Search Results - "Megchelenbrink, Wout"

Trained innate immunity, long-lasting epigenetic modulation, and skewed myelopoiesis by heme by Jentho, Elisa, Ruiz-Moreno, Cristian, Novakovic, Boris, Kourtzelis, Ioannis, Megchelenbrink, Wout. L., Martins, Rui, Chavakis, Triantafyllos, Soares, Miguel P., Kalafati, Lydia, Guerra, Joel, Roestel, Franziska, Bohm, Peter, Godmann, Maren, Grinenko, Tatyana, Eugster, Anne, Beretta, Martina, Joosten, Leo A. B., Netea, Mihai G., Bauer, Michael, Stunnenberg, Hendrik G., Weis, Sebastian

“…Trained immunity defines long-lasting adaptations of innate immunity based on transcriptional and epigenetic modifications of myeloid cells and their bone…”
Get full text

optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks by Megchelenbrink, Wout, Huynen, Martijn, Marchiori, Elena

“…Constraint-based models of metabolic networks are typically underdetermined, because they contain more reactions than metabolites. Therefore the solutions to…”
Get full text

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells by Peng, Tianran, Zhai, Yanan, Atlasi, Yaser, Ter Huurne, Menno, Marks, Hendrik, Stunnenberg, Hendrik G, Megchelenbrink, Wout

“…Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the…”
Get full text

Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages by Wang, Cheng, Nanni, Luca, Novakovic, Boris, Megchelenbrink, Wout, Kuznetsova, Tatyana, Stunnenberg, Hendrik G., Ceri, Stefano, Logie, Colin

“…Glucocorticoid receptor is a transcription factor that is ubiquitously expressed. Glucocorticoids are circadian steroids that regulate a wide range of bodily…”
Get full text

Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency by Bell, Emma, Curry, Edward W., Megchelenbrink, Wout, Jouneau, Luc, Brochard, Vincent, Tomaz, Rute A., Mau, King Hang T., Atlasi, Yaser, de Souza, Roshni A., Marks, Hendrik, Stunnenberg, Hendrik G., Jouneau, Alice, Azuara, Véronique

“…Clusters of enhancers, referred as to super-enhancers (SEs), control the expression of cell identity genes. The organisation of these clusters, and how they…”
Get full text

Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency by Atlasi, Yaser, Megchelenbrink, Wout, Peng, Tianran, Habibi, Ehsan, Joshi, Onkar, Wang, Shuang-Yin, Wang, Cheng, Logie, Colin, Poser, Ina, Marks, Hendrik, Stunnenberg, Hendrik G.

“…The mechanisms underlying enhancer activation and the extent to which enhancer–promoter rewiring contributes to spatiotemporal gene expression are not well…”
Get full text

Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival by Megchelenbrink, Wout, Katzir, Rotem, Lu, Xiaowen, Ruppin, Eytan, Notebaart, Richard A.

“…Synthetic dosage lethality (SDL) denotes a genetic interaction between two genes whereby the underexpression of gene A combined with the overexpression of gene…”
Get full text

Longitudinal single-cell transcriptomics reveals distinct patterns of recurrence in acute myeloid leukemia by Zhai, Yanan, Singh, Prashant, Dolnik, Anna, Brazda, Peter, Atlasy, Nader, del Gaudio, Nunzio, Döhner, Konstanze, Döhner, Hartmut, Minucci, Saverio, Martens, Joost, Altucci, Lucia, Megchelenbrink, Wout, Bullinger, Lars, Stunnenberg, Hendrik G

“…Abstract Background Acute myeloid leukemia (AML) is a heterogeneous and aggressive blood cancer that results from diverse genetic aberrations in the…”
Get full text

Extensive patient-to-patient single nucleus transcriptome heterogeneity in pheochromocytomas and paragangliomas by Brazda, Peter, Ruiz-Moreno, Cristian, Megchelenbrink, Wout L, Timmers, Henri J L M, Stunnenberg, Hendrik G

“…Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors with varied genetic makeup and are associated with high cardiovascular morbidity…”
Get full text

Predicting human genetic interactions from cancer genome evolution by Lu, Xiaowen, Megchelenbrink, Wout, Notebaart, Richard A, Huynen, Martijn A

“…Synthetic Lethal (SL) genetic interactions play a key role in various types of biological research, ranging from understanding genotype-phenotype relationships…”
Get full text

Publisher Correction: Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency by Atlasi, Yaser, Megchelenbrink, Wout, Peng, Tianran, Habibi, Ehsan, Joshi, Onkar, Wang, Shuang-Yin, Wang, Cheng, Logie, Colin, Poser, Ina, Marks, Hendrik, Stunnenberg, Hendrik G.

“…In the version of the article originally published, extra lines were displayed in Fig. 7. Fig. 7a contained a solid black line that extended into panel b, and…”
Get full text

Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm by Megchelenbrink, Wout, Rossell, Sergio, Huynen, Martijn A, Notebaart, Richard A, Marchiori, Elena

“…Genome-scale metabolic networks can be modeled in a constraint-based fashion. Reaction stoichiometry combined with flux capacity constraints determine the…”
Get full text

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance by Novakovic, Boris, Habibi, Ehsan, Wang, Shuang-Yin, Arts, Rob J.W., Davar, Robab, Megchelenbrink, Wout, Kim, Bowon, Kuznetsova, Tatyana, Kox, Matthijs, Zwaag, Jelle, Matarese, Filomena, van Heeringen, Simon J., Janssen-Megens, Eva M., Sharifi, Nilofar, Wang, Cheng, Keramati, Farid, Schoonenberg, Vivien, Flicek, Paul, Clarke, Laura, Pickkers, Peter, Heath, Simon, Gut, Ivo, Netea, Mihai G., Martens, Joost H.A., Logie, Colin, Stunnenberg, Hendrik G.

“…Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to…”
Get full text

Epigenomic machinery regulating pediatric AML: Clonal expansion mechanisms, therapies, and future perspectives by Chianese, Ugo, Papulino, Chiara, Megchelenbrink, Wout, Tambaro, Francesco Paolo, Ciardiello, Fortunato, Benedetti, Rosaria, Altucci, Lucia

“…Acute myeloid leukemia (AML) is a heterogeneous disease with a genetic, epigenetic, and transcriptional etiology mainly presenting somatic and germline…”
Get full text

Transcriptional Heterogeneity and Clonal Evolution between Diagnosis and Relapse in Pediatric Acute Myeloid Leukemia by Grasso, Cristoforo, Brazda, Peter, te Pas, Brigit M., Dharmadhikari, Gitanjali, Koedijk, Joost B., Goemans, Bianca F., Heidenreich, Olaf, Belderbos, Mirjam E., Zwaan, C. Michel, Stunnenberg, Hendrik G., Megchelenbrink, Wout

“…Clonal evolution of leukemia is driven by different selection pressures operating on a heterogeneous population of cells. These pressures may include…”
Get full text

WeGET: predicting new genes for molecular systems by weighted co-expression by Szklarczyk, Radek, Megchelenbrink, Wout, Cizek, Pavel, Ledent, Marie, Velemans, Gonny, Szklarczyk, Damian, Huynen, Martijn A

“…We have developed the Weighted Gene Expression Tool and database (WeGET, http://weget.cmbi.umcn.nl) for the prediction of new genes of a molecular system by…”
Get full text

TMIC-86. SPATIAL ORGANIZATION OF THE PEDIATRIC HIGH-GRADE GLIOMA TUMOR-IMMUNE LANDSCAPE by van den Broek, Thijs, Hoogendijk, Raoull, Kranendonk, Mariëtte, Ruiz, Cristian, Megchelenbrink, Wout L, Lammers, Julie, Ries, Mario G, Hoving, Eelco, van der Lugt, Jasper, Rios, Anne C, Stunnenberg, Hendrik, van Vuurden, Dannis, Zomer, Anoek

“…Abstract BACKGROUND Advances in cellular immunotherapies have shown promising results for brain tumors, including pediatric-type diffuse high-grade gliomas…”
Get full text

Predicting Human Genetic Interactions from Cancer Genome Evolution: e0125795 by Lu, Xiaowen, Megchelenbrink, Wout, Notebaart, Richard A, Huynen, Martijn A

“…Synthetic Lethal (SL) genetic interactions play a key role in various types of biological research, ranging from understanding genotype-phenotype relationships…”
Get full text