Results 21 to 30 of about 103,657 (215)
Normalization of ChIP-seq data with control
BMC Bioinformatics, 2012 Background ChIP-seq has become an important tool for identifying genome-wide protein-DNA interactions, including transcription factor binding and histone modifications. In ChIP-seq experiments, ChIP samples are usually coupled with their matching control
Liang Kun, Keleş Sündüz
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Imputation for transcription factor binding predictions based on deep learning. [PDF]
PLoS Computational Biology, 2017 Understanding the cell-specific binding patterns of transcription factors (TFs) is fundamental to studying gene regulatory networks in biological systems, for which ChIP-seq not only provides valuable data but is also considered as the gold standard ...
Qian Qin, Jianxing Feng
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Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping
BMC Research Notes, 2009 Background ChIP-Seq and ChIP-PET can potentially be used with any genome for genome wide profiling of protein-DNA interaction sites. Unfortunately, it is probable that most genome assemblies will never reach the quality of the human genome assembly ...
Sachs Laurent, Buisine Nicolas
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diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. [PDF]
PLoS ONE, 2013 ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs.
Li Shen +5 more
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SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis
BMC Bioinformatics, 2018 Background Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, an NGS library preparation method called SMART, or Switching Mechanism At the 5′ end of the RNA Transcript, is introduced to prepare ...
Dejian Zhao, Deyou Zheng
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Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq
Molecular Biomedicine, 2020 Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high ...
Shaoqian Ma, Yongyou Zhang
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Investigating transcription factor dynamics in health and disease using FRAP
FEBS Letters, EarlyView.FRAP analysis of GFP‐tagged transcription factors reveals how molecular mobility and target engagement change in response to drug treatment. By combining live‐cell imaging, quantitative model fitting, and statistical analysis, this approach uncovers transcription factor dynamics linked to disease mechanisms, providing a powerful framework for ...
Kannan Govindaraj +3 more
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STAR Protocols, 2020 Summary: Chromatin immunoprecipitation with sequencing (ChIP-seq) has been instrumental in understanding transcription factor (TF) binding during gene regulation.
Martyna Lukoseviciute +6 more
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Molecular Oncology, EarlyView.In this explorative study, the abundance of circular RNA molecules in bone marrow stem cells was found to be elevated in patients with high‐risk myelodysplastic neoplasms, and to be associated with an increased risk of progression to acute myeloid leukemia.
Eileen Wedge +17 more
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CCDC80 suppresses high‐grade serous ovarian cancer migration via negative regulation of B7‐H3
Molecular Oncology, EarlyView.PAX8 is a lineage‐specific master regulator of transcription in high‐grade serous ovarian cancer (HGSC) progression. We show for the first time that PAX8 facilitates proliferation and metastasis by repressing the cell autonomous tumor suppressor CCDC80 and inducing B7‐H3 expression.
Aya Saleh +12 more
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