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10 results for “Clustering”
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Stratification of enterochromaffin cells by single-cell expression analysis.
eLife · 2025 · 12
Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine to mediate disparate physiological responses. However, the molecular and cellular basis for …
PMID 40184163 DOI ↗
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Stratification of enterochromaffin cells by single-cell expression analysis.
bioRxiv : the preprint server for biology · 2025
Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine (5-HT) to mediate disparate physiological responses. However, the molecular and cellular basis …
PMID 37662229 DOI ↗
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Strategies for programmable manipulation of alternative splicing.
Current opinion in genetics & development · 2024 · 89: 102272
Alternative splicing (AS) plays a pivotal role in protein diversity and mRNA maturation. Programmable control of targeted AS events is of longstanding interest in RNA biology, promising correction of dysregulated splicing in disease and discovery of AS events. This review …
PMID 39471777 DOI ↗
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The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.
Scientific reports · 2022 · 12(1): 5077
Throughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to prevent the spread of the virus. However, …
PMID 35332213 DOI ↗
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ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses.
The Journal of experimental medicine · 2021 · 218(9)
Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 and autoinflammation. To identify additional endogenous dsRNA …
PMID 34297039 DOI ↗
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A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation.
Blood advances · 2021 · 5(5): 1310-1323
The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and is disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined central role, and mutations promote malignant transformation. More …
PMID 33656539 DOI ↗
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Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.
Cell · 2019 · 178(1): 107-121.e18
Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on …
PMID 31251911 DOI ↗
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iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Stem cell reports · 2017 · 8(4): 1086-1100
Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 …
PMID 28410642 DOI ↗
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High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection.
Journal of virology · 2012 · 86(1): 226-35
Human cytomegalovirus (HCMV) contributes its own set of microRNAs (miRNAs) during lytic infection of cells, likely fine-tuning conditions important for viral replication. To enhance our understanding of this component of the HCMV-host transcriptome, we have conducted deep-sequencing analysis of small …
PMID 22013051 DOI ↗
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A regulator of Dscam mutually exclusive splicing fidelity.
Nature structural & molecular biology · 2007 · 14(12): 1134-40
The Down syndrome cell adhesion molecule (Dscam) gene has essential roles in neural wiring and pathogen recognition in Drosophila melanogaster. Dscam encodes 38,016 distinct isoforms via extensive alternative splicing. The 95 alternative exons in Dscam are organized into clusters that …
PMID 21188797 DOI ↗
Datasets 9
MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy [scRNA-Seq]
Homo sapiens · GPL24676
Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for amyotrophic lateral sclerosis and frontotemporal dementia (Multiplex Analysis of PolyA-linked Sequences)
Homo sapiens · GPL11154
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]
Homo sapiens · GPL11154
Transcriptional Signature and Memory Retention of Human-induced Pluripotent Stem Cells
Homo sapiens · GPL570
Transcriptome-pathology correlations predict CSNK1E-mediated TDP-43 phosphorylation in sporadic amyotrophic lateral sclerosis
Homo sapiens · GPL20301
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq]
Homo sapiens · GPL16791
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [HiC-Seq]
Homo sapiens · GPL20795
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