Author: Roland Eils

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Preprints

The Human Cell Atlas

• Downloaded 12,681 times
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  • Site-wide: 625
  • In cell biology: 5
• Year to date:
  • Site-wide: 20,841
• Since beginning of last month:
  • Site-wide: 19,043

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

• Downloaded 5,441 times
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  • Site-wide: 1,921
  • In infectious diseases: 469
• Year to date:
  • Site-wide: 8,730
• Since beginning of last month:
  • Site-wide: 20,250

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

• Downloaded 5,115 times
• Download rankings, all-time:
  • Site-wide: 2,080
  • In genomics: 199
• Year to date:
  • Site-wide: 14,453
• Since beginning of last month:
  • Site-wide: 11,625

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

• Downloaded 5,016 times
• Download rankings, all-time:
  • Site-wide: 2,144
  • In genomics: 210
• Year to date:
  • Site-wide: 3,042
• Since beginning of last month:
  • Site-wide: 5,998

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

• Downloaded 2,525 times
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  • Site-wide: 5,746
  • In genomics: 629
• Year to date:
  • Site-wide: 109,726
• Since beginning of last month:
  • Site-wide: 114,009

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

• Downloaded 2,414 times
• Download rankings, all-time:
  • Site-wide: 6,141
  • In genomics: 674
• Year to date:
  • Site-wide: 114,757
• Since beginning of last month:
  • Site-wide: 141,043

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

• Downloaded 2,373 times
• Download rankings, all-time:
  • Site-wide: 6,292
  • In genomics: 690
• Year to date:
  • Site-wide: 38,671
• Since beginning of last month:
  • Site-wide: 61,500

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

• Downloaded 2,356 times
• Download rankings, all-time:
  • Site-wide: 6,364
  • In bioinformatics: 709
• Year to date:
  • Site-wide: 5,333
• Since beginning of last month:
  • Site-wide: 5,200

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

• Downloaded 2,175 times
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  • Site-wide: 7,148
  • In genomics: 770
• Year to date:
  • Site-wide: 89,880
• Since beginning of last month:
  • Site-wide: 124,437

The landscape of viral associations in human cancers

• Downloaded 2,022 times
• Download rankings, all-time:
  • Site-wide: 7,921
  • In cancer biology: 130
• Year to date:
  • Site-wide: 56,925
• Since beginning of last month:
  • Site-wide: 63,664

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

• Downloaded 1,843 times
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  • Site-wide: 9,117
  • In genomics: 966
• Year to date:
  • Site-wide: 66,985
• Since beginning of last month:
  • Site-wide: 78,369

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

• Downloaded 1,683 times
• Download rankings, all-time:
  • Site-wide: 10,436
  • In genomics: 1,110
• Year to date:
  • Site-wide: 61,364
• Since beginning of last month:
  • Site-wide: 43,212

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

• Downloaded 1,540 times
• Download rankings, all-time:
  • Site-wide: 11,847
  • In cancer biology: 239
• Year to date:
  • Site-wide: 63,327
• Since beginning of last month:
  • Site-wide: 36,882

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

• Downloaded 1,516 times
• Download rankings, all-time:
  • Site-wide: 12,117
  • In cancer biology: 253
• Year to date:
  • Site-wide: 2,499
• Since beginning of last month:
  • Site-wide: 1,133

Genomic footprints of activated telomere maintenance mechanisms in cancer

• Downloaded 1,478 times
• Download rankings, all-time:
  • Site-wide: 12,610
  • In genomics: 1,335
• Year to date:
  • Site-wide: 95,932
• Since beginning of last month:
  • Site-wide: 77,521

ACEseq - allele specific copy number estimation from whole genome sequencing

• Downloaded 1,428 times
• Download rankings, all-time:
  • Site-wide: 13,324
  • In bioinformatics: 1,581
• Year to date:
  • Site-wide: 31,824
• Since beginning of last month:
  • Site-wide: 23,327

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

• Downloaded 1,195 times
• Download rankings, all-time:
  • Site-wide: 17,386
  • In bioinformatics: 2,042
• Year to date:
  • Site-wide: 24,453
• Since beginning of last month:
  • Site-wide: 50,709

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

• Downloaded 1,089 times
• Download rankings, all-time:
  • Site-wide: 19,932
  • In genomics: 1,967
• Year to date:
  • Site-wide: 124,340
• Since beginning of last month:
  • Site-wide: 85,832

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

• Downloaded 957 times
• Download rankings, all-time:
  • Site-wide: 24,081
  • In cancer biology: 595
• Year to date:
  • Site-wide: 114,933
• Since beginning of last month:
  • Site-wide: 98,604

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

• Downloaded 922 times
• Download rankings, all-time:
  • Site-wide: 25,409
  • In synthetic biology: 327
• Year to date:
  • Site-wide: 72,914
• Since beginning of last month:
  • Site-wide: 76,735

Web-based design and analysis tools for CRISPR base editing

• Downloaded 873 times
• Download rankings, all-time:
  • Site-wide: 27,442
  • In bioinformatics: 3,151
• Year to date:
  • Site-wide: 109,748
• Since beginning of last month:
  • Site-wide: 87,581

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

• Downloaded 753 times
• Download rankings, all-time:
  • Site-wide: 33,695
  • In synthetic biology: 424
• Year to date:
  • Site-wide: 95,857
• Since beginning of last month:
  • Site-wide: 98,864

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

• Downloaded 738 times
• Download rankings, all-time:
  • Site-wide: 34,670
  • In bioinformatics: 3,833
• Year to date:
  • Site-wide: 104,457
• Since beginning of last month:
  • Site-wide: 88,710

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

• Downloaded 709 times
• Download rankings, all-time:
  • Site-wide: 36,658
  • In immunology: 1,096
• Year to date:
  • Site-wide: 63,623
• Since beginning of last month:
  • Site-wide: 42,886

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

• Downloaded 659 times
• Download rankings, all-time:
  • Site-wide: 40,384
  • In synthetic biology: 503
• Year to date:
  • Site-wide: 73,244
• Since beginning of last month:
  • Site-wide: 58,790

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

• Downloaded 638 times
• Download rankings, all-time:
  • Site-wide: 42,125
  • In bioinformatics: 4,500
• Year to date:
  • Site-wide: 118,863
• Since beginning of last month:
  • Site-wide: 110,423

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

• Downloaded 571 times
• Download rankings, all-time:
  • Site-wide: 48,364
  • In bioinformatics: 5,014
• Year to date:
  • Site-wide: 21,973
• Since beginning of last month:
  • Site-wide: 22,558

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

• Downloaded 481 times
• Download rankings, all-time:
  • Site-wide: 59,131
  • In cell biology: 2,598
• Year to date:
  • Site-wide: 107,793
• Since beginning of last month:
  • Site-wide: 117,078

Unraveling mitotic protein networks by 3D multiplexed epitope drug screening

• Downloaded 405 times
• Download rankings, all-time:
  • Site-wide: 70,649
  • In systems biology: 1,670
• Year to date:
  • Site-wide: 134,035
• Since beginning of last month:
  • Site-wide: 101,753

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

• Downloaded 400 times
• Download rankings, all-time:
  • Site-wide: 71,400
  • In bioinformatics: 6,781
• Year to date:
  • Site-wide: 91,735
• Since beginning of last month:
  • Site-wide: 78,212

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

• Downloaded 374 times
• Download rankings, all-time:
  • Site-wide: 76,043
  • In infectious diseases: 3,465
• Year to date:
  • Site-wide: 46,593
• Since beginning of last month:
  • Site-wide: 46,482

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

• Downloaded 289 times
• Download rankings, all-time:
  • Site-wide: 93,208
  • In genomics: 5,775
• Year to date:
  • Site-wide: 129,816
• Since beginning of last month:
  • Site-wide: 125,834

Induced aneuploidy disrupts MCF10A acini formation and CCND1 expression

• Downloaded 221 times
• Download rankings, all-time:
  • Site-wide: 108,912
  • In cancer biology: 3,303
• Year to date:
  • Site-wide: 100,052
• Since beginning of last month:
  • Site-wide: 94,083

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

• Downloaded 199 times
• Download rankings, all-time:
  • Site-wide: 114,066
  • In cancer biology: 3,478
• Year to date:
  • Site-wide: 57,261
• Since beginning of last month:
  • Site-wide: 74,303

Intratumoural heterogeneity and immune modulation in lung adenocarcinoma of female smokers and never smokers

• Downloaded 112 times
• Download rankings, all-time:
  • Site-wide: 132,899
  • In cancer biology: 4,117
• Year to date:
  • Site-wide: 38,474
• Since beginning of last month:
  • Site-wide: 4,784

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

• Downloaded 87 times
• Download rankings, all-time:
  • Site-wide: 137,311
  • In bioinformatics: 10,634
• Year to date:
  • Site-wide: 114,058
• Since beginning of last month:
  • Site-wide: 106,396