A5052123449- Single-cell and spatial transcriptomics
- Extracellular vesicles in disease
- Plant Molecular Biology Research
- Light effects on plants
- Photosynthetic Processes and Mechanisms
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Neuroinflammation and Neurodegeneration Mechanisms
- Diabetes and associated disorders
- Immune cells in cancer
- Gene Regulatory Network Analysis
- Pancreatic function and diabetes
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Vibrio bacteria research studies
- Colorectal Cancer Surgical Treatments
- Genetic factors in colorectal cancer
- Systemic Lupus Erythematosus Research
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Electrochemical Analysis and Applications
- Aquaculture disease management and microbiota
- Machine Learning in Materials Science
- Colorectal Cancer Treatments and Studies
- Circadian rhythm and melatonin
Genome Institute of Singapore
2020-2024
Agency for Science, Technology and Research
2020-2024
Institute of Chemistry, Academia Sinica
2016-2020
National Yang Ming Chiao Tung University
2020
Academia Sinica
2020
Atma Jaya Catholic University of Indonesia
2012
Abstract The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk transcriptomics. underlying epithelial cell diversity remains unclear. We analyzed 373,058 single-cell transcriptomes from 63 patients, focusing 49,155 cells. identified a pervasive genetic and transcriptomic dichotomy malignant cells, distinct gene expression, DNA copy number regulatory network. recapitulated these subtypes in 3,614 patients. two intrinsic subtypes, iCMS2 iCMS3, refine CMS....
Abstract A double-negative feedback loop formed by the morning genes CIRCADIAN CLOCK ASSOCIATED1 ( CCA1 )/ LATE ELONGATED HYPOCOTYL LHY ) and evening gene TIMING OF CAB EXPRESSION1 TOC1 contributes to regulation of circadian clock in Arabidopsis . 24-h cycle starts with peak expression at dawn. Although is targeted multiple transcriptional repressors, including PSEUDO-RESPONSE REGULATOR9 (PRR9), PRR7, PRR5 HIKING EXPEDITION (CHE), activators remain elusive. Here we use mathematical modelling...
Feature selection (marker gene selection) is widely believed to improve clustering accuracy, and thus a key component of single cell pipelines. Existing feature methods perform inconsistently across datasets, occasionally even resulting in poorer accuracy than without selection. Moreover, existing ignore information contained gene-gene correlations. Here, we introduce DUBStepR (Determining the Underlying Basis using Stepwise Regression), algorithm that leverages correlations with novel...
Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting
Quantum chemistry calculations have been very useful in providing many key detailed properties and enhancing our understanding of molecular systems. However, such calculation, especially with ab initio models, can be time-consuming. For example, the prediction charge-transfer properties, it is often necessary to work an ensemble different thermally populated structures. A possible alternative use a machine-learning based approach. In this work, we show that general electronic coupling,...
In higher plants (e.g., Arabidopsis thaliana), the core structure of circadian clock is mostly governed by a repression process with very few direct activators. With series simplified models, we studied underlying mechanism and found that consists type-2 incoherent feed-forward loops (IFFLs), one them creating pulse-like expression in PRR9/7. The double-negative feedback loop between CCA1/LHY PRR5/TOC1 generates bistable, hysteretic behavior clock. We IFFL involving PRR9/7 breaks bistability...
Vibrio cholerae is the causative organism of waterborne disease, cholera. V. has caused many epidemics and pandemics cholera for years. In this study, recovered from edible ice were investigated their genetic diversity using Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR Extragenic Palindromic (REP) PCR. Isolation was done selective medium presumptive isolates confirmed through biochemical serological assays. Seventy-five samples collected different locations Jakarta....
Abstract The transcriptomic diversity of cell types in the human body can be analysed unprecedented detail using single (SC) technologies. Unsupervised clustering SC transcriptomes, which is default technique for defining types, prone to group cells by technical, rather than biological, variation. Compared de-novo (unsupervised) clustering, we demonstrate multiple benchmarks that supervised uses reference transcriptomes as a guide, robust batch effects and data quality artifacts. Here,...
Feature selection (marker gene selection) is widely believed to improve clustering accuracy, and thus a key component of single cell pipelines. However, we found that the performance existing feature methods was inconsistent across benchmark datasets, occasionally even worse than without selection. Moreover, ignored information contained in gene-gene correlations. We therefore developed DUBStepR ( D etermining U nderlying B asis using Step wise R egression), algorithm leverages correlations...
e15603 Background: Our recent single-cell transcriptomic data indicate that colorectal cancer (CRC) can be classified into two major epithelial subtypes: iCMS2 and iCMS31. iCMS3 CRC includes MSI-H one-third of MSS tumors. The latter are enriched in KRAS, PIK3CA, BRAF mutations. subtype often exhibits chromosome instability, including copy number changes specific regions. These genomic alterations may associated with distinct histomorphological features, which assessed using hematoxylin eosin...
The circadian clock is a complex system that plays many important roles in most organisms. Previously, mathematical models have been used to sharpen our understanding of the Arabidopsis clock, which brought light each transcriptional and post-translational regulations. However, presence both regulations, instead either transcription or post-translation, raised curiosity whether combination these two regulations for clock's system. In this study, we built series simplified oscillators with...
Feature selection (marker gene selection) is widely believed to improve clustering accuracy, and thus a key component of single cell pipelines. However, we found that the performance existing feature methods was inconsistent across benchmark datasets, occasionally even worse than without selection. Moreover, ignored information contained in gene-gene correlations. We therefore developed DUBStepR (Determining Underlying Basis using Stepwise Regression), algorithm leverages correlations with...
Motivation The transcriptomic diversity of the hundreds cell types in human body can be analysed unprecedented detail using single (SC) technologies. Though clustering cellular transcriptomes is default technique for defining and subtypes, strongly influenced by technical variation. In fact, prevalent unsupervised algorithms cluster cells technical, rather than biological, Results Compared to de novo (unsupervised) methods, we demonstrate multiple benchmarks that supervised clustering, which...
Abstract The circadian clock is a complex system that plays many important roles in most organisms. Previously, mathematical models have been used to sharpen our understanding of the Arabidopsis clock. However, these are mostly dependent on transcriptional regulation, and importance post-translational regulation still rarely discussed from theoretical aspects. In this study, we built series simplified oscillators with different regulations study (specifically, 26S proteasome degradation)...