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Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data

BMC bioinformatics, 2018-01, Vol.19 (1), p.1-1, Article 1

2018

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An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment

BMC bioinformatics, 2022-05, Vol.23 (1), p.207-207, Article 207

2022

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An equivalence approach to the integrative analysis of feature lists

BMC bioinformatics, 2019-08, Vol.20 (1), p.441-13, Article 441

2019

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Statistical Analysis of Microarray Data

Methods in molecular biology (Clifton, N.J.), 2019-01, Vol.1986, p.87

2019

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Analysis of the cumulative changes in Graves’ disease thyroid glands points to IFN signature, plasmacytoid DCs and alternatively activated macrophages as chronicity determining factors

Journal of autoimmunity, 2011-05, Vol.36 (3), p.189-200

2011

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The fobitools framework: the first steps towards food enrichment analysis

Bioinformatics (Oxford, England), 2021-11, Vol.37 (21), p.3969-3971

2021

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Plasma metabolomic profiles of plant-based dietary indices reveal potential pathways for metabolic syndrome associations

Atherosclerosis, 2023-10, Vol.382, p.117285-117285, Article 117285

2023

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FOBI: an ontology to represent food intake data and associate it with metabolomic data

Database : the journal of biological databases and curation, 2020, Vol.2020

2020

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Comparative transcriptomic profile of tolerogenic dendritic cells differentiated with vitamin D3, dexamethasone and rapamycin

Scientific reports, 2018-10, Vol.8 (1), p.14985-13, Article 14985

2018

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Food and Microbiota Metabolites Associate with Cognitive Decline in Older Subjects: A 12‐Year Prospective Study

Molecular nutrition & food research, 2021-12, Vol.65 (23), p.e2100606-n/a

2021

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Circulating SOD2 Is a Candidate Response Biomarker for Neoadjuvant Therapy in Breast Cancer

Cancers, 2022-08, Vol.14 (16), p.3858

2022

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A Mediterranean Diet‐Based Metabolomic Score and Cognitive Decline in Older Adults: A Case–Control Analysis Nested within the Three‐City Cohort Study

Molecular nutrition & food research, 2024-07, Vol.68 (13), p.e2300271-n/a

2024

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Aberrant epigenome in iPSC‐derived dopaminergic neurons from Parkinson's disease patients

EMBO molecular medicine, 2015-12, Vol.7 (12), p.1529-1546

2015

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Brain transcriptomic profiling in idiopathic and LRRK2 -associated Parkinson's disease

Brain research, 2012-07, Vol.1466, p.152-157

2012

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Transcriptomics: mRNA and alternative splicing

Journal of neuroimmunology, 2012-07, Vol.248 (1), p.23-31

2012

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POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009148-e1009148

2021

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Methylation regulation of Antiviral host factors, Interferon Stimulated Genes (ISGs) and T-cell responses associated with natural HIV control

PLoS pathogens, 2020-08, Vol.16 (8), p.e1008678

2020

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Metabolic Signature of a Functional High-Catechin Tea after Acute and Sustained Consumption in Healthy Volunteers through 1H NMR Based Metabolomics Analysis of Urine

Journal of agricultural and food chemistry, 2019-03, Vol.67 (11), p.3118-3124

2019

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Dietary Sources of Anthocyanins and Their Association with Metabolome Biomarkers and Cardiometabolic Risk Factors in an Observational Study

Nutrients, 2023-02, Vol.15 (5), p.1208

2023

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Apolipoprotein E and sex modulate fatty acid metabolism in a prospective observational study of cognitive decline

Alzheimer's research & therapy, 2022-01, Vol.14 (1), p.1-12, Article 1

2022

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Hypothesis testing approaches to the exon prediction problem

Bioinformatics, 2006-12, Vol.22 (24), p.3003-3008

2006

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DNA Microarrays Technology: Overview and Current Status

Fundamentals of Advanced Omics Technologies: from Genes to Metabolites, 2014, Vol.63

2014

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Assessing Adherence to Healthy Dietary Habits Through the Urinary Food Metabolome: Results From a European Two-Center Study

Frontiers in nutrition (Lausanne), 2022-06, Vol.9, p.880770-880770

2022

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Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data

An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment

An equivalence approach to the integrative analysis of feature lists

Statistical Analysis of Microarray Data

Analysis of the cumulative changes in Graves’ disease thyroid glands points to IFN signature, plasmacytoid DCs and alternatively activated macrophages as chronicity determining factors

The fobitools framework: the first steps towards food enrichment analysis

Plasma metabolomic profiles of plant-based dietary indices reveal potential pathways for metabolic syndrome associations

FOBI: an ontology to represent food intake data and associate it with metabolomic data

Comparative transcriptomic profile of tolerogenic dendritic cells differentiated with vitamin D3, dexamethasone and rapamycin

Food and Microbiota Metabolites Associate with Cognitive Decline in Older Subjects: A 12‐Year Prospective Study

Circulating SOD2 Is a Candidate Response Biomarker for Neoadjuvant Therapy in Breast Cancer

A Mediterranean Diet‐Based Metabolomic Score and Cognitive Decline in Older Adults: A Case–Control Analysis Nested within the Three‐City Cohort Study

Aberrant epigenome in iPSC‐derived dopaminergic neurons from Parkinson's disease patients

Brain transcriptomic profiling in idiopathic and LRRK2 -associated Parkinson's disease

Transcriptomics: mRNA and alternative splicing

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

Methylation regulation of Antiviral host factors, Interferon Stimulated Genes (ISGs) and T-cell responses associated with natural HIV control

Metabolic Signature of a Functional High-Catechin Tea after Acute and Sustained Consumption in Healthy Volunteers through 1H NMR Based Metabolomics Analysis of Urine

Exploration of the Gut-Brain Axis through Metabolomics Identifies Serum Propionic Acid Associated with Higher Cognitive Decline in Older Persons

The serum metabolome mediates the concert of diet, exercise, and neurogenesis, determining the risk for cognitive decline and dementia

Dietary Sources of Anthocyanins and Their Association with Metabolome Biomarkers and Cardiometabolic Risk Factors in an Observational Study

Apolipoprotein E and sex modulate fatty acid metabolism in a prospective observational study of cognitive decline

Hypothesis testing approaches to the exon prediction problem

DNA Microarrays Technology: Overview and Current Status

Assessing Adherence to Healthy Dietary Habits Through the Urinary Food Metabolome: Results From a European Two-Center Study

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