Page Not Found
Page not found. Your pixels are in another canvas.
Sitemap
A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
About me
Page not in menu
This is a page not in th emain menu
Posts
Future Blog Post
Published:
This post will show up by default. To disable scheduling of future posts, edit config.yml and set future: false.
Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
portfolio
Universal short read adapters with variable length non-random unique molecular identifiers
Patent covering the general usage of variable length UMI barcodes for sequencing error suppression
Methods and systems for generation and error-correction of unique molecule index sets with heterogeneou smolecular lengths
Patent covering the generation of highly error tolerant variable length UMI barcodes
publications
RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing
Published in RNA, 2020
Biologically-inspired featurization of RNA transcripts enables state-of-the-art modeling of RNA subcellular localization
Recommended citation: Wu, K.E., Parker, K.R., Fazal, F.M., Chang, H.Y. and Zou, J., 2020. RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing. RNA, 26(7), pp.851-865. Vancouver https://rnajournal.cshlp.org/content/26/7/851.short
RNA-GPS predicts SARS-CoV-2 RNA residency to host mitochondria and nucleolus
Published in Cell systems, 2020
Machine learning model for RNA localization allows hypothesis generation regarding behavior of SARS-CoV-2 transcriptome
Recommended citation: Wu, K.E., Fazal, F.M., Parker, K.R., Zou, J. and Chang, H.Y., 2020. RNA-GPS predicts SARS-CoV-2 RNA residency to host mitochondria and nucleolus. Cell systems, 11(1), pp.102-108. https://www.sciencedirect.com/science/article/pii/S2405471220302374
BABEL enables cross-modality translation between multiomic profiles at single-cell resolution
Published in Proceedings of the National Academy of Sciences, 2021
BABEL enables computational imputation of single-cell multi-omic profiles with only a single modality as input
Recommended citation: Wu, K.E., Yost, K.E., Chang, H.Y. and Zou, J., 2021. BABEL enables cross-modality translation between multiomic profiles at single-cell resolution. Proceedings of the National Academy of Sciences, 118(15), p.e2023070118. https://www.pnas.org/doi/abs/10.1073/pnas.2023070118
TCR-BERT: learning the grammar of T-cell receptors for flexible antigen-binding analyses
Published in bioRxiv, 2021
Large language modeling of T-cell receptor sequences
Recommended citation: Wu, K., Yost, K.E., Daniel, B., Belk, J.A., Xia, Y., Egawa, T., Satpathy, A., Chang, H.Y. and Zou, J., 2021. TCR-BERT: learning the grammar of T-cell receptors for flexible antigen-xbinding analyses. bioRxiv. https://www.biorxiv.org/content/10.1101/2021.11.18.469186v1.full.pdf
Protein structure generation via folding diffusion
Published in Nature Communications, 2024
Generative diffusion model for protein structures; trigonometry is all you need!
Recommended citation: Wu, K. E., Yang, K. K., van den Berg, R., Alamdari, S., Zou, J. Y., Lu, A. X., & Amini, A. P. (2024). Protein structure generation via folding diffusion. Nature Communications, 15(1), 1059. https://www.nature.com/articles/s41467-024-45051-2
talks
TCR-BERT: learning the grammar of T-cell receptors for flexible antigen-binding analyses
Published:
Spotlight talk at the ICML 2022 Workshop on Computational Biology. Webpage here, pdf here.
Protein structure generation via folding diffusion
Published:
Invited talk on FoldingDiff, see details here.
Protein structure generation via folding diffusion
Published:
Invited talk on FoldingDiff at the OpenBioML journal club, see recording on YouTube.
teaching
CS 273B - Deep learning in genomics and biomedicine - course assistant
Graduate course, Stanford University, 2019
Course assistant for a course exploring cutting edge developments in the intersection of deep learning, genomics, and biomedicine. Led discussion/recitation sections and portions of lectures.