Bibliometric review of ATAC-Seq and its application in gene expression
L Luo, M Gribskov, S Wang - Briefings in Bioinformatics, 2022 - academic.oup.com
With recent advances in high-throughput next-generation sequencing, it is possible to
describe the regulation and expression of genes at multiple levels. An assay for transposase …
describe the regulation and expression of genes at multiple levels. An assay for transposase …
Identification of transcription factor binding sites using ATAC-seq
Abstract Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a
simple protocol for detection of open chromatin. Computational footprinting, the search for …
simple protocol for detection of open chromatin. Computational footprinting, the search for …
Genome-wide analysis of chromatin accessibility using ATAC-seq
T Shashikant, CA Ettensohn - Methods in cell biology, 2019 - Elsevier
Programs of gene transcription are controlled by cis-acting DNA elements, including
enhancers, silencers, and promoters. Local accessibility of chromatin has proven to be a …
enhancers, silencers, and promoters. Local accessibility of chromatin has proven to be a …
ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Background Chromatin dysregulation is associated with developmental disorders and
cancer. Numerous methods for measuring genome-wide chromatin accessibility have been …
cancer. Numerous methods for measuring genome-wide chromatin accessibility have been …
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq
ED Tarbell, T Liu - Nucleic acids research, 2019 - academic.oup.com
ATAC-seq has been widely adopted to identify accessible chromatin regions across the
genome. However, current data analysis still utilizes approaches initially designed for ChIP …
genome. However, current data analysis still utilizes approaches initially designed for ChIP …
NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA
Diverse RNA 5′ ends are generated through both transcriptional and post-transcriptional
processes. These important modes of gene regulation often vary across cell types and can …
processes. These important modes of gene regulation often vary across cell types and can …
Regulatory genome annotation of 33 insect species
Annotation of newly sequenced genomes frequently includes genes, but rarely covers
important non-coding genomic features such as the cis-regulatory modules—eg, enhancers …
important non-coding genomic features such as the cis-regulatory modules—eg, enhancers …
Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling
JB Wolpe, AL Martins, MJ Guertin - NAR Genomics and …, 2023 - academic.oup.com
Chromatin accessibility assays have revolutionized the field of transcription regulation by
providing single-nucleotide resolution measurements of regulatory features such as …
providing single-nucleotide resolution measurements of regulatory features such as …
[HTML][HTML] Calling variants in the clinic: informed variant calling decisions based on biological, clinical, and laboratory variables
ZS Bohannan, A Mitrofanova - Computational and structural biotechnology …, 2019 - Elsevier
Deep sequencing genomic analysis is becoming increasingly common in clinical research
and practice, enabling accurate identification of diagnostic, prognostic, and predictive …
and practice, enabling accurate identification of diagnostic, prognostic, and predictive …
Characterization of H5N1 influenza virus quasispecies with adaptive hemagglutinin mutations from single-virus infections of human airway cells
Y Watanabe, Y Arai, N Kawashita, MS Ibrahim… - Journal of …, 2018 - Am Soc Microbiol
Transmission of avian influenza (AI) viruses to mammals involves phylogenetic bottlenecks
that select small numbers of variants for transmission to new host species. However, little is …
that select small numbers of variants for transmission to new host species. However, little is …