Publications

Multiomics and deep learning dissect regulatory syntax in human development

Betty B Liu^*, Selin Jessa^*, Samuel H Kim^*, Yan Ting Ng^*, Soon Il Higashino, Georgi K Marinov, Derek C Chen, Benjamin E Parks, Li Li, Tri C Nguyen, Austin T Wang, Sean K Wang, Meng How Tan, Serena Y Tan, Michael Kosicki, Len A Pennacchio, Eyal Ben-David, Anca M Pasca, Anshul Kundaje^{^}, Kyle K H Farh^{^}, William J Greenleaf^{^}

Selin's postdoc work using deep learning in a new fetal single-cell atlas to study the organization of transcription factor binding sites in human development, and where they're perturbed in complex traits. Highlighted in Nature Genetics.

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells

Tong Wang, Selin Jessa, Georgi K Marinov, Sandy Klemm, Anshul Kundaje, William J Greenleaf

We present a new assay, beCasKAS, to sensitively detect off-target edits from CRISPR base editors, and show how non-coding off-target genome edits can be triaged for epigenetic dysregulation in silico using deep learning.

Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart

Andrew R Marderstein^*, Soumya Kundu^*, Evin M Padhi, Salil Deshpande, Austin Wang, Esther Robb, Ying Sun, Chang M Yun, Diego Pomales-Matos, Yilin Xie, Daniel Nachun, Selin Jessa, Anshul Kundaje^{^}, Stephen B Montgomery^{^}

A unified lexicon of predictive DNA sequence motifs from ENCODE transcription factor binding and chromatin accessibility assays

Salil Deshpande, Chang Min Yun, Vivekanandan Ramalingam, Vivian Hecht, Aman Patel, Anusri Pampari, Selin Jessa, Ryan Zhao, Austin Wang, Anshul Kundaje