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Author: Fabian J Theis

Rankings

  • All-time downloads: 110,711 (rank: 893 )
  • Categories:
    • bioengineering: 521 (rank: 7,133 (tie) )
    • bioinformatics: 80,293 (rank: 9 )
    • cell biology: 307 (rank: 27,757 (tie) )
    • developmental biology: 1,170 (rank: 3,225 (tie) )
    • genomics: 3,331 (rank: 7,336 (tie) )
    • infectious diseases: 3,272 (rank: 10,541 )
    • neuroscience: 1,016 (rank: 23,454 (tie) )
    • public and global health: 2,028 (rank: 1,904 (tie) )
    • respiratory medicine: 4,381 (rank: 188 )
    • systems biology: 14,392 (rank: 171 )

Downloads per author, site-wide

Preprints

scvi-tools: a library for deep probabilistic analysis of single-cell omics data

bioinformatics more details view paper

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Benchmarking atlas-level data integration in single-cell genomics

bioinformatics more details view paper
  • Downloaded 7,840 times
  • Download rankings, all-time:
    • Site-wide: 1,140
    • In bioinformatics: 68
  • Year to date:
    • Site-wide: 749
  • Since beginning of last month:
    • Site-wide: 1,272

Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

bioinformatics more details view paper
  • Downloaded 7,531 times
  • Download rankings, all-time:
    • Site-wide: 1,199
    • In bioinformatics: 74
  • Year to date:
    • Site-wide: 11,512
  • Since beginning of last month:
    • Site-wide: 14,264

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

bioinformatics more details view paper
  • Downloaded 6,556 times
  • Download rankings, all-time:
    • Site-wide: 1,424
    • In bioinformatics: 94
  • Year to date:
    • Site-wide: 11,130
  • Since beginning of last month:
    • Site-wide: 12,312

Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species

bioinformatics more details view paper
  • Downloaded 6,319 times
  • Download rankings, all-time:
    • Site-wide: 1,502
    • In bioinformatics: 101
  • Year to date:
    • Site-wide: 9,149
  • Since beginning of last month:
    • Site-wide: 15,118

Reconstructing cell cycle and disease progression using deep learning

bioinformatics more details view paper
  • Downloaded 6,164 times
  • Download rankings, all-time:
    • Site-wide: 1,550
    • In bioinformatics: 106
  • Year to date:
    • Site-wide: 23,871
  • Since beginning of last month:
    • Site-wide: 29,081

CellRank for directed single-cell fate mapping

bioinformatics more details view paper
  • Downloaded 6,127 times
  • Download rankings, all-time:
    • Site-wide: 1,564
    • In bioinformatics: 108
  • Year to date:
    • Site-wide: 554
  • Since beginning of last month:
    • Site-wide: 588

Assessment of batch-correction methods for scRNA-seq data with a new test metric

bioinformatics more details view paper
  • Downloaded 5,239 times
  • Download rankings, all-time:
    • Site-wide: 1,950
    • In bioinformatics: 159
  • Year to date:
    • Site-wide: 9,285
  • Since beginning of last month:
    • Site-wide: 11,604

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

systems biology more details view paper
  • Downloaded 4,296 times
  • Download rankings, all-time:
    • Site-wide: 2,572
    • In systems biology: 35
  • Year to date:
    • Site-wide: 62,603
  • Since beginning of last month:
    • Site-wide: 50,217

Query to reference single-cell integration with transfer learning

bioinformatics more details view paper
  • Downloaded 4,216 times
  • Download rankings, all-time:
    • Site-wide: 2,643
    • In bioinformatics: 230
  • Year to date:
    • Site-wide: 1,370
  • Since beginning of last month:
    • Site-wide: 2,261

scSLAM-seq reveals core features of transcription dynamics in single cells

genomics more details view paper
  • Downloaded 3,331 times
  • Download rankings, all-time:
    • Site-wide: 3,707
    • In genomics: 410
  • Year to date:
    • Site-wide: 11,610
  • Since beginning of last month:
    • Site-wide: 14,222

Integrated single cell analysis of human lung fibrosis resolves cellular origins of predictive protein signatures in body fluids

respiratory medicine more details view paper
  • Downloaded 3,017 times
  • Download rankings, all-time:
    • Site-wide: 4,262
    • In respiratory medicine: 17
  • Year to date:
    • Site-wide: 7,482
  • Since beginning of last month:
    • Site-wide: 9,933

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

systems biology more details view paper
  • Downloaded 2,984 times
  • Download rankings, all-time:
    • Site-wide: 4,325
    • In systems biology: 70
  • Year to date:
    • Site-wide: 22,758
  • Since beginning of last month:
    • Site-wide: 17,243

Compositional perturbation autoencoder for single-cell response modeling

bioinformatics more details view paper
  • Downloaded 2,882 times
  • Download rankings, all-time:
    • Site-wide: 4,544
    • In bioinformatics: 466
  • Year to date:
    • Site-wide: 412
  • Since beginning of last month:
    • Site-wide: 77

Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection

systems biology more details view paper
  • Downloaded 2,725 times
  • Download rankings, all-time:
    • Site-wide: 4,945
    • In systems biology: 82
  • Year to date:
    • Site-wide: 80,040
  • Since beginning of last month:
    • Site-wide: 83,590

Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series

bioinformatics more details view paper
  • Downloaded 2,684 times
  • Download rankings, all-time:
    • Site-wide: 5,041
    • In bioinformatics: 540
  • Year to date:
    • Site-wide: 33,664
  • Since beginning of last month:
    • Site-wide: 50,042

Deep learning does not outperform classical machine learning for cell-type annotation

bioinformatics more details view paper
  • Downloaded 2,457 times
  • Download rankings, all-time:
    • Site-wide: 5,776
    • In bioinformatics: 636
  • Year to date:
    • Site-wide: 27,631
  • Since beginning of last month:
    • Site-wide: 43,589

destiny – diffusion maps for large-scale single-cell data in R

bioinformatics more details view paper
  • Downloaded 2,414 times
  • Download rankings, all-time:
    • Site-wide: 5,908
    • In bioinformatics: 660
  • Year to date:
    • Site-wide: 31,769
  • Since beginning of last month:
    • Site-wide: 40,242

scCODA: A Bayesian model for compositional single-cell data analysis

bioinformatics more details view paper
  • Downloaded 2,269 times
  • Download rankings, all-time:
    • Site-wide: 6,463
    • In bioinformatics: 738
  • Year to date:
    • Site-wide: 1,337
  • Since beginning of last month:
    • Site-wide: 1,689

Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)

infectious diseases more details view paper
  • Downloaded 2,268 times
  • Download rankings, all-time:
    • Site-wide: 6,469
    • In infectious diseases: 968
  • Year to date:
    • Site-wide: 52,041
  • Since beginning of last month:
    • Site-wide: 65,516

Predicting antigen-specificity of single T-cells based on TCR CDR3 regions

bioinformatics more details view paper
  • Downloaded 2,242 times
  • Download rankings, all-time:
    • Site-wide: 6,581
    • In bioinformatics: 759
  • Year to date:
    • Site-wide: 25,479
  • Since beginning of last month:
    • Site-wide: 43,306

Scanpy for analysis of large-scale single-cell gene expression data

bioinformatics more details view paper
  • Downloaded 2,193 times
  • Download rankings, all-time:
    • Site-wide: 6,791
    • In bioinformatics: 793
  • Year to date:
    • Site-wide: 35,787
  • Since beginning of last month:
    • Site-wide: 43,329

Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies

public and global health more details view paper
  • Downloaded 2,028 times
  • Download rankings, all-time:
    • Site-wide: 7,610
    • In public and global health: 181
  • Year to date:
    • Site-wide: 18,054
  • Since beginning of last month:
    • Site-wide: 26,727

epiScanpy: integrated single-cell epigenomic analysis

bioinformatics more details view paper
  • Downloaded 1,993 times
  • Download rankings, all-time:
    • Site-wide: 7,821
    • In bioinformatics: 924
  • Year to date:
    • Site-wide: 9,788
  • Since beginning of last month:
    • Site-wide: 8,073

Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

systems biology more details view paper
  • Downloaded 1,691 times
  • Download rankings, all-time:
    • Site-wide: 10,013
    • In systems biology: 183
  • Year to date:
    • Site-wide: 6,931
  • Since beginning of last month:
    • Site-wide: 11,112

Impulse model-based differential expression analysis of time course sequencing data

bioinformatics more details view paper
  • Downloaded 1,688 times
  • Download rankings, all-time:
    • Site-wide: 10,043
    • In bioinformatics: 1,201
  • Year to date:
    • Site-wide: 57,291
  • Since beginning of last month:
    • Site-wide: 62,928

Swarm Learning as a privacy-preserving machine learning approach for disease classification

bioinformatics more details view paper
  • Downloaded 1,507 times
  • Download rankings, all-time:
    • Site-wide: 11,789
    • In bioinformatics: 1,410
  • Year to date:
    • Site-wide: 9,448
  • Since beginning of last month:
    • Site-wide: 9,220

FASTGenomics: An analytical ecosystem for single-cell RNA sequencing data

bioinformatics more details view paper
  • Downloaded 1,446 times
  • Download rankings, all-time:
    • Site-wide: 12,570
    • In bioinformatics: 1,510
  • Year to date:
    • Site-wide: 72,346
  • Since beginning of last month:
    • Site-wide: 94,651

Determinants of SARS-CoV-2 receptor gene expression in upper and lower airways

respiratory medicine more details view paper
  • Downloaded 1,364 times
  • Download rankings, all-time:
    • Site-wide: 13,760
    • In respiratory medicine: 47
  • Year to date:
    • Site-wide: 11,685
  • Since beginning of last month:
    • Site-wide: 16,540

Squidpy: a scalable framework for spatial single cell analysis

bioinformatics more details view paper
  • Downloaded 1,182 times
  • Download rankings, all-time:
    • Site-wide: 17,061
    • In bioinformatics: 2,028
  • Year to date:
    • Site-wide: 1,233
  • Since beginning of last month:
    • Site-wide: None

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies

systems biology more details view paper
  • Downloaded 1,054 times
  • Download rankings, all-time:
    • Site-wide: 20,227
    • In systems biology: 403
  • Year to date:
    • Site-wide: 82,167
  • Since beginning of last month:
    • Site-wide: 72,255

Cell-type specific impact of glucocorticoid receptor activation on the developing brain

neuroscience more details view paper
  • Downloaded 1,016 times
  • Download rankings, all-time:
    • Site-wide: 21,336
    • In neuroscience: 2,699
  • Year to date:
    • Site-wide: 17,075
  • Since beginning of last month:
    • Site-wide: 20,854

Self-supervised retinal thickness prediction enables deep learning from unlabeled data to boost classification of diabetic retinopathy

bioinformatics more details view paper
  • Downloaded 1,006 times
  • Download rankings, all-time:
    • Site-wide: 21,602
    • In bioinformatics: 2,542
  • Year to date:
    • Site-wide: 21,004
  • Since beginning of last month:
    • Site-wide: 27,002

Single-cell RNA sequencing reveals in vivo signatures of SARS-CoV-2-reactive T cells through 'reverse phenotyping'

infectious diseases more details view paper
  • Downloaded 1,004 times
  • Download rankings, all-time:
    • Site-wide: 21,657
    • In infectious diseases: 1,804
  • Year to date:
    • Site-wide: 4,961
  • Since beginning of last month:
    • Site-wide: 5,810

MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data

bioinformatics more details view paper
  • Downloaded 952 times
  • Download rankings, all-time:
    • Site-wide: 23,433
    • In bioinformatics: 2,748
  • Year to date:
    • Site-wide: 125,366
  • Since beginning of last month:
    • Site-wide: 130,546

Efficient parameterization of large-scale mechanistic models enables drug response prediction for cancer cell lines

systems biology more details view paper
  • Downloaded 892 times
  • Download rankings, all-time:
    • Site-wide: 25,725
    • In systems biology: 530
  • Year to date:
    • Site-wide: 80,400
  • Since beginning of last month:
    • Site-wide: 71,869

Learning interpretable latent autoencoder representations with annotations of feature sets

bioinformatics more details view paper
  • Downloaded 772 times
  • Download rankings, all-time:
    • Site-wide: 31,542
    • In bioinformatics: 3,541
  • Year to date:
    • Site-wide: 6,063
  • Since beginning of last month:
    • Site-wide: 9,855

Model-based branching point detection in single-cell data by K-Branches clustering

bioinformatics more details view paper
  • Downloaded 711 times
  • Download rankings, all-time:
    • Site-wide: 35,234
    • In bioinformatics: 3,911
  • Year to date:
    • Site-wide: 116,348
  • Since beginning of last month:
    • Site-wide: 130,043

Network reconstruction for trans acting genetic loci using multi-omics data and prior information

bioinformatics more details view paper
  • Downloaded 666 times
  • Download rankings, all-time:
    • Site-wide: 38,549
    • In bioinformatics: 4,214
  • Year to date:
    • Site-wide: 27,307
  • Since beginning of last month:
    • Site-wide: 25,753

Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells

developmental biology more details view paper
  • Downloaded 642 times
  • Download rankings, all-time:
    • Site-wide: 40,428
    • In developmental biology: 894
  • Year to date:
    • Site-wide: 27,295
  • Since beginning of last month:
    • Site-wide: 28,271

Single cell trajectory analysis of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors

developmental biology more details view paper
  • Downloaded 528 times
  • Download rankings, all-time:
    • Site-wide: 51,349
    • In developmental biology: 1,211
  • Year to date:
    • Site-wide: 3,912
  • Since beginning of last month:
    • Site-wide: 14,151

A Sparse Deep Learning Approach for Automatic Segmentation of Human Vasculature in Multispectral Optoacoustic Tomography

bioengineering more details view paper
  • Downloaded 521 times
  • Download rankings, all-time:
    • Site-wide: 52,162
    • In bioengineering: 974
  • Year to date:
    • Site-wide: 43,276
  • Since beginning of last month:
    • Site-wide: 34,836

cgCorrect: A method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics

bioinformatics more details view paper
  • Downloaded 489 times
  • Download rankings, all-time:
    • Site-wide: 56,204
    • In bioinformatics: 5,685
  • Year to date:
    • Site-wide: 123,332
  • Since beginning of last month:
    • Site-wide: 94,985

Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cells

systems biology more details view paper
  • Downloaded 483 times
  • Download rankings, all-time:
    • Site-wide: 56,957
    • In systems biology: 1,348
  • Year to date:
    • Site-wide: 132,554
  • Since beginning of last month:
    • Site-wide: 137,672

Automatic identification of relevant genes from low-dimensional embeddings of single cell RNAseq data

bioinformatics more details view paper
  • Downloaded 407 times
  • Download rankings, all-time:
    • Site-wide: 68,023
    • In bioinformatics: 6,542
  • Year to date:
    • Site-wide: 97,461
  • Since beginning of last month:
    • Site-wide: 113,986

MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data

bioinformatics more details view paper
  • Downloaded 341 times
  • Download rankings, all-time:
    • Site-wide: 79,944
    • In bioinformatics: 7,314
  • Year to date:
    • Site-wide: 96,465
  • Since beginning of last month:
    • Site-wide: 78,145

Identification and characterization of distinct murine brown adipocyte lineages

cell biology more details view paper
  • Downloaded 307 times
  • Download rankings, all-time:
    • Site-wide: 86,714
    • In cell biology: 4,015
  • Year to date:
    • Site-wide: 58,406
  • Since beginning of last month:
    • Site-wide: 99,486

Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

systems biology more details view paper
  • Downloaded 267 times
  • Download rankings, all-time:
    • Site-wide: 95,352
    • In systems biology: 2,215
  • Year to date:
    • Site-wide: 125,404
  • Since beginning of last month:
    • Site-wide: 118,847

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