• Universiteitssingel50, UNS50

    6229 ER Maastricht

    Netherlands

Research Output

2014

The first eNanoMapper prototype: A substance database to support safe-by-design

Jeliazkova, N., Doganis, P., Fadeel, B., Grafström, R., Hastings, J., Jeliazkov, V., Kohonen, P., Munteanu, C. R., Sarimveis, H., Smeets, B., Tsiliki, G., Vorgrimmler, D. & Willighagen, E. L., 1 Jan 2014, Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on. Bart Smeets, Georgia Tsiliki, David Vorgrimmler, p. 1-9

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review

Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism

Elliott, R. M., de Roos, B., Duthie, S. J., Bouwman, F. G., Rubio Aliaga, I., Crosley, L. K., Mayer, C., Polley, A. C., Heim, C., Coort, S., Evelo, C. T., Mulholland, F., Daniel, H., Mariman, E. C. & Johnson, I. T., Nov 2014, In : Genes and nutrition. 9, 6, 11 p., 432.

Research output: Contribution to journalArticleAcademicpeer-review

WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

Kutmon, M., Lotia, S., Evelo, C. T. & Pico, A. R., 1 Jan 2014, In : F1000Research. 3, p. 152

Research output: Contribution to journalArticleAcademicpeer-review

2013

A pathway approach to investigate the function and regulation of SREBPs.

Daemen, S., Kutmon, M. & Evelo, C. T. A., 1 Jan 2013, In : Genes and nutrition. 8, 3, p. 289-300

Research output: Contribution to journalArticleAcademicpeer-review

Applications of the InChI in cheminformatics with the CDK and Bioclipse.

Spjuth, O., von Berg, A., Adams, S. & Willighagen, E. L., 13 Mar 2013, In : Journal of Cheminformatics. 5, 1, p. 14 7 p., 14.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Bioclipse-R: integrating management and visualization of life science data with statistical analysis

Spjuth, O., Georgiev, V., Carlsson, L., Alvarsson, J., Berg, A., Willighagen, E., Wikberg, J. E. & Eklund, M., 1 Jan 2013, In : Bioinformatics. 29, 2, p. 286-289

Research output: Contribution to journalArticleAcademicpeer-review

CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis

Kutmon, M., Kelder, T., Mandaviya, P., Evelo, C. T. & Coort, S. L., 5 Dec 2013, In : PLOS ONE. 8, 12, 9 p., e82160.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Incorporating commercial and private data into an open linked data platform for drug discovery

Goble, C., Gray, A. J. G., Harland, L., Karapetyan, K., Loizou, A., Mikhailov, I., Rankka, Y., Senger, S., Tkachenko, V., Williams, A. J. & Willighagen, E., 1 Jan 2013, Sydney: NSW. (Lecture Notes in Computer Science, Vol. 8218).

Research output: Book/ReportBook

Open PHACTS: Meaningful linking of preclinical drug discovery knowledge

Willighagen, E. L., Brenninkmeijer, C., Evelo, C. T., Harland, L., Gray, A. J. G., Goble, C., Waagmeester, A. S. & Williams, A. J., 1 Jan 2013.

Research output: Contribution to conferenceAbstractAcademic

Personality profile of the children of long-lived parents

Antoniou, E. E., Dutta, A., Langa, K. M., Melzer, D. & Llewellyn, D., 1 Jan 2013, In : Journals of Gerontology Series B-Psychological Sciences and Social Sciences. 68, 5, p. 730-738

Research output: Contribution to journalArticleAcademicpeer-review

Safety and Efficacy of Bridging with Low Molecular Weight Heparins: A Systematic Review and Partial Meta-Analysis

Eijgenraam, P., ten Cate, H. & ten Cate-Hoek, A., Jul 2013, In : Current Pharmaceutical Design. 19, 22, p. 4014-4023

Research output: Contribution to journalArticleAcademicpeer-review

Semantic annotation of PubChem databases

Fu, G., Batchelor, C., Dumontier, M., Hastings, J., Kuecuek, H., Schurer, S. C., Vempati, U., Willighagen, E. & Bolton, E., 8 Sep 2013.

Research output: Contribution to conferenceAbstractAcademic

The ChEMBL database as linked open data

Willighagen, E. L., Waagmeester, A. S., Spjuth, O., Ansell, P., Williams, A. J., Tkachenko, V., Hastings, J., Chen, B. & Wild, D. J., 8 May 2013, In : Journal of Cheminformatics. 5, 1, 12 p., 23.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The Immediate Early Gene Product EGR1 and Polycomb Group Proteins Interact in Epigenetic Programming during Chondrogenesis

Saapen, F., van den Akker, G. G. H., Caron, M. M. J., Prickaerts, P., Rofel, C., Dahlmans, V. E. H., Surtel, D. A. M., Paulis, Y., Schweizer, F., Welting, T. J. M., Eijssen, L. M. & Voncken, J. W., 6 Mar 2013, In : PLOS ONE. 8, 3, 16 p., 58083.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R. C., Healy, L., Helma, C., Jeliazkova, N., Jeliazkova, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, S., Willighagen, E., Wiseman, J. & Hardy, B., 1 Jan 2013, In : Molecular Informatics. 32, 1, p. 47-63 17 p.

Research output: Contribution to journalArticleAcademicpeer-review

User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org.

Eijssen, L. M. T., Jaillard, M. N. L., Michiel Adriaens, M. E., Gaj, S., de Groot, P. J., Muller, M. & Evelo, C. T. A., 1 Jan 2013, In : Nucleic Acids Research. 41W1, p. W71-76

Research output: Contribution to journalArticleAcademicpeer-review

2012

Accessing, Using, and Creating Chemical Property Databases for Computational Toxicology Modeling

Williams, A. J., Ekins, S., Spjuth, O. & Willighagen, E. L., 1 Jan 2012, Computational Toxicology. Reisfeld, B. & Mayeno, A. M. (eds.). Springer, p. 221-241 (Methods in Molecular Biology; No. 929).

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

Michiel Adriaens, M. E., Jaillard, M. N. L., Eijssen, L. M. T., Mayer, C. D. & Evelo, C. T. A., 25 Jan 2012, In : BMC Genomics. 13, 1, p. 42 14 p., 42.

Research output: Contribution to journalArticleAcademicpeer-review

A survey of quantitative descriptions of molecular structure

Guha, R. & Willighagen, E., Sep 2012, In : Current Topics in Medicinal Chemistry. 12, 18, p. 1946-1956 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Bilberries potentially alleviate stress-related retinal gene expression induced by a high-fat diet in mice

Mykkanen, O. T., Kalesnykas, G., Adriaens, M., Evelo, C. T., Torronen, R. & Kaarniranta, K., 7 Sep 2012, In : Molecular Vision. 18, 247, p. 2338-2351 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Changing computational research. The challenges ahead

Neylon, C., Aerts, J., Brown, C. T., Coles, S. J., Hatton, L., Lemire, D., Millman, K. J., Murray-Rust, P., Perez, F., Saunders, N., Shah, N., Smith, A., Varoquaux, G. & Willighagen, E., 1 Jan 2012, In : Source code for biology and medicine. 7, 1, p. 2

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Cheminformatics

Wegner, J. K., Sterling, A., Guha, R., Bender, A., Faulon, J. L., Hastings, J., O'Boyle, N., Overington, J., Van Vlijmen, H. & Willighagen, E., 1 Jan 2012, In : Communications of the Acm. 55, 11, p. 65-75

Research output: Contribution to journalArticleAcademicpeer-review

136 Downloads (Pure)

Effect of supplementation with an 80:20 cis9,trans11 conjugated linoleic acid blend on the human platelet proteome.

Bachmair, E. M., Bots, M. L., Mennen, L. I., Kelder, T. A. J., Evelo, C. T. A., Horgan, G. W., Ford, I. & de Roos, B., 1 Jan 2012, In : Molecular Nutrition & Food Research. 56, 7, p. 1148-1159

Research output: Contribution to journalArticleAcademicpeer-review

Emerging practices for mapping and linking life sciences data using RDF - A case series

Marshall, M. S., Boyce, R., Deus, H. F., Zhao, J., Willighagen, E. L., Samwald, M., Pichler, E., Hajagos, J., Prud'hommeaux, E. & Stephens, S., Jul 2012, In : Journal of Web Semantics. 14, p. 2-13 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Game-Tree Search Using Proof Numbers: The First Twenty Years

Kishimoto, A., Winands, M. H. M., Müller, M. & Saito, J-T., Sep 2012, In : ICGA Journal. 35, 3, p. 131-156

Research output: Contribution to journalArticleAcademicpeer-review

GO-Elite: a flexible solution for pathway and ontology over-representation.

Zambon, A. C., Gaj, S., Ho, I., Hanspers, K., Vranizan, K., Evelo, C. T. A., Conklin, B. R., Pico, A. R. & Salomonis, N., 15 Aug 2012, In : Bioinformatics. 28, 16, p. 2209-2210 2 p.

Research output: Contribution to journalArticleAcademicpeer-review

Interactive predictive toxicology with Bioclipse and OpenTox

Willighagen, E. L., Affentranger, R., Grafström, R., Hardy, B., Jeliazkova, N. & Spjuth, O., 1 Jan 2012, Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond. Harland, L. & Forster, M. (eds.). TOC, (Woodhead Publishing Series in Biomedicine; No. 16).

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Marginal selenium deficiency down-regulates inflammation-related genes in splenic leukocytes of the mouse.

Kipp, A. P., Banning, A., van Schothorst, E. M., Meplan, C., Coort, S. L. M., Evelo, C. T. A., Keijer, J., Hesketh, J. & Brigelius Flohe, R., Sep 2012, In : Journal of Nutritional Biochemistry. 23, 9, p. 1170-1177 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

MicroRNA profiling identifies microRNA-155 as an adverse mediator of cardiac injury and dysfunction during acute viral myocarditis.

Corsten, M. F., Papageorgiou, A., Verhesen, W., Carai, P., Lindow, M., Obad, S., Summer, G., Coort, S. L. M., Hazebroek, M., van Leeuwen, R., Gijbels, M. J. J., Wijnands, E., Biessen, E. A., de Winther, M. P. J., Stassen, F. R. M., Carmeliet, P., Kauppinen, S., Schroen, B. & Heymans, S., 3 Aug 2012, In : Circulation Research. 111, 4, p. 415-425

Research output: Contribution to journalArticleAcademicpeer-review

Molecular pathways involved in prostate carcinogenesis: insights from public microarray datasets

Baetke, S. C., Michiel Adriaens, M. E., Seigneuric, R., Evelo, C. T. A. & Eijssen, L. M. T., 20 Nov 2012, In : PLOS ONE. 7, 11, 11 p., e49831.

Research output: Contribution to journalArticleAcademicpeer-review

Open PHACTS: semantic interoperability for drug discovery

Williams, A. J., Harland, L., Groth, P., Pettifer, S., Chichester, C., Willighagen, E. L., Evelo, C. T., Blomberg, N., Ecker, G., Goble, C. & Mons, B., Nov 2012, In : Drug Discovery Today. 17, 21-22, p. 1188-1198 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open source drug discovery with bioclipse.

Spjuth, O., Carlsson, L., Alvarsson, J., Georgiev, V., Willighagen, E. & Eklund, M., 1 Jan 2012, In : Current Topics in Medicinal Chemistry. 12, 18, p. 1980-6

Research output: Contribution to journalArticleAcademicpeer-review

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.

Chandan, K., van Iersel, M. P., Aladjem, M. I., Kohn, K. W. & Luna, A., 1 Jan 2012, In : Bioinformatics. 28, 6, p. 889-890 2 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
166 Downloads (Pure)

Scientific Lenses over Linked Data: An Approach to Support Task Specific Views of the Data. A Vision

Brenninkmeijer, C., Evelo, C. T. A., Goble, C., Gray, A. J. G., Groth, P., Pettifer, S., Stevens, R., Williams, A. J. & Willighagen, E. L., 1 Jan 2012, In : Linked Science.

Research output: Contribution to journalConference article in journalAcademic

Software support for SBGN maps: SBGN-ML and LibSBGN.

van Iersel, M. P., Villeger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F. T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y., Funahashi, A., Aladjem, M. I., Mi, H., Moodie, S. L., Kitano, H., Le Novere, N. & Schreiber, F., 1 Jan 2012, In : Bioinformatics. 28, 15, p. 2016-21

Research output: Contribution to journalArticleAcademicpeer-review

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

Wang, X., Wei, X., Thijssen, B., Das, J., Lipkin, S. M. & Yu, H., Feb 2012, In : Nature Biotechnology. 30, 2, p. 159-164 6 p.

Research output: Contribution to journalArticleAcademicpeer-review

Toward interoperable bioscience data

Sansone, S. A., Rocca Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral Zettler, L., Begley, K., Booth, T., Bougueleret, L., Burns, G., Chapman, B., Clark, T., Coleman, L. A., Copeland, J., Das, S., de Daruvar, A. & 30 others, de Matos, P., Dix, I., Edmunds, S., Evelo, C. T. A., Forster, M. J., Gaudet, P., Gilbert, J., Goble, C., Griffin, J. L., Jacob, D., Kleinjans, J., Harland, L., Haug, K., Hermjakob, H., Ho Sui, S. J., Laederach, A., Liang, S., Marshall, S., McGrath, A., Merrill, E., Reilly, D., Roux, M., Shamu, C. E., Shang, C. A., Steinbeck, C., Trefethen, A., Jones, B., Wolstencroft, K., Xenarios, I. & Hide, W., Feb 2012, In : Nature Genetics. 44, 2, p. 121-126 6 p.

Research output: Contribution to journalArticleAcademicpeer-review

65 Downloads (Pure)

Wikipathways: Building research communities on biological pathways

Kelder, T. A. J., van Iersel, M. P., Hanspers, K., Kutmon, M., Conklin, B. R., Evelo, C. T. A. & Pico, A. R., 1 Jan 2012, In : Nucleic Acids Research. 40, 1, p. D1301-D1307

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
263 Downloads (Pure)
2011

2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting

Bouwman, F. G., de Roos, B., Rubio Aliaga, I., Crosley, L. K., Duthie, S. J., Mayer, C., Horgan, G., Polley, A. C., Heim, C., Coort, S. L. M., Evelo, C. T. A., Mulholland, F., Johnson, I. T., Elliott, R. M., Daniel, H. & Mariman, E. C., 1 Jan 2011, In : BMC Medical Genomics. 4, 1, p. 24

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
192 Downloads (Pure)

Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention

Rubio-Aliaga, I., de Roos, B., Sailer, M., McLoughlin, G. A., Boekschoten, M. V., van Erk, M., Bachmair, E. M., van Schothorst, E. M., Keijer, J., Coort, S. L. M., Evelo, C. T. A., Gibney, M. J., Daniel, H., Muller, M., Kleemann, R. & Brennan, L., 1 Jan 2011, In : Physiological genomics. 43, 8, p. 408-416

Research output: Contribution to journalArticleAcademicpeer-review

Answering biological questions: querying a systems biology database for nutrigenomics

Evelo, C. T. A., van Bochove, G. S. & Saito, J. T., Feb 2011, In : Genes and nutrition. 6, 1, p. 81-87 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Bioinformatics: A brief introduction to changing trends in modern biology

Singh, A. & Somvanshi, P., 1 Jan 2011, OMICS: Biomedical perspectives and applications. Barth, D., Blum, K. & Madigan, M. A. (eds.). CRC Press, p. 23-39

Research output: Chapter in Book/Report/Conference proceedingChapterProfessional

Computational toxicology using the OpenTox application programming interface and Bioclipse

Willighagen, E. L., Jeliazkova, N., Hardy, B., Grafstrom, R. C. & Spjuth, O., 1 Jan 2011, In : BMC Research Notes. 4, p. 487

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Epigenetics: prenatal exposure to genistein leaves a permanent signature on the hematopoietic lineage.

Vanhees, K., Coort, S. L. M., Ruijters, E. J. B., Godschalk, R. W. L., van Schooten, F. J. & Khosrovani, S. B., 1 Jan 2011, In : Faseb Journal. 25, 2, p. 797-807

Research output: Contribution to journalArticleAcademicpeer-review

Exploratory pathway analysis

Kelder, T. A. J., 1 Jan 2011, Maastricht: Maastricht University.

Research output: ThesisDoctoral ThesisInternal

Open Access
File
361 Downloads (Pure)

Exploring pathway interactions in insulin resistant mouse liver

Kelder, T. A. J., Eijssen, L. M. T., Kleemann, R., van Erk, M., Kooistra, T. & Evelo, C. T. A., 15 Aug 2011, In : BMC Systems Biology. 5, p. 18 18 p., 127.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
204 Downloads (Pure)

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)

Luna, A., Sunshine, M. L., van Iersel, M. P., Aladjem, M. I. & Kohn, K. W., 1 Aug 2011, In : Bioinformatics. 27, 15, p. 2165-2166 2 p.

Research output: Contribution to journalArticleAcademicpeer-review