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Items: 1 to 20 of 101

1.

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 Jul 4. pii: S0888-7543(17)30054-X. doi: 10.1016/j.ygeno.2017.06.006. [Epub ahead of print]

PMID:
28684091
2.

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
3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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