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Research Output 2010 2019

  • 24 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

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
9 Downloads (Pure)

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

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

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

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

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

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

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

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

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

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
1 Citation (Scopus)

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
1 Citation (Scopus)

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
1 Citation (Scopus)

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
37 Citations (Scopus)

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
2015
3 Citations (Scopus)

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
4 Citations (Scopus)

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

620 Downloads (Pure)

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
37 Citations (Scopus)

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

2014
5 Citations (Scopus)

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

6 Citations (Scopus)

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

7 Citations (Scopus)

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
13 Citations (Scopus)

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

25 Citations (Scopus)

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
2012
235 Citations (Scopus)
198 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
2010
299 Citations (Scopus)

The BioPAX community standard for pathway data sharing

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez Flores, I., Hu, Z., Jimenez Jacinto, V., Joshi Tope, G., Kandasamy, K., Lopez Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I. & 70 others, Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M. P., Wimalaratne, S., Allen, K., Braun, B., Whirl Carrillo, M., Cheung, K. H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado Vides, J., Goto, S., Hucka, M., Le Novere, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. & Bader, G. D., 1 Jan 2010, In : Nature Biotechnology. 28, 9, p. 935-42

Research output: Contribution to journalArticleAcademicpeer-review