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If you are interested in a PhD or MS in Bioinformatics & Genomics, consider applying to our interdisciplinary graduate program here at Penn State. We have GREAT faculty, it's a very strong program, and we care about you. We don't accept the GRE. Please RT! huck.psu.edu/graduate-progr…

Our latest preprint examines cross-species prediction of transcription factor binding sites using neural networks. Really wonderful work from Kelly Cochran (Kelly Cochran), in collaboration with Divyanshi Srivastava, @avshrikumar, akshay Balsubramani, and Anshul Kundaje (anshulkundaje@bluesky): biorxiv.org/content/10.110… 1/n

Check our new paper “Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation”. biorxiv.org/content/10.110…

New preprint from Lexi Morrissey in my lab describing Allo - a new tool for allocating multi-mapped reads in regulatory genomics experiments. 1/ biorxiv.org/content/10.110…

New preprint by Sonny Arora and Jianyu Yang in our lab, in collab with Dr. B. Franklin Pugh, Minoru Ko, and Tomohiko Akiyama. We started with a simple question: are all Fox TFs pioneer factors? We investigated with the help of ChIP-exo and neural networks. 1/n biorxiv.org/content/10.110…

The Borzoi manuscript is now out in Nature Genetics: doi.org/10.1038/s41588… Borzoi predicts RNA-seq profiles in many tissues & cell types from DNA sequence as its only input. With it, we can score the impact of genetic variants on a number of gene-regulatory functions. 1/

⚡️ Our latest preprint is on bioRxiv! Shift augmentation improves DNA convolutional neural network indel effect predictions biorxiv.org/content/10.110…

I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! biorxiv.org/content/10.110…

We’re excited to share a follow-up Borzoi training run and an analysis of the capabilities that emerged. biorxiv.org/content/10.110…