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View article: Spider: a flexible and unified framework for simulating spatial transcriptomics data
Spider: a flexible and unified framework for simulating spatial transcriptomics data Open
Motivation Spatial transcriptomics (ST) technologies provide valuable insights into cellular heterogeneity by simultaneously acquiring both gene expression profiles and cellular location information. However, the limited diversity and accu…
View article: A semi-supervised Bayesian approach for marker gene trajectory inference from single-cell RNA-seq data
A semi-supervised Bayesian approach for marker gene trajectory inference from single-cell RNA-seq data Open
Motivation Trajectory inference methods are essential for extracting temporal ordering from static single-cell transcriptomic profiles, thus facilitating the accurate delineation of cellular developmental hierarchies and cell-fate transiti…
View article: CellPatch: A Flexible and Efficient Framework for Single-Cell Foundation Model Empowered by Heuristic Gene Patching
CellPatch: A Flexible and Efficient Framework for Single-Cell Foundation Model Empowered by Heuristic Gene Patching Open
The rapid advancement of foundation models has significantly enhanced the analysis of single-cell omics data, providing deeper insights into the complex cellular and genetic interactions across diverse tissues. However, existing foundation…
View article: Burden and inequalities of chronic kidney disease attributable to diet globally, regionally and temporally, 1990–2021
Burden and inequalities of chronic kidney disease attributable to diet globally, regionally and temporally, 1990–2021 Open
Background Modifiable dietary habits are a crucial means of reducing the risk of CKD. However, there is currently a lack of global-scale analysis on the burden of CKD attributable to diet. This study aimed to examine the burden of CKD pote…
View article: STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data Open
The rapid advance of spatially resolved transcriptomics technologies has yielded substantial spatial transcriptomics data. Deriving biological insights from these data poses nontrivial computational and analysis challenges, of which the mo…
View article: A global analysis of the burden of ischemic heart disease attributable to diet low in ω-3 fatty acids between 1990 and 2021
A global analysis of the burden of ischemic heart disease attributable to diet low in ω-3 fatty acids between 1990 and 2021 Open
This study untangles a significant association between a low ω-3 diet and the burden of IHD, emphasizing the importance of promoting healthy eating habits globally. Future research should further explore the impact of dietary changes on th…
View article: CellPatch: a Highly Efficient Foundation Model for Single-Cell Transcriptomics with Heuristic Patching
CellPatch: a Highly Efficient Foundation Model for Single-Cell Transcriptomics with Heuristic Patching Open
The rapid advancement of foundation models has significantly enhanced the analysis of single-cell omics data, enabling researchers to gain deeper insights into the complex interactions between cells and genes across diverse tissues. Howeve…
View article: A Novel Roseosiphovirus Infecting Dinoroseobacter shibae DFL12T Represents a New Genus
A Novel Roseosiphovirus Infecting Dinoroseobacter shibae DFL12T Represents a New Genus Open
Bacteria belonging to the Roseobacter clade are key players in marine ecosystems, contributing significantly to carbon and sulfur cycles. Marine viruses, particularly those targeting Roseobacter, play crucial roles in regulating microbial …
View article: A global analysis of the burden of ischemic heart disease attributable to diet low in fiber between 1990 and 2019
A global analysis of the burden of ischemic heart disease attributable to diet low in fiber between 1990 and 2019 Open
Our analysis underscores the substantial toll of IHD associated with low-fiber diets, particularly considering the significant regional variations. Therefore, it is imperative to sustain efforts to implement effective measures aimed at enh…
View article: STCC: consensus clustering enhances spatial domain detection for spatial transcriptomics data
STCC: consensus clustering enhances spatial domain detection for spatial transcriptomics data Open
The rapid advance of spatially resolved transcriptomics technologies has yielded substantial spatial transcriptomics data. Deriving biological insights from these data poses non-trivial computational and analysis challenges, of which the m…
View article: A longitudinal study on the effect of extreme temperature on non-accidental deaths in Hulunbuir City based on DLNM model
A longitudinal study on the effect of extreme temperature on non-accidental deaths in Hulunbuir City based on DLNM model Open
Objective To explore the frequency and effect of extreme temperature on the non-accidental death rate in Hulunbuir, a Chinese ice city. Methods From 2014 to 2018, mortality data of residents residing in Hulunbuir City were collected. The l…
View article: Spider: a flexible and unified framework for simulating spatial transcriptomics data
Spider: a flexible and unified framework for simulating spatial transcriptomics data Open
Spatial transcriptomics technology provides a valuable view for studying cellular heterogeneity due to its ability to simultaneously acquire gene expression profile and cell location information. However, benchmarking these rapidly accumul…
View article: Characterization of Oral Bacterial and Fungal Microbiome in Recovered COVID-19 Patients
Characterization of Oral Bacterial and Fungal Microbiome in Recovered COVID-19 Patients Open
COVID-19 has emerged as a global pandemic, challenging the world’s economic and health systems. Human oral microbiota comprises the second largest microbial community after the gut microbiota and is closely related to respiratory tract inf…
View article: Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data
Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data Open
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering m…
View article: Profiles of Microbial Community and Antibiotic Resistome in Wild Tick Species
Profiles of Microbial Community and Antibiotic Resistome in Wild Tick Species Open
The emergence of antibiotic-resistant bacteria poses serious threat to the public health around the world. Ticks are obligate hematophagous ectoparasites, surviving via feeding on the blood of various animal hosts.
View article: The Simultaneous Detection of Multiple Antibiotics in Milk and Pork Based on an Antibody Chip Biosensor
The Simultaneous Detection of Multiple Antibiotics in Milk and Pork Based on an Antibody Chip Biosensor Open
In the modern farming industry, the irrational or illegal use of veterinary drugs leads to residues in animal-derived food, which can seriously threaten human health. Efficient detection of low concentrations of drug residues in animal pro…
View article: Secuer: ultrafast, scalable and accurate clustering of single-cell RNA-seq data
Secuer: ultrafast, scalable and accurate clustering of single-cell RNA-seq data Open
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering m…
View article: Exosomes Derived From Dendritic Cells Infected With Toxoplasma gondii Show Antitumoral Activity in a Mouse Model of Colorectal Cancer
Exosomes Derived From Dendritic Cells Infected With Toxoplasma gondii Show Antitumoral Activity in a Mouse Model of Colorectal Cancer Open
Pathogen-based cancer therapies have been widely studied. Parasites, such as Toxoplasma gondii have elicited great interest in cancer therapy. Considering safety in clinical applications, we tried to develop an exosome-based immunomodulato…
View article: Systemic Evaluation of the Effect of Diabetes Mellitus on Breast Cancer in a Mouse Model
Systemic Evaluation of the Effect of Diabetes Mellitus on Breast Cancer in a Mouse Model Open
Breast cancer complicated with diabetes mellitus (DM) is a common disease. To evaluate the effect of preexisting DM on breast cancer progression without drug interference, we used a streptozotocin (STZ)-induced type 2 diabetes mellitus BAL…
View article: Additional file 2 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells
Additional file 2 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells Open
Additional file 2. Table S1: Detailed information for multi-strategic RNA-seq of adipo-osteogenesis of MSCs.
View article: Additional file 4 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells
Additional file 4 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells Open
Additional file 4. Table S3: Significantly differentially expressed circRNA genes in induced BMSCs from RiboMinus/RNase R data.
View article: Additional file 5 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells
Additional file 5 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells Open
Additional file 5. Table S4: Significantly differentially expressed circRNA genes in induced AMSCs from RiboMinus/RNase R data.
View article: Additional file 6 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells
Additional file 6 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells Open
Additional file 6. Table S5: Top ten significantly enriched GO terms for lineage-specific host genes of circRNAs.
View article: Additional file 7 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells
Additional file 7 of Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells Open
Additional file 7. Table S6: Oligonucleotides used in this study.