A5079973466- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Pluripotent Stem Cells Research
- Glioma Diagnosis and Treatment
- Chromosomal and Genetic Variations
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Hedgehog Signaling Pathway Studies
- Cancer, Hypoxia, and Metabolism
- Single-cell and spatial transcriptomics
- Evolution and Genetic Dynamics
- Medical Imaging and Pathology Studies
- Cancer Immunotherapy and Biomarkers
- Genomics and Rare Diseases
- MicroRNA in disease regulation
- Genetic factors in colorectal cancer
- Genetics and Neurodevelopmental Disorders
Genome Institute of Singapore
2016-2025
Agency for Science, Technology and Research
2017-2025
National Cancer Centre Singapore
2017-2025
National University of Singapore
2017-2025
University of Houston
2017
Max Planck Institute for Molecular Genetics
2011-2015
Carnegie Mellon University
2012
Stanford University
2009
University of Sheffield
2007
Charité - Universitätsmedizin Berlin
2007
X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, large number families mapping to remained unresolved suggesting that more XLID or loci are yet be Here, we investigated 405 with XLID. We employed massively parallel sequencing all exons index males. The majority these males were previously tested negative for copy variations mutations subset known by...
Abstract RNA modifications such as m6A methylation form an additional layer of complexity in the transcriptome. Nanopore direct sequencing can capture this information raw current signal for each molecule, enabling detection using supervised machine learning. However, experimental approaches provide only site-level training data, whereas modification status single molecule is missing. Here we present m6Anet, a neural-network-based method that leverages multiple instance learning framework to...
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, consortium generated over 427 million sequences from complementary DNA direct RNA datasets, encompassing human, mouse manatee species. Developers utilized these data address challenges in transcript isoform detection, quantification de novo detection. study revealed that...
Embryonic stem cell (ESC) pluripotency is governed by a gene regulatory network centered on the transcription factors Oct4 and Nanog. To date, robust self-renewing ESC states have only been obtained through chemical inhibition of signaling pathways or enforced transgene expression. Here, we show that ESCs with reduced expression resulting from heterozygosity also exhibit stabilized pluripotent state. Despite having expression, Oct4+/− increased genome-wide binding Oct4, particularly at...
Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able respire VC, Dehalococcoides sp. strains VS BAV1. Notably, respective VC reductase encoding genes, vcrAB bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes acquired horizontally independently by mechanisms. A comparative analysis included two...
B lymphocytes are important players in immune responses to cancer. However, their composition and function head neck squamous cell carcinoma (HNSCC) has not been well described. Here, we analyzed subsets HNSCC (n = 38), non-cancerous mucosa 14) peripheral blood from patients 38) healthy controls 20) by flow cytometry. Intratumoral cells contained high percentages of activated (CD86+), antigen-presenting (CD86+/CD21−) memory (IgD−/CD27+). T follicular helper (CD4+/CXCR5+/CD45RA−/CCR7−) as key...
Abstract Endogenous retroviruses (ERVs) contribute to ∼10 percent of the mouse genome. They are often silenced in differentiated somatic cells but differentially expressed at various embryonic developmental stages. A minority stem (ESCs), like 2-cell cleavage embryos, highly express ERV MERVL. However, role ERVs and mechanism their activation these still poorly understood. In this study, we investigated regulation function stage-specific ERVs, with a particular focus on totipotency marker...
Abstract The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study short read sequencing. To systematically evaluate the ability transcriptome at a resolution individual we profiled 5 cell lines cDNA sequencing Nanopore long direct RNA, amplification-free cDNA, PCR-cDNA protocols showed high level consistency, RNA being most similar. While reads generated comparable expression...
The fact that Parkinson's disease (PD) can arise from numerous genetic mutations suggests a unifying molecular pathology underlying the various backgrounds. To address this hypothesis, we took an integrated approach utilizing in vitro modeling and comprehensive transcriptome profiling to advance our understanding of PD progression concordant downstream signaling pathways across divergent predispositions. model vitro, generated neurons harboring disease-causing patient-specific, induced...
Abstract Background Deregulated gene expression is a hallmark of cancer; however, most studies to date have analyzed short-read RNA sequencing data with inherent limitations. Here, we combine PacBio long-read isoform (Iso-Seq) and Illumina paired-end comprehensively survey the transcriptome gastric cancer (GC), leading cause global mortality. Results We performed full-length analysis across 10 GC cell lines covering four major molecular subtypes (chromosomal unstable, Epstein-Barr positive,...
In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of with their full-length isoform structure. However, due to higher error rates, fusion finding algorithms designed short reads do not work. Here we present JAFFAL, identify from long-read sequencing. We validate JAFFAL using simulations, cell lines, patient data Nanopore PacBio. apply single-cell find spanning three genes demonstrating transcripts detected...
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. consortium generated over 427 million sequences from cDNA and direct RNA datasets, encompassing human, mouse, manatee species, using different protocols sequencing platforms. These data were utilized by developers address challenges in transcript isoform detection quantification, as well de novo identification....