Patrick Tan
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View article: Microproteins Simba1 and Simba2 activate Wingless signaling during the reactivation of neural stem cells in Drosophila
Microproteins Simba1 and Simba2 activate Wingless signaling during the reactivation of neural stem cells in Drosophila Open
The ability of neural stem cells (NSCs) to switch between quiescent and proliferative states is fundamental for adult neurogenesis and regeneration. Microproteins or short open reading frame (sORF)-encoded peptides (SEPs), are highly abund…
View article: Gene-Family Encoding Boosts Domain-Adapted Single-Cell Language Models
Gene-Family Encoding Boosts Domain-Adapted Single-Cell Language Models Open
Transformer-based single-cell foundation models often rely on ranked-gene (RG) sequences where genes, ranked by expression, are often not functionally related, weakening next-token learning and the structure of learned embeddings. Here, we…
View article: Case Report: Application of ex-vivo drug sensitivity testing to identify personalized treatment options for an adolescent with diffuse midline glioma
Case Report: Application of ex-vivo drug sensitivity testing to identify personalized treatment options for an adolescent with diffuse midline glioma Open
Diffuse midline glioma (DMG) is a pediatric brain cancer that has a dismal prognosis with limited treatment options. We present the treatment course and outcome of an adolescent male diagnosed with a thalamic DMG carrying a histone H3.3 K2…
View article: Glioportal: a comprehensive transcriptomic resource unveiling ligand-mediated mesenchymal transition in glioblastoma
Glioportal: a comprehensive transcriptomic resource unveiling ligand-mediated mesenchymal transition in glioblastoma Open
Background Multi-omics profiling of glioblastoma (GBM) has unraveled two aspects fundamental to its aggressiveness and lethality that is molecular heterogeneity inherent to the tumor and cellular plasticity modulated by the microenvironmen…
View article: Supplementary Figure 4 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Figure 4 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Figure 4. Clustering parameters and immune cell subtypes across clusters.
View article: Supplementary Table 2 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Table 2 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Table 2. Gene signatures, target genes, and whole transcriptome derivatives.
View article: Supplementary Figure 1 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Figure 1 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Figure 1. Quality control parameters for WES data utilized in the study.
View article: Supplementary Figure 2 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Figure 2 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Figure 2. Niche remodelling and prognostic significance of SERPINE1.
View article: Supplementary Table 6 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Table 6 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Table 6. A5 in mouse models.
View article: Supplementary Table 1 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Table 1 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Table 1. Cohort and sample overview.
View article: Supplementary Table 4 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Table 4 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Table 4. Comparisons of histological features between SC1 and SC2.
View article: Supplementary Table 5 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Table 5 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Table 5. T-test comparisons between DSP ROIs and top 20 (10 up and 10 down) discriminatory genes.
View article: Supplementary Figure 5 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Figure 5 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Figure 5. Overall survival KM curve of patients stratified by SC2 signature (Q1 vs Q4) of peritoneal samples only.
View article: Supplementary Table 3 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Table 3 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Table 3. Spatial QC metrics and cell type markers.
View article: Supplementary Methods 1 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Methods 1 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Methods 1. Supplementary Methods, DNA extraction and whole exome sequencing, Mutation calling and mutational signatures, Whole transcriptome sequencing, Spatial profiling, Methods of A5 Discovery and Validation, Other statist…
View article: Supplementary Figure 6 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Figure 6 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Figure 6. Safety profile of intravenous injection of A5.
View article: Supplementary Figure 3 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Supplementary Figure 3 from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Supplementary Figure 3. Cell type retrieval from COMET Lunaphore.
View article: Data from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Data from Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Purpose:Peritoneal metastases (PM) in colorectal cancer portend a poor prognosis. We sought to elucidate molecular features differentiating primary tumors (PT) from PMs and actionable targets facilitating transcoelomic dissemination and pr…
View article: OCCULT MOSAICISM OF KARYOTYPING IN 45,X / 46,XY DSD
OCCULT MOSAICISM OF KARYOTYPING IN 45,X / 46,XY DSD Open
INTRODUCTIONDisorder of sex development (DSD) with 45,X/46,XY mosaicism is a rare disorder. The prevalence is estimated to be less than 1:20,000. CASEA term baby, born with a good Apgar score at Hospital Sultan Abdul Halim. Genital examina…
View article: Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis
Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis Open
Purpose: Peritoneal metastases (PM) in colorectal cancer portend a poor prognosis. We sought to elucidate molecular features differentiating primary tumors (PT) from PMs and actionable targets facilitating transcoelomic dissemination and p…
View article: Single-cell Pharmacogenomic Landscapes of Epigenetic Drug Resistance Revealed by Gastric Cancer Perturb-seq
Single-cell Pharmacogenomic Landscapes of Epigenetic Drug Resistance Revealed by Gastric Cancer Perturb-seq Open
Gene expression signatures ("molecular phenotypes") are extensively utilized in cancer research. To study how gastric cancer (GC) molecular phenotypes are shaped by cell-intrinsic genetic alterations interacting with cell-extrinsic therape…
View article: A Computational Framework for Analysis of cfDNA Fragmentation Profiles
A Computational Framework for Analysis of cfDNA Fragmentation Profiles Open
Circulating cell-free DNA (cfDNA) has emerged as a promising non-invasive medium for studying tumor molecular profiles. Non-random fragmentation patterns in plasma cfDNA, particularly around nucleosome-depleted regions (NDRs) near transcri…
View article: Supplementary Figure 1-9 from Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution
Supplementary Figure 1-9 from Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution Open
(1) Supplementary Figure 1 shows morphologies of different ROI categories and their representative genes, pathways and similarities with paired scRNA-seq data. (2) Supplementary Figure 2 shows validation of findings from the discovery GeoM…
View article: Supplementary Table 1-8 from Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution
Supplementary Table 1-8 from Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution Open
(1) Supplementary Table 1 shows GeoMx DSP ROI and scRNA-seq characteristics of samples profiled; (2) Supplementary Table 2 shows clinical characteristics of GeoMx DSP ROI and scRNA-seq samples profiled; (3) Supplementary Table 3A shows con…
View article: Data from Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution
Data from Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution Open
Gastric cancer is a major cause of global cancer mortality. To explore geospatial interactions in gastric tumors, we integrated 2,138 spatial transcriptomic regions of interest with 152,423 single-cell expression profiles across 226 cancer…
View article: Determinants of diagnostic yield in a multi-ethnic Asian inherited retinal disease cohort
Determinants of diagnostic yield in a multi-ethnic Asian inherited retinal disease cohort Open
As the discovery of new genes causing inherited retinal disease (IRD) has plateaued, we look to other factors which could be used to maximize diagnostic yield. We analyzed whole-exome sequencing (WES) data from 506 IRD probands, focusing o…
View article: National Scale Genomic Engine for Precision Medicine: Singapore PRECISE-SG100K Experience
National Scale Genomic Engine for Precision Medicine: Singapore PRECISE-SG100K Experience Open
Precision medicine (PM) research in recent years has witnessed a remarkable surge in large-scale population genomics programs. In 2017, Singapore initiated the National Precision Medicine (NPM) program, a three-phase national strategy driv…
View article: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines Open
The human genome contains instructions to transcribe more than 200,000 RNAs. However, many RNA transcripts are generated from the same gene, resulting in alternative isoforms that are highly similar and that remain difficult to quantify. T…
View article: The expanding global genomics landscape: Converging priorities from national genomics programs
The expanding global genomics landscape: Converging priorities from national genomics programs Open
The global landscape of health genomics is expanding rapidly, with an increasing number of national and international initiatives, many of which are targeted toward accelerating the clinical implementation of genomic technologies and servi…