A Three-Dimensional Model of the Yeast Genome. - William Stafford Noble; Zhi-jun Duan; Mirela Andronescu; Kevin Schutz; Sean McIlwain; Yoo Jung Kim; Choli Lee; Jay Shendure; Stanley Fields; C. Anthony Blau (RECOMB, 2011)

MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. - Evan A. Boyle; Brian J. O'Roak; Beth K. Martin; Akash Kumar 013; Jay Shendure (Bioinform., 2014)

The contribution of de novo coding mutations to autism spectrum disorder. - Ivan Iossifov; Brian J. O'Roak; Stephan J. Sanders; Michael Ronemus; Niklas Krumm; Dan Levy; Holly A. Stessman; Kali T. Witherspoon; Laura Vives; Karynne E. Patterson; Joshua D. Smith; Bryan Paeper; et al. (Nat., 2014)

Understanding Spatial Genome Organization: Methods and Insights. - Vijay Ramani; Jay Shendure; Zhi-jun Duan (Genom. Proteom. Bioinform., 2016)

CADD: predicting the deleteriousness of variants throughout the human genome. - Philipp Rentzsch; Daniela M. Witten; Gregory M. Cooper; Jay Shendure; Martin Kircher (Nucleic Acids Res., 2019)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

Unsupervised manifold alignment for single-cell multi-omics data. - Ritambhara Singh; Pinar Demetci; Giancarlo Bonora; Vijay Ramani; Choli Lee; He Fang; Zhi-jun Duan; Xinxian Deng; Jay Shendure; Christine Disteche; William Stafford Noble (BCB, 2020)

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. - Hyeon-Jin Kim; Galip Gürkan Yardimci; Giancarlo Bonora; Vijay Ramani; Jie Liu 045; Ruolan Qiu; Choli Lee; Jennifer Hesson; Carol B. Ware; Jay Shendure; Zhi-jun Duan; William Stafford Noble (PLoS Comput. Biol., 2020)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)