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Items: 1 to 20 of 58

1.

The metaRbolomics Toolbox in Bioconductor and beyond.

Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S.

Metabolites. 2019 Sep 23;9(10). pii: E200. doi: 10.3390/metabo9100200. Review.

2.

Journal of Cheminformatics, ORCID, and GitHub.

Willighagen E, Jeliazkova N, Guha R.

J Cheminform. 2019 Jul 8;11(1):44. doi: 10.1186/s13321-019-0365-4. No abstract available.

3.

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.

Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

The future of metabolomics in ELIXIR.

van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C.

Version 2. F1000Res. 2017 Sep 6 [revised 2017 Jan 1];6. pii: ELIXIR-1649. doi: 10.12688/f1000research.12342.2. eCollection 2017.

11.

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
12.

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.

13.

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.

14.

Helping to improve the practice of cheminformatics.

Guha R, Willighagen E.

J Cheminform. 2017 Jun 14;9(1):40. doi: 10.1186/s13321-017-0217-z. No abstract available.

15.

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.

16.

Adverse outcome pathways: opportunities, limitations and open questions.

Leist M, Ghallab A, Graepel R, Marchan R, Hassan R, Bennekou SH, Limonciel A, Vinken M, Schildknecht S, Waldmann T, Danen E, van Ravenzwaay B, Kamp H, Gardner I, Godoy P, Bois FY, Braeuning A, Reif R, Oesch F, Drasdo D, Höhme S, Schwarz M, Hartung T, Braunbeck T, Beltman J, Vrieling H, Sanz F, Forsby A, Gadaleta D, Fisher C, Kelm J, Fluri D, Ecker G, Zdrazil B, Terron A, Jennings P, van der Burg B, Dooley S, Meijer AH, Willighagen E, Martens M, Evelo C, Mombelli E, Taboureau O, Mantovani A, Hardy B, Koch B, Escher S, van Thriel C, Cadenas C, Kroese D, van de Water B, Hengstler JG.

Arch Toxicol. 2017 Nov;91(11):3477-3505. doi: 10.1007/s00204-017-2045-3. Epub 2017 Oct 19. Review.

PMID:
29051992
17.

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management.

Lampa S, Willighagen E, Kohonen P, King A, Vrandečić D, Grafström R, Spjuth O.

J Biomed Semantics. 2017 Sep 4;8(1):35. doi: 10.1186/s13326-017-0136-y.

18.

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury.

Kohonen P, Parkkinen JA, Willighagen EL, Ceder R, Wennerberg K, Kaski S, Grafström RC.

Nat Commun. 2017 Jul 3;8:15932. doi: 10.1038/ncomms15932.

19.

SPLASH, a hashed identifier for mass spectra.

Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O.

Nat Biotechnol. 2016 Nov 8;34(11):1099-1101. doi: 10.1038/nbt.3689. No abstract available.

20.

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.

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