A5101475128- Single-cell and spatial transcriptomics
- COVID-19 Clinical Research Studies
- Cancer Genomics and Diagnostics
- SARS-CoV-2 and COVID-19 Research
- Gene expression and cancer classification
- Cancer Immunotherapy and Biomarkers
- Cytomegalovirus and herpesvirus research
- Immunotherapy and Immune Responses
- Cell Image Analysis Techniques
- Ferroptosis and cancer prognosis
- Immune responses and vaccinations
- Nanoplatforms for cancer theranostics
- Immune cells in cancer
- Angiogenesis and VEGF in Cancer
- Animal Virus Infections Studies
- Gut microbiota and health
- vaccines and immunoinformatics approaches
- Cancer Cells and Metastasis
- Long-Term Effects of COVID-19
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Advanced Fluorescence Microscopy Techniques
- Dermatological and COVID-19 studies
- Image Processing Techniques and Applications
- Advanced Surface Polishing Techniques
- Immune Response and Inflammation
Bioinformatics Institute
2023-2025
Agency for Science, Technology and Research
2016-2025
Singapore Immunology Network
2016-2024
Institute of Molecular and Cell Biology
2021-2023
A*STAR Graduate Academy
2022
Technische Universität Dresden
2020
Single-cell mass cytometry significantly increases the dimensionality of analysis as compared to fluorescence flow cytometry, providing unprecedented resolution cellular diversity in tissues. However, and interpretation these high-dimensional data poses a significant technical challenge. Here, we present cytofkit, new Bioconductor package, which integrates both state-of-the-art bioinformatics methods in-house novel algorithms offer comprehensive toolset for analysis. Cytofkit provides...
Spatially resolved transcriptomics involves a set of emerging technologies that enable the transcriptomic profiling tissues with physical location expressions. Although variety methods have been developed for data integration, most them are single-cell RNA-seq datasets without consideration spatial information. Thus, can integrate from multiple tissue slides, possibly individuals, needed. Here, we present PRECAST, integration method complex batch effects and/or biological between slides....
Spatial transcriptomics has been emerging as a powerful technique for resolving gene expression profiles while retaining tissue spatial information. These spatially resolved make it feasible to examine the complex multicellular systems of different microenvironments. To answer scientific questions with and expand our understanding how cell types states are regulated by microenvironment, first step is identify clusters integrating available Here, we introduce SC-MEB, an empirical Bayes...
The World Health Organization has defined long COVID-19 (LC) as a condition that occurs in individuals with history of SARS-CoV-2 infection who exhibit persistent symptoms after its acute phase last for at least two months and cannot be explained by an alternative diagnosis. Since we had previously reported residual viral antigens tissues convalescent patients, aimed to assess the presence such COVID tissues. Here, established virus appendix, skin, breast 2 patients exhibited LC 163 426 days...
Objectives Cholangiocarcinoma (CCA) is a heterogeneous malignancy with high mortality and dismal prognosis, an urgent clinical need for new therapies. Knowledge of the CCA epigenome largely limited to aberrant DNA methylation. Dysregulation enhancer activities has been identified affect carcinogenesis leveraged therapies but uninvestigated in CCA. Our aim identify potential therapeutic targets different subtypes through profiling. Design Integrative multiomics activity profiling diverse was...
Personalized cancer vaccines represent a transformative approach in immunotherapy, leveraging tumor-specific antigens, such as neoantigens, to stimulate durable and targeted immune responses. However, identifying immunogenic neoantigen epitopes through conventional approaches - relying on silico predictions followed by experimental validation remains significant challenge due limitations of computational tools scattering experiment data. To address these challenges, we introduce...
Introduction: Identification of immune cell types within bodily fluids, including blood samples, plays a critical role in early detection and disease monitoring public health initiatives. Although protein biomarkers present samples are useful for clinical assessment, the process sample preparation immunostaining is time-consuming costly. In this study, we an efficient rapid procedure affixing cells on glass slide downstream histological staining. Furthermore, using CD3+ T as paradigm, our...
Abstract Introduction: Characterizing the immune contexture is key to understanding tumor microenvironment, developing biomarkers, and guiding therapeutic strategies. In our previous work on colorectal cancer (CRC), we used a pathologist-guided approach annotate/count eosinophils lymphocytes. Their abundance spatial relationships with cells revealed prognostic significance. While clinically valuable, identifying this demands significant pathologist effort. Advancements in AI, particularly...
Introduction Immune checkpoint blockade (ICB) is a systemic therapeutic option for advanced hepatocellular carcinoma (HCC). However, low patient response rates necessitate the development of robust predictive biomarkers that identify individuals who will benefit from ICB. A 4-gene inflammatory signature, comprising CD8 , PD-L1 LAG-3 and STAT1 was recently shown to be associated with better overall ICB in various cancer types. Here, we examined whether tissue protein expression CD8, PD-L1,...
Clinically important broadly reactive B cells evolve during multiple infections, with re-activated after secondary infection differing from activated a primary infection. Here we studied CD27highCD38high plasmablasts patients or dengue virus Three transcriptionally and functionally distinct clusters were identified. The largest cluster 0/1 was plasma cell-related, coding for serotype cross-reactive antibodies of the IgG1 isotype, consistent memory cell activation an extrafollicular response....
Combination therapy with radioembolization (yttrium-90)-resin microspheres) followed by nivolumab has shown a promising response rate of 30.6% in Phase II trial (CA209-678) for advanced hepatocellular carcinoma (HCC); however, the mechanisms and relevant biomarkers remain unknown. By collecting both pretreatment on-treatment samples, we performed multimodal profiling tissue blood samples investigated molecular changes associated favorable responses 33 patients from trial. We found that...
Abstract Porosity, pore distribution, mean grain size, and size distribution determine the mechanical physical properties of ceramics. The quantitative structural analysis is therefore essential for characterization sintered materials. A semi-automated requires a preceding image segmentation step in which all pixels are divided into respective objects to be examined so that they can clearly assigned microstructural constituent. present work analyzes watershed transformation, IsoData, WEKA...
Abstract Spatially resolved transcriptomics involves a set of emerging technologies that enable the transcriptomic profiling tissues with physical location expressions. Although variety methods have been developed for data integration, most them are single-cell RNA-seq datasets without consideration spatial information. Thus, can integrate from multiple tissue slides, possibly individuals, needed. Here, we present PRECAST, integration method complex batch effects and/or biological between...
Abstract The World Health Organization has defined long COVID-19 (LC) as a condition where patients exhibit persistent symptoms over time after its acute phase, which cannot be explained by alternative diagnosis. Since we have previously reported residual viral antigens in tissues of convalescent patients, now aim to assess the presence such post-convalescent tissues. Here, established virus within appendix and breast tissue 2 who exhibited LC symptoms, 175 462 days upon positive diagnosis,...
Abstract The World Health Organization has defined long COVID-19 (LC) as a condition where patients exhibit persistent symptoms over time after its acute phase, which cannot be explained by alternative diagnosis. Since we have previously reported residual viral antigens in tissues of convalescent patients, now aim to assess the presence such post-convalescent tissues. Here, established virus within appendix and breast tissue 2 who exhibited LC symptoms, 175 462 days upon positive diagnosis,...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected half a billion people, including vulnerable populations such as cancer patients. While increasing evidence supports the persistence of SARS-CoV-2 months after negative nasopharyngeal swab test, effects on long-term immune memory and treatment are unclear. In this report, we examined post-COVID-19 tissue-localized responses in hepatocellular carcinoma (HCC) patient colorectal (CRC) patient. Using spatial...
Abstract Introduction The increased use of tissue-based multiplex immunohistochemistry (mIHC) in cancer research has significantly enhanced the generation spatial hyper-plex images, crucial for understanding complex tumor-immune microenvironments. This advancement led to a growing demand data analysis tools that enable quick and insightful evaluation. While existing software like Steinbock SPIAT offer foundational support, effectively managing high-dimensional voluminous cellular derive...
Abstract Objectives: Cholangiocarcinoma (CCA) is a heterogeneous malignancy with high mortality and dismal prognosis, an urgent clinical need for new therapies. Knowledge of the CCA epigenome largely limited to aberrant DNA methylation. Dysregulation enhancer activities has been identified affect carcinogenesis leveraged therapies but uninvestigated in CCA. Our aim identify potential therapeutic targets different subtypes through profiling. Design: Integrative multi-omics activity profiling...
<h3>Background</h3> Beyond conventional short-read Next-Generation Sequencing (NGS), long-read sequencing technology, like Oxford Nanopore Technologies (ONT),<sup>1</sup> enhance coverage and resolution of genomics fragments, crucial for detecting T Cell Receptors (TCRs) known their variability from VDJ recombination.<sup>2</sup> Short-read NGS sequences 3' or 5' end the cDNA template, sequencing, adapters/barcodes near constant regions hinder capturing variable regions. Long-read captures...
<h3>Background</h3> Robust deep learning (DL) models predicting cell-level biomarker expression on hematoxylin and eosin (H&E) images can enable cost-effective high-throughput evaluation for immune monitoring immunotherapy stratification.<sup>1</sup> Model generalizability is essential to real-world implementation but complicated by H&E stain variation.<sup>2 3</sup> Although scanning systems are known cause variation,<sup>2 their impact H&E-based DL prediction model performance...