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Author: Jay Shendure

Rankings

  • All-time downloads: 148,396 (rank: 598 )
  • Categories:
    • bioengineering: 4,549 (rank: 326 )
    • bioinformatics: 2,818 (rank: 5,395 )
    • cancer biology: 2,368 (rank: 2,663 (tie) )
    • developmental biology: 11,789 (rank: 42 )
    • epidemiology: 12,470 (rank: 1,261 (tie) )
    • evolutionary biology: 3,995 (rank: 913 )
    • genetics: 5,279 (rank: 3,721 )
    • genomics: 89,247 (rank: 110 )
    • infectious diseases: 8,595 (rank: 5,866 )
    • molecular biology: 7,286 (rank: 406 )

Downloads per author, site-wide

Preprints

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

genomics more details view paper
  • Downloaded 10,493 times
  • Download rankings, all-time:
    • Site-wide: 905
    • In genomics: 65
  • Year to date:
    • Site-wide: 50,576
  • Since beginning of last month:
    • Site-wide: 117,559

Cryptic transmission of SARS-CoV-2 in Washington State

epidemiology more details view paper
  • Downloaded 9,523 times
  • Download rankings, all-time:
    • Site-wide: 1,011
    • In epidemiology: 134
  • Year to date:
    • Site-wide: 8,423
  • Since beginning of last month:
    • Site-wide: 63,938

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

infectious diseases more details view paper
  • Downloaded 6,829 times
  • Download rankings, all-time:
    • Site-wide: 1,535
    • In infectious diseases: 417
  • Year to date:
    • Site-wide: 7,083
  • Since beginning of last month:
    • Site-wide: 77,112

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

molecular biology more details view paper
  • Downloaded 5,913 times
  • Download rankings, all-time:
    • Site-wide: 1,882
    • In molecular biology: 36
  • Year to date:
    • Site-wide: 6,464
  • Since beginning of last month:
    • Site-wide: 76,968

Supervised classification enables rapid annotation of cell atlases

genomics more details view paper
  • Downloaded 5,525 times
  • Download rankings, all-time:
    • Site-wide: 2,072
    • In genomics: 184
  • Year to date:
    • Site-wide: 30,370
  • Since beginning of last month:
    • Site-wide: 72,311

Accurate functional classification of thousands of BRCA1 variants with saturation genome editing

genomics more details view paper
  • Downloaded 5,392 times
  • Download rankings, all-time:
    • Site-wide: 2,135
    • In genomics: 190
  • Year to date:
    • Site-wide: 46,170
  • Since beginning of last month:
    • Site-wide: 119,358

Whole organism lineage tracing by combinatorial and cumulative genome editing

developmental biology more details view paper
  • Downloaded 4,504 times
  • Download rankings, all-time:
    • Site-wide: 2,730
    • In developmental biology: 21
  • Year to date:
    • Site-wide: 95,296
  • Since beginning of last month:
    • Site-wide: 41,929

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain by scGESTALT

developmental biology more details view paper
  • Downloaded 4,337 times
  • Download rankings, all-time:
    • Site-wide: 2,895
    • In developmental biology: 23
  • Year to date:
    • Site-wide: 105,582
  • Since beginning of last month:
    • Site-wide: 41,791

crisprQTL mapping as a genome-wide association framework for cellular genetic screens

genomics more details view paper
  • Downloaded 4,237 times
  • Download rankings, all-time:
    • Site-wide: 2,994
    • In genomics: 305
  • Year to date:
    • Site-wide: 50,550
  • Since beginning of last month:
    • Site-wide: 48,495

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

genomics more details view paper
  • Downloaded 4,080 times
  • Download rankings, all-time:
    • Site-wide: 3,156
    • In genomics: 324
  • Year to date:
    • Site-wide: 88,976
  • Since beginning of last month:
    • Site-wide: 117,692

Massively multiplex single-cell Hi-C

genomics more details view paper
  • Downloaded 4,055 times
  • Download rankings, all-time:
    • Site-wide: 3,177
    • In genomics: 327
  • Year to date:
    • Site-wide: 100,545
  • Since beginning of last month:
    • Site-wide: None

On the design of CRISPR-based single cell molecular screens

genomics more details view paper
  • Downloaded 4,034 times
  • Download rankings, all-time:
    • Site-wide: 3,212
    • In genomics: 332
  • Year to date:
    • Site-wide: 28,738
  • Since beginning of last month:
    • Site-wide: 68,469

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

genomics more details view paper
  • Downloaded 3,973 times
  • Download rankings, all-time:
    • Site-wide: 3,278
    • In genomics: 337
  • Year to date:
    • Site-wide: 55,719
  • Since beginning of last month:
    • Site-wide: 101,360

Chromatin accessibility dynamics of myogenesis at single cell resolution

genomics more details view paper
  • Downloaded 3,430 times
  • Download rankings, all-time:
    • Site-wide: 4,017
    • In genomics: 413
  • Year to date:
    • Site-wide: 53,797
  • Since beginning of last month:
    • Site-wide: 17,238

Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

genomics more details view paper
  • Downloaded 3,377 times
  • Download rankings, all-time:
    • Site-wide: 4,111
    • In genomics: 423
  • Year to date:
    • Site-wide: 64,418
  • Since beginning of last month:
    • Site-wide: None

The 4D Nucleome Project

genomics more details view paper
  • Downloaded 3,173 times
  • Download rankings, all-time:
    • Site-wide: 4,512
    • In genomics: 466
  • Year to date:
    • Site-wide: 102,967
  • Since beginning of last month:
    • Site-wide: None

Characterizing the temporal dynamics of gene expression in single cells with sci-fate

genomics more details view paper
  • Downloaded 3,158 times
  • Download rankings, all-time:
    • Site-wide: 4,549
    • In genomics: 473
  • Year to date:
    • Site-wide: 58,758
  • Since beginning of last month:
    • Site-wide: 73,444

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors

evolutionary biology more details view paper
  • Downloaded 3,041 times
  • Download rankings, all-time:
    • Site-wide: 4,758
    • In evolutionary biology: 92
  • Year to date:
    • Site-wide: 20,592
  • Since beginning of last month:
    • Site-wide: 70,469

Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing.

genomics more details view paper
  • Downloaded 2,771 times
  • Download rankings, all-time:
    • Site-wide: 5,441
    • In genomics: 561
  • Year to date:
    • Site-wide: 47,167
  • Since beginning of last month:
    • Site-wide: 117,667

Systematic reconstruction of the cellular trajectories of mammalian embryogenesis

developmental biology more details view paper
  • Downloaded 2,753 times
  • Download rankings, all-time:
    • Site-wide: 5,488
    • In developmental biology: 61
  • Year to date:
    • Site-wide: 832
  • Since beginning of last month:
    • Site-wide: 9,317

Precise genomic deletions using paired prime editing

bioengineering more details view paper
  • Downloaded 2,574 times
  • Download rankings, all-time:
    • Site-wide: 6,056
    • In bioengineering: 79
  • Year to date:
    • Site-wide: 908
  • Since beginning of last month:
    • Site-wide: 3,078

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

genomics more details view paper
  • Downloaded 2,412 times
  • Download rankings, all-time:
    • Site-wide: 6,697
    • In genomics: 712
  • Year to date:
    • Site-wide: 29,818
  • Since beginning of last month:
    • Site-wide: 72,622

Single-cell lineage and transcriptome reconstruction of metastatic cancer reveals selection of aggressive hybrid EMT states

cancer biology more details view paper
  • Downloaded 2,368 times
  • Download rankings, all-time:
    • Site-wide: 6,877
    • In cancer biology: 106
  • Year to date:
    • Site-wide: 5,256
  • Since beginning of last month:
    • Site-wide: 49,897

High-throughput mapping of meiotic crossover and chromosome mis-segregation events in interspecific hybrid mice

genetics more details view paper
  • Downloaded 2,299 times
  • Download rankings, all-time:
    • Site-wide: 7,164
    • In genetics: 318
  • Year to date:
    • Site-wide: 61,066
  • Since beginning of last month:
    • Site-wide: 116,956

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

genomics more details view paper
  • Downloaded 2,135 times
  • Download rankings, all-time:
    • Site-wide: 7,981
    • In genomics: 831
  • Year to date:
    • Site-wide: 82,060
  • Since beginning of last month:
    • Site-wide: None

Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

genomics more details view paper
  • Downloaded 1,978 times
  • Download rankings, all-time:
    • Site-wide: 8,945
    • In genomics: 914
  • Year to date:
    • Site-wide: 36,755
  • Since beginning of last month:
    • Site-wide: 72,256

A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues

bioengineering more details view paper
  • Downloaded 1,975 times
  • Download rankings, all-time:
    • Site-wide: 8,967
    • In bioengineering: 143
  • Year to date:
    • Site-wide: 5,112
  • Since beginning of last month:
    • Site-wide: None

Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells

genomics more details view paper
  • Downloaded 1,907 times
  • Download rankings, all-time:
    • Site-wide: 9,435
    • In genomics: 957
  • Year to date:
    • Site-wide: 58,526
  • Since beginning of last month:
    • Site-wide: 59,607

Multiplex Assessment of Protein Variant Abundance by Massively Parallel Sequencing

genetics more details view paper
  • Downloaded 1,878 times
  • Download rankings, all-time:
    • Site-wide: 9,648
    • In genetics: 419
  • Year to date:
    • Site-wide: 84,668
  • Since beginning of last month:
    • Site-wide: 55,966

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C

genomics more details view paper
  • Downloaded 1,871 times
  • Download rankings, all-time:
    • Site-wide: 9,695
    • In genomics: 990
  • Year to date:
    • Site-wide: 77,471
  • Since beginning of last month:
    • Site-wide: 117,741

Paired CRISPR/Cas9 guide-RNAs enable high-throughput deletion scanning (ScanDel) of a Mendelian disease locus for functionally critical non-coding elements

genomics more details view paper
  • Downloaded 1,812 times
  • Download rankings, all-time:
    • Site-wide: 10,160
    • In genomics: 1,044
  • Year to date:
    • Site-wide: 65,256
  • Since beginning of last month:
    • Site-wide: 117,531

Single cell ATAC-seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

genomics more details view paper
  • Downloaded 1,788 times
  • Download rankings, all-time:
    • Site-wide: 10,380
    • In genomics: 1,068
  • Year to date:
    • Site-wide: 97,655
  • Since beginning of last month:
    • Site-wide: 30,426

Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context

epidemiology more details view paper
  • Downloaded 1,719 times
  • Download rankings, all-time:
    • Site-wide: 11,012
    • In epidemiology: 810
  • Year to date:
    • Site-wide: 17,470
  • Since beginning of last month:
    • Site-wide: 79,564

Dynamic reorganization of nuclear architecture during human cardiogenesis

genomics more details view paper
  • Downloaded 1,662 times
  • Download rankings, all-time:
    • Site-wide: 11,549
    • In genomics: 1,186
  • Year to date:
    • Site-wide: 119,690
  • Since beginning of last month:
    • Site-wide: 55,324

The landscape of alternative polyadenylation in single cells of the developing mouse embryo

genomics more details view paper
  • Downloaded 1,604 times
  • Download rankings, all-time:
    • Site-wide: 12,170
    • In genomics: 1,249
  • Year to date:
    • Site-wide: 1,677
  • Since beginning of last month:
    • Site-wide: 94,409

The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

infectious diseases more details view paper
  • Downloaded 1,404 times
  • Download rankings, all-time:
    • Site-wide: 14,834
    • In infectious diseases: 1,659
  • Year to date:
    • Site-wide: 68,431
  • Since beginning of last month:
    • Site-wide: 94,182

Condensin-dependent chromatin condensation represses transcription globally during quiescence

molecular biology more details view paper
  • Downloaded 1,373 times
  • Download rankings, all-time:
    • Site-wide: 15,368
    • In molecular biology: 418
  • Year to date:
    • Site-wide: 65,014
  • Since beginning of last month:
    • Site-wide: 105,204

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

genomics more details view paper
  • Downloaded 1,242 times
  • Download rankings, all-time:
    • Site-wide: 17,826
    • In genomics: 1,732
  • Year to date:
    • Site-wide: 125,892
  • Since beginning of last month:
    • Site-wide: 71,777

Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy

genomics more details view paper
  • Downloaded 1,228 times
  • Download rankings, all-time:
    • Site-wide: 18,152
    • In genomics: 1,765
  • Year to date:
    • Site-wide: 78,650
  • Since beginning of last month:
    • Site-wide: 39,417

Functional Characterization of Enhancer Evolution in the Primate Lineage

genomics more details view paper
  • Downloaded 1,214 times
  • Download rankings, all-time:
    • Site-wide: 18,465
    • In genomics: 1,795
  • Year to date:
    • Site-wide: 118,163
  • Since beginning of last month:
    • Site-wide: 114,289

TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

genomics more details view paper
  • Downloaded 1,200 times
  • Download rankings, all-time:
    • Site-wide: 18,772
    • In genomics: 1,830
  • Year to date:
    • Site-wide: 13,524
  • Since beginning of last month:
    • Site-wide: 7,797

Unsupervised manifold alignment for single-cell multi-omics data

bioinformatics more details view paper
  • Downloaded 1,170 times
  • Download rankings, all-time:
    • Site-wide: 19,475
    • In bioinformatics: 2,248
  • Year to date:
    • Site-wide: 17,503
  • Since beginning of last month:
    • Site-wide: 85,604

Rapid cost-effective viral genome sequencing by V-seq

genomics more details view paper
  • Downloaded 1,026 times
  • Download rankings, all-time:
    • Site-wide: 23,616
    • In genomics: 2,231
  • Year to date:
    • Site-wide: 24,021
  • Since beginning of last month:
    • Site-wide: 10,908

A combination of transcription factors mediates inducible interchromosomal pairing

genomics more details view paper
  • Downloaded 1,002 times
  • Download rankings, all-time:
    • Site-wide: 24,449
    • In genomics: 2,288
  • Year to date:
    • Site-wide: 107,095
  • Since beginning of last month:
    • Site-wide: 119,642

Genome wide association with quantitative resistance phenotypes in Mycobacterium tuberculosis reveals novel resistance genes and regulatory regions

evolutionary biology more details view paper
  • Downloaded 954 times
  • Download rankings, all-time:
    • Site-wide: 26,321
    • In evolutionary biology: 1,124
  • Year to date:
    • Site-wide: 49,340
  • Since beginning of last month:
    • Site-wide: None

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

epidemiology more details view paper
  • Downloaded 925 times
  • Download rankings, all-time:
    • Site-wide: 27,493
    • In epidemiology: 1,529
  • Year to date:
    • Site-wide: 20,088
  • Since beginning of last month:
    • Site-wide: 52,893

Functional Testing of Thousands of Osteoarthritis-Associated Variants for Regulatory Activity

genomics more details view paper
  • Downloaded 914 times
  • Download rankings, all-time:
    • Site-wide: 27,915
    • In genomics: 2,522
  • Year to date:
    • Site-wide: 149,617
  • Since beginning of last month:
    • Site-wide: 116,072

MIPSTR: a method for multiplex genotyping of germ-line and somatic STR variation across many individuals

genomics more details view paper
  • Downloaded 880 times
  • Download rankings, all-time:
    • Site-wide: 29,458
    • In genomics: 2,617
  • Year to date:
    • Site-wide: 149,901
  • Since beginning of last month:
    • Site-wide: None

Concurrent Genome and Epigenome Editing by CRISPR-Mediated Sequence Replacement

genomics more details view paper
  • Downloaded 875 times
  • Download rankings, all-time:
    • Site-wide: 29,688
    • In genomics: 2,636
  • Year to date:
    • Site-wide: 135,284
  • Since beginning of last month:
    • Site-wide: 99,086

Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing

genomics more details view paper
  • Downloaded 864 times
  • Download rankings, all-time:
    • Site-wide: 30,214
    • In genomics: 2,667
  • Year to date:
    • Site-wide: 3,927
  • Since beginning of last month:
    • Site-wide: 60,855

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies

bioinformatics more details view paper
  • Downloaded 840 times
  • Download rankings, all-time:
    • Site-wide: 31,441
    • In bioinformatics: 3,506
  • Year to date:
    • Site-wide: 131,664
  • Since beginning of last month:
    • Site-wide: None

An open-source platform to distribute and interpret data from multiplexed assays of variant effect

genomics more details view paper
  • Downloaded 829 times
  • Download rankings, all-time:
    • Site-wide: 32,038
    • In genomics: 2,789
  • Year to date:
    • Site-wide: 119,115
  • Since beginning of last month:
    • Site-wide: 119,013

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

bioinformatics more details view paper
  • Downloaded 808 times
  • Download rankings, all-time:
    • Site-wide: 33,205
    • In bioinformatics: 3,666
  • Year to date:
    • Site-wide: 123,645
  • Since beginning of last month:
    • Site-wide: 54,262

Trans− and cis−acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome

genomics more details view paper
  • Downloaded 754 times
  • Download rankings, all-time:
    • Site-wide: 36,581
    • In genomics: 3,063
  • Year to date:
    • Site-wide: 81,193
  • Since beginning of last month:
    • Site-wide: 19,677

The dynamic three-dimensional organization of the diploid yeast genome

genomics more details view paper
  • Downloaded 682 times
  • Download rankings, all-time:
    • Site-wide: 41,890
    • In genomics: 3,386
  • Year to date:
    • Site-wide: 139,977
  • Since beginning of last month:
    • Site-wide: None

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

genomics more details view paper
  • Downloaded 645 times
  • Download rankings, all-time:
    • Site-wide: 45,072
    • In genomics: 3,577
  • Year to date:
    • Site-wide: 16,105
  • Since beginning of last month:
    • Site-wide: 62,269

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

genomics more details view paper
  • Downloaded 606 times
  • Download rankings, all-time:
    • Site-wide: 48,733
    • In genomics: 3,773
  • Year to date:
    • Site-wide: 20,018
  • Since beginning of last month:
    • Site-wide: 85,054

Autosomal dominant multiple pterygium syndrome is caused by mutations in MYH3

genetics more details view paper
  • Downloaded 571 times
  • Download rankings, all-time:
    • Site-wide: 52,559
    • In genetics: 2,324
  • Year to date:
    • Site-wide: 107,049
  • Since beginning of last month:
    • Site-wide: None

Suppressor mutations in Mecp2-null mice reveal that the DNA damage response is key to Rett syndrome pathology

genetics more details view paper
  • Downloaded 531 times
  • Download rankings, all-time:
    • Site-wide: 57,374
    • In genetics: 2,525
  • Year to date:
    • Site-wide: 85,352
  • Since beginning of last month:
    • Site-wide: None

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

genomics more details view paper
  • Downloaded 419 times
  • Download rankings, all-time:
    • Site-wide: 74,126
    • In genomics: 5,025
  • Year to date:
    • Site-wide: 80,326
  • Since beginning of last month:
    • Site-wide: None

Comparable specimen collection from both ends of at-home mid-turbinate swabs

infectious diseases more details view paper
  • Downloaded 362 times
  • Download rankings, all-time:
    • Site-wide: 84,625
    • In infectious diseases: 3,937
  • Year to date:
    • Site-wide: 43,900
  • Since beginning of last month:
    • Site-wide: None

SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

epidemiology more details view paper
  • Downloaded 303 times
  • Download rankings, all-time:
    • Site-wide: 97,603
    • In epidemiology: 4,106
  • Year to date:
    • Site-wide: 17,930
  • Since beginning of last month:
    • Site-wide: 87,450

MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis

developmental biology more details view paper
  • Downloaded 195 times
  • Download rankings, all-time:
    • Site-wide: 123,936
    • In developmental biology: 3,318
  • Year to date:
    • Site-wide: 46,692
  • Since beginning of last month:
    • Site-wide: 26,946

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