User profiles for Zhengquing Ouyang
Zhengqing OuyangAssociate Professor, Department of Biostatistics and Epidemiology, University of … Verified email at schoolph.umass.edu Cited by 21228 |
[HTML][HTML] Architecture of the human regulatory network derived from ENCODE data
Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes;
the ensemble of these binding events forms a regulatory network, constituting the wiring …
the ensemble of these binding events forms a regulatory network, constituting the wiring …
Landscape and variation of RNA secondary structure across the human transcriptome
In parallel to the genetic code for protein synthesis, a second layer of information is embedded
in all RNA transcripts in the form of RNA structure. RNA structure influences practically …
in all RNA transcripts in the form of RNA structure. RNA structure influences practically …
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
Next-generation sequencing has greatly increased the scope and the resolution of transcriptional
regulation study. RNA sequencing (RNA-Seq) and ChIP-Seq experiments are now …
regulation study. RNA sequencing (RNA-Seq) and ChIP-Seq experiments are now …
Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
Multimodal single-cell assays provide high-resolution snapshots of complex cell populations,
but are mostly limited to transcriptome plus an additional modality. Here, we describe …
but are mostly limited to transcriptome plus an additional modality. Here, we describe …
[PDF][PDF] Genome-wide measurement of RNA folding energies
RNA structural transitions are important in the function and regulation of RNAs. Here, we
reveal a layer of transcriptome organization in the form of RNA folding energies. By probing …
reveal a layer of transcriptome organization in the form of RNA folding energies. By probing …
SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
We present an integrative approach, SeqFold, that combines high-throughput RNA structure
profiling data with computational prediction for genome-scale reconstruction of RNA …
profiling data with computational prediction for genome-scale reconstruction of RNA …
Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis
Many genes initially identified for their roles in cell fate determination or signaling during
development can have a significant impact on tumorigenesis. In the developing cerebellum, …
development can have a significant impact on tumorigenesis. In the developing cerebellum, …
[HTML][HTML] Single-cell transcriptomics–based MacSpectrum reveals macrophage activation signatures in diseases
Adipose tissue macrophages (ATMs) are crucial for maintaining adipose tissue homeostasis
and mediating obesity-induced metabolic abnormalities, including prediabetic conditions …
and mediating obesity-induced metabolic abnormalities, including prediabetic conditions …
Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing
RNA structure is important for RNA function and regulation, and there is growing interest in
determining the RNA structure of many transcripts. Here we provide a detailed protocol for …
determining the RNA structure of many transcripts. Here we provide a detailed protocol for …
Multimodal single-cell analysis of cutaneous T-cell lymphoma reveals distinct subclonal tissue-dependent signatures
Cutaneous T-cell lymphoma (CTCL) is a heterogeneous group of mature T-cell neoplasms
characterized by the accumulation of clonal malignant CD4+ T cells in the skin. The most …
characterized by the accumulation of clonal malignant CD4+ T cells in the skin. The most …