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List of works by Chiara Romualdi

<i>NewWave</i>: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data

scientific article published in 2022

A data-driven network model of primary myelofibrosis: transcriptional and post-transcriptional alterations in CD34+ cells.

scientific article

A global gene evolution analysis on Vibrionaceae family using phylogenetic profile.

scientific article

A prognostic regulatory pathway in stage I epithelial ovarian cancer: new hints for the poor prognosis assessment.

scientific article

A systems biology approach to characterize the regulatory networks leading to trabectedin resistance in an in vitro model of myxoid liposarcoma

scientific article

A systems biology approach to investigate the mechanism of action of trabectedin in a model of myelomonocytic leukemia

scientific article published on 13 December 2016

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

scientific article published on 29 June 2009

Aberrant DNA methylation profiles of inherited and sporadic colorectal cancer.

scientific article

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

scientific article published on 21 September 2012

An aberrant microRNA signature in childhood T-cell lymphoblastic lymphoma affecting CDKN1B expression, NOTCH1 and growth factor signaling pathways.

scientific article

Analysis of differential miRNA expression in primary tumor and stroma of colorectal cancer patients.

scientific article

Analysis of potential factors affecting allografts contamination at retrieval.

scientific article published on 17 October 2017

Anticoagulant therapy for venous thromboembolism during pregnancy: a systematic review and a meta-analysis of the literature: a reply to a rebuttal.

scientific article

Antimicrobial use and microbiological testing in district general hospital ICUs of the Veneto region of north-east Italy

scientific article published on 15 June 2016

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

scientific article published on 21 February 2011

Beneficial Bacteria Isolated from Grapevine Inner Tissues Shape Arabidopsis thaliana Roots

scientific article published on 16 October 2015

BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes

scientific article published on 17 February 2022

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

scientific article published on 19 November 2015

Changes in Accident & Emergency Visits and Return Visits in Relation to the Enforcement of Daylight Saving Time and Photoperiod

scientific article published on 30 July 2018

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

scientific article

Circulating miRNA landscape identifies miR-1246 as promising diagnostic biomarker in high-grade serous ovarian carcinoma: A validation across two independent cohorts

scientific article published on 22 December 2016

Cognitive impairment predicts disability progression and cortical thinning in MS: An 8-year study

scientific article

Consequences of heat shock protein 72 (Hsp72) expression and activity on stress-induced apoptosis in CD30+ NPM-ALK+ anaplastic large-cell lymphomas.

scientific article published on 6 January 2012

Cortical atrophy is relevant in multiple sclerosis at clinical onset.

scientific article published on 14 March 2007

Cortical lesion load associates with progression of disability in multiple sclerosis.

scientific article published in October 2012

Cortical pathology in multiple sclerosis patients with epilepsy: a 3 year longitudinal study.

scientific article published on 2 September 2011

Defining the gene expression signature of rhabdomyosarcoma by meta-analysis.

scientific article

Denervation in murine fast-twitch muscle: short-term physiological changes and temporal expression profiling

scientific article published on 13 March 2006

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

scientific article

Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata).

scientific article

Development of mussel mRNA profiling: Can gene expression trends reveal coastal water pollution?

scientific article published on 28 September 2006

Differential gene expression profiling in genetic and multifactorial cardiovascular diseases.

scientific article published on 3 October 2006

Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics

scientific article published on 31 December 2018

Disentangling the microRNA regulatory milieu in multiple myeloma: integrative genomics analysis outlines mixed miRNA-TF circuits and pathway-derived networks modulated in t(4;14) patients.

scientific article

Evidence for relative cortical sparing in benign multiple sclerosis: a longitudinal magnetic resonance imaging study.

scientific article published on 28 August 2008

Expression profiling characterization of laminin α-2 positive MDC

scientific article published on 25 September 2006

Expression profiling of skeletal muscle in young bulls treated with steroidal growth promoters.

scientific article

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

scientific article

Gene expression profiling identifies potential relevant genes in alveolar rhabdomyosarcoma pathogenesis and discriminatesPAX3-FKHR positive and negative tumors

article

Gene expression profiling in dysferlinopathies using a dedicated muscle microarray.

scientific article

Gene flow and genetic diversity: a comparison of freshwater bryozoan populations in Europe and North America.

scientific article

Gene set analysis exploiting the topology of a pathway.

scientific article

Genotype-specific mutations in the polymerase gene of hepatitis B virus potentially associated with resistance to oral antiviral therapy ⬇️

scientific article published on September 28, 2012

Global DNA methylation profiling uncovers distinct methylation patterns of protocadherin alpha4 in metastatic and non-metastatic rhabdomyosarcoma.

scientific article

Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate

scientific article

Graphical modeling for gene set analysis: A critical appraisal.

scientific article

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

scientific article published on May 10, 2013

Gray Matter Pathology in MS: A 3-Year Longitudinal Study in a Pediatric Population ⬇️

scientific article published on March 15, 2012

High IGFBP2 expression correlates with tumor severity in pediatric rhabdomyosarcoma

scientific article

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

scientific article published on 15 January 2003

Identification of high-grade serous ovarian cancer miRNA species associated with survival and drug response in patients receiving neoadjuvant chemotherapy: a retrospective longitudinal analysis using matched tumor biopsies.

scientific article published on 17 January 2016

Impact of host genes and strand selection on miRNA and miRNA* expression.

scientific article

Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.

scientific article published on 13 January 2010

Inflammatory intrathecal profiles and cortical damage in multiple sclerosis

scientific article published on 8 March 2018

Integration analysis of microRNA and mRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity.

scientific article

KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba).

scientific article

LINE-1 hypomethylation is associated to specific clinico-pathological features in Stage I non-small cell lung cancer

scientific article published on 6 March 2017

Life at Depth: Photobacterium profundum Genome Sequence and Expression Analysis

scientific article (publication date: 4 March 2005)

Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature

scientific article

Longitudinal analysis of immune cell phenotypes in early stage multiple sclerosis: distinctive patterns characterize MRI-active patients.

scientific article published in August 2006

Low degree of cortical pathology is associated with benign course of multiple sclerosis.

scientific article published on 15 October 2012

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

scientific article published on 19 May 2010

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

scientific article

MIDAW: a web tool for statistical analysis of microarray data

scientific article

MiRNA landscape in stage I epithelial ovarian cancer defines the histotype specificities.

scientific article published on 13 June 2013

Microbiota of the Therapeutic Euganean Thermal Muds with a Focus on the Main Cyanobacteria Species

scientific article published on 15 October 2020

Microsatellite (GT)(n) is part of the von Willebrand factor (VWF) promoter region that influences the glucocorticoid-induced increase in VWF in Cushing's syndrome

scientific article published on 13 February 2010

Microsatellite unstable gastrointestinal neuroendocrine carcinomas: a new clinicopathologic entity.

scientific article

NELL1, whose high expression correlates with negative outcomes, has different methylation patterns in alveolar and embryonal rhabdomyosarcoma

scientific article

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

scientific article published in March 2005

Paradoxical GH increase during OGTT is associated to first-generation somatostatin analogs responsiveness in acromegaly

scientific article published on 01 March 2019

Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms

scientific article (publication date: April 2002)

Pharmacogenetic score predicts overall survival, progression-free survival and platinum sensitivity in ovarian cancer

scientific article published on 08 September 2020

Polymorphisms in von Willebrand factor gene promoter influence the glucocorticoid-induced increase in von Willebrand factor: the lesson learned from Cushing syndrome.

scientific article published in January 2008

Probability of conception on different days of the menstrual cycle: an ongoing exercise

scientific article published on 01 June 1997

Profiling cancer gene mutations in longitudinal epithelial ovarian cancer biopsies by targeted next-generation sequencing: a retrospective study.

scientific article published on 6 April 2015

Prognostic relevance of aberrant DNA methylation in g1 and g2 pancreatic neuroendocrine tumors

scientific article published on 05 July 2014

Pyrosequencing and de novo assembly of Antarctic krill (Euphausia superba) transcriptome to study the adaptability of krill to climate-induced environmental changes

scientific article

Regional Distribution and Evolution of Gray Matter Damage in Different Populations of Multiple Sclerosis Patients

scientific article published on 12 August 2015

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

article

Revertant fibers in the mdx murine model of Duchenne muscular dystrophy: an age- and muscle-related reappraisal

scientific article

Ripening and genotype control stilbene accumulation in healthy grapes.

scientific article

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

scientific article

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

scientific article published on 01 August 2002

Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network

scientific article published on 01 February 2019

Smokers and passive smokers gene expression profiles: Correlation with the DNA oxidation damage

article

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

scientific article published on 25 October 2019

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies.

scientific article

Synthesis of mitochondrial DNA precursors during myogenesis, an analysis in purified C2C12 myotubes.

scientific article

Systems biology approach to the dissection of the complexity of regulatory networks in the S. scrofa cardiocirculatory system

scientific article

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

scientific article published on March 2003

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

scientific article

The cortical damage, early relapses, and onset of the progressive phase in multiple sclerosis

scientific article published on 16 May 2018

The effect of fingolimod on focal and diffuse grey matter damage in active MS patients

scientific article published on 25 June 2018

The self-morningness/eveningness (Self-ME): An extremely concise and totally subjective assessment of diurnal preference

scientific article published on 9 October 2015

Tissue-specific expression and regulatory networks of pig microRNAome

scientific article

Transcriptional Characterization of Stage I Epithelial Ovarian Cancer: A Multicentric Study

scientific article published on 01 December 2019

Transcriptome Profiles of Human Visceral Adipocytes in Obesity and Colorectal Cancer Unravel the Effects of Body Mass Index and Polyunsaturated Fatty Acids on Genes and Biological Processes Related to Tumorigenesis

article

Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle

scientific article published on 01 March 2019

Usefulness of the Total Thrombus-Formation Analysis System (T-TAS) in the diagnosis and characterization of von Willebrand disease.

scientific article published on 13 June 2016

Widespread cortical thinning characterizes patients with MS with mild cognitive impairment.

scientific article published in January 2010

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

scientific article

Zebrafish Mutant Lines Reveal the Interplay between <i>nr3c1</i> and <i>nr3c2</i> in the GC-Dependent Regulation of Gene Transcription

scientific article published on 28 February 2022

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

scientific article

lncRNAs as Novel Indicators of Patients' Prognosis in Stage I Epithelial Ovarian Cancer: A Retrospective and Multicentric Study.

scientific article

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

scientific article published on 01 April 2019

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

scientific article published on 11 December 2012

microRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition.

scientific article published on January 2014

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

scientific article

rs4143815-PDL1, a New Potential Immunogenetic Biomarker of Biochemical Recurrence in Locally Advanced Prostate Cancer after Radiotherapy.

scientific article published on 27 April 2019

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

scientific article

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