JS
Jay Shendure
genomicsMutationGenome, HumanGenetic VariationSingle-Cell AnalysisChromatinEvolution, Moleculardevelopmental biologygeneticsCOVID-19
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
462 papers in the corpus · 1996–2026High-throughput identification of chromatin-opening transcription factors.42926670 · Keith, Aidan, Jain, Shruti, Daza, Riza M et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
A fluctuation test for gastruloid heterogeneity.42849438 · Regalado, Samuel G, Qiu, Chengxiang, Kottapalli, Sanjay et al.2026 · 1 citationCell. 2026
A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis.42619846 · Yu, Qi, Kim, Haedong, Seidel, Sophie et al.2026 · 3 citationsbioRxiv : the preprint server for biology. 2026
Locus-Scale Massively Parallel Reporter Assays.42539220 · McGee, Abby V, Biar, Carina G, Martin, Beth K et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Massively parallel characterization and predictive modelling of neuronal regulatory variation.42523423 · Salomon, Kilian, Deng, Chengyu, Dash, Pyaree Mohan et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.42270637 · Seidel, Sophie, Zwaans, Antoine, Regalado, Samuel et al.2026 · 7 citationsNature communications. 2026;17(1)
Gigabase-scale deletion scanning of the human genome.42282737 · Koeppel, Jonas, Keith, Aidan, Sgrizzi, Samantha et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes.41993329 · Qiu, Chengxiang, Daza, Riza M, Welsh, Ian C et al.2026 · 3 citationsbioRxiv : the preprint server for biology. 2026
Pool-packaged AAV libraries exhibit extensive length-dependent and homology-dependent chimerism.42050331 · Lalanne, Jean-Benoît, Huynh, Chau, Mich, John K et al.2026 · 1 citationNature biotechnology. 2026
Designed Minibinders Rewire Receptor Signaling to Enable Functional Human Myogenic Reprogramming.42094432 · Keshri, Riya, Foreman, Zachary, Barrett, Phillip et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
The proteomic landscape and temporal dynamics of human and mouse gastruloid development.42032312 · Garge, Riddhiman K, Lynch, Valerie, Fields, Rose et al.2026 · 1 citationNature cell biology. 2026;28(5):1015-1030
Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers.42079151 · Li, Tony, Lalanne, Jean-Benoît, Kajiwara, Emma A N et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers.42079234 · Lalanne, Jean-Benoît, Li, Tony, Kajiwara, Emma A N et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
Remembrance of inflammations past.41882082 · Qiu, Chengxiang, Shendure, Jay2026 · 1 citationNature. 2026;652(8110):569-570
A multiplex, prime editing framework for identifying drug resistance variants at scale.41722572 · Abadie, Florence M C, Suiter, Chase C, Smith, Nahum T et al.2026 · 19 citationsCell genomics. 2026;6(5):101167
Multichannel genomic recording of biological information with ENGRAM.41673323 · Nathans, Jenny F, McDiarmid, Troy A, Chen, Wei et al.2026 · 0 citationsNature protocols. 2026;21(9):3918-3943
Mammalian genome writing: Unlocking new length scales for genome engineering.41576918 · Pinglay, Sudarshan, Atwater, John T, Brosh, Ran et al.2026 · 9 citationsCell. 2026;189(2):356-374
Elucidating Neurodevelopmental Trajectories in Cancer with Topic Modeling: Revealing Persistent External Granule Layer Lineages in Medulloblastoma.41292772 · Rajendran, Ashmitha, Haldipur, Parthiv, Arora, Sonali et al.2025 · 0 citationsbioRxiv : the preprint server for biology. 2025
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording.41219485 · McDiarmid, Troy A, Taylor, Megan L, Chen, Wei et al.2026 · 4 citationsNature biotechnology. 2025
Large-scale discovery of neural enhancers for cis-regulation therapies.41278953 · McDiarmid, Troy A, Page, Nicholas F, Chardon, Florence M et al.2025 · 3 citationsbioRxiv : the preprint server for biology. 2025
A Roadmap for Predictive Human Immunology2511.03041v1 · Aly A. Khan, Jason Perera, James Zou et al.2025 · 2 citationsarXiv
Single-cell, multi-region profiling of the macaque brain across the lifespan.41279774 · Yang, Wei, Watkins, Kelsi L, DeCasien, Alex R et al.2025 · 1 citationbioRxiv : the preprint server for biology. 2025
Multiplex design and discovery of proximity handles for programmable proteome editing.41279570 · Suiter, Chase C, Ahn, Green, Chiu, Melodie et al.2025 · 3 citationsbioRxiv : the preprint server for biology. 2025
Dual-patterned pluripotent stem cells self-organize into a human embryo model with extended anterior-posterior patterning.41040184 · Liu, Zukai, Qiu, Chengxiang, Kubo, Connor A et al.2025 · 1 citationbioRxiv : the preprint server for biology. 2025
Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens.40475436 · Regalado, Samuel G, Qiu, Chengxiang, Lalanne, Jean-Benoît et al.2025 · 5 citationsbioRxiv : the preprint server for biology. 2025
Lineage recording in monoclonal gastruloids reveals heritable modes of early development.40475526 · Regalado, Samuel G, Qiu, Chengxiang, Kottapalli, Sanjay et al.2025 · 9 citationsbioRxiv : the preprint server for biology. 2025
Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity10.1101/2025.06.11.658967v1 · Arnould, C., Keukeleire, P., Inoue, F. et al.2025 · 3 citationsbioRxiv
An Improved, High-Yield Method for Isolating Nuclei from Individual Zebrafish Embryos for Single-Nucleus RNA Sequencing.40040474 · Rostomily, Clifford, Lee, Heidi, Tresenrider, Amy et al.2025 · 0 citationsZebrafish. 2025;22(2):42-45
A molecular proximity sensor based on an engineered, dual-component guide RNA.39937081 · Choi, Junhong, Chen, Wei, Liao, Hanna et al.2025 · 1 citationeLife. 2025;13
Combinatorial mapping of E3 ubiquitin ligases to their target substrates.39919746 · Suiter, Chase C, Calderon, Diego, Lee, David S et al.2025 · 20 citationsMolecular cell. 2025;85(4):829-842.e6
Technical and biological sources of noise confound multiplexed enhancer AAV screening.39868122 · Hunker, Avery C, Mich, John K, Taskin, Naz et al.2026 · 8 citationsbioRxiv : the preprint server for biology. 2025
Extensive length and homology dependent chimerism in pool-packaged AAV libraries.39868341 · Lalanne, Jean-Benoît, Mich, John K, Huynh, Chau et al.2026 · 9 citationsbioRxiv : the preprint server for biology. 2025
SARS-CoV-2 Diversity and Transmission on a University Campus across Two Academic Years during the Pandemic.39749508 · Casto, Amanda M, Paredes, Miguel I, Bennett, Julia C et al.2025 · 2 citationsClinical chemistry. 2025;71(1):192-202
The lives of cells, recorded.39587306 · Askary, Amjad, Chen, Wei, Choi, Junhong et al.2025 · 41 citationsNature reviews. Genetics. 2025;26(3):203-222
Clinical and Genomic Epidemiology of Coxsackievirus A21 and Enterovirus D68 in Homeless Shelters, King County, Washington, USA, 2019-2021.39447143 · Cox, Sarah N, Casto, Amanda M, Franko, Nicholas M et al.2024 · 1 citationEmerging infectious diseases. 2024;30(11):2250-2260
How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.39398201 · Bunne, Charlotte, Roohani, Yusuf, Rosen, Yanay et al.2026 · 415 citationsArXiv. 2024
Linking candidate causal autoimmune variants to T cell networks using genetic and epigenetic screens in primary human T cells.39416200 · Ho, Ching-Huang, Dippel, Maxwell A, McQuade, Meghan S et al.2025 · 9 citationsbioRxiv : the preprint server for biology. 2024
Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording10.1101/2024.09.30.615957v1 · McDiarmid, T. A., Taylor, M. L., Chen, W. et al.2024 · 2 citationsbioRxiv
Multi-condition and multi-modal temporal profile inference during mouse embryonic development.38496477 · Zhang, Ran, Qiu, Chengxiang, Filippova, Gala et al.2025 · 3 citationsbioRxiv : the preprint server for biology. 2024
Leukemia-derived apelin selects endothelial niche clones to promote tumorigenesis.39314385 · Baron, Chloe S, Mitchell, Olivia, Avagyan, Serine et al.2024 · 2 citationsbioRxiv : the preprint server for biology. 2024
The proteomic landscape and temporal dynamics of mammalian gastruloid development.39282277 · Garge, Riddhiman K, Lynch, Valerie, Fields, Rose et al.2026 · 2 citationsbioRxiv : the preprint server for biology. 2024
A molecular proximity sensor based on an engineered, dual-component guide RNA.37645782 · Choi, Junhong, Chen, Wei, Liao, Hanna et al.2025 · 8 citationsbioRxiv : the preprint server for biology. 2024
Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart.39187646 · Read, David F, Booth, Gregory T, Daza, Riza M et al.2024 · 22 citationsCommunications biology. 2024;7(1):1052
Retinoic acid induces human gastruloids with posterior embryo-like structures.39164488 · Hamazaki, Nobuhiko, Yang, Wei, Kubo, Connor A et al.2024 · 53 citationsNature cell biology. 2024;26(10):1790-1803
Cross-species imputation and comparison of single-cell transcriptomic profiles.37905060 · Zhang, Ran, Yang, Mu, Schreiber, Jacob et al.2025 · 12 citationsbioRxiv : the preprint server for biology. 2024
Optics-free reconstruction of 2D images via DNA barcode proximity graphs.39149271 · Liao, Hanna, Kottapalli, Sanjay, Huang, Yuqi et al.2024 · 6 citationsbioRxiv : the preprint server for biology. 2024
Symbolic recording of signalling and cis-regulatory element activity to DNA.39020177 · Chen, Wei, Choi, Junhong, Li, Xiaoyi et al.2024 · 63 citationsNature. 2024;632(8027):1073-1081
Molecular recording using DNA Typewriter.38844553 · Liao, Hanna, Choi, Junhong, Shendure, Jay2024 · 12 citationsNature protocols. 2024;19(10):2833-2862
Meningioma transcriptomic landscape demonstrates novel subtypes with regional associated biology and patient outcome.38788713 · Thirimanne, H Nayanga, Almiron-Bonnin, Damian, Nuechterlein, Nicholas et al.2024 · 29 citationsCell genomics. 2024;4(6):100566
Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years.38755171 · Perofsky, Amanda C, Hansen, Chelsea L, Burstein, Roy et al.2024 · 51 citationsNature communications. 2024;15(1):4164
Career total: at least 775 works. 462 are in this corpus.Showing the 50 most recent.
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