… single-cell Epigenome based chromatin-interaction Analysis (scEChIA) which can predict
interactions … We found that scEChIA is as accurate as Cicero, whereas using constant ρ value …

… -Accessible Chromatin using sequencing (scATAC-seq) profile. However, Cicero is designed
for predicting interactions … called jointly reconstruct cis-regulatory interaction maps (JRIM) (…

… or from single-cell chromatin accessibility data alone. By … ’s predicted CREs using independent
functional genomics data, we … , Cicero quantifies how changes in chromatin accessibility …

… Activity of distal and proximal CREs can also be used to predict … While cytosine methylation
can prevent DNA binding by … Single-cell chromatin accessibility profiling has been widely …

… We measured chromatin accessibility and nuclear gene … To corroborate predicted cell-type
annotations, we … distinct cell-types, we used Cicero to estimate gene activity scores. …

… have been developed to estimate cis-regulatory DNA interactions using epigenetic data [14–18]. …
For example, Cicero [26] employs a graphical lasso model to detect linkages between …

… single-cell chromatin accessibility data and make cell-type-specific contact map predictions.
… of peak-level significant interaction prediction using Cicero co-accessibility at various cutoffs …

… the application of single-cell epigenomic data in various contexts … A rapid and robust method
for single cell chromatin accessibility … Cicero Predicts cis-Regulatory DNA Interactions from …

… -seq data as clustering, visualization, cis-regulatory DNA … We compared Cicero predicted
interactions on human … scATAC-seq is the prediction of cis-regulatory DNA interactions (peak-to-…

… Owing to steric requirements of most DNA binding proteins, … in maize was able to predict
cell-type annotations with high … chromatin accessibility through comparison of single-cell …