Faculty Opinions recommendation of A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

By C. Semple. 2017

741 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b7d17b17ada29d400977eea73fb5c18576164360

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In Molecular Biology

Citations in the corpus

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient (2017, neutral): “…replicates are available, it is a commonpracticetouseeitherPearsonorSpearmancorrelationco-efficients between the two Hi-C data matrices as a metric for data quality (Hu et al. 2012; Imakaev et al. 2012; Gorkin et al. 2014; Rao et al. 2014; Ay and Noble 2015; Dixon et al. 2015; Servant et al. 2015).”
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction (2018, positive): “We compared EpiTensor interactions with CTCF/RNAP II ChIA-PET interactions obtained by the 3DEpiLoop predictor applied on the K562 cell line 13 , GSM970213, and with in situ Hi-C loops for the IMR90 cell line 11 .”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, positive): “…enhancers and genes within the CTCF-CTCF loops from elements outside those loops (Dixon et al., 2012; Dowen et al., 2014; Hnisz et al., 2016b; Ji et al., 2016; Lupiáñez et al., 2015; Narendra et al., 2015; Nora et al., 2012; Phillips-Cremins et al., 2013; Rao et al., 2014; Tang et al., 2015).”
Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin (2016, neutral): “We further examined the median peak-to-peak spacing within 100 kilobase (kb) windows that had been assigned to compartment A (enriched for open chromatin) or compartment B (enriched for closed chromatin) on the basis of chromatin contact maps in a lymphoblastoid cell line (Rao et al., 2014).”
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition (2017, positive): “Averaging over all genomic positions of loops and TADs identified in population Hi-C 8 (for CH12-LX cells, see Methods) revealed that both are present in individual oocytes as average enrichments (Fig.”
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom (2016, positive): “Hi-C is a widely employed method for studying how genomes are folded in three dimensions (Rao et al., 2014).”
An atlas of genetic influences on osteoporosis in humans and mice (2018, positive): “48 Instead of using HindIII restriction enzyme, we used DpnII 49 which increased coverage and insensitivity of CpG methylation.”
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data (2017, neutral): “…fast queries and can be used with a wide variety of contact mapping experiments, such as dilution Hi-C (Lieberman-Aiden et al., 2009), in situ Hi-C (Rao et al., 2014), single-cell Hi-C (Nagano et al., 2013), Hi-C 2 (Sanborn et al., 2015), ChIA-PET (Fullwood et al., 2009), HiChIP (Mumbach et al.,…”
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, positive): “Future improvements in GeneHancer will include the integration of new data sources, for both enhancer annotations (38, 39) and enhancer–gene associations, e.g. novel chromatin contact maps (83) and topologically associated domains (84).”
Comprehensive analysis of single cell ATAC-seq data with SnapATAC (2021, neutral): “Speci ﬁ cally, we monitor the running time for (1) TF-IDF transformation and Singular Value Decomposition (SVD) for LSA, (2) function “ runModels ” with topics = c(2, 5, 10, 15, 20, 25, 30, 35, 40) and “ selectModel ” function in cis -Topic.”
A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome (2016, neutral): “Raw contact matrices were constructed using in-house scripts, and then further processed using HiCNormCis (described below), or using HiCNorm (Hu et al., 2012), Vanilla Coverage (Rao et al., 2014), or ICE (Imakaev et al., 2012), where indicated.”