This paper introduces genomicBERT, a lightweight genome analysis model that improves efficiency and performance through specialized DNA vocabulary and tokenization, validated across diverse case studies.

bioRxiv · May 31, 2023 · PreprintBioinformatics

Single cell analysis of lymphatic endothelial cell fate specification and differentiation during zebrafish development

Lin Grimm, Elizabeth A. Mason, Hujun Yu, Stefanie Dudczig, Virginia Panara, Tyrone Chen, Neil Ivan Bower, Scott Paterson, Kazuhide S. Okuda, Maria Cristina Rondon-Galeano, Sakurako Kobayashi, Anne Senabouth, Anne K. Lagendijk, Joseph E. Powell, Kelly Smith, , Benjamin M. Hogan

This study uses single-cell transcriptomics to investigate Prox1's role in lymphatic endothelial cell fate specification and differentiation in zebrafish, identifying new transcriptional targets and regulatory mechanisms.

The EMBO Journal · Mar 13, 2023Peer-reviewedDevelopmental Biology

A simple, scalable approach to building a cross-platform transcriptome atlas

Paul W. Angel, Nadia Rajab, Yidi Deng, Chris M. Pacheco, Tyrone Chen, Kim‐Anh Lê Cao, Jarny Choi, Christine Anne Wells

The paper integrates hundreds of transcriptome datasets from multiple platforms to create a cross-platform blood cell atlas, enabling robust cell type clustering without batch correction.

PLoS Computational Biology · Sep 28, 2020Peer-reviewedBioinformatics