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Items: 1 to 50 of 133

1.

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

Papoutsoglou G, Lagani V, Schmidt A, Tsirlis K, Cabrero DG, Tegnér J, Tsamardinos I.

Cytometry A. 2019 Nov;95(11):1178-1190. doi: 10.1002/cyto.a.23908. Epub 2019 Nov 6.

PMID:
31692248
2.

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.

3.

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.

4.

An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems.

Zenil H, Kiani NA, Marabita F, Deng Y, Elias S, Schmidt A, Ball G, Tegnér J.

iScience. 2019 Sep 27;19:1160-1172. doi: 10.1016/j.isci.2019.07.043. Epub 2019 Aug 8.

5.

Exhaustion of CD4+ T-cells mediated by the Kynurenine Pathway in Melanoma.

Rad Pour S, Morikawa H, Kiani NA, Yang M, Azimi A, Shafi G, Shang M, Baumgartner R, Ketelhuth DFJ, Kamleh MA, Wheelock CE, Lundqvist A, Hansson J, Tegnér J.

Sci Rep. 2019 Aug 21;9(1):12150. doi: 10.1038/s41598-019-48635-x.

6.

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.

7.

Associations of Plasma 3-Methylhistidine with Frailty Status in French Cohorts of the FRAILOMIC Initiative.

Kochlik B, Stuetz W, Pérès K, Féart C, Tegner J, Rodriguez-Mañas L, Grune T, Weber D.

J Clin Med. 2019 Jul 10;8(7). pii: E1010. doi: 10.3390/jcm8071010.

8.

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.

9.

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.

10.

MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis.

Kotelnikova E, Kiani NA, Messinis D, Pertsovskaya I, Pliaka V, Bernardo-Faura M, Rinas M, Vila G, Zubizarreta I, Pulido-Valdeolivas I, Sakellaropoulos T, Faigle W, Silberberg G, Masso M, Stridh P, Behrens J, Olsson T, Martin R, Paul F, Alexopoulos LG, Saez-Rodriguez J, Tegner J, Villoslada P.

Proc Natl Acad Sci U S A. 2019 May 7;116(19):9671-9676. doi: 10.1073/pnas.1818347116. Epub 2019 Apr 19.

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.

Predictive Systems Toxicology.

Kiani NA, Shang MM, Zenil H, Tegner J.

Methods Mol Biol. 2018;1800:535-557. doi: 10.1007/978-1-4939-7899-1_25. Review.

PMID:
29934910
14.

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.

15.

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.

16.

Overexpression of endothelin B receptor in glioblastoma: a prognostic marker and therapeutic target?

Vasaikar S, Tsipras G, Landázuri N, Costa H, Wilhelmi V, Scicluna P, Cui HL, Mohammad AA, Davoudi B, Shang M, Ananthaseshan S, Strååt K, Stragliotto G, Rahbar A, Wong KT, Tegner J, Yaiw KC, Söderberg-Naucler C.

BMC Cancer. 2018 Feb 6;18(1):154. doi: 10.1186/s12885-018-4012-7.

17.

Low-algorithmic-complexity entropy-deceiving graphs.

Zenil H, Kiani NA, Tegnér J.

Phys Rev E. 2017 Jul;96(1-1):012308. doi: 10.1103/PhysRevE.96.012308. Epub 2017 Jul 7.

PMID:
29347130
18.

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
19.

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.

20.

Dynamics and heterogeneity of brain damage in multiple sclerosis.

Kotelnikova E, Kiani NA, Abad E, Martinez-Lapiscina EH, Andorra M, Zubizarreta I, Pulido-Valdeolivas I, Pertsovskaya I, Alexopoulos LG, Olsson T, Martin R, Paul F, Tegnér J, Garcia-Ojalvo J, Villoslada P.

PLoS Comput Biol. 2017 Oct 26;13(10):e1005757. doi: 10.1371/journal.pcbi.1005757. eCollection 2017 Oct.

21.

Phosphoproteomics Reveals Regulatory T Cell-Mediated DEF6 Dephosphorylation That Affects Cytokine Expression in Human Conventional T Cells.

Joshi RN, Binai NA, Marabita F, Sui Z, Altman A, Heck AJR, Tegnér J, Schmidt A.

Front Immunol. 2017 Sep 25;8:1163. doi: 10.3389/fimmu.2017.01163. eCollection 2017.

22.

Predicting Causal Relationships from Biological Data: Applying Automated Causal Discovery on Mass Cytometry Data of Human Immune Cells.

Triantafillou S, Lagani V, Heinze-Deml C, Schmidt A, Tegner J, Tsamardinos I.

Sci Rep. 2017 Oct 5;7(1):12724. doi: 10.1038/s41598-017-08582-x.

23.

HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation.

Deng Y, Zenil H, Tegnér J, Kiani NA.

Bioinformatics. 2017 Dec 15;33(24):3964-3972. doi: 10.1093/bioinformatics/btx501.

PMID:
28961895
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.

SCENERY: a web application for (causal) network reconstruction from cytometry data.

Papoutsoglou G, Athineou G, Lagani V, Xanthopoulos I, Schmidt A, Éliás S, Tegnér J, Tsamardinos I.

Nucleic Acids Res. 2017 Jul 3;45(W1):W270-W275. doi: 10.1093/nar/gkx448.

27.

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
28.

A minimal unified model of disease trajectories captures hallmarks of multiple sclerosis.

Kannan V, Kiani NA, Piehl F, Tegner J.

Math Biosci. 2017 Jul;289:1-8. doi: 10.1016/j.mbs.2017.03.006. Epub 2017 Mar 29.

29.

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.

30.

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.

31.

TGF-β Affects the Differentiation of Human GM-CSF+ CD4+ T Cells in an Activation- and Sodium-Dependent Manner.

Éliás S, Schmidt A, Kannan V, Andersson J, Tegnér J.

Front Immunol. 2016 Dec 23;7:603. doi: 10.3389/fimmu.2016.00603. eCollection 2016.

32.
33.

Corrigendum to "Methods of information theory and algorithmic complexity for network biology" [Semin. Cell Dev. Biol. 51 (2016) 32-43].

Zenil H, Kiani NA, Tegnér J.

Semin Cell Dev Biol. 2016 Dec;60:168. doi: 10.1016/j.semcdb.2016.11.006. No abstract available.

PMID:
27979328
34.

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.

35.

Adaptive input data transformation for improved network reconstruction with information theoretic algorithms.

Kannan V, Tegner J.

Stat Appl Genet Mol Biol. 2016 Dec 1;15(6):507-520. doi: 10.1515/sagmb-2016-0013.

PMID:
27875324
37.

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.

38.

Systems Toxicology: Systematic Approach to Predict Toxicity.

Kiani NA, Shang MM, Tegner J.

Curr Pharm Des. 2016;22(46):6911-6917. doi: 10.2174/1381612822666161003115629. Review.

PMID:
27697024
39.

Human cytomegalovirus may promote tumour progression by upregulating arginase-2.

Costa H, Xu X, Overbeek G, Vasaikar S, Patro CP, Kostopoulou ON, Jung M, Shafi G, Ananthaseshan S, Tsipras G, Davoudi B, Mohammad AA, Lam H, Strååt K, Wilhelmi V, Shang M, Tegner J, Tong JC, Wong KT, Söderberg-Naucler C, Yaiw KC.

Oncotarget. 2016 Jul 26;7(30):47221-47231. doi: 10.18632/oncotarget.9722.

40.

A qualitative study of how Danish drug consumption rooms influence health and well-being among people who use drugs.

Kappel N, Toth E, Tegner J, Lauridsen S.

Harm Reduct J. 2016 Jun 16;13(1):20. doi: 10.1186/s12954-016-0109-y.

41.

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.

42.

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.

43.

Human macrophages induce CD4(+)Foxp3(+) regulatory T cells via binding and re-release of TGF-β.

Schmidt A, Zhang XM, Joshi RN, Iqbal S, Wahlund C, Gabrielsson S, Harris RA, Tegnér J.

Immunol Cell Biol. 2016 Sep;94(8):747-62. doi: 10.1038/icb.2016.34. Epub 2016 May 10.

PMID:
27075967
44.

Comparative Analysis of Protocols to Induce Human CD4+Foxp3+ Regulatory T Cells by Combinations of IL-2, TGF-beta, Retinoic Acid, Rapamycin and Butyrate.

Schmidt A, Eriksson M, Shang MM, Weyd H, Tegnér J.

PLoS One. 2016 Feb 17;11(2):e0148474. doi: 10.1371/journal.pone.0148474. eCollection 2016.

45.

Evaluating network inference methods in terms of their ability to preserve the topology and complexity of genetic networks.

Kiani NA, Zenil H, Olczak J, Tegnér J.

Semin Cell Dev Biol. 2016 Mar;51:44-52. doi: 10.1016/j.semcdb.2016.01.012. Epub 2016 Feb 3. Review.

PMID:
26851626
46.

Methods of information theory and algorithmic complexity for network biology.

Zenil H, Kiani NA, Tegnér J.

Semin Cell Dev Biol. 2016 Mar;51:32-43. doi: 10.1016/j.semcdb.2016.01.011. Epub 2016 Jan 21. Review. Erratum in: Semin Cell Dev Biol. 2016 Dec;60:168.

PMID:
26802516
47.

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders.

Hofmann-Apitius M, Ball G, Gebel S, Bagewadi S, de Bono B, Schneider R, Page M, Kodamullil AT, Younesi E, Ebeling C, Tegnér J, Canard L.

Int J Mol Sci. 2015 Dec 7;16(12):29179-206. doi: 10.3390/ijms161226148. Review.

48.

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
49.

The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.

Gustafsson Sheppard N, Jarl L, Mahadessian D, Strittmatter L, Schmidt A, Madhusudan N, Tegnér J, Lundberg EK, Asplund A, Jain M, Nilsson R.

Sci Rep. 2015 Oct 13;5:15029. doi: 10.1038/srep15029.

50.

IL-1β promotes Th17 differentiation by inducing alternative splicing of FOXP3.

Mailer RK, Joly AL, Liu S, Elias S, Tegner J, Andersson J.

Sci Rep. 2015 Oct 6;5:14674. doi: 10.1038/srep14674.

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