Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells
Rooijers, Koos, Markodimitraki, Corina M, Rang, Franka J, de Vries, Sandra S, Chialastri, Alex, de Luca, Kim L, Mooijman, Dylan, Dey, Siddharth S, Kind, Jop
Published in Nature biotechnology (01.07.2019)
Published in Nature biotechnology (01.07.2019)
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Journal Article
Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species
Baglio, Serena Rubina, Rooijers, Koos, Koppers-Lalic, Danijela, Verweij, Frederik J, Pérez Lanzón, M, Zini, Nicoletta, Naaijkens, Benno, Perut, Francesca, Niessen, Hans W M, Baldini, Nicola, Pegtel, D Michiel
Published in Stem cell research & therapy (01.07.2015)
Published in Stem cell research & therapy (01.07.2015)
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Journal Article
Alcohol-derived DNA crosslinks are repaired by two distinct mechanisms
Hodskinson, Michael R, Bolner, Alice, Sato, Koichi, Kamimae-Lanning, Ashley N, Rooijers, Koos, Witte, Merlijn, Mahesh, Mohan, Silhan, Jan, Petek, Maya, Williams, David M, Kind, Jop, Chin, Jason W, Patel, Ketan J, Knipscheer, Puck
Published in Nature (London) (01.03.2020)
Published in Nature (London) (01.03.2020)
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Journal Article
p53 induces transcriptional and translational programs to suppress cell proliferation and growth
Loayza-Puch, Fabricio, Drost, Jarno, Rooijers, Koos, Lopes, Rui, Elkon, Ran, Agami, Reuven
Published in Genome biology (17.04.2013)
Published in Genome biology (17.04.2013)
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Journal Article
Ribosome profiling reveals features of normal and disease-associated mitochondrial translation
Rooijers, Koos, Loayza-Puch, Fabricio, Nijtmans, Leo G, Agami, Reuven
Published in Nature communications (03.12.2013)
Published in Nature communications (03.12.2013)
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Journal Article
The Poly(A)-Binding Protein Nuclear 1 Suppresses Alternative Cleavage and Polyadenylation Sites
Jenal, Mathias, Elkon, Ran, Loayza-Puch, Fabricio, van Haaften, Gijs, Kühn, Uwe, Menzies, Fiona M., Vrielink, Joachim A.F. Oude, Bos, Arnold J., Drost, Jarno, Rooijers, Koos, Rubinsztein, David C., Agami, Reuven
Published in Cell (27.04.2012)
Published in Cell (27.04.2012)
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Journal Article
Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA
Léveillé, Nicolas, Melo, Carlos A, Rooijers, Koos, Díaz-Lagares, Angel, Melo, Sonia A, Korkmaz, Gozde, Lopes, Rui, Moqadam, Farhad Akbari, Maia, Ana R, Wijchers, Patrick J, Geeven, Geert, den Boer, Monique L, Kalluri, Raghu, de Laat, Wouter, Esteller, Manel, Agami, Reuven
Published in Nature communications (27.03.2015)
Published in Nature communications (27.03.2015)
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Journal Article
Alternative Cleavage and Polyadenylation during Colorectal Cancer Development
MORRIS, Adam R, BOS, Arnold, DIOSDADO, Begoña, ROOIJERS, Koos, ELKON, Ran, BOLIJN, Anne S, CARVALHO, Beatriz, MEIJER, Gerrit A, AGAMI, Reuven
Published in Clinical cancer research (01.10.2012)
Published in Clinical cancer research (01.10.2012)
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Journal Article
Simultaneous quantification of protein-DNA interactions and transcriptomes in single cells with scDam&T-seq
Markodimitraki, Corina M, Rang, Franka J, Rooijers, Koos, de Vries, Sandra S, Chialastri, Alex, de Luca, Kim L, Lochs, Silke J A, Mooijman, Dylan, Dey, Siddharth S, Kind, Jop
Published in Nature protocols (01.06.2020)
Published in Nature protocols (01.06.2020)
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Journal Article
An iterative workflow for mining the human intestinal metaproteome
Rooijers, K, Kolmeder, C, Juste, C, Doré, J, Been, M. de, Boeren, S, Galan, P, Vos, W.M. de, Schaap, P.J, Beauvallet, C
Published in BMC genomics (05.01.2011)
Published in BMC genomics (05.01.2011)
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Journal Article
Using mitoribosomal profiling to investigate human mitochondrial translation
Gao, Fei, Wesolowska, Maria, Agami, Reuven, Rooijers, Koos, Loayza-Puch, Fabricio, Lawless, Conor, N. Lightowlers, Robert, Chrzanowska-Lightowlers, Zofia M. A.
Published in Wellcome open research (29.01.2018)
Published in Wellcome open research (29.01.2018)
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Journal Article
Using mitoribosomal profiling to investigate human mitochondrial translation
Gao, Fei, Wesolowska, Maria, Agami, Reuven, Rooijers, Koos, Loayza-Puch, Fabricio, Lawless, Conor, Lightowlers, Robert N, Chrzanowska-Lightowlers, Zofia M A
Published in Wellcome open research (2017)
Published in Wellcome open research (2017)
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Journal Article
Tumour-specific proline vulnerability uncovered by differential ribosome codon reading
Loayza-Puch, Fabricio, Rooijers, Koos, Buil, Levi C M, Zijlstra, Jelle, Oude Vrielink, Joachim F, Lopes, Rui, Ugalde, Alejandro Pineiro, van Breugel, Pieter, Hofland, Ingrid, Wesseling, Jelle, van Tellingen, Olaf, Bex, Axel, Agami, Reuven
Published in Nature (London) (25.02.2016)
Published in Nature (London) (25.02.2016)
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Journal Article
Exposure to arginine analog canavanine induces aberrant mitochondrial translation products, mitoribosome stalling, and instability of the mitochondrial proteome
Konovalova, Svetlana, Hilander, Taru, Loayza-Puch, Fabricio, Rooijers, Koos, Agami, Reuven, Tyynismaa, Henna
Published in The international journal of biochemistry & cell biology (01.08.2015)
Published in The international journal of biochemistry & cell biology (01.08.2015)
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Journal Article
scDam&T‐seq combines DNA adenine methyltransferase-based labeling of protein-DNA contact sites with transcriptome sequencing to analyze regulatory programs in single cells
Rooijers, Koos, Markodimitraki, Corina M., Rang, Franka J., de Vries, Sandra S., Chialastri, Alex, de Luca, Kim L., Mooijman, Dylan, Dey, Siddharth S., Kind, Jop
Published in Nature biotechnology (10.06.2019)
Published in Nature biotechnology (10.06.2019)
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Journal Article
Simultaneous quantifications of protein-DNA interactions and transcriptomes in single cells with scDam&T-seq
Markodimitraki, Corina M., Rang, Franka J., Rooijers, Koos, de Vries, Sandra S., Chialastri, Alex, de Luca, Kim L., Lochs, Silke J. A., Mooijman, Dylan, Dey, Siddharth S., Kind, Jop
Published in Nature protocols (29.04.2020)
Published in Nature protocols (29.04.2020)
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Journal Article
Parasite-induced ER stress response in hepatocytes facilitates Plasmodium liver stage infection
Inácio, Patricia, Zuzarte-Luís, Vanessa, Ruivo, Margarida TG, Falkard, Brie, Nagaraj, Nagarjuna, Rooijers, Koos, Mann, Matthias, Mair, Gunnar, Fidock, David A, Mota, Maria M
Published in EMBO reports (01.08.2015)
Published in EMBO reports (01.08.2015)
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Journal Article
TGF[beta]1-induced leucine limitation uncovered by differential ribosome codon reading
Loayza-Puch, Fabricio, Rooijers, Koos, Zijlstra, Jelle, Moumbeini, Behzad, Zaal, Esther A, Oude Vrielink, Joachim F, Lopes, Rui, Ugalde, Alejandro P, Berkers, Celia R, Agami, Reuven
Published in EMBO reports (01.04.2017)
Published in EMBO reports (01.04.2017)
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Journal Article
TGFβ1‐induced leucine limitation uncovered by differential ribosome codon reading
Loayza‐Puch, Fabricio, Rooijers, Koos, Zijlstra, Jelle, Moumbeini, Behzad, Zaal, Esther A, Oude Vrielink, Joachim F, Lopes, Rui, Ugalde, Alejandro P, Berkers, Celia R, Agami, Reuven
Published in EMBO reports (01.04.2017)
Published in EMBO reports (01.04.2017)
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Journal Article
Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA
Léveillé, Nicolas, Melo, Carlos A, Rooijers, Koos, Díaz Lagares, Angel, Melo, Sonia, Korkmaz, Gozde, Lopes, Rui, Akbari Moqadam, Farhad, Maia, Ana R, Wijchers, Patrick J, Geeven, Geert, den Boer, Monique L, Kalluri, Raghu, de Laat, Wouter, Esteller, Manel, Agami, Reuven
Published in Nature communications (27.03.2015)
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Published in Nature communications (27.03.2015)
Journal Article