Use cases

Real studies, run on PromptBio

White papers and case studies in which we apply PromptBio to public datasets: biomarker discovery, treatment-response modeling, pipeline validation, and literature mining.

5 use cases See the publications

Case study

Multi-Omics Analysis to Identify Biomarkers for Endometrial Cancer

Endometrial cancer is a prevalent malignancy affecting the uterine lining, with significant implications for women’s health. This study uses a multi-omics approach to identify biomarkers for endometrial cancer, drawing on data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). On the PromptBio platform, we integrate genomic, transcriptomic, and proteomic data to uncover molecular markers associated with different subtypes of endometrial cancer, including the aggressive copy-number high (CNV-H) subtype, and identify predictive markers for CTNNB1 mutation status and antigen presentation machinery (APM) status. The study shows how MLGenie supports biomarker discovery and points to candidate markers for diagnosis and personalized treatment.

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White paper

Multiomics Treatment Response Analysis with the PromptBio Platform

This white paper presents a reanalysis of the data from “Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer” (Cell 2023) using the PromptBio platform. The results agree closely with the original findings and add to them: optimized treatment-response prediction models built with MLGenie, homologous recombination deficiency (HRD) status prediction with PromptBio’s HRD pipeline, and integrated multi-omics treatment-response prediction.

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White paper

Validation of PromptBio Neoantigen Prediction Pipeline using TESLA data

This white paper validates the PromptBio neoantigen prediction pipeline against the benchmark dataset of the Tumor Neoantigen Selection Alliance (TESLA). It measures how accurately the pipeline identifies clinically relevant neoantigens, which are central to personalized cancer immunotherapy.

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Case study

Validation and evaluation of sepsis plasma biomarker PSP

Sepsis is a life-threatening condition that arises from the host’s dysregulated response to infection. Studies have shown that for every hour’s delay in appropriate treatment, the mortality rate of sepsis patients may increase by 7% to 10%. Novel biomarkers have emerged in clinical practice in recent years, including pancreatic stone protein (PSP). This case study uses the literature mining and data analysis capabilities of the PromptBio platform to evaluate PSP as a sepsis biomarker on publicly available data and to look for other candidate biomarkers.

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White paper

Multi-Omics Analysis of Cystic Fibrosis using Conversation-Based Interactions

This white paper, with three accompanying videos, shows how to reproduce a published multi-omics analysis through conversation on the PromptBio platform. The analysis comes from “Interactions between the gut microbiome and host gene regulation in cystic fibrosis” (Genome Medicine). Our results reproduce the key findings of the original study.

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