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Items: 1 to 50 of 70

1.

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

Jansen C, Ramirez RN, El-Ali NC, Gomez-Cabrero D, Tegner J, Merkenschlager M, Conesa A, Mortazavi A.

PLoS Comput Biol. 2019 Nov 4;15(11):e1006555. doi: 10.1371/journal.pcbi.1006555. eCollection 2019 Nov.

2.

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

Gomez-Cabrero D, Tarazona S, Ferreirós-Vidal I, Ramirez RN, Company C, Schmidt A, Reijmers T, Paul VVS, Marabita F, Rodríguez-Ubreva J, Garcia-Gomez A, Carroll T, Cooper L, Liang Z, Dharmalingam G, van der Kloet F, Harms AC, Balzano-Nogueira L, Lagani V, Tsamardinos I, Lappe M, Maier D, Westerhuis JA, Hankemeier T, Imhof A, Ballestar E, Mortazavi A, Merkenschlager M, Tegner J, Conesa A.

Sci Data. 2019 Oct 31;6(1):256. doi: 10.1038/s41597-019-0202-7.

3.

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

Kochlik B, Stuetz W, Pérès K, Pilleron S, Féart C, García García FJ, Bandinelli S, Gomez-Cabrero D, Rodriguez-Mañas L, Grune T, Weber D.

J Cachexia Sarcopenia Muscle. 2019 Aug 21. doi: 10.1002/jcsm.12479. [Epub ahead of print]

4.

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.

Fernandes SJ, Morikawa H, Ewing E, Ruhrmann S, Joshi RN, Lagani V, Karathanasis N, Khademi M, Planell N, Schmidt A, Tsamardinos I, Olsson T, Piehl F, Kockum I, Jagodic M, Tegnér J, Gomez-Cabrero D.

Sci Rep. 2019 Aug 19;9(1):11996. doi: 10.1038/s41598-019-48493-7.

5.

Current status of use of big data and artificial intelligence in RMDs: a systematic literature review informing EULAR recommendations.

Kedra J, Radstake T, Pandit A, Baraliakos X, Berenbaum F, Finckh A, Fautrel B, Stamm TA, Gomez-Cabrero D, Pristipino C, Choquet R, Servy H, Stones S, Burmester G, Gossec L.

RMD Open. 2019 Jul 18;5(2):e001004. doi: 10.1136/rmdopen-2019-001004. eCollection 2019.

6.

Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis associates with ROS pathway in monocytes.

Carlström KE, Ewing E, Granqvist M, Gyllenberg A, Aeinehband S, Enoksson SL, Checa A, Badam TVS, Huang J, Gomez-Cabrero D, Gustafsson M, Al Nimer F, Wheelock CE, Kockum I, Olsson T, Jagodic M, Piehl F.

Nat Commun. 2019 Jul 12;10(1):3081. doi: 10.1038/s41467-019-11139-3.

7.

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

Gossec L, Kedra J, Servy H, Pandit A, Stones S, Berenbaum F, Finckh A, Baraliakos X, Stamm TA, Gomez-Cabrero D, Pristipino C, Choquet R, Burmester GR, Radstake TRDJ.

Ann Rheum Dis. 2019 Jun 22. pii: annrheumdis-2019-215694. doi: 10.1136/annrheumdis-2019-215694. [Epub ahead of print]

PMID:
31229952
8.

Increased levels of soluble Receptor for Advanced Glycation End-products (RAGE) are associated with a higher risk of mortality in frail older adults.

Butcher L, Carnicero JA, Gomez Cabrero D, Dartigues JF, Pérès K, Garcia-Garcia FJ, Rodriguez-Mañas L, Erusalimsky JD; FRAILOMIC Consortium.

Age Ageing. 2019 Jun 18. pii: afz073. doi: 10.1093/ageing/afz073. [Epub ahead of print]

PMID:
31211360
9.

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

Kular L, Needhamsen M, Adzemovic MZ, Kramarova T, Gomez-Cabrero D, Ewing E, Piket E, Tegnér J, Beck S, Piehl F, Brundin L, Jagodic M.

Clin Epigenetics. 2019 May 30;11(1):86. doi: 10.1186/s13148-019-0678-1.

10.

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

Ewing E, Kular L, Fernandes SJ, Karathanasis N, Lagani V, Ruhrmann S, Tsamardinos I, Tegner J, Piehl F, Gomez-Cabrero D, Jagodic M.

EBioMedicine. 2019 May;43:411-423. doi: 10.1016/j.ebiom.2019.04.042. Epub 2019 Apr 30.

11.

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

Ferreirós-Vidal I, Carroll T, Zhang T, Lagani V, Ramirez RN, Ing-Simmons E, Gómez-Valadés AG, Cooper L, Liang Z, Papoutsoglou G, Dharmalingam G, Guo Y, Tarazona S, Fernandes SJ, Noori P, Silberberg G, Fisher AG, Tsamardinos I, Mortazavi A, Lenhard B, Conesa A, Tegner J, Merkenschlager M, Gomez-Cabrero D.

PLoS Biol. 2019 Apr 12;17(4):e2006506. doi: 10.1371/journal.pbio.2006506. eCollection 2019 Apr.

12.

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

Joshi RN, Fernandes SJ, Shang MM, Kiani NA, Gomez-Cabrero D, Tegnér J, Schmidt A.

J Leukoc Biol. 2019 Aug;106(2):413-430. doi: 10.1002/JLB.2A0618-228R. Epub 2019 Mar 18.

13.

Epigenetic Alterations Associated With Early Prenatal Dexamethasone Treatment.

Karlsson L, Barbaro M, Ewing E, Gomez-Cabrero D, Lajic S.

J Endocr Soc. 2018 Dec 12;3(1):250-263. doi: 10.1210/js.2018-00377. eCollection 2019 Jan 1.

14.

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

Tényi Á, Vela E, Cano I, Cleries M, Monterde D, Gomez-Cabrero D, Roca J.

BMJ Open Respir Res. 2018 Jun 13;5(1):e000302. doi: 10.1136/bmjresp-2018-000302. eCollection 2018.

15.

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

Kular L, Liu Y, Ruhrmann S, Zheleznyakova G, Marabita F, Gomez-Cabrero D, James T, Ewing E, Lindén M, Górnikiewicz B, Aeinehband S, Stridh P, Link J, Andlauer TFM, Gasperi C, Wiendl H, Zipp F, Gold R, Tackenberg B, Weber F, Hemmer B, Strauch K, Heilmann-Heimbach S, Rawal R, Schminke U, Schmidt CO, Kacprowski T, Franke A, Laudes M, Dilthey AT, Celius EG, Søndergaard HB, Tegnér J, Harbo HF, Oturai AB, Olafsson S, Eggertsson HP, Halldorsson BV, Hjaltason H, Olafsson E, Jonsdottir I, Stefansson K, Olsson T, Piehl F, Ekström TJ, Kockum I, Feinberg AP, Jagodic M.

Nat Commun. 2018 Jun 19;9(1):2397. doi: 10.1038/s41467-018-04732-5.

16.

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

Schmidt A, Marabita F, Kiani NA, Gross CC, Johansson HJ, Éliás S, Rautio S, Eriksson M, Fernandes SJ, Silberberg G, Ullah U, Bhatia U, Lähdesmäki H, Lehtiö J, Gomez-Cabrero D, Wiendl H, Lahesmaa R, Tegnér J.

BMC Biol. 2018 May 7;16(1):47. doi: 10.1186/s12915-018-0518-3.

17.

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

Tényi Á, Cano I, Marabita F, Kiani N, Kalko SG, Barreiro E, de Atauri P, Cascante M, Gomez-Cabrero D, Roca J.

J Transl Med. 2018 Feb 20;16(1):34. doi: 10.1186/s12967-018-1405-y.

18.

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

Pilleron S, Weber D, Pérès K, Colpo M, Gomez-Cabrero D, Stuetz W, Dartigues JF, Ferrucci L, Bandinelli S, Garcia-Garcia FJ, Grune T, Féart C; FRAILOMIC initiative.

Eur J Nutr. 2019 Feb;58(1):379-389. doi: 10.1007/s00394-017-1602-0. Epub 2018 Jan 27.

PMID:
29380043
19.

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

James T, Lindén M, Morikawa H, Fernandes SJ, Ruhrmann S, Huss M, Brandi M, Piehl F, Jagodic M, Tegnér J, Khademi M, Olsson T, Gomez-Cabrero D, Kockum I.

Hum Mol Genet. 2018 Mar 1;27(5):912-928. doi: 10.1093/hmg/ddy001.

PMID:
29325110
20.

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

Gomez-Cabrero D, Marabita F, Tarazona S, Cano I, Roca J, Conesa A, Sabatier P, Tegnér J.

Cell Syst. 2017 Dec 27;5(6):654. doi: 10.1016/j.cels.2017.12.010. No abstract available.

21.

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

Needhamsen M, Ewing E, Lund H, Gomez-Cabrero D, Harris RA, Kular L, Jagodic M.

BMC Bioinformatics. 2017 Nov 15;18(1):486. doi: 10.1186/s12859-017-1870-y.

22.

Software for the Integration of Multiomics Experiments in Bioconductor.

Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L.

Cancer Res. 2017 Nov 1;77(21):e39-e42. doi: 10.1158/0008-5472.CAN-17-0344.

23.

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

Lindén M, Ramírez Sepúlveda JI, James T, Thorlacius GE, Brauner S, Gómez-Cabrero D, Olsson T, Kockum I, Wahren-Herlenius M.

Biol Sex Differ. 2017 Oct 25;8(1):34. doi: 10.1186/s13293-017-0153-7.

24.

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

Gomez-Cabrero D, Marabita F, Tarazona S, Cano I, Roca J, Conesa A, Sabatier P, Tegnér J.

Cell Syst. 2017 Sep 27;5(3):168-175. doi: 10.1016/j.cels.2017.05.013. Epub 2017 Aug 23. Erratum in: Cell Syst. 2017 Dec 27;5(6):654.

25.

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.

Ruhrmann S, Ewing E, Piket E, Kular L, Cetrulo Lorenzi JC, Fernandes SJ, Morikawa H, Aeinehband S, Sayols-Baixeras S, Aslibekyan S, Absher DM, Arnett DK, Tegner J, Gomez-Cabrero D, Piehl F, Jagodic M.

Mult Scler. 2018 Sep;24(10):1288-1300. doi: 10.1177/1352458517721356. Epub 2017 Aug 2.

26.

Comment on "Epigenetics in the pathogenesis of RA".

Gomez-Cabrero D, Tegnér J, Ekström TJ, Ospelt C.

Semin Immunopathol. 2017 Jun;39(4):421-422. doi: 10.1007/s00281-017-0638-9. Epub 2017 May 11. No abstract available.

PMID:
28497351
27.

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

Zeitelhofer M, Adzemovic MZ, Gomez-Cabrero D, Bergman P, Hochmeister S, N'diaye M, Paulson A, Ruhrmann S, Almgren M, Tegnér JN, Ekström TJ, Guerreiro-Cacais AO, Jagodic M.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):E1678-E1687. doi: 10.1073/pnas.1615783114. Epub 2017 Feb 14.

28.

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

Gomez-Cabrero D, Menche J, Vargas C, Cano I, Maier D, Barabási AL, Tegnér J, Roca J; Synergy-COPD Consortia.

BMC Bioinformatics. 2016 Nov 22;17(Suppl 15):441. doi: 10.1186/s12859-016-1291-3.

29.

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

Gomez-Cabrero D, Almgren M, Sjöholm LK, Hensvold AH, Ringh MV, Tryggvadottir R, Kere J, Scheynius A, Acevedo N, Reinius L, Taub MA, Montano C, Aryee MJ, Feinberg JI, Feinberg AP, Tegnér J, Klareskog L, Catrina AI, Ekström TJ.

Genome Med. 2016 Nov 22;8(1):124.

30.

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

Tegnér J, Zenil H, Kiani NA, Ball G, Gomez-Cabrero D.

Philos Trans A Math Phys Eng Sci. 2016 Nov 13;374(2080). pii: 20160144. Review.

31.

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

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Aug 26;17(1):181. No abstract available.

32.

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

Lagani V, Karozou AD, Gomez-Cabrero D, Silberberg G, Tsamardinos I.

BMC Bioinformatics. 2016 Jul 27;17:290. doi: 10.1186/s12859-016-1153-z. No abstract available.

33.

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

Lagani V, Karozou AD, Gomez-Cabrero D, Silberberg G, Tsamardinos I.

BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:194. doi: 10.1186/s12859-016-1038-1. Erratum in: BMC Bioinformatics. 2016;17:290.

34.

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

Kannan V, Swartz F, Kiani NA, Silberberg G, Tsipras G, Gomez-Cabrero D, Alexanderson K, Tegnèr J.

Sci Rep. 2016 May 23;6:26170. doi: 10.1038/srep26170.

35.

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

Dueñas-Espín I, Vela E, Pauws S, Bescos C, Cano I, Cleries M, Contel JC, de Manuel Keenoy E, Garcia-Aymerich J, Gomez-Cabrero D, Kaye R, Lahr MM, Lluch-Ariet M, Moharra M, Monterde D, Mora J, Nalin M, Pavlickova A, Piera J, Ponce S, Santaeugenia S, Schonenberg H, Störk S, Tegner J, Velickovski F, Westerteicher C, Roca J.

BMJ Open. 2016 Apr 15;6(4):e010301. doi: 10.1136/bmjopen-2015-010301.

36.

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

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8. Review. Erratum in: Genome Biol. 2016;17(1):181.

37.

ChainRank, a chain prioritisation method for contextualisation of biological networks.

Tényi Á, de Atauri P, Gomez-Cabrero D, Cano I, Clarke K, Falciani F, Cascante M, Roca J, Maier D.

BMC Bioinformatics. 2016 Jan 5;17:17. doi: 10.1186/s12859-015-0864-x.

38.

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

Roca J, Cano I, Gomez-Cabrero D, Tegnér J.

Methods Mol Biol. 2016;1386:283-303. doi: 10.1007/978-1-4939-3283-2_13. Review.

PMID:
26677188
39.

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

Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L.

Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Review.

40.

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

Rodríguez-Cortez VC, Del Pino-Molina L, Rodríguez-Ubreva J, Ciudad L, Gómez-Cabrero D, Company C, Urquiza JM, Tegnér J, Rodríguez-Gallego C, López-Granados E, Ballestar E.

Nat Commun. 2015 Jun 17;6:7335. doi: 10.1038/ncomms8335.

41.

Laboratory biomarkers and frailty: presentation of the FRAILOMIC initiative.

Lippi G, Jansen-Duerr P, Viña J, Durrance-Bagale A, Abugessaisa I, Gomez-Cabrero D, Tegnér J, Grillari J, Erusalimsky J, Sinclair A, Rodriguez-Manãs L; FRAILOMIC consortium.

Clin Chem Lab Med. 2015 Sep 1;53(10):e253-5. doi: 10.1515/cclm-2015-0147. No abstract available.

PMID:
25993734
42.

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

Danielsson F, James T, Gomez-Cabrero D, Huss M.

Brief Bioinform. 2015 Nov;16(6):941-9. doi: 10.1093/bib/bbv017. Epub 2015 Mar 30.

43.

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

Hernandez C, Aibar J, de Batlle J, Gomez-Cabrero D, Soler N, Duran-Tauleria E, Garcia-Aymerich J, Altimiras X, Gomez M, Agustí A, Escarrabill J, Font D, Roca J; NEXES Consortium.

Respir Med. 2015 Apr;109(4):500-9. doi: 10.1016/j.rmed.2015.01.005. Epub 2015 Jan 28.

44.

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

Lindholm ME, Marabita F, Gomez-Cabrero D, Rundqvist H, Ekström TJ, Tegnér J, Sundberg CJ.

Epigenetics. 2014 Dec;9(12):1557-69. doi: 10.4161/15592294.2014.982445.

45.

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

Roca J, Vargas C, Cano I, Selivanov V, Barreiro E, Maier D, Falciani F, Wagner P, Cascante M, Garcia-Aymerich J, Kalko S, De Mas I, Tegnér J, Escarrabill J, Agustí A, Gomez-Cabrero D; Synergy-COPD consortium.

J Transl Med. 2014 Nov 28;12 Suppl 2:S3. doi: 10.1186/1479-5876-12-S2-S3. Epub 2014 Nov 28. Review.

46.

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

Gomez-Cabrero D, Lluch-Ariet M, Tegnér J, Cascante M, Miralles F, Roca J; Synergy-COPD consortium.

J Transl Med. 2014 Nov 28;12 Suppl 2:S2. doi: 10.1186/1479-5876-12-S2-S2. Epub 2014 Nov 28.

47.

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

Miralles F, Gomez-Cabrero D, Lluch-Ariet M, Tegnér J, Cascante M, Roca J; Synergy-COPD consortium.

J Transl Med. 2014 Nov 28;12 Suppl 2:S12. doi: 10.1186/1479-5876-12-S2-S12. Epub 2014 Nov 28. Review.

48.

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

Cascante M, de Atauri P, Gomez-Cabrero D, Wagner P, Centelles JJ, Marin S, Cano I, Velickovski F, Marin de Mas I, Maier D, Roca J, Sabatier P.

J Transl Med. 2014 Nov 28;12 Suppl 2:S11. doi: 10.1186/1479-5876-12-S2-S11. Epub 2014 Nov 28. Review.

49.

Biomedical research in a Digital Health Framework.

Cano I, Lluch-Ariet M, Gomez-Cabrero D, Maier D, Kalko S, Cascante M, Tegnér J, Miralles F, Herrera D, Roca J; Synergy-COPD consortium.

J Transl Med. 2014 Nov 28;12 Suppl 2:S10. doi: 10.1186/1479-5876-12-S2-S10. Epub 2014 Nov 28.

50.

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

Huertas-Migueláñez M, Mora D, Cano I, Maier D, Gomez-Cabrero D, Lluch-Ariet M, Miralles F.

J Transl Med. 2014 Nov 28;12 Suppl 2:S7. doi: 10.1186/1479-5876-12-S2-S7. Epub 2014 Nov 28.

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