Deep Reads¶
Paper analyses for landmark studies in pan-cancer phosphoproteomics. Each deep read provides an honest assessment — what the paper does well, where it falls short, and what design decisions define it.
| Paper | Category | Verdict |
|---|---|---|
| Geffen 2023 | Pan-Cancer Atlas | The definitive CPTAC phospho atlas |
| Cantley KinaseLibrary | Kinase Motifs | Gold standard motif reference |
| NicheCompass/decoupleR | Kinase Inference | The Swiss army knife |
| COSMOS | Pathway Reconstruction | Most ambitious multi-omics integration |
| funscoR | Functional Scoring | First systematic functional predictor |
| Krug 2020 | CPTAC Breast | Foundational CPTAC phosphoproteomics |
| benchmarKIN | Benchmark | No single method dominates |
| MIMP | Mutation Impact | Connecting genomics to phospho |