This repo contains a PyTorch implementation for the paper "Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion". The training and sampling part of the code is inspired by Score ...

Trained on sequences of length 131k, with a model size of 256 and 16 layers. Trained for 50k steps and batch size of 8. Trained with reverse-complement (RC) data ...

We identify the cell type–specific selection of T cells with a synonymous mitochondrial DNA variant in MT-CO1, reminiscent of the purifying selection of pathogenic alleles. Mechanistically, we ...

Genetic variants across the genome contribute to complex human diseases and agricultural traits, but interpreting them can be challenging. We propose a genome-wide variant effect prediction approach ...

Direct sequencing of single molecules through nanopores allows for accurate quantification and full-length characterization of native RNA or complementary DNA (cDNA) without amplification. Both ...

To link Cas9 DNA recognition to phage propagation during PACE, we developed a bacterial one-hybrid selection 20,23,24 in which the selection phage encodes a catalytically dead SpCas9 (dCas9) fused to ...

Herbal drug authentication is an important task in traditional medicine; however, it is challenged by the limitations of traditional authentication methods and the lack of trained experts. DNA ...