Jun Li

This study shows that Cxcr2 is essential for mammary gland development by coordinating epithelial-stromal interactions, leading to altered stromal architecture and immune dysregulation.

The paper identifies a genetic maternal effect on microglia development through sox17 mutation in zebrafish, showing that maternal genotype impacts microglia and yolk sac precursor cells.

The paper maps gene-by-gene-by-environment epistasis in cancer metastasis using CRISPR perturbations in mice, showing niche-dependent fitness and transcriptome convergence.

This study introduces TranScouter, a framework for predicting transcriptional responses to gene perturbations across different biological conditions, showing competitive performance in both seen and unseen perturbation scenarios.

This study uses in-situ glial cell-surface proteomics in Drosophila to identify DIP-β as a pro-longevity factor regulated by glial cells.

This study evaluates LLM-derived gene embeddings for pathway information recovery using GSEA, showing they encode substantial biological knowledge.

The paper identifies CD44 as an OPN receptor in astrocytes that regulates lipid metabolism and glial communication in Alzheimer's disease.

PEELing provides a platform for analyzing spatially-resolved proteomics data with quality assessment, contamination removal, functional annotation, and visualization tools.

The paper evaluates open-source text-embedding models as alternatives to OpenAI's for gene analysis, finding some perform as well or better than OpenAI's models.

Scouter predicts transcriptional responses to genetic perturbations using LLM embeddings, achieving higher accuracy than existing methods.

This study identifies the intracellular signaling pathway of teneurins in synaptic partner matching using Drosophila models.

This study investigates how Gq regulates wing development in Drosophila by affecting Ca2+ signaling and growth pathways, showing both Ca2+-dependent and -independent mechanisms.

The paper shows that synonymous codon substitutions in E. coli can upregulate an upstream gene through cryptic transcription, challenging the view that synonymous mutations have no phenotypic effects.

This study identifies Acj6 as a transcription factor that controls dendrite targeting in Drosophila PNs by regulating combinatorial expression of cell-surface proteins.

The paper creates a single-cell transcriptomic atlas of the adult fruit fly, identifying over 250 cell types and analyzing gene signatures and sexual dimorphism across tissues.

The paper evaluates five computational codon usage models for their ability to predict translational slowdowns using ribosome footprint data from S. cerevisiae, finding strong associations but also highlighting inconsistencies in RFP data.

The paper profiles cell-surface proteomes in Drosophila olfactory neurons across development, identifying new regulators of neural circuit assembly.

The paper identifies transcription factors that coordinate olfactory receptor expression and wiring specificity in Drosophila ORNs using single-cell RNA-sequencing and genetic analysis.

This study uses single-cell RNA sequencing to classify Drosophila olfactory projection neuron subtypes and identifies key transcription factors and molecular codes involved in their specification.