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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
Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development
Sen, Maya, Mooijman, Dylan, Chialastri, Alex, Boisset, Jean-Charles, Popovic, Mina, Heindryckx, Björn, Chuva de Sousa Lopes, Susana M., Dey, Siddharth S., van Oudenaarden, Alexander
Published in Nature communications (24.02.2021)
Published in Nature communications (24.02.2021)
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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
Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway
Ji, Ni, Middelkoop, Teije C., Mentink, Remco A., Betist, Marco C., Tonegawa, Satto, Mooijman, Dylan, Korswagen, Hendrik C., van Oudenaarden, Alexander
Published in Cell (07.11.2013)
Published in Cell (07.11.2013)
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Journal Article
Integration of multiple lineage measurements from the same cell reconstructs parallel tumor evolution
Kester, Lennart, de Barbanson, Buys, Lyubimova, Anna, Chen, Li-Ting, van der Schrier, Valérie, Alemany, Anna, Mooijman, Dylan, Peterson-Maduro, Josi, Drost, Jarno, de Ridder, Jeroen, van Oudenaarden, Alexander
Published in Cell genomics (09.02.2022)
Published in Cell genomics (09.02.2022)
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Journal Article
Description and functional validation of human enteroendocrine cell sensors
Beumer, Joep, Geurts, Maarten H., Geurts, Veerle, Andersson-Rolf, Amanda, Akkerman, Ninouk, Völlmy, Franziska, Krueger, Daniel, Busslinger, Georg A., Martínez-Silgado, Adriana, Boot, Charelle, Yousef Yengej, Fjodor A., Puschhof, Jens, Van de Wetering, Wiline J., Knoops, Kevin, López-Iglesias, Carmen, Peters, Peter J., Vivié, Judith A., Mooijman, Dylan, van Es, Johan H., Clevers, Hans
Published in Science (American Association for the Advancement of Science) (18.10.2024)
Published in Science (American Association for the Advancement of Science) (18.10.2024)
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Journal Article
Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras
Hollmann, Nele Merret, Jagtap, Pravin Kumar Ankush, Masiewicz, Pawel, Guitart, Tanit, Simon, Bernd, Provaznik, Jan, Stein, Frank, Haberkant, Per, Sweetapple, Lara Jayne, Villacorta, Laura, Mooijman, Dylan, Benes, Vladimir, Savitski, Mikhail M., Gebauer, Fátima, Hennig, Janosch
Published in Cell reports (Cambridge) (21.07.2020)
Published in Cell reports (Cambridge) (21.07.2020)
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Journal Article
A community effort to track commercial single-cell and spatial ’omic technologies and business trends
De Jonghe, Joachim, Opzoomer, James W., Vilas-Zornoza, Amaia, Crane, Peter, Nilges, Benedikt S., Vicari, Marco, Lee, Hower, Lara-Astiaso, David, Gross, Torsten, Morf, Jörg, Schneider, Kim, Cudini, Juliana, Ramos-Mucci, Lorenzo, Mooijman, Dylan, Tiklová, Katarína, Salas, Sergio Marco, Langseth, Christoffer Mattsson, Kashikar, Nachiket D., Roberts, Charles E. S., Lundeberg, Joakim, Nilsson, Mats, Shalek, Alex K., Cribbs, Adam P., Taylor-King, Jake P.
Published in Nature biotechnology (01.07.2024)
Published in Nature biotechnology (01.07.2024)
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Journal Article
Transcriptional profiling of cells sorted by RNA abundance
Klemm, Sandy, Semrau, Stefan, Wiebrands, Kay, Mooijman, Dylan, Faddah, Dina A, Jaenisch, Rudolf, van Oudenaarden, Alexander
Published in Nature methods (01.05.2014)
Published in Nature methods (01.05.2014)
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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
Different Roles for Tet1 and Tet2 Proteins in Reprogramming-Mediated Erasure of Imprints Induced by EGC Fusion
Piccolo, Francesco M., Bagci, Hakan, Brown, Karen E., Landeira, David, Soza-Ried, Jorge, Feytout, Amelie, Mooijman, Dylan, Hajkova, Petra, Leitch, Harry G., Tada, Takashi, Kriaucionis, Skirmantas, Dawlaty, Meelad M., Jaenisch, Rudolf, Merkenschlager, Matthias, Fisher, Amanda G.
Published in Molecular cell (28.03.2013)
Published in Molecular cell (28.03.2013)
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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
Transcriptionally Profiling Cells Sorted by Transcript Abundance
Klemm, Sandy, Semrau, Stefan, Wiebrands, Kay, Mooijman, Dylan, Faddah, Dina A., Jaenisch, Rudolf, van Oudenaarden, Alexander
Published in Nature methods (30.03.2014)
Published in Nature methods (30.03.2014)
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Journal Article
scTrends: A living review of commercial single-cell and spatial 'omic technologies
De Jonghe, Joachim, Opzoomer, James W, Vilas-Zornoza, Amaia, Nilges, Benedikt S, Crane, Peter, Vicari, Marco, Lee, Hower, Lara-Astiaso, David, Gross, Torsten, Morf, Jörg, Schneider, Kim, Cudini, Juliana, Ramos-Mucci, Lorenzo, Mooijman, Dylan, Tiklová, Katarína, Salas, Sergio Marco, Langseth, Christoffer Mattsson, Kashikar, Nachiket D, Schapiro, Denis, Lundeberg, Joakim, Nilsson, Mats, Shalek, Alex K, Cribbs, Adam P, Taylor-King, Jake P
Published in Cell genomics (11.12.2024)
Published in Cell genomics (11.12.2024)
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Journal Article
Different Roles for Tet1 and Tet2 Proteins in Reprogramming-Mediated Erasure of Imprints Induced by EGC Fusion
Piccolo, Francesco M., Bagci, Hakan, Brown, Karen E., Landeira, David, Soza-Ried, Jorge, Feytout, Amelie, Mooijman, Dylan, Hajkova, Petra, Leitch, Harry G., Tada, Takashi, Kriaucionis, Skirmantas, Dawlaty, Meelad M., Jaenisch, Rudolf, Merkenschlager, Matthias, Fisher, Amanda G.
Published in Molecular cell (28.03.2013)
Published in Molecular cell (28.03.2013)
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Journal Article
10x Genomics Gene Expression Flex is a powerful tool for single-cell transcriptomics of xenograft models
Llora-Batlle, Oriol, Farcas, Anca, Fransen, Doreth, Floch, Nicolas, Talbot, Sara, Schwiening, Alix, Bojko, Laura, Calver, John, Josipovic, Natasa, Lashuk, Kanstantsin, Schueler, Julia, Prodan, Andrei, Mooijman, Dylan, Mcdermott, Ultan, Consortium, Persist-Seq
Published in bioRxiv (29.01.2024)
Published in bioRxiv (29.01.2024)
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Paper
Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development
Sen, Maya, Mooijman, Dylan, Jean-Charles Boisset, Chialastri, Alex, Popovic, Mina, Heindryckx, Björn, Susana M Chuva De Sousa Lopes, Dey, Siddharth S, Alexander Van Oudenaarden
Published in bioRxiv (15.10.2019)
Published in bioRxiv (15.10.2019)
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Paper