Chengqi Lin
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View article: coFAST: Spatially-Aware Cell Clustering Algorithm with Cluster Significant Assessment
coFAST: Spatially-Aware Cell Clustering Algorithm with Cluster Significant Assessment Open
View article: Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics
Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics Open
Summary The mammalian heart is formed from multiple mesoderm-derived cell lineages. However, it remains largely unknown when and how the specification of mesoderm towards cardiac lineages is determined. Here, we systematically depict the t…
View article: Author response: Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics
Author response: Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics Open
View article: Digital reconstruction of full embryos during early mouse organogenesis
Digital reconstruction of full embryos during early mouse organogenesis Open
Early organogenesis is a crucial stage in embryonic development, characterized by extensive cell fate specification to initiate organ formation but also by a high susceptibility to developmental defects. Here, we profiled 285 serial sectio…
View article: <scp>RNF219 RING</scp> Finger Domain Mutants Drive Phase Separation to Encapsulate <scp>CCR4</scp>‐<scp>NOT</scp> and Promote Cell Proliferation
<span>RNF219 RING</span> Finger Domain Mutants Drive Phase Separation to Encapsulate <span>CCR4</span>‐<span>NOT</span> and Promote Cell Proliferation Open
RING finger protein 219 (RNF219) is a co‐factor for the CCR4‐NOT deadenylase complex in mammals. Here, we found that mutations within the C3HC4 scaffold of the RING finger domain in RNF219 are capable of forming condensates via liquid–liqu…
View article: Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors
Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors Open
Obtaining single-cell spatial information remains a challenge in spatial transcriptomics. Here we develop SEU-TCA, a method that leverages transfer component analysis to improve single-cell spatial mapping accuracy. Application to multiple…
View article: Functional Imaging of Developing Brain in Mice and Non-Human Primates
Functional Imaging of Developing Brain in Mice and Non-Human Primates Open
Despite significant advances in structural and genetic studies, investigations of early embryonic functions, such as brain activity, have long been constrained by technical challenges. Functional ultrasound (fUS) has emerged as a breakthro…
View article: LEDGF/p75 promotes transcriptional pausing through preventing SPT5 phosphorylation
LEDGF/p75 promotes transcriptional pausing through preventing SPT5 phosphorylation Open
SPT5 exhibits versatile functions in RNA Pol II promoter proximal pausing, pause release, and elongation in metazoans. However, the mechanism underlying the functional switch of SPT5 during early elongation has not been fully understood. H…
View article: The transcriptional repressor HEY2 regulates mitochondrial oxidative respiration to maintain cardiac homeostasis
The transcriptional repressor HEY2 regulates mitochondrial oxidative respiration to maintain cardiac homeostasis Open
View article: Multivariate stochastic modeling for transcriptional dynamics with cell-specific latent time using SDEvelo
Multivariate stochastic modeling for transcriptional dynamics with cell-specific latent time using SDEvelo Open
View article: 4D live tracing reveals distinct movement trajectories of meiotic chromosomes
4D live tracing reveals distinct movement trajectories of meiotic chromosomes Open
Proper chromosome alignment at the spindle equator is a prerequisite for accurate chromosome segregation during cell division. However, the chromosome movement trajectories prior to alignment remain elusive. Here, we established a 4D imagi…
View article: Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics
Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics Open
Summary The mammalian heart is formed from multiple mesoderm-derived cell lineages. However, it remains largely unknown when and how the specification of mesoderm towards cardiac lineages is determined. Here, we systematically depict the t…
View article: Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics
Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics Open
The mammalian heart is formed from multiple mesoderm-derived cell lineages. However, it remains largely unknown when and how the specification of mesoderm towards cardiac lineages is determined. Here, we systematically depict the transcrip…
View article: SpatialQC: automated quality control for spatial transcriptome data
SpatialQC: automated quality control for spatial transcriptome data Open
Summary The advent of spatial transcriptomics has revolutionized our understanding of the spatial heterogeneity in tissues, providing unprecedented insights into the cellular and molecular mechanisms underlying biological processes. Althou…
View article: Functional Imaging of Developing Brain in Mice and Non-Human Primates
Functional Imaging of Developing Brain in Mice and Non-Human Primates Open
Despite significant advances in structural and genetic studies, investigations of early embryonic functions, such as brain activity, have long been constrained by technical challenges. Functional ultrasound (fUS) has emerged as a breakthro…
View article: Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics
Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics Open
Summary The mammalian heart is formed from multiple mesoderm-derived cell lineages. However, it remains largely unknown when and how the specification of mesoderm towards cardiac lineages is determined. Here, we systematically depict the t…
View article: SDEvelo: a deep generative approach for transcriptional dynamics with cell-specific latent time and multivariate stochastic modeling
SDEvelo: a deep generative approach for transcriptional dynamics with cell-specific latent time and multivariate stochastic modeling Open
Recently, RNA velocity has driven a paradigmatic change in single-cell RNA sequencing (scRNA-seq) studies, allowing the reconstruction and prediction of directed trajectories in cell differentiation and state transitions. However, most exi…
View article: Single-cell mitochondrial lineage tracing decodes fate decision and spatial clonal architecture in human hematopoietic organoids
Single-cell mitochondrial lineage tracing decodes fate decision and spatial clonal architecture in human hematopoietic organoids Open
The ability to perform lineage tracing at the single-cell level is critical to reconstructing dynamic transitions during cell differentiation. However, prospective tracing approaches inevitably encounter outstanding challenges including ba…
View article: Distinct roles of two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA polymerase II transcription elongation
Distinct roles of two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA polymerase II transcription elongation Open
The super elongation complex (SEC) containing positive transcription elongation factor b plays a critical role in regulating transcription elongation. AFF1 and AFF4, two members of the AF4/FMR2 family, act as central scaffold proteins of S…
View article: The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release
The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release Open
View article: QSER1 preserves the suppressive status of the pro-apoptotic genes to prevent apoptosis
QSER1 preserves the suppressive status of the pro-apoptotic genes to prevent apoptosis Open
View article: Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation
Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation Open
The P-TEFb-containing super elongation complex (SEC) plays the essential role in transcriptional elongation control. The AF4/FMR2 family members AFF1 and AFF4 are the central scaffold proteins of SEC, associated with different human diseas…
View article: ZFP281-BRCA2 prevents R-loop accumulation during DNA replication
ZFP281-BRCA2 prevents R-loop accumulation during DNA replication Open
R-loops are prevalent in mammalian genomes and involved in many fundamental cellular processes. Depletion of BRCA2 leads to aberrant R-loop accumulation, contributing to genome instability. Here, we show that ZFP281 cooperates with BRCA2 i…
View article: Phase separation, transcriptional elongation control, and human diseases
Phase separation, transcriptional elongation control, and human diseases Open
View article: Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis
Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis Open
Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset…
View article: Suppression of the NTS-CPS1 regulatory axis by AFF1 in lung adenocarcinoma cells
Suppression of the NTS-CPS1 regulatory axis by AFF1 in lung adenocarcinoma cells Open
Upregulation of the neuropeptide neurotensin (NTS) in a subgroup of lung cancers has been linked to poor prognosis. However, the regulatory pathway centered on NTS in lung cancer remains unclear. Here we identified the NTS-specific enhance…
View article: Additional file 2 of Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis
Additional file 2 of Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis Open
Additional file 2: Table S1. 6164 Species Inconsistency Runs.
View article: Additional file 3 of Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis
Additional file 3 of Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis Open
Additional file 3: Table S2. 160 randomly selected Runs.
View article: RNF219 interacts with CCR4–NOT in regulating stem cell differentiation
RNF219 interacts with CCR4–NOT in regulating stem cell differentiation Open
Regulation of RNA stability plays a crucial role in gene expression control. Deadenylation is the initial rate-limiting step for the majority of RNA decay events. Here, we show that RING finger protein 219 (RNF219) interacts with the CCR4–…
View article: Diploid genome architecture revealed by multi-omic data of hybrid mice
Diploid genome architecture revealed by multi-omic data of hybrid mice Open
Although mammalian genomes are diploid, previous studies extensively investigated the average chromatin architectures without considering the differences between homologous chromosomes. We generated Hi-C, ChIP-seq, and RNA-seq data sets fr…