Search Results - "Lövkvist, Cecilia"

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models by Ekeberg, Magnus, Lövkvist, Cecilia, Lan, Yueheng, Weigt, Martin, Aurell, Erik

“…Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the…”
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Using computational modelling to reveal mechanisms of epigenetic Polycomb control by Lövkvist, Cecilia, Howard, Martin

“…The Polycomb system is essential for stable gene silencing in many organisms. This regulation is achieved in part through addition of the histone modifications…”
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Nanog, Oct4 and Tet1 interplay in establishing pluripotency by Olariu, Victor, Lövkvist, Cecilia, Sneppen, Kim

“…A few central transcription factors inside mouse embryonic stem (ES) cells and induced pluripotent stem (iPS) cells are believed to control the cells’…”
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DNA methylation in human epigenomes depends on local topology of CpG sites by Lövkvist, Cecilia, Dodd, Ian B, Sneppen, Kim, Haerter, Jan O

“…In vertebrates, methylation of cytosine at CpG sequences is implicated in stable and heritable patterns of gene expression. The classical model for…”
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A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals by Holoch, Daniel, Wassef, Michel, Lövkvist, Cecilia, Zielinski, Dina, Aflaki, Setareh, Lombard, Bérangère, Héry, Tiphaine, Loew, Damarys, Howard, Martin, Margueron, Raphaël

“…Epigenetic inheritance of gene expression states enables a single genome to maintain distinct cellular identities. How histone modifications contribute to this…”
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Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory by Lövkvist, Cecilia, Mikulski, Pawel, Reeck, Svenja, Hartley, Matthew, Dean, Caroline, Howard, Martin

“…The histone modification H3K27me3 plays a central role in Polycomb-mediated epigenetic silencing. H3K27me3 recruits and allosterically activates Polycomb…”
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CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data by Kim, Hyobin, Kumar, Amit, Lövkvist, Cecilia, Palma, António M, Martin, Patrick, Kim, Junil, Bhoopathi, Praveen, Trevino, Jose, Fisher, Paul, Madan, Esha, Gogna, Rajan, Won, Kyoung Jae

“…Cells have evolved their communication methods to sense their microenvironments and send biological signals. In addition to communication using ligands and…”
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Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis by Martin, Patrick C N, Kim, Hyobin, Lövkvist, Cecilia, Hong, Byung‐Woo, Won, Kyoung Jae

“…Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval…”
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Exploring the Link between Nucleosome Occupancy and DNA Methylation by Lövkvist, Cecilia, Sneppen, Kim, Haerter, Jan O

“…Near promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of…”
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Stabilization of epigenetic states of CpG islands by local cooperation by Sormani, Giulia, Haerter, Jan O, Lövkvist, Cecilia, Sneppen, Kim

“…DNA methylation of CpG sites is an important epigenetic mark in mammals. Active promoters are often associated with unmethylated CpG sites, whereas methylated…”
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Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states by Haerter, Jan O, Lövkvist, Cecilia, Dodd, Ian B, Sneppen, Kim

“…Inheritance of 5-methyl cytosine modification of CpG (CG/CG) DNA sequences is needed to maintain early developmental decisions in vertebrates. The standard…”
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Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models by Ekeberg, Magnus, Lövkvist, Cecilia, Lan, Yueheng, Weigt, Martin, Aurell, Erik

“…M. Ekeberg, C. L\"ovkvist, Y. Lan, M. Weigt, E. Aurell, Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models, Phys. Rev. E…”
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