case studies
Public-data walkthroughs in Forge — preprocessing, statistics, multi-omics integration, and pathway analysis on real biological questions.
Each case study is a real published dataset loaded into Forge and walked through end-to-end: data ingestion, QC, preprocessing, statistical analysis, and pathway context via the GIZMO knowledge graph. Register for a free account to explore the data interactively.
Gut Microbiome & Metabolomics
These studies pair fecal metabolomics with shotgun metagenomics from the Borenstein Lab curated resource. Each is loaded as a multi-omics project in Forge with both assays aligned by sample ID.
| Study | Condition | n | Highlights | Publication | Explore |
|---|---|---|---|---|---|
| Franzosa IBD 2019 | IBD (CD / UC / Control) | 220 | Multi-omics integration, MCIA, DIABLO group discrimination, cross-assay network | Nature Microbiology ↗ | Forge → |
| Yachida CRC 2019 | CRC stages (Healthy → Stage IV) | 347 | Stage-wise differential abundance, volcano plot, correlation network, GIZMO pathway enrichment | Nature Medicine ↗ | Forge → |
| iHMP IBDMDB 2019 | IBD (CD / UC / nonIBD) | 382 | Longitudinal multi-omics, trajectory analysis, time-course differential abundance | Nature ↗ | Forge → |
| Mars IBS 2020 | IBS subtypes (IBS-C / IBS-D / Healthy) | 444 | Longitudinal analysis, subset-specific metabolic trajectories, SNF subtype discovery | Cell ↗ | Forge → |
| Kim Adenomas 2020 | Colorectal adenomas vs. Control | ~100 | Early CRC biomarkers, fecal metabolomics + microbiome, differential abundance | CGH ↗ | Forge → |
| Sinha CRC 2016 | Colorectal cancer vs. Healthy | 131 | Fecal metabolomics, CRC biomarker identification, correlation network analysis | PLOS ONE ↗ | Forge → |
| Erawijantari Gastric Cancer 2020 | Post-gastrectomy vs. Healthy | 96 | Surgical intervention effects on gut ecology, differential microbiome-metabolome co-variation | Gut ↗ | Forge → |
| Wang ESRD 2020 | End-stage renal disease vs. Control | 287 | Uremic solute profiling, microbiome dysbiosis in renal failure, pathway enrichment | Nature Medicine ↗ | Forge → |
| Jacobs IBD Families 2016 | IBD-family members vs. Control | 90 | Subclinical metabolic signatures in at-risk relatives, early dysbiosis markers | Cell Reports ↗ | Forge → |
Pediatric & Developmental
| Study | Condition | n | Highlights | Publication | Explore |
|---|---|---|---|---|---|
| Kostic Infants Diabetes 2015 | T1D progression vs. Healthy (longitudinal) | 103 | Longitudinal microbiome development, trajectory analysis toward seroconversion | Cell Host & Microbe ↗ | Forge → |
| He Infants MFGM 2019 | Formula type vs. Breastfed (infants) | ~60 | Dietary supplementation effects on infant gut metabolome, group comparison | Microbiome ↗ | Forge → |
| Wandro Preterms 2018 | Preterm infants (longitudinal) | ~50 | Personalized microbiome-metabolome trajectories in NICU, NEC risk profiling | mSystems ↗ | Forge → |
| Kang Autism 2017 | ASD vs. Typically developing | 44 | Gut-brain axis metabolomics, differential abundance, microbiome-metabolome correlation | PLOS ONE ↗ | Forge → |
Cancer Cell Lines & Multi-Omics
| Study | Design | n | Highlights | Publication | Explore |
|---|---|---|---|---|---|
| CCLE Metabolomics | Cancer cell lines across lineages | 928 lines | Bulk metabolomics + virtual metabolomics (scATMAN) + scRNA-seq; lineage-specific metabolic programs; multi-omics late-fusion | Nature ↗ | Forge → |
Featured Case Studies
These datasets have full annotated walkthroughs inside Forge — preprocessing configuration, analysis notes, and guided interpretation.
Franzosa IBD 2019 (GeMMA-curated)
Gut microbiome and metabolome in inflammatory bowel disease. Multi-omics integration of 220 samples across CD, UC, and healthy controls.
PRACHITi HIV Cohort (ST004581)
Untargeted LC-MS metabolomics of maternal heparin plasma from HIV+ and HIV- mothers in Pune, India. Metabolon platform, 100 samples.
All datasets are publicly available through their respective repositories (MetaboLights, Metabolomics Workbench, GEO, or the Borenstein Lab curated resource). Forge does not host or redistribute the raw data — it pulls from the original sources on demand. Publication links point to the journal DOI; open-access versions are available via PubMed Central where noted.
Want to see a specific study added? Get in touch or open an issue on GitHub.