Onderzoeksoutput per jaar
Onderzoeksoutput per jaar
- 1 - 50 van 53 resultaten
Zoekresultaten
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2023
A proteomics approach to identify COPD-related changes in lung fibroblasts
Bekker, N. J. (First author), van Pijkeren, A., Wolters, J. C., Sánchez Brotons, A., Guryev, V., Woldhuis, R. R., Bischoff, R., Alkema, W., Horvatovich, P., van Nijnatten, J. L. L., van den Berge, M., Timens, W. & Brandsma, C.-A., 1 apr. 2023, In: American Journal of Physiology - Lung Cellular and Molecular Physiology. 324, 4, blz. L521-L535Onderzoeksoutput: Article › Academic › peer review
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Nailfold capillaroscopy and candidate-biomarker levels in systemic sclerosis-associated pulmonary hypertension: A cross-sectional study
Lemmers, J., van Caam, A., Kersten, B. E., van den Ende, C., Knaapen, H., van Dijk, A., Hagmolen of Ten Have, W., van den Hoogen, F., Koenen, H. J. P. M., van Leuven, S., Alkema, W., Smeets, R. L. & Vonk, M. C., 22 mei 2023, (E-pub ahead of print) In: Journal of Scleroderma and Related Disorders. 8, 3, blz. 221-230 9 blz., 3.Onderzoeksoutput: Article › Academic › peer review
Open Access -
The 3Ranker: An AI-based Algorithm for Finding Non-animal Alternative Methods
van Beuningen, N., Alkema, S., Hijlkema, N., Ulfhake, B., Frias, R., Ritskes-Hoitinga, M. & Alkema, W., 21 okt. 2023, In: Alternatives to Laboratory Animals. 51, 6, blz. 376-386 10 blz.Onderzoeksoutput: Article › Academic › peer review
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2021
Autoantibody profiles in systemic sclerosis: a comparison of diagnostic tests
Alkema, W., Koenen, H. J. P. M., Kersten, B. E., Kaffa, C., Nannenberg-Koops, J. W. & Damoiseux, J. G. M. C., 5 apr. 2021, In: Autoimmunity. 54, 3, blz. 148-155 7 blz.Onderzoeksoutput: Article › Academic › peer review
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Blood-Based Immune Profiling Combined with Machine Learning Discriminates Psoriatic Arthritis from Psoriasis Patients
Alkema, W., He, X., Kaffa, C., Joosten, I., Smeets, R. L., Koenen, H. J. P. M., Mulder, M. L. M., van den Reek, J. M. P. A., Urbano, P. C. M., Wang, X., van Cranenbroek, B., van Rijssen, E., Van Den Hoogen, F. H. J., de Jong, E. M. G. .. J. & Wenink, M. H., 12 okt. 2021, In: International Journal of Molecular Sciences. 22, 10 blz., 10990.Onderzoeksoutput: Article › Academic › peer review
Open AccessBestand122 Downloads (Pure) -
Charting host-microbe co-metabolism in skin aging and application to metagenomics data
Alkema, W., Boekhorst, J., Eijlander, R. T., Schnittger, S., de Gruyter, F., Lukovac, S., Schilling, K. & Kortman, G. A. M., 10 nov. 2021, In: PLoS ONE. 16, 11, 16 blz.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Maternal pre-pregnancy overweight and neonatal gut bacterial colonization are associated with cognitive development and gut microbiota composition in pre-school-age offspring
Guzzardi, M. A., Ederveen, T. H. A., Rizzo, F., Weisz, A., Collado, M. C., Muratori, F., Gross, G., Alkema, W. & Iozzo, P., 21 dec. 2021, In: Brain, Behavior, and Immunity. 100, blz. 311-320 10 blz.Onderzoeksoutput: Article › Academic › peer review
Open Access -
The Use of Artificial Intelligence for the Fast and Effective Identification of Three Rs-based Literature
Ritskes-Hoitinga, M. & Alkema, W., 28 sep. 2021, (E-pub ahead of print) In: ATLA Alternatives to Laboratory Animals. 49, 4, blz. 133-136 4 blz.Onderzoeksoutput: Article › Academic › peer review
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Training in Collecting, Appraising and Synthesising Evidence for EFSA scientific assessments
de Vries, R., van Luijk, J., Hooijmans, C., Wever, K., Hoffmann, S., in ’t Hout, J., Langendam, M., Tillema, A., Alkema, W. & Ritskes‐Hoitinga, M., 6 jul. 2021, (E-pub ahead of print) In: EFSA Supporting Publications. 18, 7Onderzoeksoutput: Article › Academic › peer review
Open Access -
2020
Diagnostic profiles for precision medicine in systemic sclerosis: stepping forward from single biomarkers towards pathophysiological panels
Smeets, R. L., Kersten, B. E., Joosten, I., Kaffa, C., Alkema, W., Koenen, H. J. P. M. & Vonk, M. C., 1 mei 2020, In: Autoimmunity reviews . 19, 5, 102515.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Live biotherapeutic products, a roadmap for safety assessment
Rouanet, A., Bolca, S., Bru, A., Claes, I., Cvejic, H., Girgis, H., Harper, A., Lavergne, S. N., Mathys, S., Pane, M., Pot, B., Shortt, C., Alkema, W., Bezulowsky, C., Blanquet-Diot, S., Chassard, C., Claus, S. P., Hadida, B., Hemmingsen, C. & Jeune, C. & 11 anderen, , 2020, In: Frontiers in Medicine. 7, 13 blz., 237.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Magnesium prevents vascular calcification in Klotho deficiency
Alkema, W., 1 mrt. 2020, In: Kidney International . 97, 3, blz. 487–501Onderzoeksoutput: Article › Academic › peer review
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Revealing new leads for the impact of galacto-oligosaccharides on gut commensals and gut health benefits through text mining
Sijbers, A. M., Schoemaker, R. J. W., Nauta, A. & Alkema, W., 17 apr. 2020, In: Beneficial microbes. 11, 3, blz. 283-302Onderzoeksoutput: Article › Academic › peer review
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2019
Biosynthetic homeostasis and resilience of the complement system in health and infectious disease
Willems, E., Alkema, W., Keizer-Garritsen, J., Suppers, A., van der Flier, M., Philipsen, R. H. L. A., van den Heuvel, L. P., Volokhina, E., van der Molen, R. G., Herberg, J. A., Levin, M., Wright, V. J., Ahout, I. M. L., Ferwerda, G., Emonts, M., Boeddha, N. P., Rivero-Calle, I., Torres, F. M., Wessels, H. J. C. T. & de Groot, R. & 3 anderen, , 1 jul. 2019, In: EBioMedicine. 45, blz. 303-313Onderzoeksoutput: Article › Academic › peer review
Open Access -
Establishing a health-based recommended occupational exposure limit for nitrous oxide using experimental animal data - a systematic review protocol
van Luijk, J. A. K. R., Popa, M., Swinkels, J., Menon, J. M. L., Alkema, W., Roeleveld, N., Hoffmann, S. E., Schlünssen, V., Mandrioli, D., Ritskes-Hoitinga, M. & Scheepers, P. T. J., 1 nov. 2019, In: Environmental Research. 178Onderzoeksoutput: Article › Academic › peer review
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2018
Magnesium deficiency prevents high-fat-diet-induced obesity in mice
Kurstjens, S., van Diepen, J. A., Overmars-Bos, C., Alkema, W., Bindels, R. J. M., Ashcroft, F. M., Tack, C. J. J., Hoenderop, J. G. J. & de Baaij, J. H. F., 1 sep. 2018, In: Diabetologia. 61, 9, blz. 2030-2042Onderzoeksoutput: Article › Academic › peer review
Open Access -
Primary cilia-regulated transcriptome in the renal collecting duct
Mohammed, S. G., Arjona, F. J., Verschuren, E. H. J., Bakey, Z., Alkema, W., van Hijum, S., Schmidts, M., Bindels, R. J. M. & Hoenderop, J. G. J., 8 feb. 2018, In: The FASEB Journal. 32, 7, blz. 3653-3668Onderzoeksoutput: Article › Academic › peer review
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2016
Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5
Urshev, Z., Hajo, K., Lenoci, L., Bron, P. A., Dijkstra, A., Alkema, W., Wels, M., Siezen, R. J., Minkova, S. & van Hijum, S. A. F. T., 6 okt. 2016, In: Genome Announcements. 4, 5Onderzoeksoutput: Article › Academic › peer review
Open Access -
High-throughput screening of a large collection of non-conventional yeasts reveals their potential for aroma formation in food fermentation
Gamero, A., Quintilla, R., Groenewald, M., Alkema, W., Boekhout, T. & Hazelwood, L., dec. 2016, In: Food Microbiology. 60, blz. 147-159 13 blz.Onderzoeksoutput: Article › Academic › peer review
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Strain-dependent transcriptome signatures for robustness in lactococcus lactis
Dijkstra, A. R., Alkema, W., Starrenburg, M. J. C., Hugenholtz, J., van Hijum, S. A. F. T. & Bron, P. A., 1 dec. 2016, In: PLoS ONE. 11, 12Onderzoeksoutput: Article › Academic › peer review
Open Access -
2015
Clustering analyses in peptidomics revealed that peptide profiles of infant formulae are descriptive
Lambers, T. T., Gloerich, J., van Hoffen, E., Alkema, W., Hondmann, D. H. & van Tol, E. A., jan. 2015, In: Food science & nutrition. 3, 1, blz. 81-90Onderzoeksoutput: Article › Academic › peer review
Open Access -
2014
Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress
Dijkstra, A. R., Setyawati, M. C., Bayjanov, J. R., Alkema, W., van Hijum, S. A. F. T., Bron, P. A. & Hugenholtz, J., 15 jan. 2014, In: Applied and Environmental Microbiology. 80, 2, blz. 603-611 9 blz.Onderzoeksoutput: Article › Academic › peer review
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Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness
Dijkstra, A. R., Alkema, W., Starrenburg, M. J. C., Hugenholtz, J., van Hijum, S. A. F. T. & Bron, P. A., 4 nov. 2014, In: Microbial Cell Factories. 13, 1Onderzoeksoutput: Article › Academic › peer review
Open Access -
2013
Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining
Fleuren, W. W., Toonen, E. J., Verhoeven, S., Frijters, R., Hulsen, T., Rullmann, T., van Schaik, R., de Vlieg, J. & Alkema, W., 4 feb. 2013, In: BioData Mining. 6, 1, blz. 2 1 blz.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Prednisolone induces the Wnt signalling pathway in 3T3-L1 adipocytes
Fleuren, W. W. M., Linssen, M. M. L., Toonen, E. J. M., van der Zon, G. C. M., Guigas, B., de Vlieg, J., Dokter, W. H. A., Ouwens, D. M. & Alkema, W., 19 mrt. 2013, In: Archives of Physiology and Biochemistry. 119, 2, blz. 52-64Onderzoeksoutput: Article › Academic › peer review
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2012
Assessing the metabolic effects of prednisolone in healthy volunteers using urine metabolic profiling
Ellero-Simatos, S., Szymańska, E., Rullmann, T., Dokter, W. H., Ramaker, R., Berger, R., van Iersel, T. M., Smilde, A. K., Hankemeier, T. & Alkema, W., 30 nov. 2012, In: Genome Announcements. 4, 11Onderzoeksoutput: Article › Academic › peer review
Open Access -
Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling
Smeets, R. L., Fleuren, W. W. M., He, X., Vink, P. M., Wijnands, F., Gorecka, M., Klop, H., Bauerschmidt, S., Garritsen, A., Koenen, H. J. P. M., Joosten, I., Boots, A. M. H. & Alkema, W., 14 mrt. 2012, In: Molecular Immunology. 13, 12 blz.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Org 214007-0: a novel non-steroidal selective glucocorticoid receptor modulator with full anti-inflammatory properties and improved therapeutic index
van Lierop, M.-J. C., Alkema, W., Laskewitz, A. J., Dijkema, R., van der Maaden, H. M., Smit, M. J., Plate, R., Conti, P. G. M., Jans, C. G. J. M., Timmers, C. M., van Boeckel, C. A. A., Lusher, S. J., McGuire, R., van Schaik, R. C., de Vlieg, J., Smeets, R. L., Hofstra, C. L., Boots, A. M. H., van Duin, M. & Ingelse, B. A. & 5 anderen, , 12 nov. 2012, In: PLoS ONE. 7, 11Onderzoeksoutput: Article › Academic › peer review
Open Access -
2011
CoPub update: CoPub 5.0 a text mining system to answer biological questions
Fleuren, W. W. M., Verhoeven, S., Frijters, R., Heupers, B., Polman, J., van Schaik, R., de Vlieg, J. & Alkema, W., 27 mei 2011, In: Nucleic Acids Research. 39, SUPPL. 2, blz. 450-454 5 blz., Web-Server-Issue.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Prednisolone-induced beta cell dysfunction is associated with impaired endoplasmic reticulum homeostasis in INS-1E cells
Linssen, M. M. L., van Raalte, D. H., Toonen, E. J. M., Alkema, W., van der Zon, G. C., Dokter, W. H., Diamant, M., Guigas, B. & Ouwens, D. M., 1 nov. 2011, In: Cellular Signalling. 23, 11, blz. 1708-1715Onderzoeksoutput: Article › Academic › peer review
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Prednisolone-induced changes in gene-expression profiles in healthy volunteers
Toonen, E. J. M., Fleuren, W. W. M., Nässander, U., van Lierop, M.-J. C., Bauerschmidt, S., Dokter, W. H. A. & Alkema, W., 25 jul. 2011, In: Pharmacogenomics. 12, 7, blz. 985-998Onderzoeksoutput: Article › Academic › peer review
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ss-TEA: entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs
umc, R., Fleuren, W. W. M., Verhoeven, S., van den Beld, S., Alkema, W., de Vlieg, J. & Klomp, J. P. G., 10 aug. 2011, In: Briefings in Bioinformatics. 12, blz. 332 1 blz.Onderzoeksoutput: Article › Academic › peer review
Open Access -
2010
Literature mining for the discovery of hidden connections between drugs, genes and diseases
Frijters, R., van Vugt, M., Smeets, R., van Schaik, R., de Vlieg, J. & Alkema, W., 23 sep. 2010, In: PLoS Computational Biology. 6, 9, 9.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor
Frijters, R., Fleuren, W., Toonen, E. J. M., Tuckermann, J. P., Reichardt, H. M., van der Maaden, H., van Elsas, A., van Lierop, M.-J., Dokter, W., de Vlieg, J. & Alkema, W., 5 jun. 2010, In: BMC Genomics. 11, 1Onderzoeksoutput: Article › Academic › peer review
Open Access -
2009
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
Hulsen, T., Groenen, P. M. A., de Vlieg, J. & Alkema, W., 1 jan. 2009, In: Nucleic Acids Research. 37, SUPPL. 1, blz. 731-737 7 blz., Database-Issue.Onderzoeksoutput: Article › Academic › peer review
Open Access -
2008
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
Hulsen, T., de Vlieg, J. & Alkema, W., 16 okt. 2008, In: BMC Genomics. 9Onderzoeksoutput: Article › Academic › peer review
Open Access -
CoPub: a literature-based keyword enrichment tool for microarray data analysis
Frijters, R., Heupers, B., van Beek, P., Bouwhuis, M., van Schaik, R., de Vlieg, J., Polman, J. & Alkema, W., 1 jul. 2008, In: Nucleic Acids Research. 36, Web Server issue, blz. 406-410 5 blz.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Saturation mutagenesis reveals the importance of residues alphaR145 and alphaF146 of penicillin acylase in the synthesis of beta-lactam antibiotics
Jager, S. A. W., Shapovalova, I. V., Jekel, P. A., Alkema, W. B. L., Svedas, V. K. & Janssen, D. B., 1 jan. 2008, In: Journal of Biotechnology. 133, 1, blz. 18-26Onderzoeksoutput: Article › Academic › peer review
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2007
Literature-based compound profiling: application to toxicogenomics
Frijters, R., Verhoeven, S., Alkema, W., van Schaik, R. & Polman, J., 1 nov. 2007, In: Pharmacogenomics. 8, 11, blz. 1521-1534 14 blz.Onderzoeksoutput: Article › Academic › peer review
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2006
Genome-wide analysis of mammalian promoter architecture and evolution
Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., Forrest, A. R. R., Alkema, W. B., Tan, S. L., Plessy, C., Kodzius, R., Ravasi, T., Kasukawa, T., Fukuda, S., Kanamori-Katayama, M. & Kitazume, Y. & 21 anderen, , 28 apr. 2006, In: Nature Genetics. 38, 6, blz. 626-635Onderzoeksoutput: Article › Academic › peer review
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Target validation in silico: does the virtual patient cure the pharma pipeline?
Alkema, W., Rullmann, T. & van Elsas, A., 16 sep. 2006, In: Expert Opinion on Therapeutic Targets. 10, 5, blz. 635-638Onderzoeksoutput: Article › Academic › peer review
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2004
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
Sandelin, A., Alkema, W., Engström, P., Wasserman, W. W. & Lenhard, B., 1 jan. 2004, In: Nucleic Acids Research. 32, Database-Issue, blz. 91-94 4 blz., Database-Issue.Onderzoeksoutput: Article › Academic › peer review
Open Access -
MSCAN: identification of functional clusters of transcription factor binding sites
Alkema, W. B. L., Johansson, O., Lagergren, J. & Wasserman, W. W., 1 jul. 2004, In: Nucleic Acids Research. 32, WEB SERVER ISS., blz. 195-198 4 blz., Web-Server-Issue.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Quantifying the accessibility of the metagenome by random expression cloning techniques
Gabor, E. M., Alkema, W. B. L. & Janssen, D. B., 11 aug. 2004, In: Applied and Environmental Microbiology. 6, 9, blz. 879-886Onderzoeksoutput: Article › Academic › peer review
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Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus
Alkema, W. B. L., Lenhard, B. & Wasserman, W. W., 1 jul. 2004, In: Genome Announcements. 14, 7, blz. 1362-1373 12 blz.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase
Alkema, W. B. L., Hensgens, C. M. H., Snijder, H. J., Keizer, E., Dijkstra, B. W. & Janssen, D. B., 14 jul. 2004, In: Protein Engineering, Design & Selection. 17, 5, blz. 473-480Onderzoeksoutput: Article › Academic › peer review
Open Access -
2003
Kinetics of enzyme acylation and deacylation in the penicillin acylase-catalyzed synthesis of β-lactam antibiotics
Alkema, W. B. L., de Vries, E., Floris, R. & Janssen, D. B., sep. 2003, In: European Journal of Biochemistry. 270, 18, blz. 3675-3683 9 blz.Onderzoeksoutput: Article › Academic › peer review
Open Access -
Understanding the language of gene regulation
Alkema, W. & Wasserman, W. W., 1 jan. 2003, In: Genome biology. 4, 7Onderzoeksoutput: Article › Academic › peer review
Open Access -
2002
Role of alphaArg145 and betaArg263 in the active site of penicillin acylase of Escherichia coli
Alkema, W. B. L., Prins, A. K., de Vries, E. & Janssen, D. B., jul. 2002, In: European Journal of Biochemistry. 365, 1, blz. 303-309Onderzoeksoutput: Article › Academic › peer review
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The role of hydrophobic active-site residues in substrate specificity and acyl transfer activity of penicillin acylase
Alkema, W. B. L., Dijkhuis, A.-J., De Vries, E. & Janssen, D. B., 9 apr. 2002, In: European Journal of Biochemistry. 269, 8, blz. 2093-2100Onderzoeksoutput: Article › Academic › peer review
Open Access