Curtis Lab. Stanford School of Medicine's repositories
VirtualTumorEvolution
Spatial Simulation of Tumor Growth
chromatinAnthra
Source code from the manuscript "Chromatin Regulators Mediate Anthracycline Sensitivity in Breast Cancer"
gastric_organoid_evolution
Deterministic evolution and stringent selection during pre-neoplasia
AMBRA1_paper
Scripts to reproduce results of "The AMBRA1 E3 ligase adaptor regulates Cyclin D protein stability" Chaikovsky et al. Nature 2021
cookiecutter-reproducible-science
boilerplate for reproducible and transparent science
TRIOB07
These are the processed data files related to the bulk expression data from breast tumors treated on the TRIO B07 trial (NCT00769470). Tumor or tumor bed tissue was collected and subjected to the Agilent Whole Human Genome 44K 2-color chip pre-treatment, on-treatment (after 1 cycle of HER2-targeted therapy alone, either trastuzumab, lapatinib, or the combination), and post-treatment (at definitive surgery after 6 cycles of docetaxel/carboplatin in combination with assigned HER2-targeted therapy). The raw data is available at GEO (GSE130788). The folder also includes the full protocol for the TRIO B07 trial and the gene sets assessed.
amplification_outliers
Code to reproduce the paper "Funtional screenings of amplification outlier oncogenes in organoid models of early tumorigenesis"
germline-epitopes
Scripts for evaluating germline-derived epitopes (Houlahan et al., 2023)