Publications by authors named "David Gomez-Cabrero"

79Publications

MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.

Nucleic Acids Res 2020 Oct 13. Epub 2020 Oct 13.

Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gkaa817DOI Listing
October 2020

GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.

BMC Bioinformatics 2020 Oct 7;21(1):443. Epub 2020 Oct 7.

Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain.

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http://dx.doi.org/10.1186/s12859-020-03784-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7542881PMC
October 2020

Harmonization of quality metrics and power calculation in multi-omic studies.

Nat Commun 2020 06 18;11(1):3092. Epub 2020 Jun 18.

Microbiology and Cell Science Department, Institute for Food and Agricultural Research, University of Florida, Gainesville, FL, USA.

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http://dx.doi.org/10.1038/s41467-020-16937-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7303201PMC
June 2020

Genome-wide investigation of DNA methylation in congenital adrenal hyperplasia.

J Steroid Biochem Mol Biol 2020 Jul 17;201:105699. Epub 2020 May 17.

Department of Women's and Children's Health, Karolinska Institutet, Paediatric Endocrinology Unit (QB83), Karolinska University Hospital, SE-171 76 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jsbmb.2020.105699DOI Listing
July 2020

Targeted lipidomics reveals extensive changes in circulating lipid mediators in patients with acutely decompensated cirrhosis.

J Hepatol 2020 Oct 12;73(4):817-828. Epub 2020 Apr 12.

European Foundation for the Study of Chronic Liver Failure (EF-Clif) and Grifols Chair, Barcelona, Spain; Biochemistry and Molecular Genetics Service, Hospital Clínic-IDIBAPS and CIBERehd, Barcelona, Spain; Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.jhep.2020.03.046DOI Listing
October 2020

Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma.

Front Oncol 2020 3;10:51. Epub 2020 Feb 3.

Unit of Computational Medicine, Department of Medicine, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden.

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http://dx.doi.org/10.3389/fonc.2020.00051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017805PMC
February 2020

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

Nat Commun 2020 02 4;11(1):693. Epub 2020 Feb 4.

Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK.

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http://dx.doi.org/10.1038/s41467-020-14422-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000725PMC
February 2020

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.

PLoS Comput Biol 2019 11 4;15(11):e1006555. Epub 2019 Nov 4.

Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855564PMC
November 2019

Associations of fat-soluble micronutrients and redox biomarkers with frailty status in the FRAILOMIC initiative.

J Cachexia Sarcopenia Muscle 2019 12 21;10(6):1339-1346. Epub 2019 Aug 21.

Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany.

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http://dx.doi.org/10.1002/jcsm.12479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6903435PMC
December 2019

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

Ann Rheum Dis 2020 01 22;79(1):69-76. Epub 2019 Jun 22.

Dept of Rheumatology, Clinical Immunology and Laboratory of Translational Immunology, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1136/annrheumdis-2019-215694DOI Listing
January 2020

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

Clin Epigenetics 2019 05 30;11(1):86. Epub 2019 May 30.

Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1186/s13148-019-0678-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6543588PMC
May 2019

Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg-mediated suppression of cytokine expression.

J Leukoc Biol 2019 08 18;106(2):413-430. Epub 2019 Mar 18.

Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska University Hospital and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1002/JLB.2A0618-228RDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850362PMC
August 2019

Epigenetic Alterations Associated With Early Prenatal Dexamethasone Treatment.

J Endocr Soc 2019 Jan 12;3(1):250-263. Epub 2018 Dec 12.

Department of Women's and Children's Health, Karolinska Institutet, Paediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden.

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https://academic.oup.com/jes/article/3/1/250/5239844
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http://dx.doi.org/10.1210/js.2018-00377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320242PMC
January 2019

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

BMJ Open Respir Res 2018 13;5(1):e000302. Epub 2018 Jun 13.

Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1136/bmjresp-2018-000302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018856PMC
June 2018

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

J Transl Med 2018 02 20;16(1):34. Epub 2018 Feb 20.

Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain.

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https://translational-medicine.biomedcentral.com/articles/10
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http://dx.doi.org/10.1186/s12967-018-1405-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819708PMC
February 2018

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

BMC Bioinformatics 2017 Nov 15;18(1):486. Epub 2017 Nov 15.

Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-017-1870-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688710PMC
November 2017

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

Biol Sex Differ 2017 10 25;8(1):34. Epub 2017 Oct 25.

Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1186/s13293-017-0153-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657123PMC
October 2017

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

Cell Syst 2017 09 23;5(3):168-175. Epub 2017 Aug 23.

Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, L8, 17176 Stockholm, Sweden; Science for Life Laboratory, 17121 Solna, Sweden; Biological and Environmental Sciences and Engineering Division (BESE), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.05.013DOI Listing
September 2017

Comment on "Epigenetics in the pathogenesis of RA".

Semin Immunopathol 2017 06 11;39(4):421-422. Epub 2017 May 11.

Center of Experimental Rheumatology, University Hospital Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland.

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http://dx.doi.org/10.1007/s00281-017-0638-9DOI Listing
June 2017

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

BMC Bioinformatics 2016 Nov 22;17(Suppl 15):441. Epub 2016 Nov 22.

Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1186/s12859-016-1291-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133493PMC
November 2016

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

Philos Trans A Math Phys Eng Sci 2016 Nov;374(2080)

Department of Medicine, Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden Center for Molecular Medicine, Karolinska Institutet, L8:05, 171 76 Stockholm, Sweden Department of Medicine, Unit of Clinical Epidemiology, Karolinska University Hospital L8, 17176 Stockholm, Sweden Science for Life Laboratory, Stockholm, Sweden Mucosal and Salivary Biology Division, King's College London Dental Institute, London SE1 9RT, UK.

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http://dx.doi.org/10.1098/rsta.2016.0144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052728PMC
November 2016

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

Genome Biol 2016 Aug 26;17(1):181. Epub 2016 Aug 26.

Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA.

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http://dx.doi.org/10.1186/s13059-016-1047-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000515PMC
August 2016

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

BMC Bioinformatics 2016 Jul 27;17:290. Epub 2016 Jul 27.

Institute of Computer Science, Foundation for Research and Technology - Hellas, Heraklion, Greece.

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http://dx.doi.org/10.1186/s12859-016-1153-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4963931PMC
July 2016

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

BMC Bioinformatics 2016 Jun 6;17 Suppl 5:194. Epub 2016 Jun 6.

Institute of Computer Science, Foundation for Research and Technology - Hellas, Heraklion, Greece.

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http://dx.doi.org/10.1186/s12859-016-1038-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905611PMC
June 2016

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

Methods Mol Biol 2016 ;1386:283-303

Unit of Computational Medicine, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.

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http://link.springer.com/10.1007/978-1-4939-3283-2_13
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http://dx.doi.org/10.1007/978-1-4939-3283-2_13DOI Listing
October 2016

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

Nat Commun 2015 Jun 17;6:7335. Epub 2015 Jun 17.

Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avda Gran Via 199-203, 08908L'Hospitalet de Llobregat, Barcelona, Spain.

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http://dx.doi.org/10.1038/ncomms8335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557293PMC
June 2015

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

Respir Med 2015 Apr 28;109(4):500-9. Epub 2015 Jan 28.

Hospital Clinic de Barcelona, CIBER en Enfermedades Respiratorias (CIBERES), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1016/j.rmed.2015.01.005DOI Listing
April 2015

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

PLoS One 2014 6;9(11):e111068. Epub 2014 Nov 6.

Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona and Institute of Biomedicine (IBUB), Barcelona, Catalonia, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111068PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222897PMC
July 2015

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

Am J Obstet Gynecol 2014 Nov 1;211(5):502.e1-8. Epub 2014 Jul 1.

Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; The Center for Molecular Medicine, Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.ajog.2014.05.014DOI Listing
November 2014

Serotonin regulates performance nonmonotonically in a spatial working memory network.

Cereb Cortex 2014 Sep 28;24(9):2449-63. Epub 2013 Apr 28.

Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.

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http://dx.doi.org/10.1093/cercor/bht096DOI Listing
September 2014

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

J Autoimmun 2013 Mar 8;41:6-16. Epub 2013 Jan 8.

Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.

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https://linkinghub.elsevier.com/retrieve/pii/S08968411120015
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http://dx.doi.org/10.1016/j.jaut.2012.12.005DOI Listing
March 2013

Workflow for generating competing hypothesis from models with parameter uncertainty.

Interface Focus 2011 Jun 30;1(3):438-49. Epub 2011 Mar 30.

Department of Medicine, Karolinska Institutet , Unit of Computational Medicine, Centre for Molecular Medicine , Solna, Stockholm , Sweden.

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http://dx.doi.org/10.1098/rsfs.2011.0015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262450PMC
June 2011

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

Nucleic Acids Res 2012 Mar 15;40(5):1954-68. Epub 2011 Nov 15.

Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08907 L'Hospitalet de Llobregat, Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkr1015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299990PMC
March 2012

ParkDB: a Parkinson's disease gene expression database.

Database (Oxford) 2011 18;2011:bar007. Epub 2011 May 18.

UCL, Department of Cancer Biology, University College London, Gower Street, London, UK.

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http://dx.doi.org/10.1093/database/bar007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098727PMC
September 2011