Cheng Yong Tham
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View article: Publisher Correction: NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns
Publisher Correction: NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns Open
View article: Sub-consensus haploid variant calling in Long-read sequencing technology
Sub-consensus haploid variant calling in Long-read sequencing technology Open
Background Next-generation sequencing (NGS) has become crucial in epidemiology, particularly for tracking viral evolution during outbreaks. While Oxford Nanopore Technologies (ONT) sequencing has gained popularity due to its long-read capa…
View article: Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome
Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome Open
Abundant cellular transcripts occupy most of the sequencing reads in the transcriptome, making it challenging to assay for low-abundant transcripts. Here, we utilize the adaptive sampling function of Oxford Nanopore sequencing to selective…
View article: Correspondence on NanoVar’s performance outlined by Jiang T. et al. in “Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation”
Correspondence on NanoVar’s performance outlined by Jiang T. et al. in “Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation” Open
View article: Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome
Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome Open
Abundant cellular transcripts occupy most of the sequencing reads in the transcriptome, making it challenging to assay for low abundant transcripts. Here, we utilize the adaptive sampling function of Oxford Nanopore sequencing to selective…
View article: High-throughput telomere length measurement at nucleotide resolution using the PacBio high fidelity sequencing platform
High-throughput telomere length measurement at nucleotide resolution using the PacBio high fidelity sequencing platform Open
Telomeres are specialized nucleoprotein structures at the ends of linear chromosomes. The progressive shortening of steady-state telomere length in normal human somatic cells is a promising biomarker for age-associated diseases. However, t…
View article: Simulated data for Correspondence on NanoVar's performance outlined by Jiang T. et al.
Simulated data for Correspondence on NanoVar's performance outlined by Jiang T. et al. Open
Simulated data were generated as described by Jiang et al. 2021 with several modifications due to the encountering of errors. Please refer to https://github.com/cytham/nv_benchmark_jiang/blob/main/commands.md for the commands to replicate …
View article: Simulated data for Correspondence on NanoVar's performance outlined by Jiang T. et al.
Simulated data for Correspondence on NanoVar's performance outlined by Jiang T. et al. Open
Simulated data were generated as described by Jiang et al. 2021 with several modifications due to the encountering of errors. Please refer to https://github.com/cytham/nv_benchmark_jiang/blob/main/commands.md for the commands to replicate …
View article: TIP60 acetylates H2AZ and regulates doxorubicin-induced DNA damage sensitivity through<i>RAD51</i>transcription
TIP60 acetylates H2AZ and regulates doxorubicin-induced DNA damage sensitivity through<i>RAD51</i>transcription Open
TIP60, a lysine acetyltransferase and H2AZ, a histone H2A variant are involved in transcription and DNA repair. Recent studies suggest that H2AZ acetylation is dependent on TIP60. Here, we show that TIP60 acetylates both isoforms of H2AZ i…
View article: Three-dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia
Three-dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia Open
Acute Myeloid Leukemia (AML) is a highly lethal blood cancer arising due to aberrant differentiation of haematopoietic stem cells. Here we obtained 3D genome organization maps by Hi-C in the CD34+ haematopoietic stem cells from three healt…
View article: Pre-built SV genomes
Pre-built SV genomes Open
Data stored here contains the pre-built SV-simulated genomes to be used for neural network model customization for the SV caller NanoVar. Please refer to this tutorial: https://github.com/cytham/nanovar/wiki/Model-training The SV genomes h…
View article: Pre-built SV genomes
Pre-built SV genomes Open
Data stored here contains the pre-built SV-simulated genomes to be used for neural network model customization for the SV caller NanoVar. Please refer to this tutorial: https://github.com/cytham/nanovar/wiki/Model-training The SV genomes h…
View article: NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing
NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing Open
The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are still constrained by their high s…
View article: NanoVar Simulation Datasets
NanoVar Simulation Datasets Open
The data stored here were used for benchmarking long-read structural variant (SV) callers in the publication: Tham, CY., Tirado-Magallanes, R., Goh, Y. et al. NanoVar: accurate characterization of patients’ genomic structural vari…
View article: NanoVar Simulation Datasets
NanoVar Simulation Datasets Open
The data stored here were used for benchmarking long-read structural variant (SV) callers in the publication: Tham, CY., Tirado-Magallanes, R., Goh, Y. et al. NanoVar: accurate characterization of patients’ genomic structural vari…
View article: NanoVar: Accurate Characterization of Patients’ Genomic Structural Variants Using Low-Depth Nanopore Sequencing
NanoVar: Accurate Characterization of Patients’ Genomic Structural Variants Using Low-Depth Nanopore Sequencing Open
Despite the increasing relevance of structural variants (SV) in the development of many human diseases, progress in novel pathological SV discovery remains impeded, partly due to the challenges of accurate and routine SV characterization i…
View article: NanoVar Simulation Datasets
NanoVar Simulation Datasets Open
The data stored here were used for benchmarking long-read structural variant (SV) callers in the bioRxiv preprint of "NanoVar: Accurate Characterization of Patients' Genomic Structural Variants Using Low-Depth Nanopore Sequencing" by Tham …
View article: Live-imaging of Breast Epithelial Cell Migration After the Transient Depletion of TIP60
Live-imaging of Breast Epithelial Cell Migration After the Transient Depletion of TIP60 Open
The wound-healing assay is efficient and one of the most economical ways to study cell migration in vitro. Conventionally, images are taken at the beginning and end of an experiment using a phase-contrast microscope, and the migration abil…
View article: Characterizing structural variants in AML using short and long read sequencing technologies
Characterizing structural variants in AML using short and long read sequencing technologies Open
View article: TIP60 inhibits metastasis by ablating DNMT1−SNAIL2-driven epithelial-mesenchymal transition program
TIP60 inhibits metastasis by ablating DNMT1−SNAIL2-driven epithelial-mesenchymal transition program Open
HIV-Tat-interacting protein of 60 kDa (TIP60) is a lysine acetyltransferase and known to be downregulated in multiple cancers. Among various signalling pathways, TIP60 is implicated in regulating epithelial-mesenchymal transition (EMT). He…