Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 48

1.

Learning Differential Module Networks Across Multiple Experimental Conditions.

Erola P, Bonnet E, Michoel T.

Methods Mol Biol. 2019;1883:303-321. doi: 10.1007/978-1-4939-8882-2_13.

PMID:
30547406
2.

Whole-Transcriptome Causal Network Inference with Genomic and Transcriptomic Data.

Wang L, Michoel T.

Methods Mol Biol. 2019;1883:95-109. doi: 10.1007/978-1-4939-8882-2_4.

PMID:
30547397
3.

Causal Transcription Regulatory Network Inference Using Enhancer Activity as a Causal Anchor.

Vipin D, Wang L, Devailly G, Michoel T, Joshi A.

Int J Mol Sci. 2018 Nov 15;19(11). pii: E3609. doi: 10.3390/ijms19113609.

4.

Smoking is Associated to DNA Methylation in Atherosclerotic Carotid Lesions.

Siemelink MA, van der Laan SW, Haitjema S, van Koeverden ID, Schaap J, Wesseling M, de Jager SCA, Mokry M, van Iterson M, Dekkers KF, Luijk R, Foroughi Asl H, Michoel T, Björkegren JLM, Aavik E, Ylä-Herttuala S, de Borst GJ, Asselbergs FW, El Azzouzi H, den Ruijter HM, Heijmans BT, Pasterkamp G.

Circ Genom Precis Med. 2018 Sep;11(9):e002030. doi: 10.1161/CIRCGEN.117.002030.

PMID:
30354327
5.

Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets.

Lempiäinen H, Brænne I, Michoel T, Tragante V, Vilne B, Webb TR, Kyriakou T, Eichner J, Zeng L, Willenborg C, Franzen O, Ruusalepp A, Goel A, van der Laan SW, Biegert C, Hamby S, Talukdar HA, Foroughi Asl H; CVgenes@target consortium, Pasterkamp G, Watkins H, Samani NJ, Wittenberger T, Erdmann J, Schunkert H, Asselbergs FW, Björkegren JLM.

Sci Rep. 2018 Feb 21;8(1):3434. doi: 10.1038/s41598-018-20721-6.

6.

Meta-analysis of Liver and Heart Transcriptomic Data for Functional Annotation Transfer in Mammalian Orthologs.

Reyes PFL, Michoel T, Joshi A, Devailly G.

Comput Struct Biotechnol J. 2017 Aug 26;15:425-432. doi: 10.1016/j.csbj.2017.08.002. eCollection 2017.

7.

Carbonyl reductase 1 catalyzes 20β-reduction of glucocorticoids, modulating receptor activation and metabolic complications of obesity.

Morgan RA, Beck KR, Nixon M, Homer NZM, Crawford AA, Melchers D, Houtman R, Meijer OC, Stomby A, Anderson AJ, Upreti R, Stimson RH, Olsson T, Michoel T, Cohain A, Ruusalepp A, Schadt EE, Björkegren JLM, Andrew R, Kenyon CJ, Hadoke PWF, Odermatt A, Keen JA, Walker BR.

Sci Rep. 2017 Sep 6;7(1):10633. doi: 10.1038/s41598-017-10410-1.

8.

Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data.

Wang L, Michoel T.

PLoS Comput Biol. 2017 Aug 18;13(8):e1005703. doi: 10.1371/journal.pcbi.1005703. eCollection 2017 Aug.

9.

Enhancer decommissioning by Snail1-induced competitive displacement of TCF7L2 and down-regulation of transcriptional activators results in EPHB2 silencing.

Schnappauf O, Beyes S, Dertmann A, Freihen V, Frey P, Jägle S, Rose K, Michoel T, Grosschedl R, Hecht A.

Biochim Biophys Acta. 2016 Nov;1859(11):1353-1367. doi: 10.1016/j.bbagrm.2016.08.002. Epub 2016 Aug 5.

PMID:
27504909
10.

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.

Franzén O, Ermel R, Cohain A, Akers NK, Di Narzo A, Talukdar HA, Foroughi-Asl H, Giambartolomei C, Fullard JF, Sukhavasi K, Köks S, Gan LM, Giannarelli C, Kovacic JC, Betsholtz C, Losic B, Michoel T, Hao K, Roussos P, Skogsberg J, Ruusalepp A, Schadt EE, Björkegren JL.

Science. 2016 Aug 19;353(6301):827-30. doi: 10.1126/science.aad6970.

11.

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease.

Talukdar HA, Foroughi Asl H, Jain RK, Ermel R, Ruusalepp A, Franzén O, Kidd BA, Readhead B, Giannarelli C, Kovacic JC, Ivert T, Dudley JT, Civelek M, Lusis AJ, Schadt EE, Skogsberg J, Michoel T, Björkegren JL.

Cell Syst. 2016 Mar 23;2(3):196-208. doi: 10.1016/j.cels.2016.02.002. Epub 2016 Mar 3.

12.

Human Validation of Genes Associated With a Murine Atherosclerotic Phenotype.

Pasterkamp G, van der Laan SW, Haitjema S, Foroughi Asl H, Siemelink MA, Bezemer T, van Setten J, Dichgans M, Malik R, Worrall BB, Schunkert H, Samani NJ, de Kleijn DP, Markus HS, Hoefer IE, Michoel T, de Jager SC, Björkegren JL, den Ruijter HM, Asselbergs FW.

Arterioscler Thromb Vasc Biol. 2016 Jun;36(6):1240-6. doi: 10.1161/ATVBAHA.115.306958. Epub 2016 Apr 14. Review.

PMID:
27079880
13.

Functional transcription factor target discovery via compendia of binding and expression profiles.

Banks CJ, Joshi A, Michoel T.

Sci Rep. 2016 Feb 9;6:20649. doi: 10.1038/srep20649.

14.

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations.

Melckenbeeck I, Audenaert P, Michoel T, Colle D, Pickavet M.

PLoS One. 2016 Jan 21;11(1):e0147078. doi: 10.1371/journal.pone.0147078. eCollection 2016.

15.

Microglial brain region-dependent diversity and selective regional sensitivities to aging.

Grabert K, Michoel T, Karavolos MH, Clohisey S, Baillie JK, Stevens MP, Freeman TC, Summers KM, McColl BW.

Nat Neurosci. 2016 Mar;19(3):504-16. doi: 10.1038/nn.4222. Epub 2016 Jan 18.

16.

Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource.

Devailly G, Mantsoki A, Michoel T, Joshi A.

FEBS Lett. 2015 Dec 21;589(24 Pt B):3866-70. doi: 10.1016/j.febslet.2015.11.027. Epub 2015 Nov 24.

17.

Cattle trypanosomosis: the diversity of trypanosomes and implications for disease epidemiology and control.

Auty H, Torr SJ, Michoel T, Jayaraman S, Morrison LJ.

Rev Sci Tech. 2015 Aug;34(2):587-98. Review.

PMID:
26601459
18.

Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila.

Joshi A, Beck Y, Michoel T.

J Comput Biol. 2015 Apr;22(4):253-65. doi: 10.1089/cmb.2014.0290.

PMID:
25844666
19.

Variants in ALOX5, ALOX5AP and LTA4H are not associated with atherosclerotic plaque phenotypes: the Athero-Express Genomics Study.

van der Laan SW, Foroughi Asl H, van den Borne P, van Setten J, van der Perk ME, van de Weg SM, Schoneveld AH, de Kleijn DP, Michoel T, Björkegren JL, den Ruijter HM, Asselbergs FW, de Bakker PI, Pasterkamp G.

Atherosclerosis. 2015 Apr;239(2):528-38. doi: 10.1016/j.atherosclerosis.2015.01.018. Epub 2015 Jan 20.

PMID:
25721704
20.

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells.

Joshi A, Pooley C, Freeman TC, Lennartsson A, Babina M, Schmidl C, Geijtenbeek T; FANTOM Consortium, Michoel T, Severin J, Itoh M, Lassmann T, Kawaji H, Hayashizaki Y, Carninci P, Forrest AR, Rehli M, Hume DA.

J Leukoc Biol. 2015 May;97(5):985-995. doi: 10.1189/jlb.6TA1014-477RR. Epub 2015 Feb 25.

21.

Integrative multi-omics module network inference with Lemon-Tree.

Bonnet E, Calzone L, Michoel T.

PLoS Comput Biol. 2015 Feb 13;11(2):e1003983. doi: 10.1371/journal.pcbi.1003983. eCollection 2015 Feb.

22.

Expression quantitative trait Loci acting across multiple tissues are enriched in inherited risk for coronary artery disease.

Foroughi Asl H, Talukdar HA, Kindt AS, Jain RK, Ermel R, Ruusalepp A, Nguyen KD, Dobrin R, Reilly DF, Schunkert H, Samani NJ, Braenne I, Erdmann J, Melander O, Qi J, Ivert T, Skogsberg J, Schadt EE, Michoel T, Björkegren JL; CARDIoGRAM Consortium.

Circ Cardiovasc Genet. 2015 Apr;8(2):305-15. doi: 10.1161/CIRCGENETICS.114.000640. Epub 2015 Jan 11.

PMID:
25578447
23.

SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer.

Rönsch K, Jägle S, Rose K, Seidl M, Baumgartner F, Freihen V, Yousaf A, Metzger E, Lassmann S, Schüle R, Zeiser R, Michoel T, Hecht A.

Mol Oncol. 2015 Feb;9(2):335-54. doi: 10.1016/j.molonc.2014.08.016. Epub 2014 Sep 16.

24.

Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis.

Shang MM, Talukdar HA, Hofmann JJ, Niaudet C, Asl HF, Jain RK, Rossignoli A, Cedergren C, Silveira A, Gigante B, Leander K, de Faire U, Hamsten A, Ruusalepp A, Melander O, Ivert T, Michoel T, Schadt EE, Betsholtz C, Skogsberg J, Björkegren JL.

Arterioscler Thromb Vasc Biol. 2014 Sep;34(9):2068-77. doi: 10.1161/ATVBAHA.113.302709. Epub 2014 Jun 12.

PMID:
24925974
25.

The Index-based Subgraph Matching Algorithm with General Symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration.

Houbraken M, Demeyer S, Michoel T, Audenaert P, Colle D, Pickavet M.

PLoS One. 2014 May 30;9(5):e97896. doi: 10.1371/journal.pone.0097896. eCollection 2014.

26.

Silencing of the EPHB3 tumor-suppressor gene in human colorectal cancer through decommissioning of a transcriptional enhancer.

Jägle S, Rönsch K, Timme S, Andrlová H, Bertrand M, Jäger M, Proske A, Schrempp M, Yousaf A, Michoel T, Zeiser R, Werner M, Lassmann S, Hecht A.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4886-91. doi: 10.1073/pnas.1314523111. Epub 2014 Mar 18.

27.

Plasma cholesterol-induced lesion networks activated before regression of early, mature, and advanced atherosclerosis.

Björkegren JL, Hägg S, Talukdar HA, Foroughi Asl H, Jain RK, Cedergren C, Shang MM, Rossignoli A, Takolander R, Melander O, Hamsten A, Michoel T, Skogsberg J.

PLoS Genet. 2014 Feb 27;10(2):e1004201. doi: 10.1371/journal.pgen.1004201. eCollection 2014 Feb.

28.

kruX: matrix-based non-parametric eQTL discovery.

Qi J, Asl HF, Björkegren J, Michoel T.

BMC Bioinformatics. 2014 Jan 14;15:11. doi: 10.1186/1471-2105-15-11.

29.

Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants.

Bhosale R, Jewell JB, Hollunder J, Koo AJ, Vuylsteke M, Michoel T, Hilson P, Goossens A, Howe GA, Browse J, Maere S.

Plant Cell. 2013 Aug;25(8):2865-77. doi: 10.1105/tpc.113.112268. Epub 2013 Aug 13.

30.

The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees.

Demeyer S, Michoel T, Fostier J, Audenaert P, Pickavet M, Demeester P.

PLoS One. 2013 Apr 19;8(4):e61183. doi: 10.1371/journal.pone.0061183. Print 2013.

31.

Alignment and integration of complex networks by hypergraph-based spectral clustering.

Michoel T, Nachtergaele B.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Nov;86(5 Pt 2):056111. Epub 2012 Nov 26.

PMID:
23214847
32.

Context-specific transcriptional regulatory network inference from global gene expression maps using double two-way t-tests.

Qi J, Michoel T.

Bioinformatics. 2012 Sep 15;28(18):2325-32. doi: 10.1093/bioinformatics/bts434.

PMID:
22962443
33.

MotifSuite: workflow for probabilistic motif detection and assessment.

Claeys M, Storms V, Sun H, Michoel T, Marchal K.

Bioinformatics. 2012 Jul 15;28(14):1931-2. doi: 10.1093/bioinformatics/bts293. Epub 2012 May 15.

PMID:
22592380
34.

An integrative approach to infer regulation programs in a transcription regulatory module network.

Qi J, Michoel T, Butler G.

J Biomed Biotechnol. 2012;2012:245968. doi: 10.1155/2012/245968. Epub 2012 Apr 11.

35.

Post-transcriptional regulatory networks play a key role in noise reduction that is conserved from micro-organisms to mammals.

Joshi A, Beck Y, Michoel T.

FEBS J. 2012 Sep;279(18):3501-12. doi: 10.1111/j.1742-4658.2012.08571.x. Epub 2012 Apr 10.

36.

Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks.

Michoel T, Joshi A, Nachtergaele B, Van de Peer Y.

Mol Biosyst. 2011 Oct;7(10):2769-78. doi: 10.1039/c1mb05241a. Epub 2011 Aug 23.

PMID:
21860879
37.

Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast.

Joshi A, Van de Peer Y, Michoel T.

Nucleic Acids Res. 2011 Nov;39(21):9108-17. doi: 10.1093/nar/gkr661. Epub 2011 Aug 12.

38.

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks.

Audenaert P, Van Parys T, Brondel F, Pickavet M, Demeester P, Van de Peer Y, Michoel T.

Bioinformatics. 2011 Jun 1;27(11):1587-8. doi: 10.1093/bioinformatics/btr182. Epub 2011 Apr 8.

PMID:
21478195
39.

Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data.

Bonnet E, Michoel T, Van de Peer Y.

Bioinformatics. 2010 Sep 15;26(18):i638-44. doi: 10.1093/bioinformatics/btq395.

40.

Module network inference from a cancer gene expression data set identifies microRNA regulated modules.

Bonnet E, Tatari M, Joshi A, Michoel T, Marchal K, Berx G, Van de Peer Y.

PLoS One. 2010 Apr 14;5(4):e10162. doi: 10.1371/journal.pone.0010162.

41.

Characterizing regulatory path motifs in integrated networks using perturbational data.

Joshi A, Van Parys T, Peer YV, Michoel T.

Genome Biol. 2010;11(3):R32. doi: 10.1186/gb-2010-11-3-r32. Epub 2010 Mar 11.

42.

Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development.

Vermeirssen V, Joshi A, Michoel T, Bonnet E, Casneuf T, Van de Peer Y.

Mol Biosyst. 2009 Dec;5(12):1817-30. doi: 10.1039/B908108a. Epub 2009 Jul 17.

PMID:
19763340
43.

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks.

Michoel T, De Smet R, Joshi A, Van de Peer Y, Marchal K.

BMC Syst Biol. 2009 May 7;3:49. doi: 10.1186/1752-0509-3-49.

44.

Reverse-engineering transcriptional modules from gene expression data.

Michoel T, De Smet R, Joshi A, Marchal K, Van de Peer Y.

Ann N Y Acad Sci. 2009 Mar;1158:36-43. doi: 10.1111/j.1749-6632.2008.03943.x.

PMID:
19348630
45.

Module networks revisited: computational assessment and prioritization of model predictions.

Joshi A, De Smet R, Marchal K, Van de Peer Y, Michoel T.

Bioinformatics. 2009 Feb 15;25(4):490-6. doi: 10.1093/bioinformatics/btn658. Epub 2009 Jan 9.

PMID:
19136553
46.

Analysis of a Gibbs sampler method for model-based clustering of gene expression data.

Joshi A, Van de Peer Y, Michoel T.

Bioinformatics. 2008 Jan 15;24(2):176-83. Epub 2007 Nov 22.

PMID:
18033794
47.

Validating module network learning algorithms using simulated data.

Michoel T, Maere S, Bonnet E, Joshi A, Saeys Y, Van den Bulcke T, Van Leemput K, van Remortel P, Kuiper M, Marchal K, Van de Peer Y.

BMC Bioinformatics. 2007 May 3;8 Suppl 2:S5.

48.

Helicoidal transfer matrix model for inhomogeneous DNA melting.

Michoel T, Van de Peer Y.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jan;73(1 Pt 1):011908. Epub 2006 Jan 13.

PMID:
16486186

Supplemental Content

Loading ...
Support Center