BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw...

por Kretzmer, Helene, Otto, Christian, Hoffmann, Steve
Publicado 2017

RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data

por Hetzel, Sara, Giesselmann, Pay, Reinert, Knut, Meissner, Alexander, Kretzmer, Helene
Publicado 2021

Dissecting the DNA binding landscape and gene regulatory network of p63 and p53

por Riege, Konstantin, Kretzmer, Helene, Sahm, Arne, McDade, Simon S, Hoffmann, Steve, Fischer, Martin
Publicado 2020

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data

por Jühling, Frank, Kretzmer, Helene, Bernhart, Stephan H., Otto, Christian, Stadler, Peter F., Hoffmann, Steve
Publicado 2016

Targeting oncogenic TERT promoter variants by allele-specific epigenome editing

por Kouroukli, Alexandra G., Rajaram, Nivethika, Bashtrykov, Pavel, Kretzmer, Helene, Siebert, Reiner, Jeltsch, Albert, Bens, Susanne
Publicado 2023

Topological isolation of developmental regulators in mammalian genomes

por Wu, Hua-Jun, Landshammer, Alexandro, Stamenova, Elena K., Bolondi, Adriano, Kretzmer, Helene, Meissner, Alexander, Michor, Franziska
Publicado 2021

Emergence and patterning dynamics of mouse-definitive endoderm

por Pour, Maayan, Kumar, Abhishek Sampath, Farag, Naama, Bolondi, Adriano, Kretzmer, Helene, Walther, Maria, Wittler, Lars, Meissner, Alexander, Nachman, Iftach
Publicado 2021

Self-patterning of human stem cells into post-implantation lineages

por Pedroza, Monique, Gassaloglu, Seher Ipek, Dias, Nicolas, Zhong, Liangwen, Hou, Tien-Chi Jason, Kretzmer, Helene, Smith, Zachary D., Sozen, Berna
Publicado 2023

Epigenetic regulator function through mouse gastrulation

por Grosswendt, Stefanie, Kretzmer, Helene, Smith, Zachary D., Kumar, Abhishek Sampath, Hetzel, Sara, Wittler, Lars, Klages, Sven, Timmermann, Bernd, Mukherji, Shankar, Meissner, Alexander
Publicado 2020

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer

por Bernhart, Stephan H., Kretzmer, Helene, Holdt, Lesca M., Jühling, Frank, Ammerpohl, Ole, Bergmann, Anke K., Northoff, Bernd H., Doose, Gero, Siebert, Reiner, Stadler, Peter F., Hoffmann, Steve
Publicado 2016

The DNA methylation status of the TERT promoter differs between subtypes of mature B-cell lymphomas

por Kouroukli, Alexandra G., Fischer, Anja, Kretzmer, Helene, Chteinberg, Emil, Rajaram, Nivethika, Glaser, Selina, Kolarova, Julia, Bashtrykov, Pavel, Mathas, Stephan, Drexler, Hans G., Ohno, Hitoshi, Ammerpohl, Ole, Jeltsch, Albert, Siebert, Reiner, Bens, Susanne
Publicado 2023

Molecular recording of mammalian embryogenesis

por Chan, Michelle M., Smith, Zachary D., Grosswendt, Stefanie, Kretzmer, Helene, Norman, Thomas, Adamson, Britt, Jost, Marco, Quinn, Jeffrey J., Yang, Dian, Jones, Matthew G., Khodaverdian, Alex, Yosef, Nir, Meissner, Alexander, Weissman, Jonathan S.
Publicado 2019

Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis

por Sampath Kumar, Abhishek, Tian, Luyi, Bolondi, Adriano, Hernández, Amèlia Aragonés, Stickels, Robert, Kretzmer, Helene, Murray, Evan, Wittler, Lars, Walther, Maria, Barakat, Gabriel, Haut, Leah, Elkabetz, Yechiel, Macosko, Evan Z., Guignard, Léo, Chen, Fei, Meissner, Alexander
Publicado 2023

Acute lymphoblastic leukemia displays a distinct highly methylated genome

por Hetzel, Sara, Mattei, Alexandra L., Kretzmer, Helene, Qu, Chunxu, Chen, Xiang, Fan, Yiping, Wu, Gang, Roberts, Kathryn G., Luger, Selina, Litzow, Mark, Rowe, Jacob, Paietta, Elisabeth, Stock, Wendy, Mardis, Elaine R., Wilson, Richard K., Downing, James R., Mullighan, Charles G., Meissner, Alexander
Publicado 2022

T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation

por Landshammer, Alexandro, Bolondi, Adriano, Kretzmer, Helene, Much, Christian, Buschow, René, Rose, Alina, Wu, Hua-Jun, Mackowiak, Sebastian D, Braendl, Bjoern, Giesselmann, Pay, Tornisiello, Rosaria, Parsi, Krishna Mohan, Huey, Jack, Mielke, Thorsten, Meierhofer, David, Maehr, René, Hnisz, Denes, Michor, Franziska, Rinn, John L, Meissner, Alexander
Publicado 2023

Dynamic antagonism between key repressive pathways maintains the placental epigenome

por Weigert, Raha, Hetzel, Sara, Bailly, Nina, Haggerty, Chuck, Ilik, Ibrahim A., Yung, Philip Yuk Kwong, Navarro, Carmen, Bolondi, Adriano, Kumar, Abhishek Sampath, Anania, Chiara, Brändl, Björn, Meierhofer, David, Lupiáñez, Darío G., Müller, Franz-Josef, Aktas, Tugce, Elsässer, Simon J., Kretzmer, Helene, Smith, Zachary D., Meissner, Alexander
Publicado 2023

Hijacking of transcriptional condensates by endogenous retroviruses

por Asimi, Vahid, Sampath Kumar, Abhishek, Niskanen, Henri, Riemenschneider, Christina, Hetzel, Sara, Naderi, Julian, Fasching, Nina, Popitsch, Niko, Du, Manyu, Kretzmer, Helene, Smith, Zachary D., Weigert, Raha, Walther, Maria, Mamde, Sainath, Meierhofer, David, Wittler, Lars, Buschow, René, Timmermann, Bernd, Cisse, Ibrahim I., Ameres, Stefan L., Meissner, Alexander, Hnisz, Denes
Publicado 2022

Dnmt1 has de novo activity targeted to transposable elements

por Haggerty, Chuck, Kretzmer, Helene, Riemenschneider, Christina, Kumar, Abhishek Sampath, Mattei, Alexandra L., Bailly, Nina, Gottfreund, Judith, Giesselmann, Pay, Weigert, Raha, Brändl, Björn, Giehr, Pascal, Buschow, René, Galonska, Christina, von Meyenn, Ferdinand, Pappalardi, Melissa B., McCabe, Michael T., Wittler, Lars, Giesecke-Thiel, Claudia, Mielke, Thorsten, Meierhofer, David, Timmermann, Bernd, Müller, Franz-Josef, Walter, Jörn, Meissner, Alexander
Publicado 2021

Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B-cell lymphomas

por López, Cristina, Schleussner, Nikolai, Bernhart, Stephan H., Kleinheinz, Kortine, Sungalee, Stephanie, Sczakiel, Henrike L., Kretzmer, Helene, Toprak, Umut H., Glaser, Selina, Wagener, Rabea, Ammerpohl, Ole, Bens, Susanne, Giefing, Maciej, González Sánchez, Juan C., Apic, Gordana, Hübschmann, Daniel, Janz, Martin, Kreuz, Markus, Mottok, Anja, Müller, Judith M., Seufert, Julian, Hoffmann, Steve, Korbel, Jan O., Russell, Robert B., Schüle, Roland, Trümper, Lorenz, Klapper, Wolfram, Radlwimmer, Bernhard, Lichter, Peter, Küppers, Ralf, Schlesner, Matthias, Mathas, Stephan, Siebert, Reiner
Publicado 2022

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma

por López, Cristina, Kleinheinz, Kortine, Aukema, Sietse M., Rohde, Marius, Bernhart, Stephan H., Hübschmann, Daniel, Wagener, Rabea, Toprak, Umut H., Raimondi, Francesco, Kreuz, Markus, Waszak, Sebastian M., Huang, Zhiqin, Sieverling, Lina, Paramasivam, Nagarajan, Seufert, Julian, Sungalee, Stephanie, Russell, Robert B., Bausinger, Julia, Kretzmer, Helene, Ammerpohl, Ole, Bergmann, Anke K., Binder, Hans, Borkhardt, Arndt, Brors, Benedikt, Claviez, Alexander, Doose, Gero, Feuerbach, Lars, Haake, Andrea, Hansmann, Martin-Leo, Hoell, Jessica, Hummel, Michael, Korbel, Jan O., Lawerenz, Chris, Lenze, Dido, Radlwimmer, Bernhard, Richter, Julia, Rosenstiel, Philip, Rosenwald, Andreas, Schilhabel, Markus B., Stein, Harald, Stilgenbauer, Stephan, Stadler, Peter F., Szczepanowski, Monika, Weniger, Marc A., Zapatka, Marc, Eils, Roland, Lichter, Peter, Loeffler, Markus, Möller, Peter, Trümper, Lorenz, Klapper, Wolfram, Hoffmann, Steve, Küppers, Ralf, Burkhardt, Birgit, Schlesner, Matthias, Siebert, Reiner
Publicado 2019