Li Ding

Integrated coding-noncoding genome annotation expands single-cell transcriptomic discovery and identifies clinically relevant noncoding RNAs in multiple myeloma

The paper integrates coding and noncoding genome annotations to improve transcriptomic analysis, identifying clinically relevant noncoding RNAs in multiple myeloma.

Spatial atlas highlights contribution of C. difficile in early-stage colorectal cancer

The paper creates a spatial atlas of early-stage colorectal cancer tumors to identify bacterial niches and their impact on tumor transcriptomes, highlighting C. difficile's significant influence despite low abundance.

Loss of UBP1 drives oxaliplatin resistance through a targetable dependency on translation initiation

The paper identifies UBP1 loss as a driver of oxaliplatin resistance in gastric cancer by revealing a compensatory reliance on translation initiation, which can be targeted with 4EGI.

Multimodal spatial alignment and morphology mapping with MOSAICField

MOSAICField aligns spatial slices across modalities to reconstruct 3D tissue models and map morphology, outperforming existing methods on simulated and prostate cancer data.

Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day

This paper develops a high-throughput single-cell proteomic method for PBMCs, achieving 660 cells per day with 750 protein identifications per cell and identifying low-frequency cell types.

OmniCellAgent: An AI Scientist for Omic-Driven Scientific Discovery

OmniCellAgent autonomously retrieves and analyzes scRNA-seq datasets to generate structured reports and hypotheses across disease settings.

Longitudinal multi-omic profiling uncovers immune escape and predictors of response in multiple myeloma

This study uses longitudinal multi-omic profiling to identify immune escape mechanisms and predictors of response in multiple myeloma.

Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma

This study uses linked-read sequencing to phase somatic mutations in multiple myeloma, extending haplotype blocks and revealing phasing patterns in key mutated genes.

Visualizing tumor evolution with the fishplot package for R

The paper introduces a new R package called fishplot for visualizing tumor evolution over time, providing intuitive and accurate graphical representations of clonal structure changes.