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Article
Open AccessAlignment-free clustering of large data sets of unannotated protein conserved regions using minhashing
Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput se...
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Article
Sensory experience remodels genome architecture in neural circuit to drive motor learning
Neuronal-activity-dependent transcription couples sensory experience to adaptive responses of the brain including learning and memory. Mechanisms of activity-dependent gene expression including alterations of ...
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Article
Publisher Correction: Sensory experience remodels genome architecture in neural circuit to drive motor learning
In this Letter, ‘≥’ should be ‘≤’ in the sentence: “Intra-chromosomal reads were further split into short-range reads (≥1 kb) and long-range reads (>1 kb)”. This error has been corrected online.
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Article
Circular ecDNA promotes accessible chromatin and high oncogene expression
Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultra...
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Article
An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, current tools are limited by mode...
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Article
Cell-type-specific 3D epigenomes in the develo** human cortex
Lineage-specific epigenomic changes during human corticogenesis have been difficult to study owing to challenges with sample availability and tissue heterogeneity. For example, previous studies using single-ce...
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Protocol
Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq)
Proximity ligation-assisted ChIP-Seq (PLAC-Seq), also known as HiChIP, is a method to detect and quantify chromatin contacts anchored at genomic regions bound by specific proteins or histone modifications. By ...
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Article
Open AccessSnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data
Single-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools to define chromatin loops at high resolution from scHi-C data are...
