• Universiteitssingel50, UNS50

    6229 ER Maastricht

    Netherlands

Research Output

2018

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

Open Access
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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
File
293 Downloads (Pure)

From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results

Cirillo, E., Kutmon, M., Gonzalez Hernandez, M., Hooimeijer, T., Adriaens, M. E., Eijssen, L. M. T., Parnell, L. D., Coort, S. L. & Evelo, C. T., 4 Apr 2018, In : PLOS ONE. 13, 4, p. e0193515 19 p., 0193515.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Genome-wide strategies identify downstream target genes of chick connective tissue-associated transcription factors

Orgeur, M., Martens, M., Leonte, G., Nassari, S., Bonnin, M-A., Boerno, S. T., Timmermann, B., Hecht, J., Duprez, D. & Stricker, S., Apr 2018, In : Development. 145, 7, p. 1-17 17 p., 161208.

Research output: Contribution to journalArticleAcademicpeer-review

Geospatial data and Scholia

Nielsen, F. Å., Mietchen, D. & Willighagen, E., Jun 2018, GeoLD-QuWeDa 2018 ESWC 2018 Workshops: GeoLD 2018 and QuWeDa 2018. CEUR Workshop Proceedings, Vol. 2110. p. 34-40 7 p.

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

Increasing the nanopublication recall with a BridgeDb Identifier Mapping Service

Willighagen, E., 2018, Semantic Web Applications and Tools for Health Care and Life Sciences. CEUR Workshop Proceedings, Vol. 2275. p. 1-6 6 p.

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

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

Karcher, S., Willighagen, E. L., Rumble, J., Ehrhart, F., Evelo, C. T., Fritts, M., Gaheen, S., Harper, S. L., Hoover, M. D., Jeliazkova, N., Lewinski, N., Robinson, R. L. M., Mills, K. C., Mustad, A. P., Thomas, D. G., Tsiliki, G. & Hendren, C. O., 1 Jan 2018, In : NanoImpact. 9, p. 85-101 17 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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., Grafstrom, R., Burgoon, L. D., Aladjov, H., Andon, F. T., Evelo, C. T. & Willighagen, E. L., 21 Dec 2018, In : Frontiers in Genetics. 9, 9 p., 661.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder

Rutten, B. P. F., Vermetten, E., Vinkers, C. H., Ursini, G., Daskalakis, N. P., Pishva, E., Nijs, L., Houtepen, L. C., Eijssen, L., Jaffe, A. E., Kenis, G., Viechtbauer, W., den Hove, D., Schraut, K. G., Lesch, K-P., Kleinman, J. E., Hyde, T. M., Weinberger, D. R., Schalkwyk, L., Lunnon, K. & 8 others, Mill, J., Cohen, H., Yehuda, R., Baker, D. G., Maihofer, A. X., Nievergelt, C. M., Geuze, E. & Boks, M. P. M., 1 May 2018, In : Molecular Psychiatry. 23, 5, p. 1145-1156 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Low maternal melatonin level increases autism spectrum disorder risk in children

Braam, W., Ehrhart, F., Maas, A. P. H. M., Smits, M. G. & Curfs, L., 1 Nov 2018, In : Research in Developmental Disabilities. 82, p. 79-89 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases

Townend, G. S., Ehrhart, F., van Kranen, H. J., Wilkinson, M., Jacobsen, A., Roos, M., Willighagen, E. L., van Enckevort, D., Evelo, C. T. & Curfs, L. M. G., Jul 2018, In : Human Mutation. 39, 7, p. 914-924 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Kuhn, T., Meroño-Peñuela, A., Malic, A., Poelen, J. H., Hurlbert, A. H., Ortiz, E. C., Furlong, L. I., Queralt-Rosinach, N., Chichester, C., Banda, J. M., Willighagen, E., Ehrhart, F., Evelo, C., Malas, T. B. & Dumontier, M., 18 Sep 2018, 2018 IEEE 14th International Conference on e-Science (e-Science). p. 83-92 10 p. (Proceedings of IEEE e-Science).

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

Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D

Garcia, A. M., Kutmon, M., Eijssen, L., Hewison, M., Evelo, C. T. & Coort, S. L., Feb 2018, In : Journal of Molecular Endocrinology. 60, 2, p. 95-108 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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Profiling cellular processes in adipose tissue during weight loss using time series gene expression

Tareen, S. H. K., Adriaens, M. E., Arts, I. C. W., de Kok, T. M., Vink, R. G., Roumans, N. J. T., van Baak, M. A., Mariman, E. C. M., Evelo, C. T. & Kutmon, M., Nov 2018, In : Genes. 9, 11, 16 p., 525.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Role of 1 alpha,25-Dihydroxyvitamin D-3 in Adipogenesis of SGBS Cells: New Insights into Human Preadipocyte Proliferation

Felicidade, I., Sartori, D., Coort, S. L. M., Semprebon, S. C., Niwa, A. M., D'Epiro, G. F., Biazi, B. I., Marques, L. A., Evelo, C. T., Mantovani, M. S. & Ribeiro, L. R., 1 Jan 2018, In : Cellular Physiology and Biochemistry. 48, 1, p. 407-418 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The EU NanoSafety Cluster as Linked Data visualized with Scholia

Willighagen, E., Jahn, N. & Nielsen, F. Å., Jul 2018, In : NanoSafety Cluster Newsletter. p. 6

Research output: Contribution to journalArticleAcademic

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

Slenter, D. N., Kutmon, M., Hanspers, K., Riutta, A., Windsor, J., Nunes, N., Mélius, J., Cirillo, E., Coort, S. L., Digles, D., Ehrhart, F., Giesbertz, P., Kalafati, M., Martens, M., Miller, R., Nishida, K., Rieswijk, L., Waagmeester, A., Eijssen, L. M. T., Evelo, C. T. & 2 others, Pico, A. R. & Willighagen, E. L., 4 Jan 2018, In : Nucleic Acids Research. 46, D1, p. D661-D667 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2017

A bioinformatics approach to identify molecular pathways that characterize the trabecular meshwork

Liesenborghs, I., Schouten, J. S. A. G., Eijssen, L. M. T., Kutmon, M., Gorgels, T. G. M. F., Hubens, W. H. G., Evelo, C. T., Beckers, H. J. M. & Webers, C. A. B., Apr 2017, In : Acta Ophthalmologica. 95, p. 24-24 1 p.

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

Adverse outcome pathways: opportunities, limitations and open questions

Leist, M., Ghallab, A., Graepel, R., Marchan, R., Hassan, R., Bennekou, S. H., Limonciel, A., Vinken, M., Schildknecht, S., Waldmann, T., Danen, E., van Ravenzwaay, B., Kamp, H., Gardner, I., Godoy, P., Bois, F. Y., Braeuning, A., Reif, R., Oesch, F., Drasdo, D. & 33 others, Hoehme, 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, A. H., 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, J. G., Nov 2017, In : Archives of Toxicology. 91, 11, p. 3477-3505 29 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

Cirillo, E., Parnell, L. D. & Evelo, C. T., 7 Nov 2017, In : Frontiers in Genetics. 8, 11 p., 174.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

A SCIENCE OPEN COLLECTION OF NANOSAFETY CLUSTER PUBLICATIONS

Willighagen, E., Lynch, I. & Dawson, S., 2017, In : NSC WORKING GROUP NEWS. 9, p. 7-8 2 p.

Research output: Contribution to journalEditorialProfessional

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

Kohonen, P., Parkkinen, J. A., Willighagen, E. L., Ceder, R., Wennerberg, K., Kaski, S. & Grafstrom, R. C., 3 Jul 2017, In : Nature Communications. 8, 15 p., 15932.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Willighagen, E. L., Mayfield, J. W., Alvarsson, J., Berg, A., Carlsson, L., Jeliazkova, N., Kuhn, S., Pluskal, T., Rojas-Cherto, M., Spjuth, O., Torrance, G., Evelo, C. T., Guha, R. & Steinbeck, C., 20 Sep 2017, In : Journal of Cheminformatics. 9, 1 p.

Research output: Contribution to journalErratum / corrigendumAcademic

Open Access

Helping to improve the practice of cheminformatics

Guha, R. & Willighagen, E., 14 Jun 2017, In : Journal of Cheminformatics. 9, 2 p., 40.

Research output: Contribution to journalEditorialAcademicpeer-review

Open Access

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, J. A., Xie, L., Adriaens, M., Evelo, C. T., Ford, D. & Mathers, J. C., Apr 2017, In : Molecular Nutrition & Food Research. 61, 4, 16 p., 1600713.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Myocardial and Serum Galectin-3 Expression Dynamics Marks Post-Myocardial Infarction Cardiac Remodelling

Sharma, U. C., Mosleh, W., Chaudhari, M. R., Katkar, R., Weil, B., Evelo, C., Cimato, T. R., Pokharel, S., Blankesteijn, W. M. & Suzuki, G., Jul 2017, In : Heart Lung and Circulation. 26, 7, p. 736-745 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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Persistent transcriptional responses show the involvement of feed-forward control in a repeated dose toxicity study

de Souza, T., Rieswijk, L., van den Beucken, T., Kleinjans, J. & Jennen, D., 15 Jan 2017, In : Toxicology. 375, p. 58-63

Research output: Contribution to journalArticleAcademicpeer-review

PRC1 Prevents Replication Stress during Chondrogenic Transit Amplification

Spaapen, F., Eijssen, L., Adriaens, M., Welting, T., Prickaerts, P., Salvaing, J., Dahlmans, V. E. H., Surtel, D., Kruitz, F., Kuijer, R., Takihara, Y., Marks, H., Stunnenberg, H., Wouters, B., Vidal, M. & Voncken, J., Dec 2017, In : Epigenomes. 1, 3, 31 p., 22.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Precision medicine in circadian rhythm sleep-wake disorders: current state and future perspectives

Keijzer, H., Snitselaar, M. A., Smits, M. G., Spruyt, K., Zee, P. C., Ehrhart, F. & Curfs, L. M. G., Mar 2017, In : Personalized Medicine. 14, 2, p. 171-182 12 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Proposed guidelines to evaluate scientific validity and evidence for genotype-based dietary advice

Grimaldi, K. A., van Ommen, B., Ordovas, J. M., Parnell, L. D., Mathers, J. C., Bendik, I., Brennan, L., Celis-Morales, C., Cirillo, E., Daniel, H., de Kok, B., El-Sohemy, A., Fairweather-Tait, S. J., Fallaize, R., Fenech, M., Ferguson, L. R., Gibney, E. R., Gibney, M., Gjelstad, I. M. F., Kaput, J. & 16 others, Karlsen, A. S., Kolossa, S., Lovegrove, J., Macready, A. L., Marsaux, C. F. M., Martinez, J. A., Milagro, F., Navas-Carretero, S., Roche, H. M., Saris, W. H. M., Traczyk, I., van Kranen, H., Verschuren, L., Virgili, F., Weber, P. & Bouwman, J., 15 Dec 2017, In : Genes and nutrition. 12, 12 p., 35.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management

Lampa, S., Willighagen, E., Kohonen, P., King, A., Vrandecic, D., Grafstrom, R. & Spjuth, O., 4 Sep 2017, In : Journal of biomedical semantics. 8, 13 p., 35.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Reliable Granular References to Changing Linked Data

Kuhn, T., Willighagen, E., Evelo, C., Queralt-rosinach, N., Centeno, E. & Furlong, L. I., 4 Oct 2017, The Semantic Web – ISWC 2017: 16th International Semantic Web Conference, Vienna, Austria, October 21–25, 2017, Proceedings, Part I. d'Amato, C., Fernandez, M. & Tamma, V. (eds.). 1 ed. Vol. 10587. p. 436-451 16 p. (Lecture Notes in Computer Science, Vol. 10587).

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

Scholia, Scientometrics and Wikidata

Nielsen, F. Å., Mietchen, D. & Willighagen, E., 8 Nov 2017, The Semantic Web: ESWC 2017 Satellite Events. Blomqvist, E., Hose, K. & Paulheim, H. (eds.). 1 ed. p. 237-259 23 p. (Lecture Notes in Computer Science, Vol. 10577).

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

Open Access

Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures

Curran, A. M., Fogarty Draper, C., Scott-Boyer, M-P., Valsesia, A., Roche, H. M., Ryan, M. F., Gibney, M. J., Kutmon, M., Evelo, C. T., Coort, S. L., Astrup, A., Saris, W. H., Brennan, L. & Kaput, J., 3 Nov 2017, In : Journal of Proteome Research. 16, 11, p. 4122-4133 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Willighagen, E. L., Mayfield, J. W., Alvarsson, J., Berg, A., Carlsson, L., Jeliazkova, N., Kuhn, S., Pluskal, T., Rojas-Cherto, M., Spjuth, O., Torrance, G., Evelo, C. T., Guha, R. & Steinbeck, C., 6 Jun 2017, In : Journal of Cheminformatics. 9, 19 p., 33.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The future of metabolomics in ELIXIR

Van Rijswijk, M., Beirnaert, C., Caron, C., Cascante, M., Dominguez, V., Dunn, W. B., Ebbels, T. M. D., Giacomoni, F., Gonzalez-beltran, A., Hankemeier, T., Haug, K., Izquierdo-garcia, J. L., Jimenez, R. C., Jourdan, F., Kale, N., Klapa, M. I., Kohlbacher, O., Koort, K., Kultima, K., Le Corguillé, G. & 20 others, Moreno, P., Moschonas, N. K., Neumann, S., O’donovan, C., Reczko, M., Rocca-serra, P., Rosato, A., Salek, R. M., Sansone, S., Satagopam, V., Schober, D., Shimmo, R., Spicer, R. A., Spjuth, O., Thévenot, E. A., Viant, M. R., Weber, R. J. M., Willighagen, E. L., Zanetti, G. & Steinbeck, C., 30 Oct 2017, In : F1000Research. 6, 16 p., 1649.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Open Access
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Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways

Siddiqa, A., Cirillo, E., Tareen, S. H. K., Ali, A., Kutmon, M., Eijssen, L., Ahmad, J., Evelo, C. T. & Coort, S. L., Oct 2017, In : Genomics. 109, 5-6, p. 408-418 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
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Comment: The FAIR Guiding Principles for scientific data management and stewardship

Wilkinson, M. D., Dumontier, M., Aalbersberg, IJ. 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., 't Hoen, P. A. C., 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., 15 Mar 2016, In : Scientific data. 3, 9 p., 160018.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

eNanoMapper Updates and its Collaborations with the Community #2

Willighagen, E., Tsiliki, G., Kohonen, P., Nymark, P., Chang, J., Owen, G., Rieswijk, L., Ehrhart, F., Helma, C., Rautenberg, M., Kilic, G., Jeliazkova, N., Doganis, P. & Sarimveis, H., 2016, In : NanoSafety Cluster Newsletter. Spring 2016, 7, p. 20-25

Research output: Contribution to journalArticleProfessional

Eye Gaze Technology as a Form of Augmentative and Alternative Communication for Individuals with Rett Syndrome: Experiences of Families in The Netherlands

Townend, G. S., Marschik, P. B., Smeets, E., van de Berg, R., van den Berg, M. & Curfs, L. M. G., Feb 2016, In : Journal of Developmental and Physical Disabilities. 28, 1, p. 101-112 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

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, J. A., Adriaens, M., Evelo, C. T., Ford, D. & Mathers, J. C., Sep 2016, In : Molecular Nutrition & Food Research. 60, 9, p. 2031-2042 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

Adriaens, M. E., Prickaerts, P., Beucken, T. V. D., Koch, E., Dubois, L., Dahlmans, V. E. H., Gits, C., Evelo, C. T. A., Chan-Seng-Yue, M., Wouters, B. G. & Voncken, W., 26 Oct 2016, In : Epigenetics & Chromatin. 9, p. 46 19 p.

Research output: Contribution to journalArticleAcademicpeer-review

MicroRNAs and epigenetics in chemical carcinogenesis : an integrative toxicogenomics-based approach

Rieswijk, L., 1 Jan 2016, 's-Hertogenbosch: Uitgeverij BOXPress. 220 p.

Research output: ThesisDoctoral ThesisInternal

Open Access
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New insights in Rett syndrome using pathway analysis for transcriptomics data

Ehrhart, F., Steinbusch - Coort, S., Cirillo, E., Smeets, E., Evelo, C. T. & Curfs, L., Sep 2016, In : Wiener Medizinische Wochenschrift. 166, 11, p. 346-352 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns

Digles, D., Zdrazil, B., Neefs, J. -M., Van Vlijmen, H., Herhaus, C., Caracoti, A., Brea, J., Roibas, B., Loza, M. I., Queralt-Rosinach, N., Furlong, L. I., Gaulton, A., Bartek, L., Senger, S., Chichester, C., Engkvist, O., Evelo, C. T., Franklin, N. I., Marren, D., Ecker, G. F. & 1 others, Jacoby, E., 2016, In : Medchemcomm. 7, 6, p. 1237-1244

Research output: Contribution to journalArticleAcademicpeer-review