Vivian Link

DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity biorxiv.org/content/10.110…

@cegAmorim This paper may be useful: Pouyet et al. (2018) elifesciences.org/articles/36317. They select SNPs and not regions, but they cite other methods to select regions and compare their SNP set to Gronau et al. (2011)

I'm so glad I got to be a part of this awesome team! We investigated the genomic neighborhood of the markers routinely used in forensics to create "DNA fingerprints", and found that it is enriched with variants with known phenotypic associations.

Glad to share my new preprint with @AlexCope241, George Zhang and @mwpen, in which we develop a theoretical model to investigate how mRNA and protein levels of a gene coevolve when the protein level is the target of selection. 1/n biorxiv.org/content/10.110…

There are lots of ways to build on what we did, and we're excited to start pursuing them. Every paper is a journey, and it was great to take this one with our collaborators from the @CharlestonCWKC and @nmancuso_ labs! (end)

We replicated the previous failure to find the locus using GWAS (gold), but our method, built from the same SNPs and Relate trees, finds the locus (pink), and also shows hints of signal at neighboring loci found previously in much larger GWAS samples (14/n)

Excited to share my newest preprint with @DocEdge85, as well as collaborators @jgschraiber, Caoqi Fan, @bldinh, @nmancuso_, and @CharlestonCWKC. In it, we proposed testing tree-based summaries of local relatedness to find QTLs (thread). biorxiv.org/content/10.110…

I'm hiring! Do you think, every time the perennial argument on #scitwitter about staff scientists and the postdoc exodus recurs, that you would love to find a stable staff scientist position? Do you have experience with #bioinformatics, #hpc, and #SingleCell methods? Read on!