Author: Roland Eils

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Preprints

The Human Cell Atlas

• Downloaded 12,504 times
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  • Site-wide: 512
  • In cell biology: 4
• Year to date:
  • Site-wide: 33,000
• Since beginning of last month:
  • Site-wide: 15,790

Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19

• Downloaded 5,139 times
• Download rankings, all-time:
  • Site-wide: 1,681
  • In infectious diseases: 391
• Year to date:
  • Site-wide: 5,805
• Since beginning of last month:
  • Site-wide: 7,257

SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches

• Downloaded 4,882 times
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  • Site-wide: 1,802
  • In genomics: 194
• Year to date:
  • Site-wide: 21,457
• Since beginning of last month:
  • Site-wide: 12,574

Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas

• Downloaded 4,392 times
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  • Site-wide: 2,107
  • In genomics: 245
• Year to date:
  • Site-wide: 2,301
• Since beginning of last month:
  • Site-wide: 2,441

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

• Downloaded 2,499 times
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  • Site-wide: 4,744
  • In genomics: 570
• Year to date:
  • Site-wide: 99,945
• Since beginning of last month:
  • Site-wide: 113,055

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

• Downloaded 2,388 times
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  • Site-wide: 5,105
  • In genomics: 617
• Year to date:
  • Site-wide: 118,590
• Since beginning of last month:
  • Site-wide: 65,637

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

• Downloaded 2,287 times
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  • Site-wide: 5,456
  • In genomics: 652
• Year to date:
  • Site-wide: 16,239
• Since beginning of last month:
  • Site-wide: 35,850

A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair

• Downloaded 2,137 times
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  • Site-wide: 5,989
  • In genomics: 702
• Year to date:
  • Site-wide: 104,912
• Since beginning of last month:
  • Site-wide: 53,564

The landscape of viral associations in human cancers

• Downloaded 1,963 times
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  • Site-wide: 6,791
  • In cancer biology: 113
• Year to date:
  • Site-wide: 28,068
• Since beginning of last month:
  • Site-wide: 43,551

Cell segmentation-free inference of cell types from in situ transcriptomics data

• Downloaded 1,944 times
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  • Site-wide: 6,894
  • In bioinformatics: 866
• Year to date:
  • Site-wide: 3,274
• Since beginning of last month:
  • Site-wide: 5,955

pheno-seq - linking morphological features to gene expression in 3D cell culture systems

• Downloaded 1,786 times
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  • Site-wide: 7,798
  • In genomics: 886
• Year to date:
  • Site-wide: 89,943
• Since beginning of last month:
  • Site-wide: 93,889

Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers

• Downloaded 1,623 times
• Download rankings, all-time:
  • Site-wide: 9,068
  • In genomics: 1,034
• Year to date:
  • Site-wide: 54,421
• Since beginning of last month:
  • Site-wide: 53,714

Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics

• Downloaded 1,476 times
• Download rankings, all-time:
  • Site-wide: 10,412
  • In cancer biology: 209
• Year to date:
  • Site-wide: 111,210
• Since beginning of last month:
  • Site-wide: 78,770

Genomic footprints of activated telomere maintenance mechanisms in cancer

• Downloaded 1,449 times
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  • Site-wide: 10,701
  • In genomics: 1,209
• Year to date:
  • Site-wide: 57,236
• Since beginning of last month:
  • Site-wide: 61,849

ACEseq - allele specific copy number estimation from whole genome sequencing

• Downloaded 1,301 times
• Download rankings, all-time:
  • Site-wide: 12,598
  • In bioinformatics: 1,581
• Year to date:
  • Site-wide: 60,750
• Since beginning of last month:
  • Site-wide: 24,839

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

• Downloaded 1,068 times
• Download rankings, all-time:
  • Site-wide: 16,965
  • In genomics: 1,780
• Year to date:
  • Site-wide: 115,116
• Since beginning of last month:
  • Site-wide: 93,575

Gene set inference from single-cell sequencing data using a hybrid of matrix factorization and variational autoencoders

• Downloaded 1,062 times
• Download rankings, all-time:
  • Site-wide: 17,106
  • In bioinformatics: 2,109
• Year to date:
  • Site-wide: 11,041
• Since beginning of last month:
  • Site-wide: 6,636

Resolving Drug Effects In Patient-Derived Cancer Cells Links Organoid Responses To Genome Alterations

• Downloaded 934 times
• Download rankings, all-time:
  • Site-wide: 20,653
  • In cancer biology: 500
• Year to date:
  • Site-wide: 93,393
• Since beginning of last month:
  • Site-wide: 66,641

Cell-specific CRISPR/Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins

• Downloaded 875 times
• Download rankings, all-time:
  • Site-wide: 22,705
  • In synthetic biology: 297
• Year to date:
  • Site-wide: 58,989
• Since beginning of last month:
  • Site-wide: 62,558

Web-based design and analysis tools for CRISPR base editing

• Downloaded 846 times
• Download rankings, all-time:
  • Site-wide: 23,819
  • In bioinformatics: 2,886
• Year to date:
  • Site-wide: 111,529
• Since beginning of last month:
  • Site-wide: 62,607

Computational design of anti-CRISPR proteins with improved inhibition potency and expanded specificity

• Downloaded 724 times
• Download rankings, all-time:
  • Site-wide: 29,588
  • In synthetic biology: 387
• Year to date:
  • Site-wide: 58,714
• Since beginning of last month:
  • Site-wide: 62,660

Identification and prioritisation of causal variants in human genetic disorders from exome or whole genome sequencing data

• Downloaded 711 times
• Download rankings, all-time:
  • Site-wide: 30,313
  • In bioinformatics: 3,496
• Year to date:
  • Site-wide: 81,694
• Since beginning of last month:
  • Site-wide: 110,699

Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy

• Downloaded 694 times
• Download rankings, all-time:
  • Site-wide: 31,303
  • In cancer biology: 849
• Year to date:
  • Site-wide: 8,879
• Since beginning of last month:
  • Site-wide: 5,618

Single-fluorescent protein reporters allow parallel quantification of NK cell-mediated granzyme and caspase activities in single target cells

• Downloaded 658 times
• Download rankings, all-time:
  • Site-wide: 33,634
  • In immunology: 894
• Year to date:
  • Site-wide: 33,205
• Since beginning of last month:
  • Site-wide: 47,404

Impact of cancer mutational signatures on transcription factor motifs in the human genome

• Downloaded 615 times
• Download rankings, all-time:
  • Site-wide: 36,723
  • In bioinformatics: 4,090
• Year to date:
  • Site-wide: 109,500
• Since beginning of last month:
  • Site-wide: 122,049

Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein

• Downloaded 609 times
• Download rankings, all-time:
  • Site-wide: 37,243
  • In synthetic biology: 479
• Year to date:
  • Site-wide: 82,255
• Since beginning of last month:
  • Site-wide: 41,242

Automated screening by 3D light-sheet microscopy with high spatial and temporal resolution reveals mitotic phenotypes

• Downloaded 454 times
• Download rankings, all-time:
  • Site-wide: 52,837
  • In cell biology: 2,322
• Year to date:
  • Site-wide: 99,367
• Since beginning of last month:
  • Site-wide: 112,229

The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization

• Downloaded 412 times
• Download rankings, all-time:
  • Site-wide: 58,469
  • In bioinformatics: 5,885
• Year to date:
  • Site-wide: 16,503
• Since beginning of last month:
  • Site-wide: 19,670

Unraveling mitotic protein networks by 3D multiplexed epitope drug screening

• Downloaded 391 times
• Download rankings, all-time:
  • Site-wide: 61,680
  • In systems biology: 1,532
• Year to date:
  • Site-wide: 100,413
• Since beginning of last month:
  • Site-wide: 77,989

HTSlib-js: Developer toolkit for a client-side JavaScript interface for HTSlib

• Downloaded 360 times
• Download rankings, all-time:
  • Site-wide: 66,523
  • In bioinformatics: 6,464
• Year to date:
  • Site-wide: 122,013
• Since beginning of last month:
  • Site-wide: 111,487

Delayed viral clearance and exacerbated airway hyperinflammation in hypertensive COVID-19 patients

• Downloaded 295 times
• Download rankings, all-time:
  • Site-wide: 78,204
  • In infectious diseases: 2,924
• Year to date:
  • Site-wide: 33,563
• Since beginning of last month:
  • Site-wide: 13,556

Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4

• Downloaded 276 times
• Download rankings, all-time:
  • Site-wide: 82,045
  • In genomics: 5,330
• Year to date:
  • Site-wide: 67,776
• Since beginning of last month:
  • Site-wide: 116,852

Induced aneuploidy disrupts MCF10A acini formation and CCND1 expression

• Downloaded 189 times
• Download rankings, all-time:
  • Site-wide: 100,502
  • In cancer biology: 3,077
• Year to date:
  • Site-wide: 102,485
• Since beginning of last month:
  • Site-wide: 95,967

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability

• Downloaded 133 times
• Download rankings, all-time:
  • Site-wide: 111,252
  • In cancer biology: 3,452
• Year to date:
  • Site-wide: 59,364
• Since beginning of last month:
  • Site-wide: 36,044

Integrative Ranking Of Enhancer Networks Facilitates The Discovery Of Epigenetic Markers In Cancer

• Downloaded 62 times
• Download rankings, all-time:
  • Site-wide: 122,340
  • In bioinformatics: 9,833
• Year to date:
  • Site-wide: 112,060
• Since beginning of last month:
  • Site-wide: 32,935