C. Romualdi

Latest

• A comprehensive investigation of histotype-specific microRNA and their variants in Stage I epithelial ovarian cancers
• Defective excitation-contraction coupling and mitochondrial respiration precede mitochondrial Ca2+ accumulation in spinobulbar muscular atrophy skeletal muscle
• Genome-wide profiling of patient-derived glioblastoma stem-like cells reveals recurrent genetic and transcriptomic signatures associated with brain tumors
• Spatial compartmentalization of signaling imparts source-specific functions on secreted factors
• A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes
• BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes
• Copy number alterations in stage I epithelial ovarian cancer highlight three genomic patterns associated with prognosis
• Detecting differentially expressed circular RNAs from multiple quantification methods using a generalized linear mixed model
• Hydrogen peroxide induced by nerve injury promotes axon regeneration via connective tissue growth factor
• miRNA bioinformatics and pathway analysis
• NewWave: A scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data
• PsiNorm: a scalable normalization for single-cell RNA-seq data
• The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis
• Zebrafish Mutant Lines Reveal the Interplay between nr3c1 and nr3c2 in the GC-Dependent Regulation of Gene Transcription
• A novel prognostic score to assess the risk of progression in relapsing−remitting multiple sclerosis patients
• Circulating mir-185-5p as a potential biomarker for arrhythmogenic right ventricular cardiomyopathy
• Comprehensive profiling of hypoxia-related mirnas identifies mir-23a-3p overexpression as a marker of platinum resistance and poor prognosis in high-grade serous ovarian cancer
• Genome-wide copy-number alterations in circulating tumor DNA as a novel biomarker for patients with high-grade serous ovarian cancer
• Genome-wide study of salivary miRNAs identifies miR-423-5p as promising diagnostic and prognostic biomarker in oral squamous cell carcinoma
• MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary
• MyoData: An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle
• Regional and temporal heterogeneity of epithelial ovarian cancer tumor biopsies: implications for therapeutic strategies
• A TGF-β associated genetic score to define prognosis and platinum sensitivity in advanced epithelial ovarian cancer
• Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
• Editorial: Multi-omic Data Integration in Oncology
• Expression profiles of PRKG1, SDF2L1 and PPP1R12A are predictive and prognostic factors for therapy response and survival in high-grade serous ovarian cancer
• Microbiota changes induced by microencapsulated sodium butyrate in patients with inflammatory bowel disease
• Microbiota of the therapeutic Euganean thermal muds with a focus on the main cyanobacteria species
• Pharmacogenetic score predicts overall survival, progression-free survival and platinum sensitivity in ovarian cancer
• Searching for the Source of Difference: A Graphical Model Approach
• Simulating gene silencing through intervention analysis
• Targeting p53 and histone methyltransferases restores exhausted CD8+ T cells in HCV infection
• The CSF Profile Linked to Cortical Damage Predicts Multiple Sclerosis Activity
• Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics
• FXYD5 (Dysadherin) upregulation predicts shorter survival and reveals platinum resistance in high-grade serous ovarian cancer patients
• Increased NK Cell Count in Multiple Sclerosis Patients Treated With Dimethyl Fumarate: A 2-Year Longitudinal Study
• Individual Radiosensitivity in Oncological Patients: Linking Adverse Normal Tissue Reactions and Genetic Features
• Meta Graphite-a new layer of pathway annotation to get metabolite networks
• MOSClip: multi-omic and survival pathway analysis for the identification of survival associated gene and modules
• Multisite analysis of high-grade serous epithelial ovarian cancers identifies genomic regions of focal and recurrent copy number alteration in 3q26.2 and 8q24.3
• Rs4143815-PDL1, a new potential immunogenetic biomarker of biochemical recurrence in locally advanced prostate cancer after radiotherapy
• Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba)
• Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network
• SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways
• Transcriptional characterization of stage i epithelial ovarian cancer: A multicentric study
• 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 process related to tumorigenesis
• Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle
• A systems biology approach to investigate the mechanism of action of trabectedin in a model of myelomonocytic leukemia
• Changes in Accident & Emergency Visits and Return Visits in Relation to the Enforcement of Daylight Saving Time and Photoperiod
• Inflammatory intrathecal profiles and cortical damage in multiple sclerosis
• Paradoxical GH Increase during OGTT Is Associated with First-Generation Somatostatin Analog Responsiveness in Acromegaly
• The cortical damage, early relapses, and onset of the progressive phase in multiple sclerosis
• The effect of fingolimod on focal and diffuse grey matter damage in active MS patients
• Analysis of potential factors affecting allografts contamination at retrieval
• Circulating cell-free DNA in dogs with mammary tumors: Short and long fragments and integrity index
• Circulating miRNA landscape identifies miR-1246 as promising diagnostic biomarker in high-grade serous ovarian carcinoma: A validation across two independent cohorts
• Cognitive impairment predicts disability progression and cortical thinning in MS: An 8-year study
• Cortical Thickness variability in Multiple Sclerosis: The role of lesion segmentation and filling
• KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)
• LINE-1 hypomethylation is associated to specific clinico-pathological features in Stage I non-small cell lung cancer
• LncRNAs as novel indicators of patients' prognosis in stage i epithelial ovarian cancer: A retrospective and multicentric study
• NELL1, whose high expression correlates with negative outcomes, has different methylation patterns in alveolar and embryonal rhabdomyosarcoma
• SimPATHy: A new method for simulating data from perturbed biological PATHways
• A data-driven network model of primary myelofibrosis: Transcriptional and post-transcriptional alterations in CD34+ cells
• A prognostic regulatory pathway in stage I epithelial ovarian cancer: New hints for the poor prognosis assessment
• Antimicrobial use and microbiological testing in district general hospital ICUs of the Veneto region of north-east Italy
• Characterizing genomic alterations in cancer by complementary functional associations
• COLOMBOS v3.0: Leveraging gene expression compendia for cross-species analyses
• Disentangling the microRNA regulatory milieu in multiple myeloma: Integrative genomics analysis outlines mixed miRNATF circuits and pathway-derived networks modulated in t(4;14) patients
• Global DNA methylation profiling uncovers distinct methylation patterns of protocadherin alpha4 in metastatic and non-metastatic rhabdomyosarcoma
• 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
• Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data
• Usefulness of the Total Thrombus-Formation Analysis System (T-TAS) in the diagnosis and characterization of von Willebrand disease
• A founder MYBPC3 mutation results in HCM with a high risk of sudden death after the fourth decade of life
• Aberrant DNA methylation profiles of inherited and sporadic colorectal cancer
• Beneficial bacteria isolated from grapevine inner tissues shape arabidopsis Thaliana roots
• Graphical modeling for gene set analysis: A critical appraisal
• Microsatellite unstable gastrointestinal neuroendocrine carcinomas: A new clinicopathologic entity
• Profiling cancer gene mutations in longitudinal epithelial ovarian cancer biopsies by targeted next-generation sequencing: A retrospective study
• Pyrosequencing and de novo assembly of Antarctic krill (Euphausia superba) transcriptome to study the adaptability of krill to climate-induced environmental changes
• Regional distribution and evolution of gray matter damage in different populations of multiple sclerosis patients
• The self-morningness/eveningness (Self-ME): An extremely concise and totally subjective assessment of diurnal preference
• An aberrant microRNA signature in childhood T-cell lymphoblastic lymphoma affecting CDKN1B expression, NOTCH1 and growth factor signaling pathways
• Analysis of differential miRNA expression in primary tumor and stroma of colorectal cancer patients
• Integration analysis of MicroRNA and mRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity
• Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature
• MicroRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition
• Prognostic relevance of aberrant DNA methylation in G1 and G2 pancreatic neuroendocrine tumors
• TimeClip: Pathway analysis for time course data without replicates
• Tissue-specific expression and regulatory networks of pig microRNAome
• Wiring miRNAs to pathways: A topological approach to integrate miRNA and mRNA expression profiles
• Along signal paths: An empirical gene set approach exploiting pathway topology
• Graphite Web: Web tool for gene set analysis exploiting pathway topology.
• Low degree of cortical pathology is associated with benign course of multiple sclerosis
• miR148b is a major coordinator of breast cancer progression in a relapse-associated microRNA signature by targeting ITGA5, ROCK1, PIK3CA, NRAS, and CSF1
• MiRNA landscape in stage i epithelial ovarian cancer defines the histotype specificities
• Resistance to platinum-based chemotherapy is associated with epithelial to mesenchymal transition in epithelial ovarian cancer
• Revertant Fibers in the mdx Murine Model of Duchenne Muscular Dystrophy: An Age- and Muscle-Related Reappraisal
• Synthesis of mitochondrial DNA precursors during myogenesis, an analysis in purified C2C12 myotubes
• Systems biology approach to the dissection of the complexity of regulatory networks in the S. scrofa cardiocirculatory system
• The changing clinical course of multiple sclerosis: A matter of gray matter
• A systems biology approach to characterize the regulatory networks leading to trabectedin resistance in an in vitro model of myxoid liposarcoma
• Consequences of heat shock protein 72 (Hsp72) expression and activity on stress-induced apoptosis in CD30 NPM-ALK anaplastic large-cell lymphomas
• Cortical lesion load associates with progression of disability in multiple sclerosis
• Cortical pathology in multiple sclerosis patients with epilepsy: A 3 year longitudinal study
• Genotype-specific mutations in the polymerase gene of hepatitis B virus potentially associated with resistance to oral antiviral therapy
• Graphite - a Bioconductor package to convert pathway topology to gene network
• Gray matter pathology in MS: A 3-year longitudinal study in a pediatric population
• MAGIA2: From miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update)
• Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: A retrospective study of two independent tumour tissue collections
• Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: New insights into anti-mineralogenic effect of vanadate
• High IGFBP2 expression correlates with tumor severity in pediatric rhabdomyosarcoma
• Impact of host genes and strand selection on miRNA and miRNA* expression
• Parmigene-a parallel R package for mutual information estimation and gene network reconstruction
• Statistical Test of Expression Pattern (STEPath): A new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies
• The biological Connection Markup Language: A SBGN-compliant format for visualization, filtering and analysis of biological pathways
• Gene set analysis exploiting the topology of a pathway
• Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection
• Magia, a web-based tool for miRNA and genes integrated analysis
• Magnetic resonance evidence of cerebellar cortical pathology in multiple sclerosis
• 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
• Pericentriolar material analyses in normal esophageal mucosa, Barrett's metaplasia and adenocarcinoma
• Widespread cortical thinning characterizes patients with MS with mild cognitive impairment
• A comparison on effects of normalisations in the detection of differentially expressed genes
• A modified LOESS normalization applied to microRNA arrays: A comparative evaluation
• A-MADMAN: Annotation-based microarray data meta-analysis tool
• Correlation between gene expression and clinical data through linear and nonlinear principal components analyses: Muscular dystrophies as case studies
• Cortical lesions in primary progressive multiple sclerosis: A 2-year longitudinal MR study
• Evidence for relative cortical sparing in benign multiple sclerosis: A longitudinal magnetic resonance imaging study
• Expression profiling of skeletal muscle in young bulls treated with steroidal growth promoters
• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis
• Selection of multipotent cells and enhanced muscle reconstruction by myogenic macrophage-secreted factors
• Statistical tools for gene expression analysis and systems biology and related web resources
• Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata)
• Meta-analysis of expression signatures of muscle atrophy: Gene interaction networks in early and late stages
• Morphology and evolution of cortical lesions in multiple sclerosis. A longitudinal MRI study
• Polymorphisms in von Willebrand factor gene promoter influence the glucocorticoid-induced increase in von Willebrand factor: The lesson learned from Cushing syndrome
• Ripening and genotype control stilbene accumulation in healthy grapes
• A global gene evolution analysis on Vibrionaceae family using phylogenetic profile
• Cortical atrophy is relevant in multiple sclerosis at clinical onset
• Detection of cortical inflammatory lesions by double inversion recovery magnetic resonance imaging in patients with multiple sclerosis
• Smokers and passive smokers gene expression profiles: Correlation with the DNA oxidation damage
• Defining the gene expression signature of rhabdomyosarcoma by meta-analysis
• Denervation in murine fast-twitch muscle: Short-term physiological changes and temporal expression profiling
• Development of mussel mRNA profiling: Can gene expression trends reveal coastal water pollution?
• Differential gene expression profiling in genetic and multifactorial cardiovascular diseases
• Expression analysis of androgen-responsive genes in the prostate of veal calves treated with anabolic hormones
• Expression profiling characterization of laminin α-2 positive MDC
• Gene expression profiling identifies potential relevant genes in alveolar rhabdomyosarcoma pathogenesis and discriminates PAX3-FKHR positive and negative tumors
• Longitudinal analysis of immune cell phenotypes in early stage multiple sclerosis: Distinctive patterns characterize MRI-active patients
• 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
• A leukemia-enriched cDNA microarray platform identifies new transcripts with relevance to the biology of pediatric acute lymphoblastic leukemia
• Life at depth: Photobacterium profundum genome sequence and expression analysis
• MIDAW: A web tool for statistical analysis of microarray data
• Novel genes, possibly relevant for molecular diagnosis or therapy of human rhabdomyosarcoma, detected by genomic expression profiling
• RAP: A new computer program for de novo identification of repeated sequences in whole genomes
• Territorial male gobies respond aggressively to sneakers but do not adjust their sperm expenditure
• Altered glucose metabolism and proteolysis in pancreatic cancer cell conditioned myoblasts: Searching for a gene expression pattern with a microarray analysis of 5000 skeletal muscle genes
• Disease genes and intracellular protein networks
• Application of a cDNA micoarray for the analysis of muscular dystrophies and childhood leukemias
• IDEG6: A web tool for detection of differentially expressed genes in multiple tag sampling experiments
• Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration.
• Pattern recognition in gene expression profiling using DNA array: A comparative study of different statistical methods applied to cancer classification
• TRAIT (TRAnscript Integrated Table): A knowledgebase of human skeletal muscle transcripts
• Differential expression of genes coding of ribosomal proteins in different human tissues
• Gene expression profiling in skeletal muscle using a dedicated microarray
• Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms
• Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices
• Detecting differentially expressed genes in multiple tag sampling experiments: Comparative evaluation of statistical tests
• Gene flow and genetic diversity: A comparison of freshwater bryozoan populations in Europe and North America
• The human adult skeletal muscle transcriptional profile reconstructed by a novel computational approach
• Probability of conception on different days of the menstrual cycle: An ongoing exercise