Nelson L.S. Tang

In-silico cell sorting revealed granulocyte-specific single-cell-type gene expression from peripheral blood bulk expression data and its application as host response biomarkers to discriminate bacterial and viral infections

The paper develops an in-silico cell sorting method to identify granulocyte-specific gene expression biomarkers from bulk blood data, enabling discrimination between bacterial and viral infections.

Compositional data modeling of high-dimensional single cell RNA-seq (CoDA-hd): its advantages over commonly used normalization approaches

This paper introduces CoDA-hd, a compositional data analysis approach for scRNA-seq, showing its advantages in dimension reduction, clustering, and trajectory inference compared to log-normalization.

A map of Non-translated RNA (nt-RNA) junctions in cancer genomes: a database resource of unproductive splicing

This paper identifies and characterizes toxic junctions from non-translated RNA in cancer genomes, revealing their abundance and potential as biomarkers.

Monocyte single cell-type gene expression measured in peripheral blood by DIRECT LS-TA method: the ratio-based biomarkers of (IFI27/PSAP) showed superior performance than interferon score in triage patients with viral infection

This paper develops a ratio-based biomarker (DIRECT LS-TA) using monocyte-specific gene expression ratios in peripheral blood to improve viral infection triage, outperforming the IFN score in diagnostic accuracy.

'Trans-differentiation of neutrophils from plasmablast' is an artefact caused by over-reliance on machine algorithms in single cell RNA sequencing analysis: Lesson learnt and steps ahead

The paper shows that trans-differentiation of plasmablasts to neutrophils in scRNA-seq data is an artefact caused by low-quality cells and highlights the need for improved statistical standards and quality control in single-cell analysis.

Direct single cell-type gene expression analysis in Whole blood: Novel ratio-based gene expression biomarkers using 2 novel monocyte reference genes (PSAP and CTSS) for monitoring bacterial infection

The paper develops a ratio-based biomarker (DIRECT LS-TA) to quantify monocyte-specific gene expression directly from whole blood without cell sorting, showing potential for bacterial infection diagnosis.

Low-Rank Full Matrix Factorization for dropout imputation in single cell RNA-seq and benchmarking with imputation algorithms for downstream applications

This paper develops an imputation algorithm for single-cell RNA-seq and benchmarks it against other methods across various downstream analyses.

Simultaneous transcriptome and methylome profiles of single mouse oocytes provide novel insights on maturation and aging

The paper analyzes transcriptome and methylome data from mouse oocytes to understand aging and maturation, identifying biomarkers and a predictive model for oocyte quality.

Single-cell RNA-Seq Resolves Cellular Heterogeneity and Transcriptional Dynamics in Spermatogonial Stem Cells Establishment

This study uses single-cell RNA sequencing to analyze spermatogonial stem cell establishment in mice, identifying key molecular transitions and novel markers.