Michael Q. Zhang
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View article: Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture Open
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
View article: Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture Open
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
View article: Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture Open
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
View article: Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture Open
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
View article: Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture Open
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
View article: Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture Open
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
View article: Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture Open
Supplementary Figure from Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
View article: Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation
Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation Open
View article: HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells
HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells Open
Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) techniques hold great value in evaluating the heterogeneity and spatial characteristics of hematopoietic cells within tissues. These two techniques are highly compleme…
View article: Single‐cell multi‐omics deciphers hepatocyte dedifferentiation and illuminates maintenance strategies
Single‐cell multi‐omics deciphers hepatocyte dedifferentiation and illuminates maintenance strategies Open
Due to the similarity to human hepatocytes, porcine hepatocytes play an important role in hepatic research and drug evaluation. However, once hepatocytes were cultured in vitro, it was often prone to dedifferentiate, resulting in the loss …
View article: Bridging the Dimensional Gap from Planar Spatial Transcriptomics to 3D Cell Atlases
Bridging the Dimensional Gap from Planar Spatial Transcriptomics to 3D Cell Atlases Open
Spatial transcriptomics (ST) has revolutionized our understanding of tissue architecture, yet constructing comprehensive three-dimensional (3D) cell atlases remains challenging due to technical limitations and high cost. Current approaches…
View article: Sequential-GAM constructs the single-cell geometric 3D genome structure
Sequential-GAM constructs the single-cell geometric 3D genome structure Open
Three-dimensional structure of the chromatin is crucial for cell identity and gene regulation. However, how genome-wide hierarchical geometric structure is organized in single cells remains elusive. Here we developed Sequential-GAM (Sequen…
View article: Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer
Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer Open
KRASG12C inhibitors (adagrasib and sotorasib) have shown clinical promise in targeting KRASG12C-mutated lung cancers; however, most patients eventually develop resistance. In lung patients with adenocarcinoma with KRA…
View article: ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features Open
The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, and gradient boosting to pr…
View article: A Survey on Deep Learning in Edge-Cloud Collaboration: Model Partitioning, Privacy Preservation, and Prospects
A Survey on Deep Learning in Edge-Cloud Collaboration: Model Partitioning, Privacy Preservation, and Prospects Open
View article: SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and technologies
SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and technologies Open
Properly integrating spatially resolved transcriptomics (SRT) generated from different batches into a unified gene-spatial coordinate system could enable the construction of a comprehensive spatial transcriptome atlas. Here, we propose SPI…
View article: Adeno-to-squamous transition drives resistance to KRAS inhibition in<i>LKB1</i>mutant lung cancer
Adeno-to-squamous transition drives resistance to KRAS inhibition in<i>LKB1</i>mutant lung cancer Open
Summary KRAS G12C inhibitors including adagrasib and sortorasib have shown clinical promise in targeting KRAS G12C -mutated lung cancers, however, most patients eventually develop drug resistance. In lung adenocarcinoma patients with co-oc…
View article: Chromatin-associated RNA Dictates the ecDNA Interactome in the Nucleus
Chromatin-associated RNA Dictates the ecDNA Interactome in the Nucleus Open
Extrachromosomal DNA (ecDNA) promotes cancer by driving copy number heterogeneity and amplifying oncogenes along with functional enhancers. More recent studies suggest two additional mechanisms for further enhancing their oncogenic potenti…
View article: iSMOD: an integrative browser for image-based single-cell multi-omics data
iSMOD: an integrative browser for image-based single-cell multi-omics data Open
Genomic and transcriptomic image data, represented by DNA and RNA fluorescence in situ hybridization (FISH), respectively, together with proteomic data, particularly that related to nuclear proteins, can help elucidate gene regulation in r…
View article: Aging-induced pseudouridine synthase 10 impairs hematopoietic stem cells
Aging-induced pseudouridine synthase 10 impairs hematopoietic stem cells Open
Aged hematopoietic stem cells (HSC) exhibit compromised reconstitution capacity and differentiation-bias towards myeloid lineage, however, the molecular mechanism behind it remains not fully understood. In this study, we observed that the …
View article: Data from Integrative Genomic Analysis of Gemcitabine Resistance in Pancreatic Cancer by Patient-derived Xenograft Models
Data from Integrative Genomic Analysis of Gemcitabine Resistance in Pancreatic Cancer by Patient-derived Xenograft Models Open
Purpose:Gemcitabine is most commonly used for pancreatic cancer. However, the molecular features and mechanisms of the frequently occurring resistance remain unclear. This work aims at exploring the molecular features of gemcitabine resist…
View article: Data from Integrative Genomic Analysis of Gemcitabine Resistance in Pancreatic Cancer by Patient-derived Xenograft Models
Data from Integrative Genomic Analysis of Gemcitabine Resistance in Pancreatic Cancer by Patient-derived Xenograft Models Open
Purpose:Gemcitabine is most commonly used for pancreatic cancer. However, the molecular features and mechanisms of the frequently occurring resistance remain unclear. This work aims at exploring the molecular features of gemcitabine resist…
View article: Publisher Correction: SODB facilitates comprehensive exploration of spatial omics data
Publisher Correction: SODB facilitates comprehensive exploration of spatial omics data Open
View article: Development and Experimental Validation of a Novel Prognostic Signature for Gastric Cancer
Development and Experimental Validation of a Novel Prognostic Signature for Gastric Cancer Open
Background: Gastric cancer is a malignant tumor with high morbidity and mortality. Therefore, the accurate recognition of prognostic molecular markers is the key to improving treatment efficacy and prognosis. Methods: In this study, we dev…
View article: SOTIP is a versatile method for microenvironment modeling with spatial omics data
SOTIP is a versatile method for microenvironment modeling with spatial omics data Open
View article: Accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features
Accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features Open
The three-dimensional (3D) genome organization influences diverse nuclear processes. Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and Hi-C are powerful methods to study the 3D genome organization. However, ChIA-PE…
View article: Profiling and characterization of constitutive chromatin-enriched RNAs
Profiling and characterization of constitutive chromatin-enriched RNAs Open
View article: Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture Open
Prostate cancer is one of the most heritable human cancers. Genome-wide association studies have identified at least 185 prostate cancer germline risk alleles, most noncoding. We used integrative three-dimensional (3D) spatial genomics to …
View article: CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming
CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming Open
CTCF mediates chromatin insulation and long-distance enhancer-promoter (EP) interactions; however, little is known about how these regulatory functions are partitioned among target genes in key biological processes. Here, we show that Ctcf…
View article: Avian influenza viruses suppress innate immunity by inducing trans-transcriptional readthrough via SSU72
Avian influenza viruses suppress innate immunity by inducing trans-transcriptional readthrough via SSU72 Open
Innate immunity plays critical antiviral roles. The highly virulent avian influenza viruses (AIVs) H5N1, H7N9, and H5N6 can better escape host innate immune responses than the less virulent seasonal H1N1 virus. Here, we report a mechanism …