Search Results - "Lindeboom, Rik"

To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases by Supek, Fran, Lehner, Ben, Lindeboom, Rik G.H.

“…The nonsense-mediated mRNA decay (NMD) pathway degrades some but not all mRNAs bearing premature termination codons (PTCs). Decades of work have elucidated the…”
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The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy by Lindeboom, Rik G. H., Vermeulen, Michiel, Lehner, Ben, Supek, Fran

“…Premature termination codons (PTCs) can result in the production of truncated proteins or the degradation of messenger RNAs by nonsense-mediated mRNA decay…”
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The rules and impact of nonsense-mediated mRNA decay in human cancers by Lindeboom, Rik G H, Supek, Fran, Lehner, Ben

“…Ben Lehner and colleagues analyze data from matched exomes and transcriptomes from tumors across 27 cancer types to elucidate rules linking premature…”
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Towards a Human Cell Atlas: Taking Notes from the Past by Lindeboom, Rik G.H., Regev, Aviv, Teichmann, Sarah A.

“…Comprehensively characterizing the cellular composition and organization of tissues has been a long-term scientific challenge that has limited our ability to…”
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Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids by Artegiani, Benedetta, van Voorthuijsen, Lisa, Lindeboom, Rik G.H., Seinstra, Daniëlle, Heo, Inha, Tapia, Pablo, López-Iglesias, Carmen, Postrach, Daniel, Dayton, Talya, Oka, Rurika, Hu, Huili, van Boxtel, Ruben, van Es, Johan H., Offerhaus, Johan, Peters, Peter J., van Rheenen, Jacco, Vermeulen, Michiel, Clevers, Hans

“…The deubiquitinating enzyme BAP1 is a tumor suppressor, among others involved in cholangiocarcinoma. BAP1 has many proposed molecular targets, while its…”
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Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins by Suo, Chenqu, Polanski, Krzysztof, Dann, Emma, Lindeboom, Rik G. H., Vilarrasa-Blasi, Roser, Vento-Tormo, Roser, Haniffa, Muzlifah, Meyer, Kerstin B., Dratva, Lisa M., Tuong, Zewen Kelvin, Clatworthy, Menna R., Teichmann, Sarah A.

“…Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in…”
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Single-Molecule Imaging Uncovers Rules Governing Nonsense-Mediated mRNA Decay by Hoek, Tim A., Khuperkar, Deepak, Lindeboom, Rik G.H., Sonneveld, Stijn, Verhagen, Bram M.P., Boersma, Sanne, Vermeulen, Michiel, Tanenbaum, Marvin E.

“…Nonsense-mediated decay (NMD) is a surveillance system that degrades mRNAs containing a premature termination codon (PTC) and plays important roles in protein…”
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N 6 -methyladenosine (m 6 A) recruits and repels proteins to regulate mRNA homeostasis by Edupuganti, Raghu R, Geiger, Simon, Lindeboom, Rik G H, Shi, Hailing, Hsu, Phillip J, Lu, Zhike, Wang, Shuang-Yin, Baltissen, Marijke P A, Jansen, Pascal W T C, Rossa, Martin, Müller, Markus, Stunnenberg, Hendrik G, He, Chuan, Carell, Thomas, Vermeulen, Michiel

“…RNA modifications are integral to the regulation of RNA metabolism. One abundant mRNA modification is N -methyladenosine (m A), which affects various aspects…”
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ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage by Spruijt, Cornelia G., Luijsterburg, Martijn S., Menafra, Roberta, Lindeboom, Rik G.H., Jansen, Pascal W.T.C., Edupuganti, Raghu Ram, Baltissen, Marijke P., Wiegant, Wouter W., Voelker-Albert, Moritz C., Matarese, Filomena, Mensinga, Anneloes, Poser, Ina, Vos, Harmjan R., Stunnenberg, Hendrik G., van Attikum, Haico, Vermeulen, Michiel

“…NuRD (nucleosome remodeling and histone deacetylase) is a versatile multi-protein complex with roles in transcription regulation and the DNA damage response…”
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Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq by Neikes, Hannah K., Kliza, Katarzyna W., Gräwe, Cathrin, Wester, Roelof A., Jansen, Pascal W. T. C., Lamers, Lieke A., Baltissen, Marijke P., van Heeringen, Simon J., Logie, Colin, Teichmann, Sarah A., Lindeboom, Rik G. H., Vermeulen, Michiel

“…Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the impact of…”
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Single-cell multi-omics analysis of the immune response in COVID-19 by Stephenson, Emily, Reynolds, Gary, Botting, Rachel A., Calero-Nieto, Fernando J., Morgan, Michael D., Tuong, Zewen Kelvin, Bach, Karsten, Sungnak, Waradon, Worlock, Kaylee B., Yoshida, Masahiro, Kumasaka, Natsuhiko, Kania, Katarzyna, Engelbert, Justin, Olabi, Bayanne, Spegarova, Jarmila Stremenova, Wilson, Nicola K., Mende, Nicole, Jardine, Laura, Gardner, Louis C. S., Goh, Issac, Horsfall, Dave, McGrath, Jim, Webb, Simone, Mather, Michael W., Lindeboom, Rik G. H., Dann, Emma, Huang, Ni, Polanski, Krzysztof, Prigmore, Elena, Gothe, Florian, Scott, Jonathan, Payne, Rebecca P., Baker, Kenneth F., Hanrath, Aidan T., Schim van der Loeff, Ina C. D., Barr, Andrew S., Sanchez-Gonzalez, Amada, Bergamaschi, Laura, Mescia, Federica, Barnes, Josephine L., Kilich, Eliz, de Wilton, Angus, Saigal, Anita, Saleh, Aarash, Janes, Sam M., Smith, Claire M., Gopee, Nusayhah, Wilson, Caroline, Coupland, Paul, Coxhead, Jonathan M., Kiselev, Vladimir Yu, van Dongen, Stijn, Bacardit, Jaume, King, Hamish W., Rostron, Anthony J., Simpson, A. John, Hambleton, Sophie, Laurenti, Elisa, Lyons, Paul A., Meyer, Kerstin B., Nikolić, Marko Z., Duncan, Christopher J. A., Smith, Kenneth G. C., Teichmann, Sarah A., Clatworthy, Menna R., Marioni, John C., Göttgens, Berthold, Haniffa, Muzlifah

“…Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus…”
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A spatially resolved atlas of the human lung characterizes a gland-associated immune niche by Madissoon, Elo, Oliver, Amanda J., Kleshchevnikov, Vitalii, Wilbrey-Clark, Anna, Polanski, Krzysztof, Richoz, Nathan, Ribeiro Orsi, Ana, Mamanova, Lira, Bolt, Liam, Elmentaite, Rasa, Pett, J. Patrick, Huang, Ni, Xu, Chuan, He, Peng, Dabrowska, Monika, Pritchard, Sophie, Tuck, Liz, Prigmore, Elena, Perera, Shani, Knights, Andrew, Oszlanczi, Agnes, Hunter, Adam, Vieira, Sara F., Patel, Minal, Lindeboom, Rik G. H., Campos, Lia S., Matsuo, Kazuhiko, Nakayama, Takashi, Yoshida, Masahiro, Worlock, Kaylee B., Nikolić, Marko Z., Georgakopoulos, Nikitas, Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Bayraktar, Omer Ali, Clatworthy, Menna R., Stegle, Oliver, Kumasaka, Natsuhiko, Teichmann, Sarah A., Meyer, Kerstin B.

“…Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To…”
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Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data by Drost, Felix, An, Yang, Bonafonte-Pardàs, Irene, Dratva, Lisa M., Lindeboom, Rik G. H., Haniffa, Muzlifah, Teichmann, Sarah A., Theis, Fabian, Lotfollahi, Mohammad, Schubert, Benjamin

“…Recent advances in single-cell immune profiling have enabled the simultaneous measurement of transcriptome and T cell receptor (TCR) sequences, offering great…”
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Integrative multi‐omics analysis of intestinal organoid differentiation by Lindeboom, Rik GH, van Voorthuijsen, Lisa, Oost, Koen C, Rodríguez‐Colman, Maria J, Luna‐Velez, Maria V, Furlan, Cristina, Baraille, Floriane, Jansen, Pascal WTC, Ribeiro, Agnès, Burgering, Boudewijn MT, Snippert, Hugo J, Vermeulen, Michiel

“…Intestinal organoids accurately recapitulate epithelial homeostasis in vivo , thereby representing a powerful in vitro system to investigate lineage…”
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Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation by Bonnet, Jacques, Lindeboom, Rik G.H., Pokrovsky, Daniil, Stricker, Georg, Çelik, Muhammed Hasan, Rupp, Ralph A.W., Gagneur, Julien, Vermeulen, Michiel, Imhof, Axel, Müller, Jürg

“…Gene transcription in eukaryotes is regulated through dynamic interactions of a variety of different proteins with DNA in the context of chromatin. Here, we…”
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Liver Colonization by Colorectal Cancer Metastases Requires YAP-Controlled Plasticity at the Micrometastatic Stage by Heinz, Maria C, Peters, Niek A, Oost, Koen C, Lindeboom, Rik G H, van Voorthuijsen, Lisa, Fumagalli, Arianna, van der Net, Mirjam C, de Medeiros, Gustavo, Hageman, Joris H, Verlaan-Klink, Ingrid, Borel Rinkes, Inne H M, Liberali, Prisca, Gloerich, Martijn, van Rheenen, Jacco, Vermeulen, Michiel, Kranenburg, Onno, Snippert, Hugo J G

“…Micrometastases of colorectal cancer can remain dormant for years prior to the formation of actively growing, clinically detectable lesions (i.e.,…”
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RNF43 truncations trap CK1 to drive niche‐independent self‐renewal in cancer by Spit, Maureen, Fenderico, Nicola, Jordens, Ingrid, Radaszkiewicz, Tomasz, Lindeboom, Rik GH, Bugter, Jeroen M, Cristobal, Alba, Ootes, Lars, van Osch, Max, Janssen, Eline, Boonekamp, Kim E, Hanakova, Katerina, Potesil, David, Zdrahal, Zbynek, Boj, Sylvia F, Medema, Jan Paul, Bryja, Vitezslav, Koo, Bon‐Kyoung, Vermeulen, Michiel, Maurice, Madelon M

“…Wnt/β‐catenin signaling is a primary pathway for stem cell maintenance during tissue renewal and a frequent target for mutations in cancer. Impaired Wnt…”
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Decoding chromatin states by proteomic profiling of nucleosome readers by Lukauskas, Saulius, Tvardovskiy, Andrey, Nguyen, Nhuong V., Stadler, Mara, Faull, Peter, Ravnsborg, Tina, Özdemir Aygenli, Bihter, Dornauer, Scarlett, Flynn, Helen, Lindeboom, Rik G. H., Barth, Teresa K., Brockers, Kevin, Hauck, Stefanie M., Vermeulen, Michiel, Snijders, Ambrosius P., Müller, Christian L., DiMaggio, Peter A., Jensen, Ole N., Schneider, Robert, Bartke, Till

“…DNA and histone modifications combine into characteristic patterns that demarcate functional regions of the genome 1 , 2 . While many ‘readers’ of individual…”
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Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs by Smits, Arne H, Lindeboom, Rik G H, Perino, Matteo, van Heeringen, Simon J, Veenstra, Gert Jan C, Vermeulen, Michiel

“…While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus…”
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Quantifying genome-wide transcription factor binding affinities for chromatin using BANC-seq by Wester, Roelof A, Neikes, Hannah K, Lindeboom, Rik G H, Vermeulen, Michiel

“…Transcription factors (TFs) bind specific DNA sequences to regulate transcription. Apart from DNA sequences, local factors such as DNA accessibility and…”
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