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DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter
2016
Bioinformatics
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Results: Using DNase-seq data from the ENCODE project, we show that a large degree of previously uncharacterized site-to-site variability exists in footprint signal across motif sites for a transcription ...
Motivation: Identifying the locations of transcription factor binding sites is critical for understanding how gene transcription is regulated across different cell types and conditions. ...
We also thank Tatsunori Hashimoto for his support in updating PIQ for compatibility with our motif site evaluation sets. ...
doi:10.1093/bioinformatics/btw740
pmid:27993786
pmcid:PMC6075477
fatcat:gal7s2ar6jegde3fnx5gttzrsy
TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence
2020
Genome Research
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Thus, identification of transcription factor binding sites (TFBSs) is key to understanding gene expression and whole regulatory networks within a cell. ...
TRACE incorporates DNase-seq data and PWMs within a multivariate Hidden Markov Model (HMM) to detect footprint-like regions with matching motifs. ...
Identification of cis-regulatory elements where transcription factors (TFs) bind remains a key goal in deciphering transcriptional regulatory circuits. ...
doi:10.1101/gr.258228.119
pmid:32660981
pmcid:PMC7397869
fatcat:duzc7zeefbewris7ndyokcaz3q
TRACE: transcription factor footprinting using DNase I hypersensitivity data and DNA sequence
[article]
2019
bioRxiv
pre-print
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Thus, identification of transcription factor binding sites is key to understanding gene expression and whole regulatory networks within a cell. ...
Trace incorporates DNase-seq data and PWMs within a multivariate Hidden Markov Model (HMM) to detect footprint-like regions with matching motifs. ...
(B) Predicted binding sites from TRACE using our 10-motif CTCF model match corresponding region of transcription factor binding obtained by ChIP-seq experiments with DNA binding motifs by the ENCODE Factorbook ...
doi:10.1101/801001
fatcat:yhzkj3rt4vhllnxycs25w3i4ue
Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning
2021
Nucleic Acids Research
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Epitome achieves state-of-the-art accuracy when predicting transcription factor binding sites on novel cellular contexts and can further improve predictions as more epigenetic signals are collected from ...
We propose Epitome, a deep neural network that learns similarities of chromatin accessibility between well characterized reference cell types and a query cellular context, and copies over signal of transcription ...
ACKNOWLEDGEMENTS We thank Gunjan Baid, Alex Ku, Roman Kuhn, Joseph Gonzalez, Jennifer Listgarten, and Esther Rolf for their support. ...
doi:10.1093/nar/gkab676
pmid:34379786
pmcid:PMC8565335
fatcat:p4stdsffqrc3xauc4uxjmekfzy
Epitome: Predicting epigenetic events in novel cell types with multi-cell deep ensemble learning
[article]
2021
bioRxiv
pre-print
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Epitome achieves state-of-the-art accuracy when predicting transcription factor binding sites on novel cellular contexts and can further improve predictions as more epigenetic signals are collected from ...
We propose Epitome, a deep neural network that learns similarities of chromatin accessibility between well characterized reference cell types and a query cellular context, and copies over signal of transcription ...
Because DeFCoM and other footprinting methods are motif centric, they are only designed to predict binding in regions centered around motifs. ...
doi:10.1101/2021.06.10.447140
fatcat:xaidfhe4pzbu5pgim5avcreaym
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
2020
Genome Biology
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, motif enrichment, footprinting, and nucleosome position analysis). ...
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. ...
Availability of data and materials The raw sequencing data to produce the fragment size distribution, TSS enrichment plot, and peak tracks from Corces et al. ...
doi:10.1186/s13059-020-1929-3
pmid:32014034
fatcat:xowyj2wc5vfkvisoceizn7tdra
Deciphering Transcriptional Regulatory Circuits: Transcription Factor Binding and Regulatory Variants Identification
2022
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Identification of transcription factor binding sites remains a crucial goal in deciphering transcriptional regulatory circuits. ...
In this dissertation, I develop an improved footprinting algorithm to map transcription factor binding sites genome-wide, study regulatory variants associated with transcription factor binding affinity ...
ACKNOWLEDGEMENTS The work presented in this dissertation could not have been accomplished without the support of so many people. First and foremost, I would like to thank my advisor, Dr. ...
doi:10.7302/4546
fatcat:leshz4qqhbdi3pz7udlwr7nrfe