Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

By Eitan Yaffe, Amos Tanay. Nature Genetics, 2011

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View Paper: https://www.semanticscholar.org/paper/d946fd6324a3338a3e5825b58d52f2e197849355

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Citations in the corpus

A decade of 3C technologies: insights into nuclear organization. (2012, methodology): “For a more thorough statistical definition of 4C, HiC, or ChIA-PET interactions, we refer to Lieberman-Aiden et al. (2009), Li et al. (2010), Splinter et al. (2011), and Yaffe and Tanay (2011).”
Formation of Chromosomal Domains by Loop Extrusion (2015, background): “For these simulations, we converted ChIP-seq data for CTCF and cohesin over a 15Mb region of human chromosome 14 into BE occupancy and directionality (Methods).”
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient (2017, methodology): “It has been found effective in commonly-used Hi-C normalization methods (Imakaev et al. 2012; Yaffe and Tanay 2011).”
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data (2015, result): “While Hi-C background depends on a number of known parameters, such as fragment length and GC content [10], we, along with others [7, 8, 30], have opted to avoid any specific assumptions about noise structure, particularly given the increased complexity and asymmetric nature of capture Hi-C noise co”
CTCF Binding Polarity Determines Chromatin Looping. (2015, background): “, 2006) and is enriched at boundaries of topological domains (Dixon et al., 2012; Yaffe and Tanay, 2011).”
Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM) (2017, neutral): “However, 3C-based approaches have important limitations, due to their reliance on digestion and ligation to capture interacting DNA segments15–20.”
A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping (2014, positive): “These findings expand on earlier reports suggesting three compartments in human cells (Yaffe and Tanay, 2011).”
Genome-wide mapping and analysis of chromosome architecture (2016, methodology): “Next, an empirical distrib ution was used to estimate such combinational bias effects, leading to a statistically effective but computationally intensive bias-removal method 77 .”
Three-dimensional folding and functional organization principles of the Drosophila genome. (2012, methodology): “The functions Flen and Fgc correct for technical biases given fragment lengths (alen, blen) and GC contents (agc, bgc), as described in Yaffe and Tanay (2011).”
A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome (2016, neutral): “HiCNormCis then takes into account biases from three known factors known to bias observed Hi-C contact counts, including effective fragment length, GC content and mappability (Yaffe and Tanay, 2011) (related to Figure 2, Figure S2).”
Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture (2015, methodology): “Processing of the aligned reads and normalization of the interaction matrices were performed as previously described (Yaffe and Tanay, 2011; Sofueva et al., 2013).”