Name
Title | ||
|---|---|---|
Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data. |
Abstract | ||
|---|---|---|
Motivation: Computational prediction of transcription factor (TF) binding sites in the genome remains a challenging task. Here, we present Romulus, a novel computational method for identifying individual TF binding sites from genome sequence information and cell-type-specific experimental data, such as DNase-seq. It combines the strengths of previous approaches, and improves robustness by reducing the number of free parameters in the model by an order of magnitude. Results: We show that Romulus significantly outperforms existing methods across three sources of DNase-seq data, by assessing the performance of these tools against ChIP-seq profiles. The difference was particularly significant when applied to binding site prediction for low-information-content motifs. Our method is capable of inferring multiple binding modes for a single TF, which differ in their DNase I cut profile. Finally, using the model learned by Romulus and ChIP-seq data, we introduce Binding in Closed Chromatin (BCC) as a quantitative measure of TF pioneer factor activity. Uniquely, our measure quantifies a defining feature of pioneer factors, namely their ability to bind closed chromatin. |
Year | DOI | Venue |
|---|---|---|
2016 | 10.1093/bioinformatics/btw209 | BIOINFORMATICS |
Field | DocType | Volume |
Genome,Data mining,Binding site,DNA binding site,Computer science,Robustness (computer science),DNase-Seq,Bioinformatics,Chromatin immunoprecipitation,Chromatin,Pioneer factor | Journal | 32 |
Issue | ISSN | Citations |
16 | 1367-4803 | 3 |
PageRank | References | Authors |
0.41 | 3 | 3 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Aleksander Jankowski | 1 | 34 | 3.47 |
| Jerzy Tiuryn | 2 | 1210 | 126.00 |
| Shyam Prabhakar | 3 | 3 | 0.74 |