Case Studies – Sprout Informatics

Case Study 1

A state-of-the-art neural network to predict novel RNA processing drug targets

Mining over 400,000 public RNA sequencing datasets to identify poison exons and building a deep learning framework to predict the best candidates for drug target screening.

Case Study 2

Large-scale data mining and development of target profiling dashboards to enable indication selection

Mining over 36,000 samples spanning common and rare cancers to identify indications with the greatest differential gene expression and build interactive dashboards for target profiling.

Case Study 3

Deconvoluting phenotypic mechanism of action using public data

Leveraging external public data to uncover the mechanism of action for unknown chemical matter by analyzing transcriptomic fingerprints and overlaying them on known pathway networks.

Case Study 4

Target profiling in bulk and single-cell RNA-seq expression data reveals differential co-expression patterns by data type

A large-scale meta-analysis of bulk and single-cell RNA-seq data showing how Siglec-15 and PD-L1 co-expression varies across cancer indications, informing combination immunotherapy strategies.

Case Study 5

Development of a novel single-cell RNA-seq quantification pipeline for a target gene isoform enables target profiling by cell type

Creating a novel algorithm and pipeline for pseudo-bulk isoform-level quantification at the single-cell level to identify cell types producing target proteins.

Case Study 6

Clinical analysis support in late-stage microbiome therapeutics elucidates the relationship between engraftment and therapeutic response

Building a best-in-class bacterial classification pipeline that enabled unprecedented resolution for the first FDA-approved oral microbiome therapeutic.