Nature Biotech. 2016 release

This code corresponds to the experiments, results and models that accompany our 2016 Nat. Biotech paper: doi:10.1038/nbt.3437.

After publication, a small indexing bug (#1) was found that had no substantial effect on the model or reported results (all Spearman correlations reported in the paper remain the same), but has been corrected in future versions to avoid confusion. This bug was fixed starting in commit 8d11972.

On 6/11/2016 we became aware that there are small differences in the exact values between the bug-fixed version and the original version even though the Spearman correlations (and therefore quality of the model) remain the same.