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Research Output

  • 32 Article
  • 3 Conference Abstract/Poster in journal
  • 2 Review article
  • 1 Doctoral Thesis
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

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

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

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

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

2018

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

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

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

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

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

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

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

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

2016

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
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
3 Citations (Scopus)

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

15 Citations (Scopus)

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

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

14 Citations (Scopus)

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

7 Citations (Scopus)
2013

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
9 Citations (Scopus)

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

44 Citations (Scopus)
2012

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

12 Citations (Scopus)

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

9 Citations (Scopus)
2011

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
9 Citations (Scopus)
193 Downloads (Pure)
2009

Reduction of colonic inflammation in HLA-B27 transgenic rats by feeding Marie Ménard apples, rich in polyphenols.

Castagnini, C., Luceri, C., Toti, S., Bigagli, E., Caderni, G., Femia, A. P., Giovannelli, L., Lodovici, M., Pitozzi, V., Salvadori, M., Messerini, L., Martin, R., Zoetendal, E. G., Gaj, S., Eijssen, L. M., Evelo, C. T., Renard, C. M., Baron, A. & Dolara, P., 1 Jan 2009, In : British Journal of Nutrition. 102, 11, p. 1620-1628

Research output: Contribution to journalArticleAcademicpeer-review

22 Citations (Scopus)
2008

Altered myocardial gene expression reveals possible maladaptive processes in heterozygous and homozygous cardiac myosin-binding protein C knockout mice.

Eijssen, L. M. T., van den Bosch, B. J. C., Vignier, N., Lindsey, P. J., van den Burg, C. M. M., Carrier, L., Doevendans, P. A. F. M., van der Vusse, G. J. & Smeets, H. J., 1 Jan 2008, In : Genomics. 91, 1, p. 52-60

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Scopus)

A novel stepwise analysis procedure of genome-wide expression profiles identifies transcript signatures of thiamine genes as classifiers of mitochondrial mutants.

Eijssen, L. M. T., Lindsey, P. J., Peeters, R., Westra, R. L., van Eijsden, R. G. E., Bolotin-Fukuhara, M., Smeets, H. J. & Vlietinck, R. F. M., 1 Jan 2008, In : Yeast. 25, 2, p. 129-140

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Termination of damaged protein repair defines the occurrence of symptoms in carriers of the m.3243A > G tRNA(Leu) mutation.

van Eijsden, R., Eijssen, L. M., Lindsey, P., van den Burg, C., de Wit, E., Rubio-Gozalbo, M. E., de Die-Smulders, C. E. M., Ayoubi, T., Sluiter, W., de Coo, I. & Smeets, H., 1 Jan 2008, In : Journal of Medical Genetics. 45, 8, p. 525-534

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)

The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation

Baccini, M., Bachmaier, E. M., Biggeri, A., Boekschoten, M. V., Bouwman, F. G., Brennan, L., Caesar, R., Cinti, S., Coort, S. L. M., Crosley, K., Daniel, H., Drevon, C. A., Duthie, S. J., Eijssen, L. M. T., Elliott, R. M., van Erk, M., Evelo, C. T. A., Gibney, M., Heim, C., Horgan, G. W. & 1 others, Johnson, I. T., 1 Jan 2008, In : Genes and nutrition. 3(3-4), p. 147-151

Research output: Contribution to journalArticleAcademicpeer-review

18 Citations (Scopus)

Validating nutrient-related gene expression changes from microarrays using RT(2) PCR-arrays

Gaj, S., Eijssen, L. M., Mensink, R. P. & Evelo, C. T., 1 Jan 2008, In : Genes and nutrition. 3, 3-4, p. 153-7

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)
2006

Analysis of microarray gene expression data sets

Eijssen, L. M. T., 1 Jan 2006, Maastricht: Universiteit Maastricht. 236 p.

Research output: ThesisDoctoral ThesisInternal

Open Access
File
659 Downloads (Pure)

Chip-based mtDNA mutation screening enables fast and reliable genetic diagnosis of OXPHOS patients

van Eijsden, R. G., Gerards, M., Eijssen, L. M., Hendrickx, A. T., Jongbloed, R. J. E., Wokke, J. H., Hintzen, R. Q., Rubio-Gozalbo, M. E., De Coo, I. F., Briem, E., Tiranti, V. & Smeets, H. J., 1 Jan 2006, In : Genetics in Medicine. 8, 10, p. 620-627

Research output: Contribution to journalArticleAcademicpeer-review

30 Citations (Scopus)