Author: Roland Eils

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Preprints

The Human Cell Atlas

• Downloaded 12,616 times
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  • Site-wide: 583
  • In cell biology: 4
• Year to date:
  • Site-wide: 19,893
• Since beginning of last month:
  • Site-wide: 16,035

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

• Downloaded 5,346 times
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  • Site-wide: 1,818
  • In infectious diseases: 435
• Year to date:
  • Site-wide: 7,387
• Since beginning of last month:
  • Site-wide: 9,408

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

• Downloaded 5,013 times
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  • Site-wide: 1,975
  • In genomics: 196
• Year to date:
  • Site-wide: 15,784
• Since beginning of last month:
  • Site-wide: 15,857

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

• Downloaded 4,820 times
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  • Site-wide: 2,091
  • In genomics: 219
• Year to date:
  • Site-wide: 2,589
• Since beginning of last month:
  • Site-wide: 3,096

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

• Downloaded 2,517 times
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  • Site-wide: 5,311
  • In genomics: 599
• Year to date:
  • Site-wide: 98,194
• Since beginning of last month:
  • Site-wide: 75,385

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

• Downloaded 2,409 times
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  • Site-wide: 5,682
  • In genomics: 647
• Year to date:
  • Site-wide: 95,456
• Since beginning of last month:
  • Site-wide: 89,254

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

• Downloaded 2,338 times
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  • Site-wide: 5,946
  • In genomics: 670
• Year to date:
  • Site-wide: 34,408
• Since beginning of last month:
  • Site-wide: 41,537

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

• Downloaded 2,178 times
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  • Site-wide: 6,580
  • In bioinformatics: 772
• Year to date:
  • Site-wide: 5,429
• Since beginning of last month:
  • Site-wide: 10,074

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

• Downloaded 2,163 times
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  • Site-wide: 6,653
  • In genomics: 741
• Year to date:
  • Site-wide: 80,756
• Since beginning of last month:
  • Site-wide: 57,024

The landscape of viral associations in human cancers

• Downloaded 2,002 times
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  • Site-wide: 7,448
  • In cancer biology: 123
• Year to date:
  • Site-wide: 46,920
• Since beginning of last month:
  • Site-wide: 43,038

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

• Downloaded 1,828 times
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  • Site-wide: 8,558
  • In genomics: 929
• Year to date:
  • Site-wide: 54,709
• Since beginning of last month:
  • Site-wide: 53,989

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

• Downloaded 1,650 times
• Download rankings, all-time:
  • Site-wide: 9,968
  • In genomics: 1,084
• Year to date:
  • Site-wide: 69,771
• Since beginning of last month:
  • Site-wide: 87,559

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

• Downloaded 1,506 times
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  • Site-wide: 11,370
  • In cancer biology: 228
• Year to date:
  • Site-wide: 74,566
• Since beginning of last month:
  • Site-wide: 56,933

Genomic footprints of activated telomere maintenance mechanisms in cancer

• Downloaded 1,464 times
• Download rankings, all-time:
  • Site-wide: 11,847
  • In genomics: 1,289
• Year to date:
  • Site-wide: 94,421
• Since beginning of last month:
  • Site-wide: 78,596

ACEseq - allele specific copy number estimation from whole genome sequencing

• Downloaded 1,367 times
• Download rankings, all-time:
  • Site-wide: 13,172
  • In bioinformatics: 1,598
• Year to date:
  • Site-wide: 35,835
• Since beginning of last month:
  • Site-wide: 23,102

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

• Downloaded 1,152 times
• Download rankings, all-time:
  • Site-wide: 17,076
  • In bioinformatics: 2,058
• Year to date:
  • Site-wide: 19,908
• Since beginning of last month:
  • Site-wide: 30,530

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

• Downloaded 1,102 times
• Download rankings, all-time:
  • Site-wide: 18,207
  • In cancer biology: 419
• Year to date:
  • Site-wide: 3,423
• Since beginning of last month:
  • Site-wide: 3,163

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

• Downloaded 1,078 times
• Download rankings, all-time:
  • Site-wide: 18,823
  • In genomics: 1,905
• Year to date:
  • Site-wide: 126,582
• Since beginning of last month:
  • Site-wide: 112,565

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

• Downloaded 948 times
• Download rankings, all-time:
  • Site-wide: 22,648
  • In cancer biology: 551
• Year to date:
  • Site-wide: 105,405
• Since beginning of last month:
  • Site-wide: 95,670

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

• Downloaded 903 times
• Download rankings, all-time:
  • Site-wide: 24,356
  • In synthetic biology: 316
• Year to date:
  • Site-wide: 67,414
• Since beginning of last month:
  • Site-wide: 66,826

Web-based design and analysis tools for CRISPR base editing

• Downloaded 862 times
• Download rankings, all-time:
  • Site-wide: 25,947
  • In bioinformatics: 3,044
• Year to date:
  • Site-wide: 106,505
• Since beginning of last month:
  • Site-wide: 85,944

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

• Downloaded 741 times
• Download rankings, all-time:
  • Site-wide: 32,089
  • In synthetic biology: 414
• Year to date:
  • Site-wide: 87,500
• Since beginning of last month:
  • Site-wide: 87,669

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

• Downloaded 725 times
• Download rankings, all-time:
  • Site-wide: 33,061
  • In bioinformatics: 3,710
• Year to date:
  • Site-wide: 103,432
• Since beginning of last month:
  • Site-wide: 110,391

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

• Downloaded 689 times
• Download rankings, all-time:
  • Site-wide: 35,435
  • In immunology: 1,008
• Year to date:
  • Site-wide: 55,965
• Since beginning of last month:
  • Site-wide: 48,917

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

• Downloaded 637 times
• Download rankings, all-time:
  • Site-wide: 39,268
  • In synthetic biology: 497
• Year to date:
  • Site-wide: 72,629
• Since beginning of last month:
  • Site-wide: 99,718

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

• Downloaded 631 times
• Download rankings, all-time:
  • Site-wide: 39,778
  • In bioinformatics: 4,324
• Year to date:
  • Site-wide: 106,736
• Since beginning of last month:
  • Site-wide: 118,423

The COVID-19 PHARMACOME: A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization

• Downloaded 489 times
• Download rankings, all-time:
  • Site-wide: 54,240
  • In bioinformatics: 5,507
• Year to date:
  • Site-wide: 25,570
• Since beginning of last month:
  • Site-wide: 32,165

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

• Downloaded 469 times
• Download rankings, all-time:
  • Site-wide: 56,710
  • In cell biology: 2,474
• Year to date:
  • Site-wide: 108,014
• Since beginning of last month:
  • Site-wide: 100,620

Unraveling mitotic protein networks by 3D multiplexed epitope drug screening

• Downloaded 398 times
• Download rankings, all-time:
  • Site-wide: 67,127
  • In systems biology: 1,618
• Year to date:
  • Site-wide: 128,364
• Since beginning of last month:
  • Site-wide: 126,398

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

• Downloaded 380 times
• Download rankings, all-time:
  • Site-wide: 70,011
  • In bioinformatics: 6,683
• Year to date:
  • Site-wide: 101,025
• Since beginning of last month:
  • Site-wide: 96,385

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

• Downloaded 349 times
• Download rankings, all-time:
  • Site-wide: 75,420
  • In infectious diseases: 3,224
• Year to date:
  • Site-wide: 38,713
• Since beginning of last month:
  • Site-wide: 38,065

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

• Downloaded 284 times
• Download rankings, all-time:
  • Site-wide: 88,658
  • In genomics: 5,586
• Year to date:
  • Site-wide: 118,348
• Since beginning of last month:
  • Site-wide: 126,381

Induced aneuploidy disrupts MCF10A acini formation and CCND1 expression

• Downloaded 206 times
• Download rankings, all-time:
  • Site-wide: 105,798
  • In cancer biology: 3,231
• Year to date:
  • Site-wide: 100,229
• Since beginning of last month:
  • Site-wide: 83,667

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

• Downloaded 179 times
• Download rankings, all-time:
  • Site-wide: 111,683
  • In cancer biology: 3,431
• Year to date:
  • Site-wide: 48,366
• Since beginning of last month:
  • Site-wide: 40,313

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

• Downloaded 75 times
• Download rankings, all-time:
  • Site-wide: 131,180
  • In bioinformatics: 10,315
• Year to date:
  • Site-wide: 117,015
• Since beginning of last month:
  • Site-wide: 94,663