Shaolong Cao
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View article: Integrated proteomics and single-cell transcriptomics reveal potential therapeutic targets in Wilson’s disease patients
Integrated proteomics and single-cell transcriptomics reveal potential therapeutic targets in Wilson’s disease patients Open
Purpose Wilson’s Disease (WD), an autosomal recessive ATP7B mutations disorder causing copper accumulation, poses diagnostic challenges. This study used proteomics and single-cell transcriptomics to identify WD mechanisms and therapeutic t…
View article: SpaceSequest: A unified pipeline for spatial transcriptomics data analysis
SpaceSequest: A unified pipeline for spatial transcriptomics data analysis Open
Spatial transcriptomics has emerged as one of the most powerful tools for gaining biological insights, enabling researchers to uncover intricate relationships between gene expression patterns and tissue architecture. Recent advances in the…
View article: Comparative snRNAseq study of C9orf72, SOD1, and sALS spinal cord
Comparative snRNAseq study of C9orf72, SOD1, and sALS spinal cord Open
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by the loss of motor neurons, yet the cell-type specific molecular alterations within the spinal cords are not well characterized. In this study, …
View article: Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles
Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles Open
View article: Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles
Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles Open
Traditional gene expression deconvolution methods assess a limited number of cell types, therefore do not capture the full complexity of the tumor microenvironment (TME). Here, we integrate nine deconvolution tools to assess 79 TME cell ty…
View article: Viral-mediated knockdown of Atxn2 attenuates TDP-43 pathology and muscle dysfunction in the PFN1C71G ALS mouse model
Viral-mediated knockdown of Atxn2 attenuates TDP-43 pathology and muscle dysfunction in the PFN1C71G ALS mouse model Open
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron loss and muscle atrophy. Hyperphosphorylated aggregation of the RNA-binding protein, TDP-43, in the motor cortex and spinal…
View article: Integrated transcriptome and metabolome analyses reveals the mechanisms of function loss of Lr29 leaf rust resistance gene at high temperatures in wheat
Integrated transcriptome and metabolome analyses reveals the mechanisms of function loss of Lr29 leaf rust resistance gene at high temperatures in wheat Open
Leaf rust (LR) is one of the most common diseases of wheat. The resistance gene Lr29 provides wide resistance to LR, but loses its function under high temperatures. Despite the importance of this gene, the mechanism of resistance is unclea…
View article: Identification of a Novel Substrate for eEF2K and the AURKA‐SOX8 as the Related Pathway in TNBC
Identification of a Novel Substrate for eEF2K and the AURKA‐SOX8 as the Related Pathway in TNBC Open
Eukaryotic elongation factor 2 kinase (eEF2K) has been considered as a putative target for cancer therapy; however, the underlying mechanisms of eEF2K in triple‐negative breast cancer (TNBC) progression remain to be fully elucidated. In th…
View article: Spatial transcriptomics reveals heterogeneous cell–cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions
Spatial transcriptomics reveals heterogeneous cell–cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions Open
The cuprizone (CPZ) model is widely used for modeling demyelination in multiple sclerosis (MS) and for testing potential remyelination therapies. We integrated single-cell and spatial transcriptomics (ST) to fine map the spatial cellular a…
View article: ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU
ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU Open
The rise of large-scale single-cell RNA-seq data has introduced challenges in data processing due to its slow speed. Leveraging advancements in GPU computing ecosystems, such as CuPy, and building on Scanpy and rapids-singlecell package, w…
View article: <i>ScaleSC</i> : a superfast and scalable single-cell RNA-seq data analysis pipeline powered by GPU
<i>ScaleSC</i> : a superfast and scalable single-cell RNA-seq data analysis pipeline powered by GPU Open
Summary The rise of large-scale single-cell RNA-seq data has introduced challenges in data processing due to its slow speed. Leveraging advancements in Graphics Processing Unit (GPU) computing ecosystems, such as CuPy and Compute Unified D…
View article: Rhabdomyolysis Occurred Again after Changing Chemotherapy Regimens in Ovarian Cancer: A Case Report
Rhabdomyolysis Occurred Again after Changing Chemotherapy Regimens in Ovarian Cancer: A Case Report Open
Introduction: The incidence of chemotherapy-induced rhabdomyolysis is rare, but it is a syndrome that may cause death and should be paid attention to clinically. Case Presentation: Here, we report a case of rhabdomyolysis in an ovarian can…
View article: Editorial: Application of novel statistical and machine-learning methods to high-dimensional clinical cancer and (multi-) omics data volume II
Editorial: Application of novel statistical and machine-learning methods to high-dimensional clinical cancer and (multi-) omics data volume II Open
View article: Subclonal mutation load predicts survival and response to immunotherapy in cancers with low to moderate tumor mutation burden
Subclonal mutation load predicts survival and response to immunotherapy in cancers with low to moderate tumor mutation burden Open
Intra-tumor heterogeneity is characterized by a diverse population of tumor clones and subclones which are important drivers of tumor evolution and therapeutic response. However, accurate subclonal reconstruction at scale remains challengi…
View article: Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction Open
View article: Issue Information – Editorial Board
Issue Information – Editorial Board Open
View article: DOP19 High dimensional profiling of IL-23-responsive cells revealed molecular signatures that predict response to anti-IL-23 therapy in patients with Crohn’s Disease
DOP19 High dimensional profiling of IL-23-responsive cells revealed molecular signatures that predict response to anti-IL-23 therapy in patients with Crohn’s Disease Open
Background The interleukin (IL)-23 signaling plays a crucial role in the pathogenesis of Crohn’s disease (CD). IL-23 activates T-helper (Th) 17 cells, IL-17-secreting CD8 T (Tc)17 cells, gd T cells, nature killer (NK) T cells, and group 3 …
View article: CRISPR–Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames
CRISPR–Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames Open
View article: Clinically impactful metabolic subtypes of pancreatic ductal adenocarcinoma (PDAC)
Clinically impactful metabolic subtypes of pancreatic ductal adenocarcinoma (PDAC) Open
Background: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease characterized by a diverse tumor microenvironment. The heterogeneous cellular composition of PDAC makes it challenging to study molecular features of tumor cells using…
View article: CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames
CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames Open
Processing and Analysis code for generating manuscript figures
View article: <i>TP53</i> gain-of-function mutation modulates the immunosuppressive microenvironment in non-HPV-associated oral squamous cell carcinoma
<i>TP53</i> gain-of-function mutation modulates the immunosuppressive microenvironment in non-HPV-associated oral squamous cell carcinoma Open
Background TP53 , the most mutated gene in solid cancers, has a profound impact on most hallmarks of cancer. Somatic TP53 mutations occur in high frequencies in head and neck cancers, including oral squamous cell carcinoma (OSCC). Our stud…
View article: scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing
scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing Open
Background Single-cell RNA sequencing is a state-of-the-art technology to understand gene expression in complex tissues. With the growing amount of data being generated, the standardization and automation of data analysis are critical to g…
View article: Author Correction: The evolutionary history of 2,658 cancers
Author Correction: The evolutionary history of 2,658 cancers Open
View article: Additional file 2 of scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing
Additional file 2 of scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing Open
Additional file 2: Supplementary Table S2. An example of NEBULA differential expression analysis results. FDR: False discovery rate. The NEBULA-HL method was used.
View article: Additional file 3 of scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing
Additional file 3 of scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing Open
Additional file 3: Supplementary Table S3. Detailed comparison of multiple single-cell RNA-seq data visualization software.
View article: Additional file 1 of scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing
Additional file 1 of scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing Open
Additional file 1: Supplementary Table S1. Detailed comparison of multiple single-cell RNA-seq data processing workflows.
View article: Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig Open
View article: Author Correction: Inferring structural variant cancer cell fraction
Author Correction: Inferring structural variant cancer cell fraction Open
View article: The origin of bladder cancer from mucosal field effects
The origin of bladder cancer from mucosal field effects Open
[This corrects the article DOI: 10.1016/j.isci.2022.104551.].
View article: Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression Open