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Author: Oliver Stegle

Rankings

  • All-time downloads: 123,106 (rank: 766 )
  • Categories:
    • bioinformatics: 32,611 (rank: 85 )
    • cancer biology: 2,136 (rank: 2,566 (tie) )
    • cell biology: 1,131 (rank: 7,209 (tie) )
    • developmental biology: 9,112 (rank: 64 )
    • genetic and genomic medicine: 2,020 (rank: 879 (tie) )
    • genetics: 16,971 (rank: 826 )
    • genomics: 54,879 (rank: 141 )
    • neuroscience: 358 (rank: 55,514 (tie) )
    • systems biology: 3,888 (rank: 904 )

Downloads per author, site-wide

Preprints

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

genomics more details view paper
  • Downloaded 12,873 times
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    • Site-wide: 596
    • In genomics: 40
  • Year to date:
    • Site-wide: 3,207
  • Since beginning of last month:
    • Site-wide: 5,451

Accurate prediction of single-cell DNA methylation states using deep learning

bioinformatics more details view paper
  • Downloaded 6,339 times
  • Download rankings, all-time:
    • Site-wide: 1,495
    • In bioinformatics: 100
  • Year to date:
    • Site-wide: 46,771
  • Since beginning of last month:
    • Site-wide: 45,958

LIMIX: genetic analysis of multiple traits

genetics more details view paper
  • Downloaded 6,260 times
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    • Site-wide: 1,516
    • In genetics: 52
  • Year to date:
    • Site-wide: 21,707
  • Since beginning of last month:
    • Site-wide: 25,594

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

developmental biology more details view paper
  • Downloaded 6,234 times
  • Download rankings, all-time:
    • Site-wide: 1,526
    • In developmental biology: 10
  • Year to date:
    • Site-wide: 24,234
  • Since beginning of last month:
    • Site-wide: 18,555

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

genomics more details view paper
  • Downloaded 5,373 times
  • Download rankings, all-time:
    • Site-wide: 1,885
    • In genomics: 178
  • Year to date:
    • Site-wide: 20,708
  • Since beginning of last month:
    • Site-wide: 19,197

Multi-Omics factor analysis - a framework for unsupervised integration of multi-omic data sets

bioinformatics more details view paper
  • Downloaded 5,071 times
  • Download rankings, all-time:
    • Site-wide: 2,032
    • In bioinformatics: 174
  • Year to date:
    • Site-wide: 29,132
  • Since beginning of last month:
    • Site-wide: 23,303

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

genomics more details view paper
  • Downloaded 4,943 times
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    • Site-wide: 2,108
    • In genomics: 213
  • Year to date:
    • Site-wide: 26,887
  • Since beginning of last month:
    • Site-wide: 21,489

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

genomics more details view paper
  • Downloaded 4,232 times
  • Download rankings, all-time:
    • Site-wide: 2,633
    • In genomics: 287
  • Year to date:
    • Site-wide: 23,863
  • Since beginning of last month:
    • Site-wide: 21,467

Kipoi: accelerating the community exchange and reuse of predictive models for genomics

bioinformatics more details view paper
  • Downloaded 4,041 times
  • Download rankings, all-time:
    • Site-wide: 2,805
    • In bioinformatics: 252
  • Year to date:
    • Site-wide: 13,706
  • Since beginning of last month:
    • Site-wide: 11,010

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics

genomics more details view paper
  • Downloaded 3,991 times
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    • Site-wide: 2,869
    • In genomics: 318
  • Year to date:
    • Site-wide: 483
  • Since beginning of last month:
    • Site-wide: 440

Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis

bioinformatics more details view paper
  • Downloaded 3,653 times
  • Download rankings, all-time:
    • Site-wide: 3,265
    • In bioinformatics: 317
  • Year to date:
    • Site-wide: 49,617
  • Since beginning of last month:
    • Site-wide: 58,143

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

genetics more details view paper
  • Downloaded 3,153 times
  • Download rankings, all-time:
    • Site-wide: 4,015
    • In genetics: 165
  • Year to date:
    • Site-wide: 3,678
  • Since beginning of last month:
    • Site-wide: 7,428

SpatialDE - Identification of spatially variable genes

genomics more details view paper
  • Downloaded 3,131 times
  • Download rankings, all-time:
    • Site-wide: 4,061
    • In genomics: 454
  • Year to date:
    • Site-wide: 39,509
  • Since beginning of last month:
    • Site-wide: 57,873

Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects

bioinformatics more details view paper
  • Downloaded 2,960 times
  • Download rankings, all-time:
    • Site-wide: 4,375
    • In bioinformatics: 449
  • Year to date:
    • Site-wide: 108,472
  • Since beginning of last month:
    • Site-wide: 134,020

Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation

systems biology more details view paper
  • Downloaded 2,937 times
  • Download rankings, all-time:
    • Site-wide: 4,426
    • In systems biology: 74
  • Year to date:
    • Site-wide: 84,621
  • Since beginning of last month:
    • Site-wide: 86,127

A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation

developmental biology more details view paper
  • Downloaded 2,878 times
  • Download rankings, all-time:
    • Site-wide: 4,552
    • In developmental biology: 49
  • Year to date:
    • Site-wide: 19,980
  • Since beginning of last month:
    • Site-wide: 26,448

Common genetic variation drives molecular heterogeneity in human iPSCs

genomics more details view paper
  • Downloaded 2,840 times
  • Download rankings, all-time:
    • Site-wide: 4,636
    • In genomics: 508
  • Year to date:
    • Site-wide: 62,030
  • Since beginning of last month:
    • Site-wide: 53,773

MOFA+: a probabilistic framework for comprehensive integration of structured single-cell data

bioinformatics more details view paper
  • Downloaded 2,605 times
  • Download rankings, all-time:
    • Site-wide: 5,249
    • In bioinformatics: 561
  • Year to date:
    • Site-wide: 27,447
  • Since beginning of last month:
    • Site-wide: 46,832

Single-cell RNA-seq of differentiating iPS cells reveals dynamic genetic effects on gene expression

genomics more details view paper
  • Downloaded 2,556 times
  • Download rankings, all-time:
    • Site-wide: 5,407
    • In genomics: 595
  • Year to date:
    • Site-wide: 55,743
  • Since beginning of last month:
    • Site-wide: 34,338

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

genomics more details view paper
  • Downloaded 2,537 times
  • Download rankings, all-time:
    • Site-wide: 5,473
    • In genomics: 602
  • Year to date:
    • Site-wide: 44,298
  • Since beginning of last month:
    • Site-wide: 43,422

A linear mixed model approach to study multivariate gene-environment interactions

genetics more details view paper
  • Downloaded 2,410 times
  • Download rankings, all-time:
    • Site-wide: 5,926
    • In genetics: 272
  • Year to date:
    • Site-wide: 59,767
  • Since beginning of last month:
    • Site-wide: 34,130

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

bioinformatics more details view paper
  • Downloaded 2,279 times
  • Download rankings, all-time:
    • Site-wide: 6,424
    • In bioinformatics: 730
  • Year to date:
    • Site-wide: 5,292
  • Since beginning of last month:
    • Site-wide: 7,059

The Polygenic and Monogenic Basis of Blood Traits and Diseases

genetic and genomic medicine more details view paper
  • Downloaded 2,020 times
  • Download rankings, all-time:
    • Site-wide: 7,644
    • In genetic and genomic medicine: 28
  • Year to date:
    • Site-wide: 27,459
  • Since beginning of last month:
    • Site-wide: 56,084

Dissecting indirect genetic effects from peers in laboratory mice

genetics more details view paper
  • Downloaded 1,569 times
  • Download rankings, all-time:
    • Site-wide: 11,169
    • In genetics: 529
  • Year to date:
    • Site-wide: 21,182
  • Since beginning of last month:
    • Site-wide: 8,398

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

bioinformatics more details view paper
  • Downloaded 1,543 times
  • Download rankings, all-time:
    • Site-wide: 11,433
    • In bioinformatics: 1,376
  • Year to date:
    • Site-wide: 60,903
  • Since beginning of last month:
    • Site-wide: 43,907

Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO

bioinformatics more details view paper
  • Downloaded 1,448 times
  • Download rankings, all-time:
    • Site-wide: 12,535
    • In bioinformatics: 1,508
  • Year to date:
    • Site-wide: 3,732
  • Since beginning of last month:
    • Site-wide: 3,710

Screening for genes that accelerate the epigenetic ageing clock in humans reveals a role for the H3K36 methyltransferase NSD1

genomics more details view paper
  • Downloaded 1,443 times
  • Download rankings, all-time:
    • Site-wide: 12,605
    • In genomics: 1,347
  • Year to date:
    • Site-wide: 64,930
  • Since beginning of last month:
    • Site-wide: 57,808

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

cancer biology more details view paper
  • Downloaded 1,428 times
  • Download rankings, all-time:
    • Site-wide: 12,847
    • In cancer biology: 274
  • Year to date:
    • Site-wide: 90,615
  • Since beginning of last month:
    • Site-wide: 64,134

Systematic assessment of regulatory effects of human disease variants in pluripotent cells

genomics more details view paper
  • Downloaded 1,418 times
  • Download rankings, all-time:
    • Site-wide: 12,984
    • In genomics: 1,382
  • Year to date:
    • Site-wide: 29,247
  • Since beginning of last month:
    • Site-wide: 55,948

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

bioinformatics more details view paper
  • Downloaded 1,405 times
  • Download rankings, all-time:
    • Site-wide: 13,158
    • In bioinformatics: 1,572
  • Year to date:
    • Site-wide: 70,161
  • Since beginning of last month:
    • Site-wide: 70,599

LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies

genomics more details view paper
  • Downloaded 1,313 times
  • Download rankings, all-time:
    • Site-wide: 14,573
    • In genomics: 1,518
  • Year to date:
    • Site-wide: 63,557
  • Since beginning of last month:
    • Site-wide: 64,283

Robustness and applicability of functional genomics tools on scRNA-seq data

bioinformatics more details view paper
  • Downloaded 1,267 times
  • Download rankings, all-time:
    • Site-wide: 15,400
    • In bioinformatics: 1,845
  • Year to date:
    • Site-wide: 50,172
  • Since beginning of last month:
    • Site-wide: 59,195

Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for twelve immune-mediated diseases

genomics more details view paper
  • Downloaded 1,261 times
  • Download rankings, all-time:
    • Site-wide: 15,502
    • In genomics: 1,589
  • Year to date:
    • Site-wide: 28,959
  • Since beginning of last month:
    • Site-wide: 27,238

Identifying extrinsic versus intrinsic drivers of variation in cell behaviour in human iPS cell lines from healthy donors

cell biology more details view paper
  • Downloaded 1,131 times
  • Download rankings, all-time:
    • Site-wide: 18,210
    • In cell biology: 585
  • Year to date:
    • Site-wide: 40,702
  • Since beginning of last month:
    • Site-wide: 49,771

Genome-wide Analysis of Differential Transcriptional and Epigenetic Variability Across Human Immune Cell Types

genomics more details view paper
  • Downloaded 1,096 times
  • Download rankings, all-time:
    • Site-wide: 19,063
    • In genomics: 1,909
  • Year to date:
    • Site-wide: 122,511
  • Since beginning of last month:
    • Site-wide: 133,657

Genome-scale oscillations in DNA methylation during exit from pluripotency

genomics more details view paper
  • Downloaded 1,058 times
  • Download rankings, all-time:
    • Site-wide: 20,109
    • In genomics: 2,007
  • Year to date:
    • Site-wide: 129,380
  • Since beginning of last month:
    • Site-wide: 132,654

Joint genetic analysis using variant sets reveals polygenic gene-context interactions

genetics more details view paper
  • Downloaded 962 times
  • Download rankings, all-time:
    • Site-wide: 23,046
    • In genetics: 1,099
  • Year to date:
    • Site-wide: 132,071
  • Since beginning of last month:
    • Site-wide: 113,168

Genomic determinants of protein abundance variation in colorectal cancer cells

systems biology more details view paper
  • Downloaded 951 times
  • Download rankings, all-time:
    • Site-wide: 23,496
    • In systems biology: 478
  • Year to date:
    • Site-wide: 95,578
  • Since beginning of last month:
    • Site-wide: 86,161

Tandem duplications lead to loss of fitness effects in CRISPR-Cas9 data

genomics more details view paper
  • Downloaded 818 times
  • Download rankings, all-time:
    • Site-wide: 29,029
    • In genomics: 2,660
  • Year to date:
    • Site-wide: 108,585
  • Since beginning of last month:
    • Site-wide: 111,277

Genomic Rearrangements Considered as Quantitative Traits

genetics more details view paper
  • Downloaded 813 times
  • Download rankings, all-time:
    • Site-wide: 29,320
    • In genetics: 1,404
  • Year to date:
    • Site-wide: 118,827
  • Since beginning of last month:
    • Site-wide: 113,157

Genetic Analyses of Blood Cell Structure for Biological and Pharmacological Inference

genetics more details view paper
  • Downloaded 802 times
  • Download rankings, all-time:
    • Site-wide: 29,905
    • In genetics: 1,435
  • Year to date:
    • Site-wide: 22,378
  • Since beginning of last month:
    • Site-wide: 33,204

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage

genomics more details view paper
  • Downloaded 800 times
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    • Site-wide: 29,967
    • In genomics: 2,712
  • Year to date:
    • Site-wide: 130,694
  • Since beginning of last month:
    • Site-wide: 135,943

Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans

genomics more details view paper
  • Downloaded 731 times
  • Download rankings, all-time:
    • Site-wide: 33,979
    • In genomics: 2,962
  • Year to date:
    • Site-wide: 82,567
  • Since beginning of last month:
    • Site-wide: 117,923

Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma

cancer biology more details view paper
  • Downloaded 708 times
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    • Site-wide: 35,449
    • In cancer biology: 953
  • Year to date:
    • Site-wide: 109,117
  • Since beginning of last month:
    • Site-wide: 110,608

Multi-Tissue DNA Methylation Age Predictor In Mouse

genomics more details view paper
  • Downloaded 649 times
  • Download rankings, all-time:
    • Site-wide: 39,868
    • In genomics: 3,316
  • Year to date:
    • Site-wide: 122,449
  • Since beginning of last month:
    • Site-wide: 116,752

Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats

genomics more details view paper
  • Downloaded 630 times
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    • Site-wide: 41,385
    • In genomics: 3,417
  • Year to date:
    • Site-wide: 129,997
  • Since beginning of last month:
    • Site-wide: 108,652

Interactions between genetic variation and cellular environment in skeletal muscle gene expression

genetics more details view paper
  • Downloaded 592 times
  • Download rankings, all-time:
    • Site-wide: 44,726
    • In genetics: 2,074
  • Year to date:
    • Site-wide: 116,821
  • Since beginning of last month:
    • Site-wide: 126,823

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease

genomics more details view paper
  • Downloaded 494 times
  • Download rankings, all-time:
    • Site-wide: 55,602
    • In genomics: 4,213
  • Year to date:
    • Site-wide: 59,540
  • Since beginning of last month:
    • Site-wide: 43,718

Multi-omics characterization of interaction-mediated control of human protein abundance levels

genomics more details view paper
  • Downloaded 460 times
  • Download rankings, all-time:
    • Site-wide: 60,063
    • In genomics: 4,418
  • Year to date:
    • Site-wide: 135,536
  • Since beginning of last month:
    • Site-wide: 110,006

Genome-wide scale analyses identify novel BMI genotype-environment interactions using a conditional false discovery rate

genetics more details view paper
  • Downloaded 410 times
  • Download rankings, all-time:
    • Site-wide: 67,491
    • In genetics: 3,080
  • Year to date:
    • Site-wide: 66,207
  • Since beginning of last month:
    • Site-wide: 48,086

Using the past to estimate sensory uncertainty

neuroscience more details view paper
  • Downloaded 358 times
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    • Site-wide: 76,663
    • In neuroscience: 11,674
  • Year to date:
    • Site-wide: 135,703
  • Since beginning of last month:
    • Site-wide: 127,668

scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation

genomics more details view paper
  • Downloaded 232 times
  • Download rankings, all-time:
    • Site-wide: 103,232
    • In genomics: 6,099
  • Year to date:
    • Site-wide: 12,808
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    • Site-wide: 8,182

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