Results 91 to 100 of about 574,745 (303)

Model-based Analysis of ChIP-Seq (MACS) [PDF]

Genome Biology, 2008
AbstractWe present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites.
Zhang, Yong, Liu, Tao, Meyer, Clifford A., Eeckhoute, Jerome, Johnson, David S., Nusbaum, Chad, Myers, Richard M., Brown, Myles, Li, Wei, Liu, Xiaole S., Bernstein, Bradley E.   +10 more
openaire   +4 more sources

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

BMC Genomics, 2019
Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are ...
Jonas Ibn-Salem, Miguel A. Andrade-Navarro   +1 more
doaj   +1 more source

Shape-based peak identification for ChIP-Seq [PDF]

BMC Bioinformatics, 2011
We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments.
Valerie Hower, Steven N. Evans, Lior Pachter   +2 more
openaire   +6 more sources

Using cell‐free RNA to identify B‐ and T‐cell clonality for diagnosis and monitoring of B‐ and T‐cell neoplasms

FEBS Open Bio, EarlyView.
Using peripheral blood for determining B‐cell or T‐cell clonality is more reliable when we use cell‐free RNA (cfRNA) because cells release blood significantly more RNA than DNA. Next‐generation sequencing (NGS) of cfRNA allows us to evaluate fragment cfRNA and evaluate clonality reliably without the need for prior determination of the specific dominant
Adam Albitar, Sally Agersborg, Ahmed Charifa, Pooja Phull, Noa Biran, David Vesole, Harsh Parmar, Andrew Pecora, Andrew Ip, Andre Goy, David Siegel, Maher Albitar   +11 more
wiley   +1 more source

RACS: rapid analysis of ChIP-Seq data for contig based genomes

BMC Bioinformatics, 2019
Background Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely-used molecular method to investigate the function of chromatin-related proteins by identifying their associated DNA sequences on a genomic scale.
Alejandro Saettone, Marcelo Ponce, Syed Nabeel-Shah, Jeffrey Fillingham   +3 more
doaj   +1 more source

An Epigenetic Fate Converter Based on Nuclei‐Targeting Lipid Nanoparticles Drives Neuronal Programming of Stem Cells for Spinal Cord Repair

Advanced Functional Materials, EarlyView.
Schematic illustration of LNP‐MPG nuclei‐targeting delivery of HMW‐FGF2 promoting histone acetylation to regulate the fate of DPSCs and treat spinal cord injury. LNPs components include pHMW‐FGF2 plasmid, DSPC, Dlin‐MC3‐DMA, cholesterol, and PEG2000, and are modified with MPG to form HMW‐FGF2@LNP‐MPG (HLM). HLM nuclei‐targets DPSCs to deliver HMW‐FGF2,
Heng Zhou, Qiang Qin, Xiqin Li, Hanyu Ding, Chun Xu, Yan He, Qingsong Ye   +6 more
wiley   +1 more source

vanrooij-lab/chip-seq-pipeline2: chip-seq-pipeline2

<p>chip-seq-pipeline2</p ...
Jin wook Lee, Soo Lee, J. Seth Strattan
core   +1 more source

In silico pooling of ChIP-seq control experiments.

PLoS ONE, 2014
As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation.
Guannan Sun, Rajini Srinivasan, Camila Lopez-Anido, Holly A Hung, John Svaren, Sündüz Keleş   +5 more
doaj   +1 more source

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

BMC Genomics, 2011
Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone ...
Karchenko Peter V, Bishop Eric, Ho Joshua WK, Nègre Nicolas, White Kevin P, Park Peter J   +5 more
doaj   +1 more source

An Engineered Biomimetic Nanoreactor With Cascade Functions for Targeted and Combinatorial Therapy of Ischemic Stroke

Advanced Healthcare Materials, EarlyView.
Preparation of RVG‐modified erythrocyte membrane‐coated HMPB nanocarriers loaded with L‐arginine and NBP (RM@HPAN) and its neuroprotective mechanism. After intravenous injection, RM@HPAN achieves prolonged circulation, RVG‐29‐mediated BBB penetration, and ischemic accumulation.
Shaofa Li, Ying Wu, Huimin Wei, Jinyong Teng, Zaizhi Yang, Jufang Chen, Bao Liao, Xiaoqin Huang, Lanqing Meng, Tong Li   +9 more
wiley   +1 more source