Experts and Doctors on gene expression profiling in Netherlands

Summary

Locale: Netherlands
Topic: gene expression profiling

Top Publications

  1. Dik W, Pike Overzet K, Weerkamp F, de Ridder D, de Haas E, Baert M, et al. New insights on human T cell development by quantitative T cell receptor gene rearrangement studies and gene expression profiling. J Exp Med. 2005;201:1715-23 pubmed
    ..Our data demonstrate that a number of key events occur earlier than assumed previously; therefore, human T cell development is much more similar to murine T cell development than reported before. ..
  2. Makama M, Drukker C, Rutgers E, Slaets L, Cardoso F, Rookus M, et al. An association study of established breast cancer reproductive and lifestyle risk factors with tumour subtype defined by the prognostic 70-gene expression signature (MammaPrint®). Eur J Cancer. 2017;75:5-13 pubmed publisher
    ..Using prognostic gene expression profiles, we have indications that specific reproductive factors may be associated with prognostic tumour subtypes beyond hormone receptor status. ..
  3. Maczuga P, Verheij J, van der Loos C, van Logtenstein R, Hooijer G, Martier R, et al. Therapeutic expression of hairpins targeting apolipoprotein B100 induces phenotypic and transcriptome changes in murine liver. Gene Ther. 2014;21:60-70 pubmed publisher
    ..The increased hepatocyte profileration by AAV-shRNA may have severe long-term effects indicating that AAV-mediated RNA interference therapy using artificial miRNA may be a safer approach for familial hypercholesterolemia therapy. ..
  4. Buitendijk G, Rochtchina E, Myers C, van Duijn C, Lee K, Klein B, et al. Prediction of age-related macular degeneration in the general population: the Three Continent AMD Consortium. Ophthalmology. 2013;120:2644-2655 pubmed publisher
    ..Our prediction model is robust and distinguishes well between those who will develop late AMD and those who will not. Estimated risks were lower in these population-based studies than in previous case-control studies. ..
  5. Nandoe Tewarie R, Bossers K, Ritfeld G, Blits B, Grotenhuis J, Verhaagen J, et al. Early passage bone marrow stromal cells express genes involved in nervous system development supporting their relevance for neural repair. Restor Neurol Neurosci. 2011;29:187-201 pubmed publisher
    ..Our gene profiling results suggested a decreased plasticity and repair aptitude of long-term cultured BMSC. Our data indicated the use of early passage BMSC for neural repair approaches. ..
  6. Li A, van Luijk N, Ter Beek M, Caspers M, Punt P, van der Werf M. A clone-based transcriptomics approach for the identification of genes relevant for itaconic acid production in Aspergillus. Fungal Genet Biol. 2011;48:602-11 pubmed publisher
    ..Interestingly, this cluster is directly linked to the large lovastatin gene cluster. ..
  7. Linares D, Kok J, Poolman B. Genome sequences of Lactococcus lactis MG1363 (revised) and NZ9000 and comparative physiological studies. J Bacteriol. 2010;192:5806-12 pubmed publisher
  8. Thygesen H, Zwinderman A. Modelling the correlation between the activities of adjacent genes in Drosophila. BMC Bioinformatics. 2005;6:10 pubmed
    ..Correlation between the activities of adjacent genes is higher than between non-adjacent genes. In the data we analyzed, this appeared, for the most part, to be a constant effect that applied to all pairs of adjacent genes. ..
  9. van Spronsen M, van Battum E, Kuijpers M, Vangoor V, Rietman M, Pothof J, et al. Developmental and activity-dependent miRNA expression profiling in primary hippocampal neuron cultures. PLoS ONE. 2013;8:e74907 pubmed publisher
    ..Identification and characterization of miRNA targets may further elucidate translational control mechanisms involved in hippocampal development, differentiation and activity-depended processes. ..

More Information

Publications27

  1. Eisinga R, Breitling R, Heskes T. The exact probability distribution of the rank product statistics for replicated experiments. FEBS Lett. 2013;587:677-82 pubmed publisher
    ..In this paper we relate the rank product statistic to number theory and provide a derivation of its exact probability distribution and the true tail probabilities. ..
  2. Bouwens M, van de Rest O, Dellschaft N, Bromhaar M, de Groot L, Geleijnse J, et al. Fish-oil supplementation induces antiinflammatory gene expression profiles in human blood mononuclear cells. Am J Clin Nutr. 2009;90:415-24 pubmed publisher
    ..These results are the first to show that intake of EPA+DHA for 26 wk can alter the gene expression profiles of PBMCs to a more antiinflammatory and antiatherogenic status. This trial was registered at clinicaltrials.gov as NCT00124852. ..
  3. Wansleeben C, van Gurp L, de Graaf P, Mousson F, Marc Timmers H, Meijlink F. An ENU-induced point mutation in the mouse Btaf1 gene causes post-gastrulation embryonic lethality and protein instability. Mech Dev. 2011;128:279-88 pubmed publisher
    ..5 displaying growth arrest and edema. Analyses in vitro suggest that the altered protein is less stable and, independent from this, functionally impaired in releasing of TBP from chromatin, but not in binding to TBP. ..
  4. Jiang J, Mathijs K, Timmermans L, Claessen S, Hecka A, Weusten J, et al. Omics-based identification of the combined effects of idiosyncratic drugs and inflammatory cytokines on the development of drug-induced liver injury. Toxicol Appl Pharmacol. 2017;332:100-108 pubmed publisher
    ..Overall, our study provides a potential mechanism to explain the role of inflammation in idiosyncratic drug reactions. ..
  5. Afzal M, Kuipers O, Shafeeq S. Niacin-mediated Gene Expression and Role of NiaR as a Transcriptional Repressor of niaX, nadC, and pnuC in Streptococcus pneumoniae. Front Cell Infect Microbiol. 2017;7:70 pubmed publisher
    ..The putative operator site of NiaR (5'-TACWRGTGTMTWKACASYTRWAW-3') in the promoter regions of niaX, nadC, and pnuC is predicted and further confirmed by promoter mutational experiments. ..
  6. Stanford S, Svensson M, Sacchetti C, Pilo C, Wu D, Kiosses W, et al. Receptor Protein Tyrosine Phosphatase α-Mediated Enhancement of Rheumatoid Synovial Fibroblast Signaling and Promotion of Arthritis in Mice. Arthritis Rheumatol. 2016;68:359-69 pubmed publisher
    ..By regulating the phosphorylation of Src and FAK, RPTPα mediates proinflammatory and proinvasive signaling in RA FLS, correlating with the promotion of disease in an FLS-dependent model of RA. ..
  7. Jacobs C, van der Zee M. Immune competence in insect eggs depends on the extraembryonic serosa. Dev Comp Immunol. 2013;41:263-9 pubmed publisher
    ..Drosophila eggs and serosa-less Tribolium eggs, however, show little to no upregulation of any of the tested immune genes. We conclude that the extraembryonic serosa is crucial for the early immune competence of the Tribolium egg...
  8. Schepers A, Snippert H, Stange D, van den Born M, van Es J, van de Wetering M, et al. Lineage tracing reveals Lgr5+ stem cell activity in mouse intestinal adenomas. Science. 2012;337:730-5 pubmed publisher
    ..The Lgr5(+) cells are intermingled with Paneth cells near the adenoma base, a pattern reminiscent of the architecture of the normal crypt niche...
  9. Waters A. Parasitology. Guilty until proven otherwise. Science. 2003;301:1487-8 pubmed
  10. Sieuwerts S, Molenaar D, van Hijum S, Beerthuyzen M, Stevens M, Janssen P, et al. Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus. Appl Environ Microbiol. 2010;76:7775-84 pubmed publisher
    ..In addition, the postgenomic analysis of the responses of L. bulgaricus to mixed-culture growth allows a deeper understanding of the ecology and interactions of this important industrial food fermentation process...
  11. van der Veen S, Abee T. Importance of SigB for Listeria monocytogenes static and continuous-flow biofilm formation and disinfectant resistance. Appl Environ Microbiol. 2010;76:7854-60 pubmed publisher
  12. Kaufmann K, Wellmer F, Muiño J, Ferrier T, Wuest S, Kumar V, et al. Orchestration of floral initiation by APETALA1. Science. 2010;328:85-9 pubmed publisher
    ..Our results further imply that AP1 orchestrates floral initiation by integrating growth, patterning, and hormonal pathways. ..
  13. Snippert H, Haegebarth A, Kasper M, Jaks V, van Es J, Barker N, et al. Lgr6 marks stem cells in the hair follicle that generate all cell lineages of the skin. Science. 2010;327:1385-9 pubmed publisher
    ..Adult Lgr6+ cells executed long-term wound repair, including the formation of new hair follicles. We conclude that Lgr6 marks the most primitive epidermal stem cell...
  14. Barker N, Huch M, Kujala P, van de Wetering M, Snippert H, van Es J, et al. Lgr5(+ve) stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell Stem Cell. 2010;6:25-36 pubmed publisher
    ..The Lgr5 stem cell marker and culture method described here will be invaluable tools for accelerating research into gastric epithelial renewal, inflammation/infection, and cancer. ..
  15. Wesseling S, Joles J, van Goor H, Bluyssen H, Kemmeren P, Holstege F, et al. Transcriptome-based identification of pro- and antioxidative gene expression in kidney cortex of nitric oxide-depleted rats. Physiol Genomics. 2007;28:158-67 pubmed
    ..Interaction between NO synthesis and heme degradation pathways for blood pressure regulation was not found...
  16. Kovács Á, van Hartskamp M, Kuipers O, van Kranenburg R. Genetic tool development for a new host for biotechnology, the thermotolerant bacterium Bacillus coagulans. Appl Environ Microbiol. 2010;76:4085-8 pubmed publisher
    ..Here, we present a targeted gene disruption system using the Cre-lox system, development of a LacZ reporter assay for monitoring gene transcription, and heterologous d-lactate dehydrogenase expression. ..
  17. Riemer P, Rydenfelt M, Marks M, van Eunen K, Thedieck K, Herrmann B, et al. Oncogenic β-catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids. J Cell Biol. 2017;216:1567-1577 pubmed publisher
    ..Our work defines phenotypes, signaling network states, and vulnerabilities of transgenic intestinal organoids as a novel approach to understanding oncogene activities and guiding the development of targeted therapies. ..
  18. Schreuder K, Kuijer A, Rutgers E, Smorenburg C, van Dalen T, Siesling S. Impact of gene-expression profiling in patients with early breast cancer when applied outside the guideline directed indication area. Eur J Cancer. 2017;84:270-277 pubmed publisher
    ..7% vs. 52.2%, respectively. GEP is frequently used outside the indicated area and significantly influenced the administration of adjuvant CT, although adherence to the test result was limited. ..