Aaron Watkins James

AmbiDose: per-cell removal budgets for ambient RNA contamination

AmbiDose removes ambient RNA contamination in single-cell RNA sequencing by using cell-specific removal budgets and ambient profiles, achieving high specificity for same-species UMIs.

TxNova: recovery of recurrent unannotated intergenic splice loci from existing bulk RNA-seq alignments

TxNova identifies recurrent unannotated intergenic splice junctions from bulk RNA-seq alignments, providing candidate leads for experimental validation.

scFair: Geometry-Aware Gene Budgets and Same-Rank Extension for Highly Variable Gene Selection

scFair improves highly variable gene selection by automatically setting list length and adding a tail to reduce bias from fixed cutoffs.

scATrans: annotating single-cell differential expression as transcription- or stabilization-weighted using unspliced RNA

scATrans annotates single-cell differential expression as transcription- or stabilization-weighted using unspliced RNA, without additional experiments, and recovers mechanism-specific biology from standard scRNA-seq data.

Nutrient flux governs osteogenic fate commitment through the SLC3A1-cystine Axis

This study identifies SLC3A1-mediated cystine transport as a key regulator of osteogenic fate commitment and shows cystine supplementation promotes bone regeneration and mitigates osteoporosis.

Mapping Somatosensory Afferent Circuitry to Bone Identifies Neurotrophic Signals Required for Fracture Healing

The paper identifies neurotrophic signals, particularly FGF9, required for fracture healing by mapping somatosensory afferent circuitry to bone and analyzing gene expression changes in DRG neurons.

Sensorineural regulation of skull healing implicates FGF1 signaling in non-healing bone

The paper identifies FGF1 signaling as a sensorineural-skeletal interaction that impairs bone healing in critical-sized defects by promoting osteoprogenitor proliferation and inhibiting differentiation.

TrkA+ sensory neurons regulate osteosarcoma proliferation and vascularization to promote disease progression

This study shows that TrkA+ sensory neurons promote osteosarcoma progression by enhancing tumor growth, vascularization, and metastasis, and that inhibiting these neurons reduces disease severity and improves survival.