Search Results - "Stadler, Michael"

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors by Barisic, Darko, Stadler, Michael B., Iurlaro, Mario, Schübeler, Dirk

“…Chromatin remodelling complexes evict, slide, insert or replace nucleosomes, which represent an intrinsic barrier for access to DNA. These remodellers function…”
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Self-organization and symmetry breaking in intestinal organoid development by Serra, Denise, Mayr, Urs, Boni, Andrea, Lukonin, Ilya, Rempfler, Markus, Challet Meylan, Ludivine, Stadler, Michael B., Strnad, Petr, Papasaikas, Panagiotis, Vischi, Dario, Waldt, Annick, Roma, Guglielmo, Liberali, Prisca

“…Intestinal organoids are complex three-dimensional structures that mimic the cell-type composition and tissue organization of the intestine by recapitulating…”
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Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation by Kaluscha, Sebastian, Domcke, Silvia, Wirbelauer, Christiane, Stadler, Michael B., Durdu, Sevi, Burger, Lukas, Schübeler, Dirk

“…Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition…”
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A mixed integer linear programming approach for optimal DER portfolio, sizing, and placement in multi-energy microgrids by Mashayekh, Salman, Stadler, Michael, Cardoso, Gonçalo, Heleno, Miguel

“…•This paper presents a MILP model for optimal design of multi-energy microgrids.•Our microgrid design includes optimal technology portfolio, placement, and…”
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QuasR: quantification and annotation of short reads in R by Gaidatzis, Dimos, Lerch, Anita, Hahne, Florian, Stadler, Michael B

“…QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality…”
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Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation by Gaidatzis, Dimos, Burger, Lukas, Florescu, Maria, Stadler, Michael B

“…Comparing exon and intron reads in RNA-seq data reveals the levels of nascent and steady-state RNA. RNA-seq experiments generate reads derived not only from…”
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Preprocessing choices affect RNA velocity results for droplet scRNA-seq data by Soneson, Charlotte, Srivastava, Avi, Patro, Rob, Stadler, Michael B

“…Experimental single-cell approaches are becoming widely used for many purposes, including investigation of the dynamic behaviour of developing biological…”
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Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function by Avrahami, Dana, Li, Changhong, Zhang, Jia, Schug, Jonathan, Avrahami, Ran, Rao, Shilpa, Stadler, Michael B., Burger, Lukas, Schübeler, Dirk, Glaser, Benjamin, Kaestner, Klaus H.

“…Aging is driven by changes of the epigenetic state that are only partially understood. We performed a comprehensive epigenomic analysis of the pancreatic β…”
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Wobble base-pairing slows in vivo translation elongation in metazoans by Stadler, Michael, Fire, Andrew

“…In the universal genetic code, most amino acids can be encoded by multiple trinucleotide codons, and the choice among available codons can influence…”
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Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution by Cowan, Cameron S., Renner, Magdalena, De Gennaro, Martina, Gross-Scherf, Brigitte, Goldblum, David, Hou, Yanyan, Munz, Martin, Rodrigues, Tiago M., Krol, Jacek, Szikra, Tamas, Cuttat, Rachel, Waldt, Annick, Papasaikas, Panagiotis, Diggelmann, Roland, Patino-Alvarez, Claudia P., Galliker, Patricia, Spirig, Stefan E., Pavlinic, Dinko, Gerber-Hollbach, Nadine, Schuierer, Sven, Srdanovic, Aldin, Balogh, Marton, Panero, Riccardo, Kusnyerik, Akos, Szabo, Arnold, Stadler, Michael B., Orgül, Selim, Picelli, Simone, Hasler, Pascal W., Hierlemann, Andreas, Scholl, Hendrik P.N., Roma, Guglielmo, Nigsch, Florian, Roska, Botond

“…Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed…”
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Mammalian SWI/SNF continuously restores local accessibility to chromatin by Iurlaro, Mario, Stadler, Michael B., Masoni, Francesca, Jagani, Zainab, Galli, Giorgio G., Schübeler, Dirk

“…Chromatin accessibility is a hallmark of regulatory regions, entails transcription factor (TF) binding and requires nucleosomal reorganization. However, it…”
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Phenotypic landscape of intestinal organoid regeneration by Lukonin, Ilya, Serra, Denise, Challet Meylan, Ludivine, Volkmann, Katrin, Baaten, Janine, Zhao, Rui, Meeusen, Shelly, Colman, Karyn, Maurer, Francisca, Stadler, Michael B., Jenkins, Jeremy, Liberali, Prisca

“…The development of intestinal organoids from single adult intestinal stem cells in vitro recapitulates the regenerative capacity of the intestinal epithelium 1…”
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mutscan-a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data by Soneson, Charlotte, Bendel, Alexandra M, Diss, Guillaume, Stadler, Michael B

“…Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by selective enrichment of sequences with…”
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Identification of active regulatory regions from DNA methylation data by Burger, Lukas, Gaidatzis, Dimos, Schübeler, Dirk, Stadler, Michael B

“…We have recently shown that transcription factor binding leads to defined reduction in DNA methylation, allowing for the identification of active regulatory…”
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The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells by Horvathova, Ivana, Voigt, Franka, Kotrys, Anna V., Zhan, Yinxiu, Artus-Revel, Caroline G., Eglinger, Jan, Stadler, Michael B., Giorgetti, Luca, Chao, Jeffrey A.

“…RNA degradation plays a fundamental role in regulating gene expression. In order to characterize the spatiotemporal dynamics of RNA turnover in single cells,…”
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Gene bivalency at Polycomb domains regulates cranial neural crest positional identity by Minoux, Maryline, Holwerda, Sjoerd, Vitobello, Antonio, Kitazawa, Taro, Kohler, Hubertus, Stadler, Michael B., Rijli, Filippo M.

“…The cranial neural crest cells are multipotent cells that provide head skeletogenic mesenchyme and are crucial for craniofacial patterning. We analyzed the…”
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DNA-binding factors shape the mouse methylome at distal regulatory regions by Stadler, Michael B., Murr, Rabih, Burger, Lukas, Ivanek, Robert, Lienert, Florian, Schöler, Anne, Nimwegen, Erik van, Wirbelauer, Christiane, Oakeley, Edward J., Gaidatzis, Dimos, Tiwari, Vijay K., Schübeler, Dirk

“…Methylation of cytosines is an essential epigenetic modification in mammalian genomes, yet the rules that govern methylation patterns remain largely elusive…”
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Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos by Albright, Ashley R, Stadler, Michael R, Eisen, Michael B

“…Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as…”
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PIK3CA(H1047R) induces multipotency and multi-lineage mammary tumours by Koren, Shany, Reavie, Linsey, Couto, Joana Pinto, De Silva, Duvini, Stadler, Michael B, Roloff, Tim, Britschgi, Adrian, Eichlisberger, Tobias, Kohler, Hubertus, Aina, Olulanu, Cardiff, Robert D, Bentires-Alj, Mohamed

“…The adult mouse mammary epithelium contains self-sustained cell lineages that form the inner luminal and outer basal cell layers, with stem and progenitor…”
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Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome by Schübeler, Dirk, Weber, Michael, Hellmann, Ines, Stadler, Michael B, Ramos, Liliana, Pääbo, Svante, Rebhan, Michael

“…To gain insight into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase…”
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