Search Results - "Krueger, Felix"

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications by KRUEGER, Felix, ANDREWS, Simon R

“…A combination of bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot of a cell's epigenomic state by revealing its…”
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Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data by Olova, Nelly, Krueger, Felix, Andrews, Simon, Oxley, David, Berrens, Rebecca V, Branco, Miguel R, Reik, Wolf

“…Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research…”
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Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution by Booth, Michael J., Branco, Miguel R., Ficz, Gabriella, Oxley, David, Krueger, Felix, Reik, Wolf, Balasubramanian, Shankar

“…5-Methylcytosine can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by the ten-eleven translocation (TET) enzymes. We introduce oxidative…”
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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells by Clark, Stephen J., Argelaguet, Ricard, Kapourani, Chantriolnt-Andreas, Stubbs, Thomas M., Lee, Heather J., Alda-Catalinas, Celia, Krueger, Felix, Sanguinetti, Guido, Kelsey, Gavin, Marioni, John C., Stegle, Oliver, Reik, Wolf

“…Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome…”
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Resetting transcription factor control circuitry toward ground-state pluripotency in human by Takashima, Yasuhiro, Guo, Ge, Loos, Remco, Nichols, Jennifer, Ficz, Gabriella, Krueger, Felix, Oxley, David, Santos, Fatima, Clarke, James, Mansfield, William, Reik, Wolf, Bertone, Paul, Smith, Austin

“…Current human pluripotent stem cells lack the transcription factor circuitry that governs the ground state of mouse embryonic stem cells (ESC). Here, we report…”
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The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells by Seisenberger, Stefanie, Andrews, Simon, Krueger, Felix, Arand, Julia, Walter, Jörn, Santos, Fátima, Popp, Christian, Thienpont, Bernard, Dean, Wendy, Reik, Wolf

“…Genome-wide DNA methylation reprogramming occurs in mouse primordial germ cells (PGCs) and preimplantation embryos, but the precise dynamics and biological…”
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Multi-omics profiling of mouse gastrulation at single-cell resolution by Argelaguet, Ricard, Clark, Stephen J., Mohammed, Hisham, Stapel, L. Carine, Krueger, Christel, Kapourani, Chantriolnt-Andreas, Imaz-Rosshandler, Ivan, Lohoff, Tim, Xiang, Yunlong, Hanna, Courtney W., Smallwood, Sebastien, Ibarra-Soria, Ximena, Buettner, Florian, Sanguinetti, Guido, Xie, Wei, Krueger, Felix, Göttgens, Berthold, Rugg-Gunn, Peter J., Kelsey, Gavin, Dean, Wendy, Nichols, Jennifer, Stegle, Oliver, Marioni, John C., Reik, Wolf

“…Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan and is associated with…”
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Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq by Kara, Neesha, Krueger, Felix, Rugg-Gunn, Peter, Houseley, Jonathan

“…Faithful replication of the entire genome requires replication forks to copy large contiguous tracts of DNA, and sites of persistent replication fork stalling…”
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SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes [version 2; peer review: 3 approved] by Krueger, Felix, Andrews, Simon R

“…Sequencing reads overlapping polymorphic sites in diploid mammalian genomes may be assigned to one allele or the other. This holds the potential to detect gene…”
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Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism by Hahn, Oliver, Grönke, Sebastian, Stubbs, Thomas M, Ficz, Gabriella, Hendrich, Oliver, Krueger, Felix, Andrews, Simon, Zhang, Qifeng, Wakelam, Michael J, Beyer, Andreas, Reik, Wolf, Partridge, Linda

“…Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan in diverse…”
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Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation by Ficz, Gabriella, Branco, Miguel R., Seisenberger, Stefanie, Santos, Fátima, Krueger, Felix, Hore, Timothy A., Marques, C. Joana, Andrews, Simon, Reik, Wolf

“…Fine-tuning DNA methylation by Tet proteins The modified DNA base 5-hydroxymethylcytosine (5hmC), sometimes called the sixth base, is present in the mammalian…”
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Multi-tissue DNA methylation age predictor in mouse by Stubbs, Thomas M, Bonder, Marc Jan, Stark, Anne-Katrien, Krueger, Felix, von Meyenn, Ferdinand, Stegle, Oliver, Reik, Wolf

“…DNA methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether…”
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Dynamic CpG island methylation landscape in oocytes and preimplantation embryos by Kelsey, Gavin, Smallwood, Sébastien A, Tomizawa, Shin-ichi, Krueger, Felix, Ruf, Nico, Carli, Natasha, Segonds-Pichon, Anne, Sato, Shun, Hata, Kenichiro, Andrews, Simon R

“…Elucidating how and to what extent CpG islands (CGIs) are methylated in germ cells is essential to understand genomic imprinting and epigenetic reprogramming…”
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Transcription-induced formation of extrachromosomal DNA during yeast ageing by Hull, Ryan M, King, Michelle, Pizza, Grazia, Krueger, Felix, Vergara, Xabier, Houseley, Jonathan

“…Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation and is implicated in the…”
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FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency by Ficz, Gabriella, Hore, Timothy A., Santos, Fátima, Lee, Heather J., Dean, Wendy, Arand, Julia, Krueger, Felix, Oxley, David, Paul, Yu-Lee, Walter, Jörn, Cook, Simon J., Andrews, Simon, Branco, Miguel R., Reik, Wolf

“…Genome-wide erasure of DNA methylation takes place in primordial germ cells (PGCs) and early embryos and is linked with pluripotency. Inhibition of Erk1/2 and…”
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Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape by Veselovska, Lenka, Smallwood, Sebastien A, Saadeh, Heba, Stewart, Kathleen R, Krueger, Felix, Maupetit-Méhouas, Stéphanie, Arnaud, Philippe, Tomizawa, Shin-Ichi, Andrews, Simon, Kelsey, Gavin

“…Previously, a role was demonstrated for transcription in the acquisition of DNA methylation at imprinted control regions in oocytes. Definition of the oocyte…”
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Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions by Thompson, Oliver, von Meyenn, Ferdinand, Hewitt, Zoe, Alexander, John, Wood, Andrew, Weightman, Richard, Gregory, Sian, Krueger, Felix, Andrews, Simon, Barbaric, Ivana, Gokhale, Paul J., Moore, Harry D., Reik, Wolf, Milo, Marta, Nik-Zainal, Serena, Yusa, Kosuke, Andrews, Peter W.

“…The occurrence of repetitive genomic changes that provide a selective growth advantage in pluripotent stem cells is of concern for their clinical application…”
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Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues by Hanna, Courtney W, Pérez-Palacios, Raquel, Gahurova, Lenka, Schubert, Michael, Krueger, Felix, Biggins, Laura, Andrews, Simon, Colomé-Tatché, Maria, Bourc'his, Deborah, Dean, Wendy, Kelsey, Gavin

“…Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on the parent of origin and is typically…”
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The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome by Gdula, Michal R., Nesterova, Tatyana B., Pintacuda, Greta, Godwin, Jonathan, Zhan, Ye, Ozadam, Hakan, McClellan, Michael, Moralli, Daniella, Krueger, Felix, Green, Catherine M., Reik, Wolf, Kriaucionis, Skirmantas, Heard, Edith, Dekker, Job, Brockdorff, Neil

“…The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically…”
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Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression by Strogantsev, Ruslan, Krueger, Felix, Yamazawa, Kazuki, Shi, Hui, Gould, Poppy, Goldman-Roberts, Megan, McEwen, Kirsten, Sun, Bowen, Pedersen, Roger, Ferguson-Smith, Anne C

“…Selective maintenance of genomic epigenetic imprints during pre-implantation development is required for parental origin-specific expression of imprinted…”
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