Shendure, Jay

High-resolution comparative analysis of great ape genomes

Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., et al. (2018) · Science

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 350

Recurrent de novo mutations implicate novel genes underlying simplex autism risk

O'Roak, B. J., Stessman, H. A., Boyle, E. A., Witherspoon, K. T., Martin, B., Lee, C., Vives, L., Baker, C., Hiatt, J. B., Nickerson, D. A., et al. (2014) · Nature Communications

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 336

Long-read sequence assembly of the gorilla genome

Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 333

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Inoue, F., Kircher, M., Martin, B., Cooper, G. M., Witten, D. M., McManus, M. T., Ahituv, N., & Shendure, J. (2017) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 331

Transcriptome-wide miR-155 Binding Map Reveals Widespread Noncanonical MicroRNA Targeting

Loeb, G. B., Khan, A. A., Canner, D., Hiatt, J. B., Shendure, J., Darnell, R. B., Leslie, C. S., & Rudensky, A. Y. (2012) · Molecular Cell

MicroRNA in disease regulationPlant Molecular Biology Research

Cited by 311

Predicting cellular responses to complex perturbations in high‐throughput screens

Lotfollahi, M., Klimovskaia Susmelj, A., De Donno, C., Hetzel, L., Ji, Y., Ibarra, I. L., Srivatsan, S. R., Naghipourfar, M., Daza, R. M., Martin, B., et al. (2023) · Molecular Systems Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 307

Highly scalable generation of DNA methylation profiles in single cells

Mulqueen, R. M., Pokholok, D., Norberg, S. J., Torkenczy, K. A., Fields, A. J., Sun, D., Sinnamon, J. R., Shendure, J., Trapnell, C., O'Roak, B. J., et al. (2018) · Nature Biotechnology

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 289

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

Liu, S., Huang, S., Chen, F., Zhao, L., Yuan, Y., Francis, S. S., Fang, L., Li, Z., Lin, L., Liu, R., et al. (2018) · Cell

Genetic Associations and EpidemiologyForensic and Genetic Research

Cited by 279

On the design of CRISPR-based single-cell molecular screens

Hill, A. J., McFaline-Figueroa, J. L., Starita, L. M., Gasperini, M. J., Matreyek, K. A., Packer, J., Jackson, D., Shendure, J., & Trapnell, C. (2018) · Nature Methods

CRISPR and Genetic EngineeringSingle-cell and spatial transcriptomics

Cited by 262

Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks

Agarwal, V., & Shendure, J. (2018) · Cell Reports

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 243

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

Agarwal, V., & Shendure, J. (2020) · Cell Reports

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 243

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

Smith, R. P., Taher, L., Patwardhan, R. P., Kim, M. J., Inoue, F., Shendure, J., Ovcharenko, I., & Ahituv, N. (2013) · Nature Genetics

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 239

A suppressor screen in Mecp2 mutant mice implicates cholesterol metabolism in Rett syndrome

Buchovecky, C. M., Turley, S. D., Brown, H. M., Kyle, S. M., McDonald, J. G., Liu, B., Pieper, A. A., Huang, W., Katz, D. M., Russell, D. W., et al. (2013) · Nature Genetics

Genetics and Neurodevelopmental DisordersAutism Spectrum Disorder Research

Cited by 234

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

Kircher, M., Xiong, C., Martin, B., Schubach, M., Inoue, F., Bell, R. J. A., Costello, J. F., Shendure, J., & Ahituv, N. (2019) · Nature Communications

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 234

A systematic evaluation of the design and context dependencies of massively parallel reporter assays

Klein, J. C., Agarwal, V., Inoue, F., Keith, A., Martin, B., Kircher, M., Ahituv, N., & Shendure, J. (2020) · Nature Methods

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 226

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

Chen, W., McKenna, A., Schreiber, J., Haeussler, M., Yin, Y., Agarwal, V., Noble, W. S., & Shendure, J. (2019) · Nucleic Acids Research

CRISPR and Genetic EngineeringDNA Repair Mechanisms

Cited by 216

Estimating the human mutation rate using autozygosity in a founder population.

Campbell, C. D., Chong, J. X., Malig, M., Ko, A., Dumont, B. L., Han, L., Vives, L., O'Roak, B. J., Sudmant, P. H., Shendure, J., et al. (2012) · Nature Genetics

Genomics and Rare DiseasesEvolution and Genetic Dynamics

Cited by 215

Computational discovery of sense-antisense transcription in the human and mouse genomes

Shendure, J., & Church, G. M. (2002) · Genome Biology

Cancer-related molecular mechanisms researchRNA Research and Splicing

Cited by 191

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

Amini, S., Pushkarev, D., Christiansen, L., Kostem, E., Royce, T., Turk, C., Pignatelli, N., Adey, A., Kitzman, J. O., Vijayan, K., et al. (2014) · Nature Genetics

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 189

De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability

Küry, S., van Woerden, G. M., Besnard, T., Proietti Onori, M., Latypova, X., Towne, M. C., Cho, M. T., Prescott, T. E., Ploeg, M. A., Sanders, S., et al. (2017) · The American Journal of Human Genetics

Genetics and Neurodevelopmental DisordersGenomics and Rare Diseases

Cited by 185

Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis

Starita, L. M., Pruneda, J. N., Lo, R. S., Fowler, D. M., Kim, H. J., Hiatt, J. B., Shendure, J., Brzovic, P. S., Fields, S., & Klevit, R. E. (2013) · Proceedings of the National Academy of Sciences

Ubiquitin and proteasome pathwaysProtein Degradation and Inhibitors

Cited by 183

The power of multiplexed functional analysis of genetic variants

Gasperini, M., Starita, L., & Shendure, J. (2016) · Nature Protocols

Genomics and Rare DiseasesCRISPR and Genetic Engineering

Cited by 160

FlashFry: A fast and flexible tool for large-scale CRISPR target design

McKenna, A., & Shendure, J. (2018) · BMC Biology

CRISPR and Genetic EngineeringRNA regulation and disease

Cited by 152

Massively parallel characterization of transcriptional regulatory elements

Agarwal, V., Inoue, F., Schubach, M., Penzar, D., Martin, B. K., Dash, P. M., Keukeleire, P., Zhang, Z., Sohota, A., Zhao, J., et al. (2025) · Nature

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 146