26 Result(s)
within
William J. Greenleaf
Agriculture
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Article
Open AccessSystematic benchmarking of single-cell ATAC-sequencing protocols
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of syst...
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Open AccessIntegration of spatial and single-cell data across modalities with weakly linked features
Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integra...
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Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases
Genome-wide association studies have identified many loci associated with hair and skin disease, but identification of causal variants requires deciphering of gene-regulatory networks in relevant cell types. W...
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High-throughput biochemistry in RNA sequence space: predicting structure and function
RNAs are central to fundamental biological processes in all known organisms. The set of possible intramolecular interactions of RNA nucleotides defines the range of alternative structural conformations of a sp...
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Open AccessTargeted profiling of human extrachromosomal DNA by CRISPR-CATCH
Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agaros...
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Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks
Gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed, it can lead to disease. To understand how gene expression disruptions perco...
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Open AccessSingle-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single-cell chromatin accessibility prof...
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The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation
Transcription factors bind DNA sequence motif vocabularies in cis-regulatory elements (CREs) to modulate chromatin state and gene expression during cell state transitions. A quantitative understanding of how moti...
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Open AccessAuthor Correction: ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
A Correction to this paper has been published: https://doi.org/10.1038/s41588-021-00850-x.
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Open AccessTranscription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum
Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem ...
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Open AccessArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological mea...
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Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases
Genome-wide association studies of neurological diseases have identified thousands of variants associated with disease phenotypes. However, most of these variants do not alter coding sequences, making it diffi...
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Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia
Identifying the causes of human diseases requires deconvolution of abnormal molecular phenotypes spanning DNA accessibility, gene expression and protein abundance1–3. We present a single-cell framework that integ...
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Landscape of stimulation-responsive chromatin across diverse human immune cells
A hallmark of the immune system is the interplay among specialized cell types transitioning between resting and stimulated states. The gene regulatory landscape of this dynamic system has not been fully charac...
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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion
Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for map** transposa...
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Chromatin accessibility and the regulatory epigenome
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome refle...
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Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens
Phagocytosis is required for a broad range of physiological functions, from pathogen defense to tissue homeostasis, but the mechanisms required for phagocytosis of diverse substrates remain incompletely unders...
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Challenges and recommendations for epigenomics in precision health
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Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
High-resolution contact maps of active enhancers and target genes generated by H3K27ac HiChIP in primary human cells provide rational guides to link noncoding disease-associated risk variants to candidate caus...
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Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation
Adam Rubin, Brook Barajas, Mayra Furlan-Magaril and colleagues studied dynamic chromatin across the genome of differentiating human skin keratinocytes, identifying both stable and reorganizing classes of trans...
