• Universiteitssingel50, UNS50

    6229 ER Maastricht

    Netherlands

Research Output

2016

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

McKay, J. A., Xie, L., Adriaens, M., Evelo, C. T., Ford, D. & Mathers, J. C., 22 Oct 2016, In : Nutrients. 8, 10, 20 p., 661.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Adriaens, M. E., Prickaerts, P., Chan-Seng-Yue, M., van den Beucken, T., Dahlmans, V. E. H., Eijssen, L. M., Beck, T., Wouters, B. G., Voncken, W. & Evelo, C. T. A., 1 Nov 2016, In : Epigenetics & Chromatin. 9, 48.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Reactome from a WikiPathways Perspective

Bohler, A., Wu, G., Kutmon, M., Pradhana, L. A., Steinbusch - Coort, S., Hanspers, K., Haw, R., Pico, A. R. & Evelo, C. T., May 2016, In : PLoS Computational Biology. 12, 5, e1004941.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes

Ehrhart, F., Steinbusch - Coort, S., Cirillo, E., Smeets, E., Evelo, C. T. & Curfs, L. M. G., 25 Nov 2016, In : Orphanet Journal of Rare Diseases. 11, 13 p., 158.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

SPLASH, a hashed identifier for mass spectra

Wohlgemuth, G., Mehta, S. S., Mejia, R. F., Neumann, S., Pedrosa, D., Pluskal, T., Schymanski, E. L., Willighagen, E. L., Wilson, M., Wishart, D. S., Arita, M., Dorrestein, P. C., Bandeira, N., Wang, M., Schulze, T., Salek, R. M., Steinbeck, C., Nainala, V. C., Mistrik, R., Nishioka, T. & 1 others, Fiehn, O., Nov 2016, In : Nature Biotechnology. 34, 11, p. 1099-1101

Research output: Contribution to journalComment/Letter to the editorAcademicpeer-review

Open Access
File
94 Downloads (Pure)

The systems biology format converter

Rodriguez, N., Pettit, J-B., Pezze, P. D., Li, L., Henry, A., van Iersel, M. P., Jalowicki, G., Kutmon, M., Natarajan, K. N., Tolnay, D., Stefan, M. I., Evelo, C. T. & Le Novere, N., 5 Apr 2016, In : BMC Bioinformatics. 17, 154.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Waagmeester, A., Kutmon, M., Riutta, A., Miller, R., Willighagen, E. L., Evelo, C. T. & Pico, A. R., Jun 2016, In : PLoS Computational Biology. 12, 6, 11 p., e1004989.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

WikiPathways: capturing the full diversity of pathway knowledge

Kutmon, M., Riutta, A., Nunes, N., Hanspers, K., Willighagen, E. L., Bohler, A., Melius, J., Waagmeester, A., Sinha, S. R., Miller, R., Coort, S. L., Cirillo, E., Smeets, B., Evelo, C. T. & Pico, A. R., 4 Jan 2016, In : Nucleic Acids Research. 44, D1, p. D488-D494 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

XMetDB: an open access database for xenobiotic metabolism

Spjuth, O., Rydberg, P., Willighagen, E. L., Evelo, C. T. & Jeliazkova, N., 15 Sep 2016, In : Journal of Cheminformatics. 8, 47.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2015

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

Eijssen, L. M. T., Goelela, V. S., Kelder, T., Adriaens, M. E., Evelo, C. T. & Radonjic, M., 1 Jan 2015, In : BMC Genomics. 16, 482.

Research output: Contribution to journalArticleAcademicpeer-review

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

Bohler, A., Eijssen, L. M., van Iersel, M. P., Leemans, C., Willighagen, E. L., Kutmon, M., Jaillard, M. & Evelo, C. T., 1 Jan 2015, In : BMC Bioinformatics. 16, 267.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Classification of mild cognitive impairment and Alzheimer's Disease with machine-learning techniques using H-1 Magnetic Resonance Spectroscopy data

Munteanu, C., Fernandez-Lozano, C., Mato Abad, V., Pita Fernandez, S., Alvarez-Linera, J., Antonio Hernandez-Tamames, J. & Pazos, A., 1 Jan 2015, In : Expert Systems with Applications. 42, 15-16, p. 6205-6214

Research output: Contribution to journalArticleAcademicpeer-review

Classification of signaling proteins based on molecular star graph descriptors using Machine Learning models

Fernandez-Lozano, C., Cuinas, R. F., Seoane, J. A., Fernandez-Blanco, E., Dorado, J. & Munteanu, C., 1 Jan 2015, In : Journal of Theoretical Biology. 384, p. 50-58

Research output: Contribution to journalArticleAcademicpeer-review

Comparing social reciprocity in preserved speech variant and typical Rett syndrome during the early years of life

Townend, G. S., Bartl-Pokorny, K. D., Sigafoos, J., Curfs, L. M. G., Bölte, S., Poustka, L., Einspieler, C. & Marschik, P. B., 15 Jul 2015, In : Research in Developmental Disabilities. 43-44, p. 80-86 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Differences in gene expression profiles between human preimplantation embryos cultured in two different IVF culture media

Kleijkers, S. H., Eijssen, L. M., Coonen, E., Derhaag, J. G., Mantikou, E., Jonker, M. J., Mastenbroek, S., Repping, S., Evers, J. L., Dumoulin, J. C. & van Montfoort, A. P., 1 Jan 2015, In : Human Reproduction. 30, 10, p. 2303-2311

Research output: Contribution to journalArticleAcademicpeer-review

diXa: a data infrastructure for chemical safety assessment

Hendrickx, D., Aerts, H., Caiment, F., Clark, D., Ebbels, T. M., Evelo, C. T., Gmuender, H., Hebels, D. G., Herwig, R., Hescheler, J., Jennen, D. G., Jetten, M. J., Kanterakis, S., Keun, H. C., Matser, V., Overington, J. P., Pilicheva, E., Sarkans, U., Segura-Lepe, M. P., Sotiriadou, I. & 4 others, Wittenberger, T., Wittwehr, C., Zanzi, A. & Kleinjans, J. C., 1 May 2015, In : Bioinformatics. 31, 9, p. 1505-1507 3 p.

Research output: Contribution to journalArticleAcademicpeer-review

Enabling open science: Wikidata for research (Wiki4R)

Mietchen, D., Hagedorn, G., Willighagen, E., Rico, M., Gómez-Pérez, A., Aibar, E., Rafes, K., Germain, C., Dunning, A., Pintscher, L. & Kinzler, D., 1 Jan 2015, In : Research Ideas and Outcomes. 1, e7573.

Research output: Contribution to journalArticleProfessional

Open Access

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment

Hastings, J., Jeliazkova, N., Owen, G., Tsiliki, G., Munteanu, C. R., Steinbeck, C. & Willighagen, E., 1 Jan 2015, In : Journal of biomedical semantics. 6, 10.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

eNanoMapper updates and its collaborations with the community

Willighagen, E., Ehrhart, F., Rieswijk, L., Jeliazkova, N., Evelo, C. T. A., Farcal, L., Hardy, B. & Sarimveis, H., 1 Jan 2015, In : NanoSafety Cluster Newsletter. 6, p. 14-17

Research output: Contribution to journalArticleProfessional

Graph-Based Processing of Macromolecular Information

Munteanu, C. R., Aguiar-Pulido, V., Freire, A., Martinez-Romero, M., Porto-Pazos, A. B., Pereira, J. & Dorado, J., 2015, In : Current Bioinformatics. 10, 5, p. 606-631

Research output: Contribution to journalArticleAcademicpeer-review

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

Kutmon, M., Coort, S. L., de Nooijer, K., Lemmens, C. & Evelo, C. T., 1 Jan 2015, In : Genes and nutrition. 10, 5, 35.

Research output: Contribution to journalArticleAcademicpeer-review

Managing biological data in pathways and networks

Kutmon, M., 1 Jan 2015, 's-Hertogenbosch: Uitgeverij BOXPress. 142 p.

Research output: ThesisDoctoral ThesisInternal

Open Access
File
801 Downloads (Pure)

Metabolite BridgeDb ID Mapping Database (20150717)

Willighagen, E., 1 Jan 2015, In : FigShare. July 2015

Research output: Contribution to journalArticleProfessional

NanoWiki (release 1),

Willighagen, E., 1 Jan 2015, In : FigShare. March 2015

Research output: Contribution to journalArticleProfessional

PathVisio 3: An Extendable Pathway Analysis Toolbox

Kutmon, M., van Iersel, M., Bohler, A., Kelder, T., Nunes, N., Pico, A. R. & Evelo, C. T., Feb 2015, In : PLoS Computational Biology. 11, 2, 13 p., e1004085.

Research output: Contribution to journalArticleAcademicpeer-review

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Fu, G., Batchelor, C., Dumontier, M., Hastings, J., Willighagen, E. & Bolton, E., 1 Jan 2015, In : Journal of Cheminformatics. 7, p. 34

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Puzzling with the pathways of life

Evelo, C. T. A., 6 Mar 2015, Maastricht: Maastricht University. 13 p.

Research output: Book/ReportInaugural speech

Open Access
File
235 Downloads (Pure)

Rett Syndrome as a Rare Disease: A European Perspective

Townend, G. S., van Kranen, H. J., van der Stel, R., van den Berg, M., Smeets, E., van Waardenburg, D. & Curfs, L. M. G., 1 Jan 2015, In : Public Health Genomics. 18, 4, p. 233-236 4 p.

Research output: Contribution to journalArticleAcademicpeer-review

RRegrs: an R package for computer-aided model selection with multiple regression models

Tsiliki, G., Munteanu, C. R., Seoane, J. A., Fernandez-Lozano, C., Sarimveis, H. & Willighagen, E. L., 1 Jan 2015, In : Journal of Cheminformatics. 7, 46.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands

Eijssen, L., Evelo, C., Kok, R., Mons, B. & Hooft, R., 1 Jan 2015, In : F1000Research. 4, 33.

Research output: Contribution to journalArticleAcademicpeer-review

The eNanoMapper database for nanomaterial safety information

Jeliazkova, N., Chomenidis, C., Doganis, P., Fadeel, B., Grafstrom, R., Hardy, B., Hastings, J., Hegi, M., Jeliazkov, V., Kochev, N., Kohonen, P., Munteanu, C. R., Sarimveis, H., Smeets, B., Sopasakis, P., Tsiliki, G., Vorgrimmler, D. & Willighagen, E., 1 Jan 2015, In : Beilstein Journal of Nanotechnology. 6, p. 1609-1634

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures.

Grafstrom, R. C., Nymark, P., Hongisto, V., Spjuth, O., Ceder, R., Willighagen, E., Hardy, B., Kaski, S. & Kohonen, P., Nov 2015, In : ATLA-Alternatives to laboratory animals. 43, 5, p. 325-332

Research output: Contribution to journalArticleAcademicpeer-review

Using the RRegrs r package for automating predictive modelling

Tsiliki, G., Munteanu, C., Seoane, J., Fernandez-Lozano, C., Sarimveis, H. & Willighagen, E., 1 Jan 2015, Proceedings of MOL2NET. F009

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademic

WikiPathways SD file (v.1)

Willighagen, E., 1 Jan 2015, In : FigShare. March 2015

Research output: Contribution to journalArticleProfessional

2014

Altered gene expression in human placentas after IVF/ICSI

Nelissen, E. C. M., Dumoulin, J. C. M., Busato, F., Ponger, L., Eijssen, L. M., Evers, J. L. H., Tost, J. & van Montfoort, A. P. A., Dec 2014, In : Human Reproduction. 29, 12, p. 2821-2831 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

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

Kutmon, M., Evelo, C. T. & Coort, S. L., 1 Jan 2014, In : BMC Genomics. 15, p. 971

Research output: Contribution to journalArticleAcademicpeer-review

Applying linked data approaches to pharmacology: Architectural decisions and implementation

Gray, A. J. G., Groth, P., Loizou, A., Askjaer, S., Brenninkmeijer, C., Burger, K., Chichester, C., Evelo, C. T., Goble, C., Harland, L., Pettifer, S., Thompson, M., Waagmeester, A. & Williams, A. J., 1 Jan 2014, In : Semantic web. 5, 2, p. 101-113 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

A systems biology approach to unravel the effects of cadmium exposure on Arabidopsis thaliana

Bohler, S., Bohler, A., Deckers, J., Vangronsveld, J., Noben, J. P., Evelo, C., Renaut, J. & Cuypers, A., 1 Jan 2014, Systems Biology for Food, Feed and Health. Wageningen

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

Open Access
File
89 Downloads (Pure)

Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life

Kaput, J., van Ommen, B., Kremer, B., Priami, C., Monteiro, J. P., Morine, M., Pepping, F., Diaz, Z., Fenech, M., He, Y., Albers, R., Drevon, C. A., Evelo, C. T. A., Hancock, R. E., Ijsselmuiden, C., Lumey, L. H., Minihane, A. M., Muller, M., Murgia, C., Radonjic, M. & 2 others, Sobral, B. & West, K. P. . J., 1 Jan 2014, In : Genes and nutrition. 9, 1, 9 p., 378.

Research output: Contribution to journalArticleAcademicpeer-review

eNanoMapper: Opportunities and challenges in using ontologies to enable data integration for nanomaterial risk assessment

Hastings, J., Willighagen, E., Owen, G., Jeliazkova, N. & Steinbeck, C., 2014, Proceedings of the 17th Annual Bio-Ontologies Meeting . p. 18-21

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Identification of platelet function defects by multi-parameter assessment of thrombus formation

de Witt, S. M., Swieringa, F., Cavill, R., Lamers, M. M., van Kruchten, R., Mastenbroek, T., Baaten, C., Coort, S., Pugh, N., Schulz, A., Scharrer, I., Jurk, K., Zieger, B., Clemetson, K. J., Farndale, R. W., Heemskerk, J. W. & Cosemans, J. M., Jul 2014, In : Nature Communications. 5, 13 p., 4257.

Research output: Contribution to journalArticleAcademicpeer-review

Increased levels of CCR7 ligands in carotid atherosclerosis: different effects in macrophages and smooth muscle cells

Halvorsen, B., Dahl, T. B., Smedbakken, L. M., Singh, A., Michelsen, A. E., Skjelland, M., Krohg-Sorensen, K., Russell, D., Hoepken, U. E., Lipp, M., Damas, J. K., Holm, S., Yndestad, A., Biessen, E. A. & Aukrust, P., 1 Apr 2014, In : Cardiovascular Research. 102, 1, p. 148-156

Research output: Contribution to journalArticleAcademicpeer-review

Integrated visualization of a multi-omics study of starvation in mouse intestine

van Iersel, M. P., Sokolovic, M., Lenaerts, K., Kutmon, M., Bouwman, F. G., Lamers, W. H., Mariman, E. C. & Evelo, C. T., 1 Jan 2014, In : Journal of integrative bioinformatics. 11, 1, 235.

Research output: Contribution to journalArticleAcademicpeer-review

LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design

Munteanu, C., Pedreira, N., Dorado, J., Pazos, A., Perez-Montoto, L. G., Ubeira, F. M. & Gonzalez-Diaz, H., Apr 2014, In : Molecular Informatics. 33, 4, p. 276-285 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice

Schraut, K. G., Jakob, S. B., Weidner, M. T., Schmitt, A. G., Scholz, C. J., Strekalova, T., El Hajj, N., Eijssen, L. M., Domschke, K., Reif, A., Haaf, T., Ortega, G., Steinbusch, H. W., Lesch, K. P. & Van den Hove, D. L., Oct 2014, In : Translational Psychiatry. 4, 10 p., e473.

Research output: Contribution to journalArticleAcademicpeer-review

Scientific Lenses to Support Multiple Views over Linked Chemistry Data

Batchelor, C., Brenninkmeijer, C. A., Chichester, C., Davies, M., Digles, D., Dunlop, I., Evelo, C., Gaulton, A., Goble, C., Gray, A. G., Groth, P., Harland, L., Karapetyan, K., Loizou, A., Overington, J., Pettifer, S., Steele, J., Stevens, R., Tkachenko, V., Waagmeester, A. & 2 others, Williams, A. & Willighagen, E., 1 Jan 2014, The Semantic Web - ISWC 2014. Mika, P., Tudorache, T., Bernstein, A., Welty, C., Knoblock, C., Vrandečić, D., Groth, P., Noy, N., Janowicz, K. & Goble, C. (eds.). Italy: Springer, p. 98-113 (Lecture Notes in Computer Science).

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Summary of the Spring 2014 NSC Database Survey, figshare

Mustad, A. P., Smeets, B., Jeliazkova, N., Jeliazkov, V. & Willighagen, E., 2014, Creative Commons SABY 4.0.

Research output: Book/ReportReport

Open Access

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, J. M., Tipney, H., Siebes, R., Waagmeester, A., Bradley, G., Chau, C. H., Richter, L., Brea, J., Evelo, C. T., Jacoby, E., Senger, S., Loza, M. I., Ecker, G. F. & Chichester, C., 18 Dec 2014, In : PLOS ONE. 9, 12, 32 p., e115460.

Research output: Contribution to journalArticleAcademicpeer-review