Shendure, Jay

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Cusanovich, D. A., Hill, A. J., Aghamirzaie, D., Daza, R. M., Pliner, H. A., Berletch, J. B., Filippova, G. N., Huang, X., Christiansen, L., DeWitt, W. S., et al. (2018) · Cell

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 759

De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes

Finding of Rare Disease Genes (FORGE) Canada Consortium, Rivière, J.-B., Mirzaa, G. M., O'Roak, B. J., Beddaoui, M., Alcantara, D., Conway, R. L., St-Onge, J., Schwartzentruber, J. A., Gripp, K. W., et al. (2012) · Nature Genetics

Fetal and Pediatric Neurological DisordersGenomics and Rare Diseases

Cited by 741

The 4D nucleome project

the 4D Nucleome Network, Dekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., Mirny, L. A., O’Shea, C. C., Park, P. J., et al. (2017) · Nature

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 732

Refining analyses of copy number variation identifies specific genes associated with developmental delay

Coe, B. P., Witherspoon, K., Rosenfeld, J. A., van Bon, B. W. M., Vulto-van Silfhout, A. T., Bosco, P., Friend, K. L., Baker, C., Buono, S., Vissers, L. E. L. M., et al. (2014) · Nature Genetics

Genomic variations and chromosomal abnormalitiesGenetics and Neurodevelopmental Disorders

Cited by 720

A brief history of human disease genetics

Claussnitzer, M., Cho, J. H., Collins, R., Cox, N. J., Dermitzakis, E. T., Hurles, M. E., Kathiresan, S., Kenny, E. E., Lindgren, C. M., MacArthur, D. G., et al. (2020) · Nature

Genetic Associations and EpidemiologyGenomics and Rare Diseases

Cited by 697

Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1

Carvill, G. L., Heavin, S. B., Yendle, S. C., McMahon, J. M., O'Roak, B. J., Cook, J., Khan, A., Dorschner, M. O., Weaver, M., Calvert, S., et al. (2013) · Nature Genetics

Epilepsy research and treatmentGenomics and Rare Diseases

Cited by 687

Diversity of Human Copy Number Variation and Multicopy Genes

Sudmant, P. H., Kitzman, J. O., Antonacci, F., Alkan, C., Malig, M., Tsalenko, A., Sampas, N., Bruhn, L., Shendure, J., 1000 Genomes Project, et al. (2010) · Science

Genomic variations and chromosomal abnormalitiesGenome Rearrangement Algorithms

Cited by 667

The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

Chong, J. X., Buckingham, K. J., Jhangiani, S. N., Boehm, C., Sobreira, N., Smith, J. D., Harrell, T. M., McMillin, M. J., Wiszniewski, W., Gambin, T., et al. (2015) · The American Journal of Human Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 643

CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores

Rentzsch, P., Schubach, M., Shendure, J., & Kircher, M. (2021) · Genome Medicine

Genomics and Rare DiseasesRNA Research and Splicing

Cited by 640

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

Gasperini, M., Hill, A. J., McFaline-Figueroa, J. L., Martin, B., Kim, S., Zhang, M. D., Jackson, D., Leith, A., Schreiber, J., Noble, W. S., et al. (2019) · Cell

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 613

Massively parallel functional dissection of mammalian enhancers in vivo

Patwardhan, R. P., Hiatt, J. B., Witten, D. M., Kim, M. J., Smith, R. P., May, D., Lee, C., Andrie, J. M., Lee, S.-I., Cooper, G. M., et al. (2012) · Nature Biotechnology

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 536

Supervised classification enables rapid annotation of cell atlases

Pliner, H. A., Shendure, J., & Trapnell, C. (2019) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 498

Multiplex assessment of protein variant abundance by massively parallel sequencing

Matreyek, K. A., Starita, L. M., Stephany, J. J., Martin, B., Chiasson, M. A., Gray, V. E., Kircher, M., Khechaduri, A., Dines, J. N., Hause, R. J., et al. (2018) · Nature Genetics

Genomics and Rare DiseasesCancer Genomics and Diagnostics

Cited by 436

A de novo convergence of autism genetics and molecular neuroscience

Krumm, N., O’Roak, B. J., Shendure, J., & Eichler, E. E. (2014) · Trends in Neurosciences

Genetics and Neurodevelopmental DisordersAutism Spectrum Disorder Research

Cited by 423

Massively multiplex chemical transcriptomics at single-cell resolution

Srivatsan, S. R., McFaline-Figueroa, J. L., Ramani, V., Saunders, L., Cao, J., Packer, J., Pliner, H. A., Jackson, D. L., Daza, R. M., Christiansen, L., et al. (2020) · Science

Single-cell and spatial transcriptomicsAdvanced Proteomics Techniques and Applications

Cited by 401

Towards a comprehensive catalogue of validated and target-linked human enhancers

Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 396

Somatic mutations in cerebral cortical malformations

Jamuar, S. S., Lam, A.-T. N., Kircher, M., D’Gama, A. M., Wang, J., Barry, B. J., Zhang, X., Hill, R. S., Partlow, J. N., Rozzo, A., et al. (2014) · New England Journal of Medicine

Fetal and Pediatric Neurological DisordersGenomics and Rare Diseases

Cited by 392

TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome

National Heart, L., Boileau, C., Guo, D.-C., Hanna, N., Regalado, E. S., Detaint, D., Gong, L., Varret, M., Prakash, S. K., Li, A. H., et al. (2012) · Nature Genetics

Connective tissue disorders researchAortic Disease and Treatment Approaches

Cited by 382

Variant interpretation: functional assays to the rescue

Starita, L. M., Ahituv, N., Dunham, M. J., Kitzman, J. O., Roth, F. P., Seelig, G., Shendure, J., & Fowler, D. M. (2017) · The American Journal of Human Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 381

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

Patwardhan, R. P., Lee, C., Litvin, O., Young, D. L., Pe'er, D., & Shendure, J. (2009) · Nature Biotechnology

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 377

PI3K/AKT pathway mutations cause a spectrum of brain malformations from megalencephaly to focal cortical dysplasia

Jansen, L. A., Mirzaa, G. M., Ishak, G. E., O'Roak, B. J., Hiatt, J. B., Roden, W. H., Gunter, S. A., Christian, S. L., Collins, S., Adams, C., et al. (2015) · Brain

Fetal and Pediatric Neurological DisordersEpilepsy research and treatment

Cited by 364

The cis-regulatory dynamics of embryonic development at single-cell resolution

Cusanovich, D. A., Reddington, J. P., Garfield, D. A., Daza, R. M., Aghamirzaie, D., Marco-Ferreres, R., Pliner, H. A., Christiansen, L., Qiu, X., Steemers, F. J., et al. (2018) · Nature

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 363

Saturation editing of genomic regions by multiplex homology-directed repair

Findlay, G. M., Boyle, E. A., Hause, R. J., Klein, J. C., & Shendure, J. (2014) · Nature

CRISPR and Genetic EngineeringDNA Repair Mechanisms

Cited by 362

Global survey of escape from X inactivation by RNA-sequencing in mouse

Yang, F., Babak, T., Shendure, J., & Disteche, C. M. (2010) · Genome Research

Genetic and Clinical Aspects of Sex Determination and Chromosomal AbnormalitiesEpigenetics and DNA Methylation

Cited by 350