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Author: O Stegle

Rankings

  • All-time downloads: 106,126 (rank: 285 out of 426,771)
  • Categories:
    • bioinformatics: 27,487 (rank: 87 out of 36,221)
    • cancer biology: 2,044 (rank: 1,873 out of 30,504)
    • cell biology: 1,024 (rank: 6,044 (tie) out of 32,960)
    • developmental biology: 8,650 (rank: 51 out of 17,001)
    • genetics: 15,236 (rank: 855 out of 38,051)
    • genomics: 47,584 (rank: 139 out of 44,673)
    • neuroscience: 312 (rank: 49,313 (tie) out of 72,417)
    • systems biology: 3,789 (rank: 744 out of 12,484)

Downloads per author, site-wide

Preprints

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

genomics more details view paper
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    • In genomics: 39 out of 6,265
  • Year to date:
    • Site-wide: 562 out of 101,039
  • Since beginning of last month:
    • Site-wide: 1,333 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 6,217 times
  • Download rankings, all-time:
    • Site-wide: 610 out of 101,039
    • In bioinformatics: 89 out of 9,276
  • Year to date:
    • Site-wide: 22,948 out of 101,039
  • Since beginning of last month:
    • Site-wide: 31,877 out of 101,039

LIMIX: genetic analysis of multiple traits

genetics more details view paper
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    • In genetics: 48 out of 5,026
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    • Site-wide: 17,903 out of 101,039
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    • Site-wide: 16,658 out of 101,039

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

developmental biology more details view paper
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    • In developmental biology: 7 out of 3,018
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    • Site-wide: 5,048 out of 101,039
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    • Site-wide: 8,629 out of 101,039

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

genomics more details view paper
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    • Site-wide: 837 out of 101,039
    • In genomics: 165 out of 6,265
  • Year to date:
    • Site-wide: 3,783 out of 101,039
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    • Site-wide: 12,208 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 4,872 times
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    • Site-wide: 915 out of 101,039
    • In bioinformatics: 150 out of 9,276
  • Year to date:
    • Site-wide: 17,330 out of 101,039
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    • Site-wide: 9,550 out of 101,039

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

genomics more details view paper
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    • In genomics: 195 out of 6,265
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    • Site-wide: 4,422 out of 101,039
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    • Site-wide: 5,407 out of 101,039

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

genomics more details view paper
  • Downloaded 4,024 times
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    • Site-wide: 1,292 out of 101,039
    • In genomics: 260 out of 6,265
  • Year to date:
    • Site-wide: 10,053 out of 101,039
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    • Site-wide: 30,377 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 3,674 times
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    • Site-wide: 1,498 out of 101,039
    • In bioinformatics: 250 out of 9,276
  • Year to date:
    • Site-wide: 4,086 out of 101,039
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    • Site-wide: 6,201 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 3,516 times
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    • Site-wide: 1,623 out of 101,039
    • In bioinformatics: 271 out of 9,276
  • Year to date:
    • Site-wide: 13,976 out of 101,039
  • Since beginning of last month:
    • Site-wide: 22,599 out of 101,039

SpatialDE - Identification of spatially variable genes

genomics more details view paper
  • Downloaded 3,011 times
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    • Site-wide: 2,159 out of 101,039
    • In genomics: 402 out of 6,265
  • Year to date:
    • Site-wide: 21,984 out of 101,039
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    • Site-wide: 13,001 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 2,914 times
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    • Site-wide: 2,266 out of 101,039
    • In bioinformatics: 393 out of 9,276
  • Year to date:
    • Site-wide: 49,825 out of 101,039
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    • Site-wide: 38,532 out of 101,039

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

systems biology more details view paper
  • Downloaded 2,877 times
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    • Site-wide: 2,313 out of 101,039
    • In systems biology: 58 out of 2,566
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    • Site-wide: 49,316 out of 101,039
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    • Site-wide: 57,472 out of 101,039

Common genetic variation drives molecular heterogeneity in human iPSCs

genomics more details view paper
  • Downloaded 2,756 times
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    • Site-wide: 2,469 out of 101,039
    • In genomics: 456 out of 6,265
  • Year to date:
    • Site-wide: 42,763 out of 101,039
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    • Site-wide: 86,960 out of 101,039

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

developmental biology more details view paper
  • Downloaded 2,646 times
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    • Site-wide: 2,635 out of 101,039
    • In developmental biology: 41 out of 3,018
  • Year to date:
    • Site-wide: 2,010 out of 101,039
  • Since beginning of last month:
    • Site-wide: 12,734 out of 101,039

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

genomics more details view paper
  • Downloaded 2,464 times
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    • Site-wide: 2,982 out of 101,039
    • In genomics: 543 out of 6,265
  • Year to date:
    • Site-wide: 9,868 out of 101,039
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    • Site-wide: 23,446 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 2,408 times
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    • Site-wide: 3,099 out of 101,039
    • In bioinformatics: 539 out of 9,276
  • Year to date:
    • Site-wide: 1,399 out of 101,039
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    • Site-wide: 6,611 out of 101,039

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

genomics more details view paper
  • Downloaded 2,408 times
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    • Site-wide: 3,102 out of 101,039
    • In genomics: 565 out of 6,265
  • Year to date:
    • Site-wide: 11,250 out of 101,039
  • Since beginning of last month:
    • Site-wide: 6,879 out of 101,039

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

genetics more details view paper
  • Downloaded 2,341 times
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    • Site-wide: 3,244 out of 101,039
    • In genetics: 240 out of 5,026
  • Year to date:
    • Site-wide: 716 out of 101,039
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    • Site-wide: 1,615 out of 101,039

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

genetics more details view paper
  • Downloaded 2,314 times
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    • Site-wide: 3,319 out of 101,039
    • In genetics: 245 out of 5,026
  • Year to date:
    • Site-wide: 28,331 out of 101,039
  • Since beginning of last month:
    • Site-wide: 27,796 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 1,423 times
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    • Site-wide: 7,485 out of 101,039
    • In bioinformatics: 1,269 out of 9,276
  • Year to date:
    • Site-wide: 40,736 out of 101,039
  • Since beginning of last month:
    • Site-wide: None out of 101,039

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

cancer biology more details view paper
  • Downloaded 1,375 times
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    • Site-wide: 7,921 out of 101,039
    • In cancer biology: 212 out of 3,624
  • Year to date:
    • Site-wide: 58,191 out of 101,039
  • Since beginning of last month:
    • Site-wide: 65,226 out of 101,039

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 1,361 times
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    • Site-wide: 8,068 out of 101,039
    • In genomics: 1,212 out of 6,265
  • Year to date:
    • Site-wide: 26,998 out of 101,039
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    • Site-wide: 42,500 out of 101,039

Dissecting the mechanisms underlying indirect genetic effects on biomedical phenotypes: a study of 170 behavioural, physiological and morphological phenotypes measured in adult laboratory mice

genetics more details view paper
  • Downloaded 1,342 times
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    • Site-wide: 8,271 out of 101,039
    • In genetics: 559 out of 5,026
  • Year to date:
    • Site-wide: 10,441 out of 101,039
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    • Site-wide: 23,821 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 1,332 times
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    • Site-wide: 8,378 out of 101,039
    • In bioinformatics: 1,400 out of 9,276
  • Year to date:
    • Site-wide: 42,181 out of 101,039
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    • Site-wide: 27,804 out of 101,039

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

genomics more details view paper
  • Downloaded 1,230 times
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    • Site-wide: 9,563 out of 101,039
    • In genomics: 1,390 out of 6,265
  • Year to date:
    • Site-wide: 8,897 out of 101,039
  • Since beginning of last month:
    • Site-wide: 13,688 out of 101,039

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

genomics more details view paper
  • Downloaded 1,227 times
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    • Site-wide: 9,622 out of 101,039
    • In genomics: 1,393 out of 6,265
  • Year to date:
    • Site-wide: 33,425 out of 101,039
  • Since beginning of last month:
    • Site-wide: 39,730 out of 101,039

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

bioinformatics more details view paper
  • Downloaded 1,131 times
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    • Site-wide: 11,014 out of 101,039
    • In bioinformatics: 1,759 out of 9,276
  • Year to date:
    • Site-wide: 11,838 out of 101,039
  • Since beginning of last month:
    • Site-wide: 24,309 out of 101,039

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

genomics more details view paper
  • Downloaded 1,066 times
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    • Site-wide: 12,086 out of 101,039
    • In genomics: 1,650 out of 6,265
  • Year to date:
    • Site-wide: 2,374 out of 101,039
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    • Site-wide: 9,124 out of 101,039

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

genomics more details view paper
  • Downloaded 1,055 times
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    • Site-wide: 12,325 out of 101,039
    • In genomics: 1,674 out of 6,265
  • Year to date:
    • Site-wide: 56,947 out of 101,039
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    • Site-wide: 63,697 out of 101,039

Genome-scale oscillations in DNA methylation during exit from pluripotency

genomics more details view paper
  • Downloaded 1,031 times
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    • Site-wide: 12,769 out of 101,039
    • In genomics: 1,722 out of 6,265
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    • Site-wide: 72,949 out of 101,039
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    • Site-wide: 41,161 out of 101,039

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 1,024 times
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    • Site-wide: 12,907 out of 101,039
    • In cell biology: 518 out of 5,230
  • Year to date:
    • Site-wide: 52,079 out of 101,039
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    • Site-wide: 56,221 out of 101,039

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

genetics more details view paper
  • Downloaded 938 times
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    • Site-wide: 14,865 out of 101,039
    • In genetics: 954 out of 5,026
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    • Site-wide: 92,085 out of 101,039

Genomic determinants of protein abundance variation in colorectal cancer cells

systems biology more details view paper
  • Downloaded 912 times
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    • Site-wide: 15,608 out of 101,039
    • In systems biology: 415 out of 2,566
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    • Site-wide: 86,525 out of 101,039

Genomic Rearrangements Considered as Quantitative Traits

genetics more details view paper
  • Downloaded 776 times
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    • Site-wide: 20,015 out of 101,039
    • In genetics: 1,243 out of 5,026
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    • Site-wide: 95,371 out of 101,039

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

genomics more details view paper
  • Downloaded 773 times
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    • Site-wide: 20,102 out of 101,039
    • In genomics: 2,369 out of 6,265
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    • Site-wide: 87,273 out of 101,039

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

genomics more details view paper
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    • Site-wide: 20,345 out of 101,039
    • In genomics: 2,382 out of 6,265
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    • Site-wide: 69,645 out of 101,039

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

cancer biology more details view paper
  • Downloaded 669 times
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    • Site-wide: 24,891 out of 101,039
    • In cancer biology: 785 out of 3,624
  • Year to date:
    • Site-wide: 82,728 out of 101,039
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    • Site-wide: 76,553 out of 101,039

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

genomics more details view paper
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    • Site-wide: 24,912 out of 101,039
    • In genomics: 2,719 out of 6,265
  • Year to date:
    • Site-wide: 23,018 out of 101,039
  • Since beginning of last month:
    • Site-wide: 64,080 out of 101,039

Multi-Tissue DNA Methylation Age Predictor In Mouse

genomics more details view paper
  • Downloaded 615 times
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    • Site-wide: 27,997 out of 101,039
    • In genomics: 2,926 out of 6,265
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    • Site-wide: 75,859 out of 101,039
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    • Site-wide: 82,554 out of 101,039

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

genomics more details view paper
  • Downloaded 602 times
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    • Site-wide: 28,811 out of 101,039
    • In genomics: 2,983 out of 6,265
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    • Site-wide: 32,531 out of 101,039
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    • Site-wide: 82,957 out of 101,039

Genetic Analyses of Blood Cell Structure for Biological and Pharmacological Inference

genetics more details view paper
  • Downloaded 595 times
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    • Site-wide: 29,243 out of 101,039
    • In genetics: 1,747 out of 5,026
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    • Site-wide: 5,780 out of 101,039
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    • Site-wide: 15,157 out of 101,039

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

genetics more details view paper
  • Downloaded 550 times
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    • Site-wide: 32,285 out of 101,039
    • In genetics: 1,883 out of 5,026
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    • Site-wide: 71,973 out of 101,039

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

genomics more details view paper
  • Downloaded 439 times
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    • Site-wide: 42,526 out of 101,039
    • In genomics: 3,875 out of 6,265
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    • Site-wide: 96,977 out of 101,039
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    • Site-wide: 92,025 out of 101,039

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

genomics more details view paper
  • Downloaded 416 times
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    • Site-wide: 45,154 out of 101,039
    • In genomics: 4,025 out of 6,265
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    • Site-wide: 53,446 out of 101,039
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    • Site-wide: 80,796 out of 101,039

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

genetics more details view paper
  • Downloaded 326 times
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    • Site-wide: 57,157 out of 101,039
    • In genetics: 3,138 out of 5,026
  • Year to date:
    • Site-wide: 14,704 out of 101,039
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    • Site-wide: 66,947 out of 101,039

Using the past to estimate sensory uncertainty

neuroscience more details view paper
  • Downloaded 312 times
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    • Site-wide: 59,339 out of 101,039
    • In neuroscience: 10,486 out of 18,002
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  • Since beginning of last month:
    • Site-wide: 62,401 out of 101,039

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