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List of works by David Gomez-Cabrero

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

scientific article

A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions

scientific article

A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

scientific article

A survey of best practices for RNA-seq data analysis

scientific article

Abundance and diversity of resistomes differ between healthy human oral cavities and gut

scientific article published on 04 February 2020

An Introduction to Uncertainty in the Development of Computational Models of Biological Processes

article

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

scientific article published on 19 February 2013

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

scientific article

Assessing the consistency of public human tissue RNA-seq data sets

scientific article

Assessment of health status and program performance in patients on long-term oxygen therapy

scientific article published on 28 January 2015

Biomedical research in a Digital Health Framework

scientific article (publication date: 28 November 2014)

Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using Linked Self-Organizing Maps

article

Cesarean delivery and hematopoietic stem cell epigenetics in the newborn infant: implications for future health?

scientific article published on July 2014

ChainRank, a chain prioritisation method for contextualisation of biological networks

scientific article published on 5 January 2016

Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization

scientific article published on 06 November 2019

Chronic Obstructive Pulmonary Disease heterogeneity: challenges for health risk assessment, stratification and management

scientific article

Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression

scientific article

Comment on "Epigenetics in the pathogenesis of RA".

scientific article

Comparison of the prevalence and distribution of human papillomavirus infection and cervical lesions between urban and native habitants of an Amazonian region of Peru

scientific article published on 6 August 2012

Computational Modeling Under Uncertainty: Challenges and Opportunities

Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction

scientific article

DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis.

scientific article

Data Integration: Towards Understanding Biological Complexity

Data integration in the era of omics: current and future challenges

scientific article

Distribution of human papillomavirus types in women from Valencia, Spain, with abnormal cytology.

scientific article published in March 2010

EULAR points to consider for the use of big data in rheumatic and musculoskeletal diseases

scientific article published on 22 June 2019

Editorial overview

Epigenetic Alterations Associated With Early Prenatal Dexamethasone Treatment

scientific article published on 12 December 2018

Epigenetic alterations in autoimmune disease

scientific article published on 23 November 2011

Erratum to: A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions

scientific article published on 27 July 2016

Erratum to: A survey of best practices for RNA-seq data analysis

scientific article published on 26 August 2016

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation

article

From Systems Understanding to Personalized Medicine: Lessons and Recommendations Based on a Multidisciplinary and Translational Analysis of COPD.

scientific article published on January 2016

From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration

scientific article

Functional and transcriptomic analysis of extracellular vesicles identifies calprotectin as a new prognostic marker in peripheral arterial disease (PAD)

scientific article published on 19 February 2020

Functional genomics analysis of vitamin D effects on CD4+ T cells in vivo in experimental autoimmune encephalomyelitis .

scientific article published on 14 February 2017

Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology

scientific article published on 23 August 2017

Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology

scientific article published on 01 December 2017

High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis

scientific article

Hypermethylation of MIR21 in CD4+ T cells from patients with relapsing-remitting multiple sclerosis associates with lower miRNA-21 levels and concomitant up-regulation of its target genes

scientific article published on August 2017

Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression

scientific article published on 8 January 2013

Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma

scientific article published on 03 February 2020

Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients

scientific article published on 8 January 2018

Implementation of the CDC translational informatics platform--from genetic variants to the national Swedish Rheumatology Quality Register

scientific article published on 2 April 2013

Importance of mitochondrial P(O2) in maximal O2 transport and utilization: a theoretical analysis

scientific article published on 5 September 2013

Introduction to Data Types in Epigenomics

Laboratory biomarkers and frailty: presentation of the FRAILOMIC initiative

scientific article published on 14 March 2015

List of Contributors

Methylome characterization of CD4+ T cells in multiple sclerosis — Establishing a role for miR-21 in autoimmune disease

scholarly article by Sabrina Ruhrmann et al published October 2014 in Journal of Neuroimmunology

Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition

scientific article

Network Biology Empowering Detection and Understanding of Interactions Between Genetic Factors in Development of Complex Phenotypes

article

Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients.

scientific article published on 20 February 2018

Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis.

scientific article

Neuroswarm: A Methodology to Explore the Constraints that Function Imposes on Simulation Parameters in Large-Scale Networks of Biological Neurons

Non-HLA genes PTPN22, CDK6 and PADI4 are associated with specific autoantibodies in HLA-defined subgroups of rheumatoid arthritis

scientific article published on 20 August 2014

Optimization in Biology Parameter Estimation and the Associated Optimization Problem

Oxygen pathway modeling estimates high reactive oxygen species production above the highest permanent human habitation

scientific article

ParkDB: a Parkinson's disease gene expression database

scientific article

Patterns of circulating fat-soluble vitamins and carotenoids and risk of frailty in four European cohorts of older adults.

scientific article

Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes

scientific article published on 15 November 2011

Predictive medicine: outcomes, challenges and opportunities in the Synergy-COPD project

scientific article

Prevalence and distribution of human papillomavirus findings in swab specimens from gynaecology clinics of the east coast of Spain

scientific article published in July 2010

Proposals for enhanced health risk assessment and stratification in an integrated care scenario

scientific article published on 15 April 2016

Public data and open source tools for multi-assay genomic investigation of disease

scientific article

Reconciling coherent oscillation with modulation of irregular spiking activity in selective attention: gamma-range synchronization between sensory and executive cortical areas

scientific article published on February 2010

Risk and temporal order of disease diagnosis of comorbidities in patients with COPD: a population health perspective.

scientific article

STATegra EMS: an Experiment Management System for complex next-generation omics experiments

scientific article

STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse

scientific article published on 31 October 2019

Serotonin regulates performance nonmonotonically in a spatial working memory network

scientific article

Sex influences eQTL effects of SLE and Sjögren's syndrome-associated genetic polymorphisms

scientific article published on 25 October 2017

Simulation environment and graphical visualization environment: a COPD use-case

scientific article

Software For The Integration Of Multi-Omics Experiments In Bioconductor

Software for the Integration of Multiomics Experiments in Bioconductor

scientific article

Synergy-COPD: a systems approach for understanding and managing chronic diseases

scientific article published on 28 November 2014

Systems Medicine: from molecular features and models to the clinic in COPD.

scientific article published on 28 November 2014

The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research

scientific article

The Multiple Sclerosis Genomic Map: Role of peripheral immune cells and resident microglia in susceptibility

scholarly article published 13 July 2017

The Travelling Salesman’s Problem: A self-adapting PSO-ACS algorithm

The salivary proteome reflects some traits of dietary habits in diabetic and non-diabetic older adults

scientific article published in 2021

The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

scientific article published on 7 May 2018

Unsupervised Cell Segmentation and Labelling in Neural Tissue Images

scientific article published on 21 April 2021

Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies.

scientific article published on 15 November 2017

Workflow for generating competing hypothesis from models with parameter uncertainty

scientific article published on 30 March 2011

Workforce preparation: the Biohealth computing model for Master and PhD students

scientific article

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