# Drug discovery bioinformatics: mechanism, repurposing and biomarkers
URL: https://omicsquest.com/services/drug-discovery-bioinformatics/

OmicsQuest supports drug discovery programs with omics-driven mechanism-of-action studies, connectivity mapping against CMap/LINCS L1000, drug repurposing, single-cell pharmacotranscriptomics, response and resistance biomarker discovery, patient stratification and translational analysis of clinical samples. We combine transcriptomic, proteomic and imaging readouts with chemistry databases such as ChEMBL. Pricing starts at $79/hour.

## Analyses
### Mechanism of action
- **Transcriptomic MoA**: Pathway, TF and kinase activity shifts after treatment.
- **Connectivity mapping**: Signature matching against CMap/LINCS L1000.
- **Morphological MoA**: Cell Painting similarity to reference compounds.
- **Single-cell drug response**: Cell-type-specific responses with multiplexed scRNA-seq (sci-Plex, MIX-Seq style).
### Repurposing and combinations
- **Signature reversal**: Compounds that reverse disease signatures.
- **Network-based repurposing**: Drug-target proximity to disease modules.
- **Synergy analysis**: Bliss, Loewe and ZIP synergy scoring from dose matrices.
### Translational biomarkers
- **Response biomarkers**: Baseline and on-treatment predictors with cross-validation.
- **Resistance mechanisms**: Clonal and transcriptional programs enriched in non-responders.
- **Patient stratification**: Molecular subtyping and enrichment strategies for trials.
- **Pharmacodynamic markers**: Target engagement signatures for dose selection.

## Deliverables
- MoA and pathway reports
- Ranked repurposing or combination candidates
- Validated biomarker models with performance metrics
- Figures and methods

## Mistakes we avoid
- **Confusing toxicity with mechanism**: At high doses, many compounds produce generic stress signatures. We profile across doses and filter generic responses.
- **Biomarkers that only work in-sample**: We use nested cross-validation and independent cohorts before calling a biomarker.
- **Ignoring cell-line context**: MoA signatures differ by cell line. We test consistency across contexts.

## FAQ
**Can you analyze clinical trial samples?**
Yes, for exploratory and translational research. We work within your data governance, and we do not produce clinical diagnostic reports.

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Source: https://omicsquest.com/services/drug-discovery-bioinformatics/ | OmicsQuest, contact@omicsquest.com