Network-guided identification of candidate biomarkers for COPD-associated comorbidities using deep learning and real-world transcriptomic data
Manuscript submitted to bioRxiv · 2026
Science and references
Expertise demonstrated through scientific publications.
Our experience spans more than 50 publications and competitively funded projects across multiple therapeutic areas. This knowledge strengthens each new study and supports work with further diseases and treatments.
Recent research
Latest research
Manuscripts submitted to bioRxiv. Read the full text in PDF.
Virtual Human Twins for In Silico Clinical Trials in Depression: A Systems Medicine Comparison of Escitalopram, Citalopram and Duloxetine
Manuscript submitted to bioRxiv · 2026
Published experience
Bringing scientific knowledge to every project.
The areas below show direct experience supported by publications and publicly documented research projects.
50+scientific publications
Oncology and precision medicine
Experience in pancreatic, colorectal, gastric, kidney, lung and blood cancers, and tumour biomarkers.
View publications and projects
Publications
- Digital patient modeling identifies predictive biomarkers of regorafenib response in elderly metastatic colorectal cancerFrontiers in Systems Biology, 2025
- A decision support system based on artificial intelligence and systems biology for the simulation of pancreatic cancer patient statusCPT: Pharmacometrics & Systems Pharmacology, 2023
- The LEGACy study: molecular phenotypes and personalized clinical decision making in gastric cancerBMC Cancer, 2022
- Exploring the synergistic effects of cabozantinib and a PD-1 inhibitor in metastatic renal cell carcinoma with machine learningOncotarget, 2022
- Head-to-head evaluation of brigatinib and alectinib as first-line treatment for ALK-positive NSCLCOncotarget, 2021
- Systems biology drug screening identifies statins as enhancers of current therapies in chronic lymphocytic leukemiaScientific Reports, 2020
- Biological relationships between miRNAs used for colorectal cancer screeningJournal of Molecular Biomarkers & Diagnosis, 2018
- Functional, structural and contextual analysis of a BRCA1 variant of uncertain clinical significanceJournal of Cancer Genetics and Biomarkers, 2017
- Potato carboxypeptidase inhibitor is an epidermal growth factor antagonist that inhibits tumor cell growthJournal of Biological Chemistry, 1998
Publicly documented projects
- LEGACy — Personalized medicine in gastric cancerHorizon 2020 · 825832
- Extracellular vesicles in prostate cancerHorizon 2020 · 860303
- Exploitation of the secretory pathway for cancer therapyHorizon 2020 · 859962
Neurology, neurodegeneration and mental health
Modelling and analysis in multiple sclerosis, ALS, Alzheimer's disease, brain ageing, ADHD and mental health.
View publications and projects
Publications
- Computational head-to-head comparison of lisdexamfetamine and methylphenidateFrontiers in Psychiatry, 2021
- Psychosocial impact of the COVID-19 pandemic: identification of the most vulnerable populationsBMJ Open, 2021
- Aging increases hippocampal Dusp2 through a cholesterol loss-mediated RTK/p38MAPK mechanismFrontiers in Neurology, 2019
- Neuroprotective drug for nerve trauma revealed using artificial intelligenceScientific Reports, 2018
- Novel neuroprotective multicomponent therapy for amyotrophic lateral sclerosis designed by networked systemsPLOS ONE, 2016
- Signaling networks in multiple sclerosis: a systems-based approach to developing new pharmacological therapiesMultiple Sclerosis Journal, 2015
- Systems biology identifies presenilin-1-interacting proteins and drug targets in Alzheimer’s diseaseAlzheimer's & Dementia, 2012
Publicly documented projects
Diabetes, metabolism and kidney disease
Research in type 2 diabetes, diabetic nephropathy, nutrition, microalbuminuria, and cognitive and retinal complications.
View publications and projects
Publications
- Urinary proteome analysis identified neprilysin and VCAM as proteins involved in diabetic nephropathyJournal of Diabetes Research, 2018
- Systems biology and nutrition: effects of a protein-rich ketogenic diet in patients with type 2 diabetes [title translated from Spanish]Alimentación, Nutrición y Salud, 2011
- Revealing the molecular relationship between type 2 diabetes and the metabolic changes induced by a low-carbohydrate ketogenic dietNutrition & Metabolism, 2010
- Adding questions about cardiovascular risk factors improves the ability of the ADA questionnaire to identify unknown diabetic patients in SpainAvances en Diabetología, 2010
- Microirbe: epidemiology of microalbuminuria in people with diabetes and hypertension in SpainAvances en Diabetología, 2005
Publicly documented projects
- RECOGNISED — Retinal and cognitive dysfunction in type 2 diabetesHorizon 2020 · 847749
Cardiovascular medicine, hepatology and gastroenterology
Experience in heart failure, myocardial injury, cirrhosis, NAFLD, associated kidney function and irritable bowel syndrome.
View publications and projects
Publications
- In-silico simulated prototype-patients to study a potential adverse effect of sacubitril and valsartanPLOS ONE, 2020
- A novel method for prevention of hypoxic cardiomyocyte injuryCardiology in Belarus, 2019
- Characterization of inflammatory response in cirrhosis associated with kidney outcome and survivalLiver International, 2019
- Systems biology applied to NAFLD: treatment selection based on the mechanism of action of nutraceuticalsNutrafoods, 2014
Publicly documented projects
- LIVERHOPE — Simvastatin and rifaximin in decompensated cirrhosisHorizon 2020 · 731875
- DISCOvERIE — Diagnosis and prevention of comorbidities in irritable bowel syndromeHorizon 2020 · 848228
Immunology, rheumatology and inflammatory diseases
Applications in psoriasis, spondyloarthritis, rheumatoid arthritis, periodontal inflammation and adaptive immunity.
View publications and projects
Publications
- A quantitative systems pharmacology model for certolizumab pegol treatment in moderate-to-severe psoriasisFrontiers in Immunology, 2023
- Female gender and age are associated with suboptimal response to TNF inhibitors in axial spondyloarthritisArthritis Care & Research, 2022
Publicly documented projects
Infectious diseases and vaccines
Research in tuberculosis, malaria, COVID-19, bacterial infections and host-pathogen interactions.
View publications and projects
Publications
- In-silico drug repurposing predicts pirfenidone and melatonin to reduce SARS-CoV-2 progression and respiratory distressPLOS ONE, 2020
- Antigen-stimulated PBMC transcriptional protective signatures for malaria immunizationScience Translational Medicine, 2020
- Phage spread dynamics in clonal bacterial populations depends on features of the founder cellMicrobiological Research, 2001
- RecA-dependent viral burst in bacterial colonies during entry into stationary phaseFEMS Microbiology Letters, 1999
- Viral spread within ageing bacterial populationsGene, 1997
Publicly documented projects
Ophthalmology and sensory disorders
Mechanistic analysis in diabetic macular oedema, macular degeneration, ocular safety and visual disorders.
View publications and projects
Publications
- Aflibercept off-target effects in diabetic macular edema: an in silico modeling approachInternational Journal of Molecular Sciences, 2024
- Biomarkers of macular degeneration prognosis in simulated patients exposed to heart-failure treatmentbioRxiv, 2019
Publicly documented projects
Reproductive, bone, urological and population health
Work on embryo implantation, osteoporosis, urological health, skin ageing and smoking prevention.
View publications
Publications
- Proteomics-based drug repositioning to improve in vitro fertilization implantationSystems Biology in Reproductive Medicine, 2021
- Methods for diagnosing perceived age on the basis of an ensemble of phenotypic featuresClinical, Cosmetic and Investigational Dermatology, 2014
- Prevalence of vertebral fracture in postmenopausal women with lumbar osteopenia: OSTEOXPRESS studyAging Clinical and Experimental Research, 2010
- Risk of non-vertebral fractures in postmenopausal women receiving antiresorptive treatment [title translated from Spanish]Progresos de Obstetricia y Ginecología, 2009
- Reasons for quitting smoking in Spain by sex and age [title translated from Spanish]Gaceta Sanitaria, 2009
- Profile of patients seeking to quit smoking in primary and specialist care [title translated from Spanish]Revista Clínica Española, 2009
- Profile of smokers wishing to quit: a socioeconomic perspective [title translated from Spanish]Revista Española de Economía de la Salud, 2009
- Prevalence of ejaculatory dysfunction secondary to alpha-blocker therapy in benign prostatic hyperplasiaActas Urológicas Españolas, 2008
Systems biology, data and molecular modelling
Methods spanning real-world data, transcriptomics, biological networks, proteins, biosensors and computational discovery.
View publications
Publications
- The usage of transcriptomics datasets as sources of real-world data for clinical triallingbioRxiv, 2022
- CuBlock: a cross-platform normalization method for gene-expression microarraysBioinformatics, 2021
- Same drug, new purposeEuropean Biopharmaceutical Review, 2015
- Virtual-organism toy-model for systems-biology approaches to medical-target discoveryarXiv, 2014
- Systems biology solutions to the microarray nightmareInnovations in Pharmaceutical Technology, 2013
- Towards a molecular characterization of pathological pathwaysFEBS Letters, 2008
- Artistic representation of the human interactome built with AxPathBuilderNature Chemical Biology cover, 2008
- Classification of protein disulphide-bridge topologiesJournal of Computer-Aided Molecular Design, 2001
- Human A2 pro-carboxypeptidase model: improving homology modeling through secondary-structure predictionJournal of Computer-Aided Molecular Design, 2000
- Corrigendum: mechanisms of antibody-enzymatic reactivation in beta-galactosidase molecular sensorsFEBS Letters, 2000
- Detection of molecular interactions using a peptide-displaying bacteriophage biosensorBiochemical and Biophysical Research Communications, 1999
- Distinct mechanisms of antibody-enzymatic reactivation in beta-galactosidase molecular sensorsFEBS Letters, 1998
- Effects of counter-ions and volume on the simulated dynamics of solvated proteinsProtein Engineering, 1998
- Protein similarities beyond disulphide-bridge topologyJournal of Molecular Biology, 1998
- Statistical analysis of loop geometry in a non-redundant database of proteinsJournal of Molecular Modeling, 1998
Beyond these areas
Published experience opens the way to further therapeutic areas.
We can work with other diseases, treatments and populations. We define the scientific question, incorporate available knowledge and adapt the simulation to each project's therapeutic context, involving clinical specialists where they add value.
Science in practice