Shendure, Jay

A general framework for estimating the relative pathogenicity of human genetic variants

Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 6,183

Next-generation DNA sequencing

Shendure, J., & Ji, H. (2008) · Nature Biotechnology

Genomics and Phylogenetic StudiesGenetics, Bioinformatics, and Biomedical Research

Cited by 4,509

The single-cell transcriptional landscape of mammalian organogenesis

Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019) · Nature

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 4,490

CADD: predicting the deleteriousness of variants throughout the human genome

Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J., & Kircher, M. (2019) · Nucleic Acids Research

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 3,534

The contribution of de novo coding mutations to autism spectrum disorder

Iossifov, I., O’Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., Stessman, H. A., Witherspoon, K. T., Vives, L., Patterson, K. E., et al. (2014) · Nature

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 2,585

The complete genome sequence of a Neanderthal from the Altai Mountains

Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 2,254

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

O’Roak, B. J., Vives, L., Girirajan, S., Karakoc, E., Krumm, N., Coe, B. P., Levy, R., Ko, A., Lee, C., Smith, J. D., et al. (2012) · Nature

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 2,165

Targeted capture and massively parallel sequencing of 12 human exomes

Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E. E., et al. (2009) · Nature

Genomics and Rare DiseasesGenomics and Phylogenetic Studies

Cited by 2,030

A high-coverage genome sequence from an archaic denisovan individual

Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 1,967

Exome sequencing identifies the cause of a mendelian disorder

Ng, S. B., Buckingham, K. J., Lee, C., Bigham, A. W., Tabor, H. K., Dent, K. M., Huff, C. D., Shannon, P. T., Jabs, E. W., Nickerson, D. A., et al. (2010) · Nature Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 1,957

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O., & Shendure, J. (2013) · Nature Biotechnology

Genomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Cited by 1,470

Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

Cao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S. N., Steemers, F. J., et al. (2017) · Science

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 1,402

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., Steemers, F. J., Trapnell, C., & Shendure, J. (2015) · Science

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 1,248

Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

O’Roak, B. J., Vives, L., Fu, W., Egertson, J. D., Stanaway, I. B., Phelps, I. G., Carvill, G., Kumar, A., Lee, C., Ankenman, K., et al. (2012) · Science

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 1,240

Guidelines for investigating causality of sequence variants in human disease

MacArthur, D. G., Manolio, T. A., Dimmock, D. P., Rehm, H. L., Shendure, J., Abecasis, G. R., Adams, D. R., Altman, R. B., Antonarakis, S. E., Ashley, E. A., et al. (2014) · Nature

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 1,224

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

O'Roak, B. J., Deriziotis, P., Lee, C., Vives, L., Schwartz, J. J., Girirajan, S., Karakoc, E., MacKenzie, A. P., Ng, S. B., Baker, C., et al. (2011) · Nature Genetics

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 1,203

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

Roach, J. C., Glusman, G., Smit, A. F. A., Huff, C. D., Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M., et al. (2010) · Science

Genomics and Rare DiseasesGenomics and Phylogenetic Studies

Cited by 1,084

Genome evolution in the allotetraploid frog Xenopus laevis

Session, A. M., Uno, Y., Kwon, T., Chapman, J. A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M., et al. (2016) · Nature

Chromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Cited by 949

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

Cao, J., Cusanovich, D. A., Ramani, V., Aghamirzaie, D., Pliner, H. A., Hill, A. J., Daza, R. M., McFaline-Figueroa, J. L., Packer, J. S., Christiansen, L., et al. (2018) · Science

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 938

Accurate classification of BRCA1 variants with saturation genome editing

Findlay, G. M., Daza, R. M., Martin, B., Zhang, M. D., Leith, A. P., Gasperini, M., Janizek, J. D., Huang, X., Starita, L. M., & Shendure, J. (2018) · Nature

BRCA gene mutations in cancerGenomics and Rare Diseases

Cited by 843

Disruptive CHD8 Mutations Define a Subtype of Autism Early in Development

Bernier, R., Golzio, C., Xiong, B., Stessman, H. A., Coe, B. P., Penn, O., Witherspoon, K., Gerdts, J., Baker, C., Vulto-van Silfhout, A. T., et al. (2014) · Cell

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 798

Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data

Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., et al. (2018) · Molecular Cell

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 789

Whole-organism lineage tracing by combinatorial and cumulative genome editing

McKenna, A., Findlay, G. M., Gagnon, J. A., Horwitz, M. S., Schier, A. F., & Shendure, J. (2016) · Science

CRISPR and Genetic EngineeringSingle-cell and spatial transcriptomics

Cited by 766

A human cell atlas of fetal gene expression

Cao, J., O’Day, D. R., Pliner, H. A., Kingsley, P. D., Deng, M., Daza, R. M., Zager, M. A., Aldinger, K. A., Blecher-Gonen, R., Zhang, F., et al. (2020) · Science

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 764