v ABSTRACTOFTHEDISSERTATION EfficientAlgorithmsfortheAnalysisofHi-CContactMaps by AbbasRoayaeiArdakany DoctorofPhilosophy,GraduatePrograminComputerScience UniversityofCalifornia,Riverside,December2019 Dr.StefanoLonardi,Chairperson Thisdissertationdealswiththeanalysisofhigh-throughputchromatinconformationcap- ture(Hi-C)...
Results By carefully examining the properties of Hi-C maps and integrating various recent advances in deep learning, we developed a Hi-C Super-Resolution (HiCSR) framework capable of accurately recovering the fine details, textures, and substructures found in high resolution contact maps. This was...
DiffGR is a novel statistical method for detecting differential genomic regions at TAD level between two Hi-C contact maps. Briefly, DiffGR utilizes the stratum-adjusted correlation coefficient (SCC), which can effectively eliminate the genomic-distance effect in Hi-C data, to measure the similarity...
d An example of contact domain splitting (between the dashed lines) coupled with chromatin state switching (shown by Hi-C maps and histone ChIP-seq tracks) around BCAT1 locus in Capan-1 and PANC-1 cells (*p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001). ...
Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome architecture assays.The phrase 'chromosomal contact maps produced by genome architecture assays' may be faithfully reduced to 'Hi-C data.' Applying that change yields:Fit-Hi-C is a ...
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We present Mustache, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. Mustache employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps. Mustache is sca
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Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet. 43, 1059–1065 (2011). Article CAS PubMed Google Scholar Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. ...
Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks ...