Mengbo Li

hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data

hoodscanR identifies and analyzes cell neighborhoods in spatial transcriptomics data, revealing transcriptional differences in tumor cells across neighborhoods.

Termination dynamics set RNAPII elongation rate and gate the response to CDK12 inactivation

The paper identifies SCAF4-CPA and KHDRBS1/SAM68 as key regulators of RNAPII termination under CDK12 inactivation, showing termination dynamics influence elongation rate and response to inhibition.

INTS12 Bridges Integrator and NELF to Prevent the Release of Non-processive RNA Polymerase II Complexes

This paper identifies INTS12's role in stabilizing the Integrator-NELF complex to prevent the release of defective RNA Polymerase II complexes, showing its importance in transcription regulation and cellular toxicity.

IdentifiHR: predicting homologous recombination deficiency in high-grade serous ovarian carcinoma using gene expression

IdentifiHR predicts homologous recombination deficiency in high-grade serous ovarian carcinoma using gene expression, achieving 85% accuracy in TCGA and 91% in an independent cohort.

Orchestrating Spatial Transcriptomics Analysis with Bioconductor

The paper provides an open-source online book for analyzing spatial transcriptomics data using Bioconductor in R, with reproducible code and datasets.

Improved marker detection for rare population in single-cell transcriptomics through text mining-inspired scoring approach

The paper introduces smartid, a method for accurately detecting markers in rare cell populations using a modified TF-IDF approach with Gaussian Mixture Model, improving cell type annotation in single-cell RNA-seq data.

Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR

The paper introduces limma and edgeR pipelines for differential transcript usage analysis that account for read-to-transcript ambiguity, improving power and FDR control in small and large datasets.

Preserving tissue structure through density-based spatial analysis with scider

The paper introduces scider, a spatial analysis framework that preserves tissue structure by identifying regions of interest using kernel density estimation, enabling multi-sample analysis and revealing spatial patterns.

Quantification and differential analysis of mass spectrometry proteomics data with probabilistic recovery of information from missing values

The paper introduces limpa, a package for quantifying and analyzing MS proteomics data, handling missing values probabilistically to improve differential expression analysis.

Missing values are informative in label-free shotgun proteomics data: estimating the detection probability curve

The paper argues that missing values in label-free shotgun proteomics data are informative and proposes a statistical method to estimate the detection probability curve as a function of intensity.

Guiding and interpreting brain network classification with transcriptional data

This paper introduces a method to improve fMRI network classification by integrating transcriptional data, enhancing prediction accuracy for schizophrenia and enabling biological interpretation of functional connectivity features.