publications

2025

1. 

   The lives of cells, recorded

   Amjad Askary, Wei Chen, Junhong Choi, Lucia Y. Du, Michael B. Elowitz, James A. Gagnon, Alexander F. Schier, Sophie Seidel, Jay Shendure, Tanja Stadler, and Martin Tran

   Nature Reviews Genetics, 2025

2. 

   Molecular circuits for genomic recording of cellular events

   Wei Chen, and Junhong Choi

   Trends in Genetics, 2025
3. Computational design of sequence-specific DNA-binding proteins

   Cameron J Glasscock, Robert J Pecoraro, Ryan McHugh, Lindsey A Doyle, Wei Chen, Olivier Boivin, Beau Lonnquist, Emily Na, Yuliya Politanska, Hugh K Haddox, and  others

   Nature Structural & Molecular Biology, 2025
4. Design of intrinsically disordered region binding proteins

   Kejia Wu, Hanlun Jiang, Derrick R Hicks, Caixuan Liu, Edin Muratspahić, Theresa A Ramelot, Yuexuan Liu, Kerrie McNally, Sebastian Kenny, Andrei Mihut, and  others

   Science, 2025
5. A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording

   Troy A McDiarmid, Megan L Taylor, Wei Chen, Florence M Chardon, Junhong Choi, Hanna Liao, Xiaoyi Li, Haedong Kim, Jean-Benoı̂t Lalanne, Tony Li, and  others

   Nature Biotechnology, 2025

2024

1. Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists

   Matthias Glögl, Aditya Krishnakumar, Robert J Ragotte, Inna Goreshnik, Brian Coventry, Asim K Bera, Alex Kang, Emily Joyce, Green Ahn, Buwei Huang, and  others

   Science, 2024

2. 

   Chromatin context-dependent regulation and epigenetic manipulation of prime editing

   Xiaoyi Li, Wei Chen, Beth K. Martin, Diego Calderon, Choli Lee, Junhong Choi, Florence M. Chardon, Troy McDiarmid, Haedong Kim, Jean-Benoît Lalanne, Jenny F. Nathans, and Jay Shendure

   Cell, 2024

3. 

   Symbolic recording of signalling and cis-regulatory element activity to DNA

   Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F Nathans, Beth Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoı̂t Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, and Jay Shendure

   Nature, 2024

2022

1. 

   Precise genomic deletions using paired prime editing

   Junhong Choi, Wei Chen, Chase C Suiter, Choli Lee, Florence M Chardon, Wei Yang, Anh Leith, Riza M Daza, Beth Martin, and Jay Shendure

   Nature Biotechnology, 2022

2. 

   A time-resolved, multi-symbol molecular recorder via sequential genome editing

   Junhong Choi, Wei Chen, Anna Minkina, Florence M. Chardon, Chase C. Suiter, Samuel G. Regalado, Silvia Domcke, Nobuhiko Hamazaki, Choli Lee, Beth Martin, Riza M. Daza, and Jay Shendure

   Nature, 2022
3. SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

   Sanjay Srivatsan, Sarah Heidl, Brian Pfau, Beth K Martin, Peter D Han, Weizhi Zhong, Katrina Raay, Evan McDermot, Jordan Opsahl, Luis Gamboa, and  others

   Clinical Chemistry, 2022

2020

1. Trans MPRA: A framework for assaying the role of many trans-acting factors at many enhancers

   Diego Calderon, Andria Ellis, Riza M Daza, Beth Martin, Jacob M Tome, Wei Chen, Florence M Chardon, Anh Leith, Choli Lee, Cole Trapnell, and  others

   BioRxiv, 2020

2019

1. 

   Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

   Wei Chen, Aaron McKenna, Jacob Schreiber, Maximilian Haeussler, Yi Yin, Vikram Agarwal, William Stafford Noble, and Jay Shendure

   Nucleic acids research, 2019

2018

1. Identifying novel enhancer elements with CRISPR-based screens

   Jason C Klein, Wei Chen, Molly Gasperini, and Jay Shendure

   ACS chemical biology, 2018
2. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

   Alexander B. Rosenberg, Charles M. Roco, Richard A. Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas T. Graybuck, David J. Peeler, Sumit Mukherjee, Wei Chen, S. Pun, D. Sellers, Bosiljka Tasic, and Georg Seelig

   Science, 2018