Author: Roland Eils

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Preprints

The Human Cell Atlas

• Downloaded 12,560 times
• Download rankings, all-time:
  • Site-wide: 550
  • In cell biology: 4
• Year to date:
  • Site-wide: 18,657
• Since beginning of last month:
  • Site-wide: 12,573

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

• Downloaded 5,259 times
• Download rankings, all-time:
  • Site-wide: 1,746
  • In infectious diseases: 418
• Year to date:
  • Site-wide: 5,660
• Since beginning of last month:
  • Site-wide: 4,443

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

• Downloaded 4,955 times
• Download rankings, all-time:
  • Site-wide: 1,884
  • In genomics: 194
• Year to date:
  • Site-wide: 13,250
• Since beginning of last month:
  • Site-wide: 12,028

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

• Downloaded 4,459 times
• Download rankings, all-time:
  • Site-wide: 2,199
  • In genomics: 246
• Year to date:
  • Site-wide: 5,349
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 2,507 times
• Download rankings, all-time:
  • Site-wide: 5,020
  • In genomics: 585
• Year to date:
  • Site-wide: 97,700
• Since beginning of last month:
  • Site-wide: 78,577

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

• Downloaded 2,402 times
• Download rankings, all-time:
  • Site-wide: 5,361
  • In genomics: 629
• Year to date:
  • Site-wide: 79,913
• Since beginning of last month:
  • Site-wide: 55,221

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

• Downloaded 2,322 times
• Download rankings, all-time:
  • Site-wide: 5,635
  • In genomics: 660
• Year to date:
  • Site-wide: 21,703
• Since beginning of last month:
  • Site-wide: 18,929

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

• Downloaded 2,148 times
• Download rankings, all-time:
  • Site-wide: 6,299
  • In genomics: 721
• Year to date:
  • Site-wide: 85,377
• Since beginning of last month:
  • Site-wide: 80,903

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

• Downloaded 2,066 times
• Download rankings, all-time:
  • Site-wide: 6,660
  • In bioinformatics: 795
• Year to date:
  • Site-wide: 4,316
• Since beginning of last month:
  • Site-wide: 3,969

The landscape of viral associations in human cancers

• Downloaded 1,968 times
• Download rankings, all-time:
  • Site-wide: 7,138
  • In cancer biology: 118
• Year to date:
  • Site-wide: 62,664
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 1,812 times
• Download rankings, all-time:
  • Site-wide: 8,094
  • In genomics: 907
• Year to date:
  • Site-wide: 45,001
• Since beginning of last month:
  • Site-wide: 37,943

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

• Downloaded 1,644 times
• Download rankings, all-time:
  • Site-wide: 9,408
  • In genomics: 1,053
• Year to date:
  • Site-wide: 46,215
• Since beginning of last month:
  • Site-wide: 30,335

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

• Downloaded 1,491 times
• Download rankings, all-time:
  • Site-wide: 10,833
  • In cancer biology: 217
• Year to date:
  • Site-wide: 73,598
• Since beginning of last month:
  • Site-wide: 52,712

Genomic footprints of activated telomere maintenance mechanisms in cancer

• Downloaded 1,455 times
• Download rankings, all-time:
  • Site-wide: 11,223
  • In genomics: 1,253
• Year to date:
  • Site-wide: 85,574
• Since beginning of last month:
  • Site-wide: 67,406

ACEseq - allele specific copy number estimation from whole genome sequencing

• Downloaded 1,322 times
• Download rankings, all-time:
  • Site-wide: 12,972
  • In bioinformatics: 1,601
• Year to date:
  • Site-wide: 47,111
• Since beginning of last month:
  • Site-wide: 46,442

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

• Downloaded 1,127 times
• Download rankings, all-time:
  • Site-wide: 16,542
  • In bioinformatics: 2,030
• Year to date:
  • Site-wide: 12,125
• Since beginning of last month:
  • Site-wide: 15,044

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

• Downloaded 1,067 times
• Download rankings, all-time:
  • Site-wide: 17,913
  • In genomics: 1,857
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 935 times
• Download rankings, all-time:
  • Site-wide: 21,726
  • In cancer biology: 528
• Year to date:
  • Site-wide: 120,671
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 896 times
• Download rankings, all-time:
  • Site-wide: 23,137
  • In cancer biology: 572
• Year to date:
  • Site-wide: 3,637
• Since beginning of last month:
  • Site-wide: 3,671

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

• Downloaded 891 times
• Download rankings, all-time:
  • Site-wide: 23,322
  • In synthetic biology: 298
• Year to date:
  • Site-wide: 54,838
• Since beginning of last month:
  • Site-wide: 43,733

Web-based design and analysis tools for CRISPR base editing

• Downloaded 854 times
• Download rankings, all-time:
  • Site-wide: 24,743
  • In bioinformatics: 2,951
• Year to date:
  • Site-wide: 101,714
• Since beginning of last month:
  • Site-wide: 64,830

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

• Downloaded 727 times
• Download rankings, all-time:
  • Site-wide: 31,004
  • In synthetic biology: 398
• Year to date:
  • Site-wide: 98,980
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 721 times
• Download rankings, all-time:
  • Site-wide: 31,349
  • In bioinformatics: 3,561
• Year to date:
  • Site-wide: 80,586
• Since beginning of last month:
  • Site-wide: 66,417

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

• Downloaded 671 times
• Download rankings, all-time:
  • Site-wide: 34,529
  • In immunology: 938
• Year to date:
  • Site-wide: 49,365
• Since beginning of last month:
  • Site-wide: 43,171

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

• Downloaded 631 times
• Download rankings, all-time:
  • Site-wide: 37,431
  • In synthetic biology: 476
• Year to date:
  • Site-wide: 48,498
• Since beginning of last month:
  • Site-wide: 37,576

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

• Downloaded 613 times
• Download rankings, all-time:
  • Site-wide: 38,881
  • In bioinformatics: 4,278
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 469 times
• Download rankings, all-time:
  • Site-wide: 53,604
  • In bioinformatics: 5,512
• Year to date:
  • Site-wide: 15,559
• Since beginning of last month:
  • Site-wide: 13,076

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

• Downloaded 464 times
• Download rankings, all-time:
  • Site-wide: 54,151
  • In cell biology: 2,376
• Year to date:
  • Site-wide: 88,884
• Since beginning of last month:
  • Site-wide: 51,719

Unraveling mitotic protein networks by 3D multiplexed epitope drug screening

• Downloaded 396 times
• Download rankings, all-time:
  • Site-wide: 63,826
  • In systems biology: 1,556
• Year to date:
  • Site-wide: 110,059
• Since beginning of last month:
  • Site-wide: 90,627

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

• Downloaded 374 times
• Download rankings, all-time:
  • Site-wide: 67,377
  • In bioinformatics: 6,511
• Year to date:
  • Site-wide: 84,250
• Since beginning of last month:
  • Site-wide: 54,527

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

• Downloaded 324 times
• Download rankings, all-time:
  • Site-wide: 75,977
  • In infectious diseases: 3,053
• Year to date:
  • Site-wide: 31,353
• Since beginning of last month:
  • Site-wide: 32,093

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: 84,037
  • In genomics: 5,411
• Year to date:
  • Site-wide: 84,443
• Since beginning of last month:
  • Site-wide: 78,205

Induced aneuploidy disrupts MCF10A acini formation and CCND1 expression

• Downloaded 198 times
• Download rankings, all-time:
  • Site-wide: 102,559
  • In cancer biology: 3,145
• Year to date:
  • Site-wide: 90,435
• Since beginning of last month:
  • Site-wide: 62,160

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

• Downloaded 155 times
• Download rankings, all-time:
  • Site-wide: 111,267
  • In cancer biology: 3,443
• Year to date:
  • Site-wide: 44,225
• Since beginning of last month:
  • Site-wide: 31,788

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

• Downloaded 68 times
• Download rankings, all-time:
  • Site-wide: 125,924
  • In bioinformatics: 10,023
• Year to date:
  • Site-wide: 108,996
• Since beginning of last month:
  • Site-wide: 86,757