisognin, 2012, Nucleic Acids Res..

A-MADMAN: Annotation-based microarray data meta-analysis tool

Chiara Romualdi, Davide Risso, Silvio Bicciato, 2009, BMC Bioinformatics.

MAGIA, a web-based tool for miRNA and Genes Integrated Analysis

Gabriele Sales, Chiara Romualdi, Andrea Bisognin, 2010, Nucleic Acids Res..

MIDAW: a web tool for statistical analysis of microarray data

Chiara Romualdi, Nicola Vitulo, Gerolamo Lanfranchi, 2005, Nucleic Acids Res..

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

Enrica Calura, Chiara Romualdi, Duccio Cavalieri, 2011, Bioinform..

Morphology and evolution of cortical lesions in multiple sclerosis. A longitudinal MRI study

Marco Rovaris, Massimo Filippi, Chiara Romualdi, 2008, NeuroImage.

Differential expression of genes coding for ribosomal proteins in different human tissues

Chiara Romualdi, Stefania Bortoluzzi, Gian Antonio Danieli, 2001, Bioinform..

graphite - a Bioconductor package to convert pathway topology to gene network

Gabriele Sales, Enrica Calura, Chiara Romualdi, 2012, BMC Bioinformatics.

Correlation between gene expression and clinical data through linear and nonlinear principal components analyses: muscular dystrophies as case studies.

Alessandro Giuliani, Chiara Romualdi, Romualdo Benigni, 2009, Omics : a journal of integrative biology.

The Power of Alignment-Free Histogram-based Functions: a Comprehensive Genome Scale Experimental Analysis - Version 1 pdf

Umberto Ferraro Petrillo, Giuseppe Cattaneo, Raffaele Giancarlo, 2021, ArXiv.

PsiNorm: a scalable normalization for single-cell RNA-seq data

Chiara Romualdi, Davide Risso, Graziano Martello, 2021, Bioinform..

The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis

Giuseppe Cattaneo, Raffaele Giancarlo, Chiara Romualdi, 2021, Bioinform..

Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration.

Chiara Romualdi, Barbara Celegato, G. Lanfranchi, 2003, Nucleic acids research.

Parallel protein and transcript profiles of FSHD patient muscles correlate to the D4Z4 arrangement and reveal a common impairment of slow to fast fibre differentiation and a general deregulation of MyoD‐dependent genes

Chiara Romualdi, Cecilia Gelfi, Mario Pescatori, 2006, Proteomics.

Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: a retrospective study of two independent tumour tissue collections.

Enrica Calura, Chiara Romualdi, Duccio Cavalieri, 2011, The Lancet. Oncology.

Expression profiling characterization of laminin α-2 positive MDC

Chiara Romualdi, Marina Fanin, Milena Bellin, 2006 .

Gene expression profiling identifies potential relevant genes in alveolar rhabdomyosarcoma pathogenesis and discriminates PAX3‐FKHR positive and negative tumors

Cesare Furlanello, Chiara Romualdi, Giuseppe Jurman, 2006, International journal of cancer.

Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles

Enrica Calura, Chiara Romualdi, Paolo Martini, 2014, Nucleic acids research.

Resistance to platinum-based chemotherapy is associated with epithelial to mesenchymal transition in epithelial ovarian cancer.

Chiara Romualdi, Duccio Cavalieri, Alberto Zambelli, 2013, European journal of cancer.

Pattern recognition in gene expression profiling using DNA array: a comparative study of different statistical methods applied to cancer classification.

Stefano Toppo, Giorgio Valle, Chiara Romualdi, 2003, Human molecular genetics.

Magnetic resonance evidence of cerebellar cortical pathology in multiple sclerosis

Chiara Romualdi, Massimiliano Calabrese, Francesca Rinaldi, 2009, Journal of Neurology, Neurosurgery & Psychiatry.

IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments.

Chiara Romualdi, Stefania Bortoluzzi, Gian Antonio Danieli, 2003, Physiological genomics.

Circulating Cell-Free DNA in Dogs with Mammary Tumors: Short and Long Fragments and Integrity Index

Chiara Romualdi, Chiara Bedin, Marco Agostini, 2017, PloS one.

miR148b is a major coordinator of breast cancer progression in a relapse‐associated microRNA signature by targeting ITGA5, ROCK1, PIK3CA, NRAS, and CSF1

Chiara Romualdi, Francesca Orso, Daniela Taverna, 2013, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Analysis of Differential miRNA Expression in Primary Tumor and Stroma of Colorectal Cancer Patients

Enrica Calura, Chiara Romualdi, Giancarlo Troncone, 2014, BioMed research international.

A leukemia-enriched cDNA microarray platform identifies new transcripts with relevance to the biology of pediatric acute lymphoblastic leukemia.

Chiara Romualdi, Nicola Vitulo, Giuseppe Basso, 2005, Haematologica.

Detection of cortical inflammatory lesions by double inversion recovery magnetic resonance imaging in patients with multiple sclerosis.

Chiara Romualdi, Massimiliano Calabrese, Paolo Gallo, 2007, Archives of neurology.

Novel genes, possibly relevant for molecular diagnosis or therapy of human rhabdomyosarcoma, detected by genomic expression profiling.

Chiara Romualdi, Stefania Bortoluzzi, Gian Antonio Danieli, 2005, Gene.

Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System

Enrica Calura, Chiara Romualdi, Paolo Martini, 2013, International journal of molecular sciences.

The changing clinical course of multiple sclerosis: A matter of gray matter

Chiara Romualdi, Massimiliano Calabrese, Francesca Rinaldi, 2013, Annals of neurology.

Cortical atrophy is relevant in multiple sclerosis at clinical onset

Chiara Romualdi, Bruce Fischl, Massimiliano Calabrese, 2007, Journal of Neurology.

Characterizing genomic alterations in cancer by complementary functional associations

Gabriela Alexe, Chiara Romualdi, Pablo Tamayo, 2016, Nature Biotechnology.

Gene expression profiling in dysferlinopathies using a dedicated muscle microarray.

Giorgio Valle, Chiara Romualdi, Marina Fanin, 2002, Human molecular genetics.