• Universiteitssingel50, UNS50

    6229 ER Maastricht

    Netherlands

Research Output

2020

Adoption of the Citation Typing Ontology by the Journal of Cheminformatics

Willighagen, E., 28 Jul 2020, In : Journal of Cheminformatics. 12, 1, 3 p., 47.

Research output: Contribution to journalEditorialAcademic

Open Access

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Ostaszewski, M., Mazein, A., Gillespie, M. E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A. R., Willighagen, E. L., Evelo, C. T., Hasenauer, J., Schreiber, F., Dräger, A., Demir, E., Wolkenhauer, O., Furlong, L. I., Barillot, E., Dopazo, J., Orta-resendiz, A., Messina, F., Valencia, A. & 5 others, Funahashi, A., Kitano, H., Auffray, C., Balling, R. & Schneider, R., 5 May 2020, In : Scientific data. 7, 1, 4 p., 136.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models

Sarathy, C., Kutmon, M., Lenz, M., Adriaens, M. E., Evelo, C. T. & Arts, I. C. W., 12 Feb 2020, In : Metabolites. 10, 2, 14 p., 66.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Identification of Biological Pathways Contributing to Marbling in Skeletal Muscle to Improve Beef Cattle Breeding

Roudbari, Z., Coort, S. L., Kutmon, M., Eijssen, L., Melius, J., Sadkowski, T. & Evelo, C. T., 7 Feb 2020, In : Frontiers in Genetics. 10, 12 p., 1370.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Identification of microRNAs in skeletal muscle associated with lung cancer cachexia

van de Worp, W. R. P. H., Schols, A. M. W. J., Dingemans, A-M. C., Op den Kamp, C. M. H., Degens, J. H. R. J., Kelders, M. C. J. M., Coort, S., Woodruff, H. C., Kratassiouk, G., Harel-Bellan, A., Theys, J., van Helvoort, A. & Langen, R. C. J., Apr 2020, In : Journal of cachexia, sarcopenia and muscle. 11, 2, p. 452-463 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
88 Downloads (Pure)

Learning cheminformatics

Guha, R. & Willighagen, E., 20 Jan 2020, In : Journal of Cheminformatics. 12, 1, 2 p., 4.

Research output: Contribution to journalEditorialAcademic

Open Access

Modelling molecular processes in weight loss: Regulation of metabolic flexibility

Tareen, S. H. K., 2020, Maastricht: Maastricht University. 158 p.

Research output: ThesisDoctoral ThesisInternal

Open Access
File
94 Downloads (Pure)

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment

Afantitis, A., Melagraki, G., Isigonis, P., Tsoumanis, A., Varsou, D. D., Valsami-jones, E., Papadiamantis, A., Ellis, L. A., Sarimveis, H., Doganis, P., Karatzas, P., Tsiros, P., Liampa, I., Lobaskin, V., Greco, D., Serra, A., Kinaret, P. A. S., Saarimäki, L. A., Grafström, R., Kohonen, P. & 33 others, Nymark, P., Willighagen, E., Puzyn, T., Rybinska-fryca, A., Lyubartsev, A., Alstrup Jensen, K., Brandenburg, J. G., Lofts, S., Svendsen, C., Harrison, S., Maier, D., Tamm, K., Jänes, J., Sikk, L., Dusinska, M., Longhin, E., Rundén-pran, E., Mariussen, E., El Yamani, N., Unger, W., Radnik, J., Tropsha, A., Cohen, Y., Leszczynski, J., Ogilvie Hendren, C., Wiesner, M., Winkler, D., Suzuki, N., Yoon, T. H., Choi, J., Sanabria, N., Gulumian, M. & Lynch, I., 7 Mar 2020, In : Computational and Structural Biotechnology Journal. 18, p. 583-602 20 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

Risk Governance of Emerging Technologies Demonstrated in Terms of its Applicability to Nanomaterials

Isigonis, P., Afantitis, A., Antunes, D., Bartonova, A., Beitollahi, A., Bohmer, N., Bouman, E., Chaudhry, Q., Cimpan, M. R., Cimpan, E., Doak, S., Dupin, D., Fedrigo, D., Fessard, V., Gromelski, M., Gutleb, A. C., Halappanavar, S., Hoet, P., Jeliazkova, N., Jomini, S. & 25 others, Lindner, S., Linkov, I., Longhin, E. M., Lynch, I., Malsch, I., Marcomini, A., Mariussen, E., de la Fuente, J. M., Melagraki, G., Murphy, F., Neaves, M., Packroff, R., Pfuhler, S., Puzyn, T., Rahman, Q., Pran, E. R., Semenzin, E., Serchi, T., Steinbach, C., Trump, B., Vrcek, I. V., Warheit, D., Wiesner, M. R., Willighagen, E. & Dusinska, M., 10 Sep 2020, In : Small. 16, 36, 12 p., 2003303.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

SCIENCE FORUM Wikidata as a knowledge graph for the life sciences

Waagmeester, A., Stupp, G., Burgstaller-muehlbacher, S., Good, B. M., Griffith, M., Griffith, O. L., Hanspers, K., Hermjakob, H., Hudson, T. S., Hybiske, K., Keating, S. M., Manske, M., Mayers, M., Mietchen, D., Mitraka, E., Pico, A. R., Putman, T., Riutta, A., Queralt-rosinach, N., Schriml, L. M. & 10 others, Shafee, T., Slenter, D., Stephan, R., Thornton, K., Tsueng, G., Tu, R., Ul-hasan, S., Willighagen, E., Wu, C. & Su, A. I., 17 Mar 2020, In : Elife. 9, 15 p., 52614.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Open Access

The aqueous humor proteome of primary open angle glaucoma: An extensive review

Hubens, W. H. G., Mohren, R. J. C., Liesenborghs, Eijssen, L. M. T., Ramdas, W. D., Webers, C. A. B. & Gorgels, T. G. M. F., Aug 2020, In : Experimental Eye Research. 197, 11 p., 108077.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access
2019

A bioinformatics workflow to decipher transcriptomic data from vitamin D studies

Muñoz García, A., Eijssen, L. M., Kutmon, M., Sarathy, C., Cengo, A., Hewison, M., Evelo, C. T., Lenz, M. & Coort, S. L., May 2019, In : Journal of Steroid Biochemistry and Molecular Biology. 189, p. 28-35 8 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access
Open Access

Alzheimer's disease-associated (hydroxy)methylomic changes in the brain and blood

Lardenoije, R., Roubroeks, J. A. Y., Pishva, E., Leber, M., Wagner, H., Iatrou, A., Smith, A. R., Smith, R. G., Eijssen, L. M. T., Kleineidam, L., Kawalia, A., Hoffmann, P., Luck, T., Riedel-Heller, S., Jessen, F., Maier, W., Wagner, M., Hurlemann, R., Kenis, G., Ali, M. & 9 others, del Sol, A., Mastroeni, D., Delvaux, E., Coleman, P. D., Mill, J., Rutten, B. P. F., Lunnon, K., Ramirez, A. & van den Hove, D. L. A., 27 Nov 2019, In : Clinical epigenetics. 11, 1, 15 p., 164.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

Miller, R. A., Ehrhart, F., Eijssen, L. M. T., Slenter, D. N., Curfs, L. M. G., Evelo, C. T., Willighagen, E. L. & Kutmon, M., 21 Feb 2019, In : Frontiers in Genetics. 10, 10 p., 59.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Challenges in evaluating the oculomotor function in individuals with Rett syndrome using electronystagmography

de Breet, L. H. M., Townend, G. S., Curfs, L. M. G., Kingma, H., Smeets, E. E. J., Lucieer, F., Widdershoven, J. & van de Berg, R., Mar 2019, In : European Journal of Paediatric Neurology. 23, 2, p. 262-269 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Circulating Serum MicroRNAs as Potential Diagnostic Biomarkers of Posttraumatic Stress Disorder: A Pilot Study

Snijders, C., Krauskopf, J., Pishva, E., Eijssen, L., Machiels, B., Kleinjans, J., Kenis, G., van den Hove, D., Kim, M. O., Boks, M. P. M., Vinkers, C. H., Vermetten, E., Geuze, E., Rutten, B. P. F. & de Nijs, L., 22 Nov 2019, In : Frontiers in Genetics. 10, 10 p., 1042.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

AstraZeneca-Sanger Drug Combinatio, 17 Jun 2019, In : Nature Communications. 10, 17 p., 2674.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Kutmon, M., Ehrhart, F., Willighagen, E. L., Evelo, C. T. & Coort, S. L., 13 Aug 2019, In : F1000Research. 7, p. 743

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
58 Downloads (Pure)
Open Access
File
554 Downloads (Pure)

Identification of Cholecystokinin by Genome-Wide Profiling as Potential Mediator of Serotonin-Dependent Behavioral Effects of Maternal Separation in the Amygdala

Weidner, M. T., Lardenoije, R., Eijssen, L., Mogavero, F., De Groodt, L. P. M. T., Popp, S., Palme, R., Foerstner, K. U., Strekalova, T., Steinbusch, H. W. M., Schmitt-Boehrer, A. G., Glennon, J. C., Waider, J., van den Hove, D. L. A. & Lesch, K-P., 10 May 2019, In : Frontiers in Neuroscience. 13, 17 p., 460.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Journal of Cheminformatics, ORCID, and GitHub

Willighagen, E., Jeliazkova, N. & Guha, R., 8 Jul 2019, In : Journal of Cheminformatics. 11, 2 p., 44.

Research output: Contribution to journalEditorialAcademicpeer-review

Open Access

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

Ehrhart, F., Janssen, K. J. M., Coort, S. L., Evelo, C. T. & Curfs, L. M. G., 21 Oct 2019, In : World Journal of Biological Psychiatry. 20, 9, p. 670-682 13 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access
176 Downloads (Pure)

Rett syndrome and developmental regression

Smeets, E. E., Townend, G. S. & Curfs, L. M. G., Sep 2019, In : Neuroscience and Biobehavioral Reviews. 104, p. 100-101 2 p.

Research output: Contribution to journalEditorialAcademicpeer-review

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, C. T. & Curfs, L. M. G., 2019, In : Molecular Psychiatry. 24, 1, p. 10-17 8 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

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

van der Kolk, B. W., Kalafati, M., Adriaens, M., van Greevenbroek, M. M. J., Vogelzangs, N., Saris, W. H. M., Astrup, A., Valsesia, A., Langin, D., van der Kallen, C. J. H., Eussen, S. J. P. M., Schalkwijk, C. G., Stehouwer, C. D. A., Goossens, G. H., Arts, I. C. W., Jocken, J. W. E., Evelo, C. T. & Blaak, E. E., Dec 2019, In : Diabetes. 68, 12, p. 2247-2258 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

The FAIR Guiding Principles for scientific data management and stewardship (vol 15, 160018, 2016)

Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J-W., Santos, L. B. D. S., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A. & 33 others, Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., Hoen, P. A. C. T., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 19 Mar 2019, In : Scientific data. 6, 2 p., 6.

Research output: Contribution to journalErratum / corrigendumAcademic

Open Access

The metaRbolomics Toolbox in Bioconductor and beyond

Stanstrup, J., Broeckling, C. D., Helmus, R., Hoffmann, N., Mathe, E., Naake, T., Nicolotti, L., Peters, K., Rainer, J., Salek, R. M., Schulze, T., Schymanski, E. L., Stravs, M. A., Thevenot, E. A., Treutler, H., Weber, R. J. M., Willighagen, E., Witting, M. & Neumann, S., Oct 2019, In : Metabolites. 9, 10, 55 p., 200.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

The signature of the healthy trabecular meshwork

Liesenborghs, I., Eijssen, L. M. T., Kutmon, M., Evelo, C. T., Gorgels, T. G. M. F., Hubens, W. H. G., Beckers, H. J. M., Webers, C. A. B. & Schouten, J. S. A. G., Mar 2019, In : Acta Ophthalmologica. 97, p. 25-25 1 p.

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

Transcriptomic analysis of vitamin D responses in uterine and peripheral NK cells

Tamblyn, J. A., Jeffery, L. E., Susarla, R., Lissauer, D. M., Coort, S. L., Garcia, A. M., Knoblich, K., Fletcher, A. L., Bulmer, J. N., Kilby, M. D. & Hewison, M., Aug 2019, In : Reproduction. 158, 2, p. 211-221 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

2018

Abdominal subcutaneous adipose tissue gene expression in relation to tissue-specific insulin resistance in human obesity

CODAM study, Maastricht Study & DiOGenes Consortium, Oct 2018, In : Diabetologia. 61, p. S110-S110 1 p.

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

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, C. T., Hongisto, V., Kohonen, P., Willighagen, E. & Grafstrom, R. C., Mar 2018, In : Toxicological Sciences. 162, 1, p. 264-275 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
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A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

Orgeur, M., Martens, M., Boerno, S. T., Timmermann, B., Duprez, D. & Stricker, S., Jan 2018, In : Biology Open. 7, 1, p. 1-8 8 p., 028498.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Advancing food, nutrition, and health research in Europe by connecting and building research infrastructures in a DISH-RI: Results of the EuroDISH project

Snoek, H. M., Eijssen, L. M. T., Geurts, M., Vors, C., Brown, K. A., Bogaardt, M-J., Dhonukshe-Rutten, R. A. M., Evelo, C. T., Fezeu, L. K., Finglas, P. M., Laville, M., Ocke, M., Perozzi, G., Poppe, K., Slimani, N., Tetens, I., Timotijevic, L., Zimmermann, K. & van't Veer, P., Mar 2018, In : Trends in Food Science & Technology. 73, p. 58-66 9 p.

Research output: Contribution to journalReview articleAcademicpeer-review

A simple and efficient toolset for analysing mitochondrial trafficking in neuronal cells

Shahen, V. A., Cantrill, L. C., Bahram Sangani, N., Christodoulou, J. & Gold, W. A., 1 Jan 2018, In : Acta Histochemica. 120, 8, p. 797-805 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Bioinformatical pathway analyses to discover the molecular pathogenesis of primary open angle glaucoma

Liesenborghs, I., Kutmon, M., Eijssen, L. M. T., Gorgels, T. G. M. F., Evelo, C. T., Beckers, H. J. M., Webers, C. A. B. & Schouten, J. S. A. G., Mar 2018, In : Acta Ophthalmologica. 96, p. 18-19 2 p.

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

Biological pathways leading from ANGPTL8 to Diabetes Mellitus: a co-expression network based analysis

Siddiqa, A., Cirillo, E., Tareen, S. H. K., Ali, A., Kutmon, M., Eijssen, L. M. T., Ahmad, J., Evelo, C. T. & Coort, S. L., 21 Dec 2018, In : Frontiers in physiology. 9, 15 p., 1841.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Current developments in the genetics of Rett and Rett-like syndrome

Ehrhart, F., Sangani, N. B. & Curfs, L. M. G., 1 Mar 2018, In : Current Opinion in Psychiatry. 31, 2, p. 103-108 6 p.

Research output: Contribution to journalReview articleAcademicpeer-review

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., Bauza Martinez, J., Odena, A., Oliveira, E., Coort, S. L., Evelo, C. T., Mariman, E. C. M., Schuhmacher, M. & Kumar, V., 15 Sep 2018, In : Journal of Proteomics. 187, p. 106-125 20 p.

Research output: Contribution to journalArticleAcademicpeer-review

Early development in Rett syndrome: the benefits and difficulties of a birth cohort approach

Marschik, P. B., Lemcke, S., Einspieler, C., Zhang, D., Bolte, S., Townend, G. S. & Lauritsen, M. B., 1 Jan 2018, In : Developmental Neurorehabilitation. 21, 1, p. 68-72 5 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Exploring the cellular network of metabolic flexibility in the adipose tissue

Tareen, S. H. K., Kutmon, M., Adriaens, M., Mariman, E., de Kok, T., Arts, I. & Evelo, C., 5 Jul 2018, In : Genes and nutrition. 13, 8 p., 17.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

Forced to cooperate: mechano-chemical interactions in cardiac sarcomeres

Dupuis, L., 2018, Maastricht: Maastricht University. 119 p.

Research output: ThesisDoctoral ThesisInternal

Open Access
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