Ming Tang

Chromatin Landscape of Cancer Cell Lines Identifies Enhancer Subtypes

The paper identifies enhancer subtypes in cancer cell lines and tumors, revealing distinct epigenetic patterns and potential therapeutic targets.

FUSED: CROSS-DOMAIN INTEGRATION OF FOUNDATION MODELS FOR CANCER DRUG RESPONSE PREDICTION

The paper introduces FUSED, a method that integrates foundation models across domains to improve cancer drug response prediction by reducing input features and enhancing performance.

The tidyomics ecosystem: Enhancing omic data analyses

The paper introduces tidyomics, an ecosystem bridging Bioconductor and tidy R to streamline omic analysis using data from the Human Cell Atlas.

Monkeybread: A Python toolkit for the analysis of cellular niches in single-cell resolution spatial transcriptomics data

Monkeybread identifies cellular niches in spatial transcriptomics data, revealing immunogenic and tolerogenic macrophage populations in melanoma tumors.

Fast alignment and preprocessing of chromatin profiles with Chromap

Chromap provides a fast and accurate method for aligning and preprocessing chromatin profiles, outperforming existing tools in speed while maintaining alignment accuracy.

Perifornical Area Urocortin-3 Neurons Promote Infant-directed Neglect and Aggression

This study identifies PeFAUcn3 neurons as a circuit controlling infant-directed neglect and aggression by linking their activation to specific behavioral responses.

CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data

CHIPS is a Snakemake pipeline for processing chromatin profiling data, providing quality control metrics and reproducible analysis workflows for ChIP-seq, ATAC-seq, and DNase-seq experiments.

The histologic phenotype of lung cancers may be driven by transcriptomic features rather than genomic characteristics

This study shows that transcriptomic features, not genomic characteristics, drive the histologic phenotype of lung cancers.

Evaluating single-cell cluster stability using the Jaccard similarity index

The paper introduces tools to evaluate single-cell clustering stability using subsampling and the Jaccard similarity index, with an R package and Snakemake workflow for implementation.

HieRFIT: Hierarchical Random Forest for Information Transfer

HieRFIT improves cell type classification accuracy by using hierarchical random forests with prior cell type relationships, showing effectiveness in cross-dataset and cross-species analyses.

Super-enhancer impairment is a link between MLL4 inactivated lung tumors and their vulnerability to glycolysis pathway inhibition

The paper shows that MLL4 loss in lung cancer promotes glycolysis and that inhibiting glycolysis selectively targets MLL4-mutant lung tumors.