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Items: 1 to 50 of 129

1.

Logical modelling reveals the PDC-PDK interaction as the regulatory switch driving metabolic flexibility at the cellular level.

Tareen SH, Kutmon M, Arts IC, de Kok TM, Evelo CT, Adriaens ME.

Genes Nutr. 2019 Sep 9;14:27. doi: 10.1186/s12263-019-0647-5. eCollection 2019.

2.

Subcutaneous Adipose Tissue and Systemic Inflammation Are Associated With Peripheral but Not Hepatic Insulin Resistance in Humans.

van der Kolk BW, Kalafati M, Adriaens M, van Greevenbroek MMJ, Vogelzangs N, Saris WHM, Astrup A, Valsesia A, Langin D, van der Kallen CJH, Eussen SJPM, Schalkwijk CG, Stehouwer CDA, Goossens GH, Arts ICW, Jocken JWE, Evelo CT, Blaak EE.

Diabetes. 2019 Dec;68(12):2247-2258. doi: 10.2337/db19-0560. Epub 2019 Sep 6.

PMID:
31492661
3.

Network Analysis of Genome-Wide Association Studies for Chronic Obstructive Pulmonary Disease in the Context of Biological Pathways.

Mount S, Cirillo E, Stewart K, Coort S, Evelo CT, Wesselius A, Zeegers MP, Schols AMWJ.

Am J Respir Crit Care Med. 2019 Dec 1;200(11):1439-1441. doi: 10.1164/rccm.201904-0902LE. No abstract available.

PMID:
31343902
4.

Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma.

Liesenborghs I, Eijssen LMT, Kutmon M, Gorgels TGMF, Evelo CT, Beckers HJM, Webers CAB, Schouten JSAG.

Acta Ophthalmol. 2019 Jun 14. doi: 10.1111/aos.14154. [Epub ahead of print]

PMID:
31197946
5.

Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes.

Ehrhart F, Coort SL, Eijssen L, Cirillo E, Smeets EE, Bahram Sangani N, Evelo CT, Curfs LMG.

World J Biol Psychiatry. 2019 Mar 25:1-14. doi: 10.1080/15622975.2019.1593501. [Epub ahead of print]

PMID:
30907210
6.

Addendum: The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, Hoen PAC', Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Jan Velterop, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2019 Mar 19;6(1):6. doi: 10.1038/s41597-019-0009-6. No abstract available.

7.

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome.

Miller RA, Ehrhart F, Eijssen LMT, Slenter DN, Curfs LMG, Evelo CT, Willighagen EL, Kutmon M.

Front Genet. 2019 Feb 21;10:59. doi: 10.3389/fgene.2019.00059. eCollection 2019.

8.

A bioinformatics workflow to decipher transcriptomic data from vitamin D studies.

Muñoz García A, Eijssen LM, Kutmon M, Sarathy C, Cengo A, Hewison M, Evelo CT, Lenz M, Coort SL.

J Steroid Biochem Mol Biol. 2019 May;189:28-35. doi: 10.1016/j.jsbmb.2019.01.003. Epub 2019 Feb 1. Review.

9.

Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus-A Co-expression Network Based Analysis.

Siddiqa A, Cirillo E, Tareen SHK, Ali A, Kutmon M, Eijssen LMT, Ahmad J, Evelo CT, Coort SL.

Front Physiol. 2018 Dec 21;9:1841. doi: 10.3389/fphys.2018.01841. eCollection 2018.

10.

Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials.

Martens M, Verbruggen T, Nymark P, Grafström R, Burgoon LD, Aladjov H, Torres Andón F, Evelo CT, Willighagen EL.

Front Genet. 2018 Dec 21;9:661. doi: 10.3389/fgene.2018.00661. eCollection 2018.

11.

Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform.

Miller RA, Woollard P, Willighagen EL, Digles D, Kutmon M, Loizou A, Waagmeester A, Senger S, Evelo CT.

Version 2. F1000Res. 2018 Jan 17 [revised 2018 Jan 1];7:75. doi: 10.12688/f1000research.13197.2. eCollection 2018.

12.

Profiling Cellular Processes in Adipose Tissue during Weight Loss Using Time Series Gene Expression.

Tareen SHK, Adriaens ME, Arts ICW, de Kok TM, Vink RG, Roumans NJT, van Baak MA, Mariman ECM, Evelo CT, Kutmon M.

Genes (Basel). 2018 Oct 29;9(11). pii: E525. doi: 10.3390/genes9110525.

13.

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations.

Karcher S, Willighagen EL, Rumble J, Ehrhart F, Evelo CT, Fritts M, Gaheen S, Harper SL, Hoover MD, Jeliazkova N, Lewinski N, Marchese Robinson RL, Mills KC, Mustad AP, Thomas DG, Tsiliki G, Ogilvie Hendren C.

NanoImpact. 2018 Jan;9:85-101. doi: 10.1016/j.impact.2017.11.002.

14.

Differential protein expression of hippocampal cells associated with heavy metals (Pb, As, and MeHg) neurotoxicity: Deepening into the molecular mechanism of neurodegenerative diseases.

Karri V, Ramos D, Martinez JB, Odena A, Oliveira E, Coort SL, Evelo CT, Mariman ECM, Schuhmacher M, Kumar V.

J Proteomics. 2018 Sep 15;187:106-125. doi: 10.1016/j.jprot.2018.06.020. Epub 2018 Jul 12.

PMID:
30017948
15.

Role of 1α,25-Dihydroxyvitamin D3 in Adipogenesis of SGBS Cells: New Insights into Human Preadipocyte Proliferation.

Felicidade I, Sartori D, Coort SLM, Semprebon SC, Niwa AM, D'Epiro GFR, Biazi BI, Marques LA, Evelo CT, Mantovani MS, Ribeiro LR.

Cell Physiol Biochem. 2018;48(1):397-408. doi: 10.1159/000491770. Epub 2018 Jul 17.

16.

Exploring the cellular network of metabolic flexibility in the adipose tissue.

Tareen SHK, Kutmon M, Adriaens ME, Mariman ECM, de Kok TM, Arts ICW, Evelo CT.

Genes Nutr. 2018 Jul 5;13:17. doi: 10.1186/s12263-018-0609-3. eCollection 2018. Review.

17.

CyTargetLinker app update: A flexible solution for network extension in Cytoscape.

Kutmon M, Ehrhart F, Willighagen EL, Evelo CT, Coort SL.

Version 2. F1000Res. 2018 Jun 14 [revised 2019 Jan 1];7. pii: ELIXIR-743. doi: 10.12688/f1000research.14613.2. eCollection 2018.

18.

Review and gap analysis: molecular pathways leading to fetal alcohol spectrum disorders.

Ehrhart F, Roozen S, Verbeek J, Koek G, Kok G, van Kranen H, Evelo CT, Curfs LMG.

Mol Psychiatry. 2019 Jan;24(1):10-17. doi: 10.1038/s41380-018-0095-4. Epub 2018 Jun 11. Review.

19.

MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases.

Townend GS, Ehrhart F, van Kranen HJ, Wilkinson M, Jacobsen A, Roos M, Willighagen EL, van Enckevort D, Evelo CT, Curfs LMG.

Hum Mutat. 2018 Jul;39(7):914-924. doi: 10.1002/humu.23542. Epub 2018 May 21.

20.

From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results.

Cirillo E, Kutmon M, Gonzalez Hernandez M, Hooimeijer T, Adriaens ME, Eijssen LMT, Parnell LD, Coort SL, Evelo CT.

PLoS One. 2018 Apr 4;13(4):e0193515. doi: 10.1371/journal.pone.0193515. eCollection 2018.

21.

Prader-Willi syndrome and Angelman syndrome: Visualisation of the molecular pathways for two chromosomal disorders.

Ehrhart F, Janssen KJM, Coort SL, Evelo CT, Curfs LMG.

World J Biol Psychiatry. 2018 Mar 1:1-13. doi: 10.1080/15622975.2018.1439594. [Epub ahead of print]

PMID:
29425059
22.

Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D.

Muñoz Garcia A, Kutmon M, Eijssen L, Hewison M, Evelo CT, Coort SL.

J Mol Endocrinol. 2018 Feb;60(2):95-108. doi: 10.1530/JME-17-0186. Epub 2017 Dec 12.

23.

A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.

Cirillo E, Parnell LD, Evelo CT.

Front Genet. 2017 Nov 7;8:174. doi: 10.3389/fgene.2017.00174. eCollection 2017. Review.

24.

A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions.

Nymark P, Rieswijk L, Ehrhart F, Jeliazkova N, Tsiliki G, Sarimveis H, Evelo CT, Hongisto V, Kohonen P, Willighagen E, Grafström RC.

Toxicol Sci. 2018 Mar 1;162(1):264-275. doi: 10.1093/toxsci/kfx252.

PMID:
29149350
25.

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E, Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida K, Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL.

Nucleic Acids Res. 2018 Jan 4;46(D1):D661-D667. doi: 10.1093/nar/gkx1064.

26.

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C.

J Cheminform. 2017 Sep 20;9(1):53. doi: 10.1186/s13321-017-0231-1. No abstract available.

27.

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C.

J Cheminform. 2017 Jun 6;9(1):33. doi: 10.1186/s13321-017-0220-4. Erratum in: J Cheminform. 2017 Sep 20;9(1):53.

28.

Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures.

Curran AM, Fogarty Draper C, Scott-Boyer MP, Valsesia A, Roche HM, Ryan MF, Gibney MJ, Kutmon M, Evelo CT, Coort SL, Astrup A, Saris WH, Brennan L, Kaput J.

J Proteome Res. 2017 Nov 3;16(11):4122-4133. doi: 10.1021/acs.jproteome.7b00501. Epub 2017 Oct 4.

PMID:
28950061
29.

Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways.

Siddiqa A, Cirillo E, Tareen SHK, Ali A, Kutmon M, Eijssen LMT, Ahmad J, Evelo CT, Coort SL.

Genomics. 2017 Oct;109(5-6):408-418. doi: 10.1016/j.ygeno.2017.06.006. Epub 2017 Jul 4.

30.

Maternal folate depletion during early development and high fat feeding from weaning elicit similar changes in gene expression, but not in DNA methylation, in adult offspring.

McKay JA, Xie L, Adriaens M, Evelo CT, Ford D, Mathers JC.

Mol Nutr Food Res. 2017 Apr;61(4). doi: 10.1002/mnfr.201600713. Epub 2017 Feb 6.

PMID:
27928883
31.

Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes.

Ehrhart F, Coort SL, Cirillo E, Smeets E, Evelo CT, Curfs LM.

Orphanet J Rare Dis. 2016 Nov 25;11(1):158. Review.

32.

Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia.

Adriaens ME, Prickaerts P, Chan-Seng-Yue M, van den Beucken T, Dahlmans VEH, Eijssen LM, Beck T, Wouters BG, Voncken JW, Evelo CTA.

Epigenetics Chromatin. 2016 Nov 1;9:48. doi: 10.1186/s13072-016-0090-4. eCollection 2016.

33.

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3.

Prickaerts P, Adriaens ME, Beucken TVD, Koch E, Dubois L, Dahlmans VEH, Gits C, Evelo CTA, Chan-Seng-Yue M, Wouters BG, Voncken JW.

Epigenetics Chromatin. 2016 Oct 26;9:46. doi: 10.1186/s13072-016-0086-0. eCollection 2016.

34.

Organ-Specific Gene Expression Changes in the Fetal Liver and Placenta in Response to Maternal Folate Depletion.

McKay JA, Xie L, Adriaens M, Evelo CT, Ford D, Mathers JC.

Nutrients. 2016 Oct 22;8(10). pii: E661.

35.

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.

Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibás B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E.

Medchemcomm. 2016 Jun 1;7(6):1237-1244. Epub 2016 May 11.

36.

XMetDB: an open access database for xenobiotic metabolism.

Spjuth O, Rydberg P, Willighagen EL, Evelo CT, Jeliazkova N.

J Cheminform. 2016 Sep 15;8:47. doi: 10.1186/s13321-016-0161-3. eCollection 2016.

37.

New insights in Rett syndrome using pathway analysis for transcriptomics data.

Ehrhart F, Coort SL, Cirillo E, Smeets E, Evelo CT, Curfs L.

Wien Med Wochenschr. 2016 Sep;166(11-12):346-52. doi: 10.1007/s10354-016-0488-4. Epub 2016 Aug 12.

38.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen EL, Evelo CT, Pico AR.

PLoS Comput Biol. 2016 Jun 23;12(6):e1004989. doi: 10.1371/journal.pcbi.1004989. eCollection 2016 Jun.

39.

Reactome from a WikiPathways Perspective.

Bohler A, Wu G, Kutmon M, Pradhana LA, Coort SL, Hanspers K, Haw R, Pico AR, Evelo CT.

PLoS Comput Biol. 2016 May 20;12(5):e1004941. doi: 10.1371/journal.pcbi.1004941. eCollection 2016 May.

40.

Gene promoter DNA methylation patterns have a limited role in orchestrating transcriptional changes in the fetal liver in response to maternal folate depletion during pregnancy.

McKay JA, Adriaens M, Evelo CT, Ford D, Mathers JC.

Mol Nutr Food Res. 2016 Sep;60(9):2031-42. doi: 10.1002/mnfr.201600079. Epub 2016 Jun 6.

41.

The systems biology format converter.

Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N.

BMC Bioinformatics. 2016 Apr 5;17:154. doi: 10.1186/s12859-016-1000-2.

42.

The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18. Erratum in: Sci Data. 2019 Mar 19;6(1):6.

43.

WikiPathways: capturing the full diversity of pathway knowledge.

Kutmon M, Riutta A, Nunes N, Hanspers K, Willighagen EL, Bohler A, Mélius J, Waagmeester A, Sinha SR, Miller R, Coort SL, Cirillo E, Smeets B, Evelo CT, Pico AR.

Nucleic Acids Res. 2016 Jan 4;44(D1):D488-94. doi: 10.1093/nar/gkv1024. Epub 2015 Oct 19.

44.

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

Bohler A, Eijssen LM, van Iersel MP, Leemans C, Willighagen EL, Kutmon M, Jaillard M, Evelo CT.

BMC Bioinformatics. 2015 Aug 23;16:267. doi: 10.1186/s12859-015-0708-8.

45.

Integrative network-based analysis of mRNA and microRNA expression in 1,25-dihydroxyvitamin D3-treated cancer cells.

Kutmon M, Coort SL, de Nooijer K, Lemmens C, Evelo CT.

Genes Nutr. 2015 Sep;10(5):35. doi: 10.1007/s12263-015-0484-0. Epub 2015 Aug 15.

46.

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

Eijssen LM, Goelela VS, Kelder T, Adriaens ME, Evelo CT, Radonjic M.

BMC Genomics. 2015 Jun 30;16:482. doi: 10.1186/s12864-015-1689-8.

47.

PathVisio 3: an extendable pathway analysis toolbox.

Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT.

PLoS Comput Biol. 2015 Feb 23;11(2):e1004085. doi: 10.1371/journal.pcbi.1004085. eCollection 2015 Feb.

48.

The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research.

Ratnam J, Zdrazil B, Digles D, Cuadrado-Rodriguez E, Neefs JM, Tipney H, Siebes R, Waagmeester A, Bradley G, Chau CH, Richter L, Brea J, Evelo CT, Jacoby E, Senger S, Loza MI, Ecker GF, Chichester C.

PLoS One. 2014 Dec 18;9(12):e115460. doi: 10.1371/journal.pone.0115460. eCollection 2014.

49.

diXa: a data infrastructure for chemical safety assessment.

Hendrickx DM, Aerts HJ, Caiment F, Clark D, Ebbels TM, Evelo CT, Gmuender H, Hebels DG, Herwig R, Hescheler J, Jennen DG, Jetten MJ, Kanterakis S, Keun HC, Matser V, Overington JP, Pilicheva E, Sarkans U, Segura-Lepe MP, Sotiriadou I, Wittenberger T, Wittwehr C, Zanzi A, Kleinjans JC.

Bioinformatics. 2015 May 1;31(9):1505-7. doi: 10.1093/bioinformatics/btu827. Epub 2014 Dec 12.

50.

A network biology workflow to study transcriptomics data of the diabetic liver.

Kutmon M, Evelo CT, Coort SL.

BMC Genomics. 2014 Nov 15;15:971. doi: 10.1186/1471-2164-15-971.

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