James C. Costello

The paper identifies a transcriptomic signature predicting stromal innervation in NMIBC and links it to clinical outcomes.

This study shows estradiol suppresses microglial immunity and promotes breast cancer brain metastasis, with E2 suppression enhancing anti-tumor responses and synergizing with radiotherapy.

HetNetEX provides exact asymptotic inference for connectivity in heterogeneous biomedical knowledge graphs, outperforming XSwap in speed and accuracy.

The paper introduces a section-aware RAG system for Down syndrome research that prioritizes experimental results to generate accurate, cited responses.

The paper identifies eIF3d and eIF3e as mediators of hypoxia-induced translational control and shows that small molecules can inhibit this process.

The paper shows that loss of the Y chromosome in bladder cancer drives metabolic reprogramming through DDR2, enhancing glycolysis and tumor aggressiveness.

CLAMP integrates genetic associations and drug signatures with large-scale RNA-seq data to identify interpretable gene modules linked to complex diseases.

curatedPCaData harmonizes prostate cancer datasets to enable meta-analysis and clinical insights across multiple cohorts.

The paper develops predictive models for preterm birth using maternal blood multi-omics data, finding transcriptomic and proteomic markers can predict gestational age and spontaneous preterm birth with high accuracy.

This paper introduces SOPHIE, a method using generative neural networks to distinguish common from specific transcriptional responses across datasets.

This study shows that Prdm3 and Prdm16 regulate Wnt/β-catenin activity to control craniofacial chondrocyte differentiation and development.

The paper tests reconstruction algorithms for chromosome conformations using fluorescence microscopy and finds they can produce near-perfect reconstructions with sufficient fluorescent colors.

GSEA-InContext Explorer is a Shiny app that performs and visualizes gene set enrichment analysis using two methods, allowing users to compare results across experiments and identify significant gene sets.

The paper improves a method for inferring chromosome conformation from labeled loci images, enhancing accuracy and scalability for large-scale problems.

This study identifies low MSH2 protein levels as a marker of cisplatin resistance in bladder cancer using in vitro and clinical data.

The paper introduces a method to simulate heterogeneous populations using Boolean networks, capturing rare cellular events without modeling individual cells.

GSEA-InContext identifies common and experiment-specific gene set enrichment patterns by comparing an experiment to a background compendium of transcriptomic data.

This paper presents a crowdsourced challenge to predict early discontinuation of docetaxel in mCRPC patients using clinical data from multiple trials, finding that ensemble models outperform individual models.