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Author: Fabian J Theis

Rankings

  • All-time downloads: 75,799 (rank: 532 out of 426,025)
  • Categories:
    • bioengineering: 406 (rank: 6,447 (tie) out of 13,236)
    • bioinformatics: 57,686 (rank: 27 out of 36,200)
    • cell biology: 210 (rank: 26,415 (tie) out of 32,894)
    • developmental biology: 463 (rank: 7,879 (tie) out of 16,934)
    • genomics: 2,986 (rank: 7,074 (tie) out of 44,631)
    • neuroscience: 723 (rank: 25,720 (tie) out of 72,365)
    • systems biology: 13,325 (rank: 162 out of 12,462)

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Preprints

CellRank for directed single-cell fate mapping

bioinformatics more details view paper

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

bioinformatics more details view paper
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Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

bioinformatics more details view paper
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    • In bioinformatics: 91 out of 9,260
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Reconstructing cell cycle and disease progression using deep learning

bioinformatics more details view paper
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Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species

bioinformatics more details view paper
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Benchmarking atlas-level data integration in single-cell genomics

bioinformatics more details view paper
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    • In bioinformatics: 133 out of 9,260
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Assessment of batch-correction methods for scRNA-seq data with a new test metric

bioinformatics more details view paper
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DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

systems biology more details view paper
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scSLAM-seq reveals core features of transcription dynamics in single cells

genomics more details view paper
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    • In genomics: 407 out of 6,254
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An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

systems biology more details view paper
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    • In systems biology: 64 out of 2,563
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Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection

systems biology more details view paper
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    • In systems biology: 69 out of 2,563
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Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series

bioinformatics more details view paper
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    • In bioinformatics: 483 out of 9,260
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Query to reference single-cell integration with transfer learning

bioinformatics more details view paper
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    • In bioinformatics: 580 out of 9,260
  • Year to date:
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    • Site-wide: 205 out of 100,856

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

bioinformatics more details view paper
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    • In bioinformatics: 616 out of 9,260
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Deep learning does not outperform classical machine learning for cell-type annotation

bioinformatics more details view paper
  • Downloaded 2,225 times
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    • In bioinformatics: 631 out of 9,260
  • Year to date:
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    • Site-wide: 12,204 out of 100,856

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

bioinformatics more details view paper
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    • Site-wide: 4,052 out of 100,856
    • In bioinformatics: 718 out of 9,260
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    • Site-wide: 9,104 out of 100,856

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

bioinformatics more details view paper
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    • In bioinformatics: 719 out of 9,260
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Impulse model-based differential expression analysis of time course sequencing data

bioinformatics more details view paper
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    • In bioinformatics: 1,075 out of 9,260
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    • Site-wide: 34,305 out of 100,856

epiScanpy: integrated single-cell epigenomic analysis

bioinformatics more details view paper
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    • In bioinformatics: 1,086 out of 9,260
  • Year to date:
    • Site-wide: 7,170 out of 100,856
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    • Site-wide: 7,279 out of 100,856

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

bioinformatics more details view paper
  • Downloaded 1,375 times
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    • In bioinformatics: 1,346 out of 9,260
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Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

systems biology more details view paper
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    • In systems biology: 265 out of 2,563
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Swarm Learning as a privacy-preserving machine learning approach for disease classification

bioinformatics more details view paper
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    • In bioinformatics: 1,869 out of 9,260
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    • Site-wide: 3,088 out of 100,856

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

systems biology more details view paper
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MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data

bioinformatics more details view paper
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    • In bioinformatics: 2,331 out of 9,260
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Efficient parameterization of large-scale mechanistic models enables drug response prediction for cancer cell lines

systems biology more details view paper
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Cell-type specific impact of glucocorticoid receptor activation on the developing brain

neuroscience more details view paper
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    • In neuroscience: 3,640 out of 17,976
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    • Site-wide: 9,099 out of 100,856

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

bioinformatics more details view paper
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    • In bioinformatics: 3,339 out of 9,260
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Self-supervised retinal thickness prediction enables deep learning from unlabeled data to boost classification of diabetic retinopathy

bioinformatics more details view paper
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Network reconstruction for trans acting genetic loci using multi-omics data and prior information

bioinformatics more details view paper
  • Downloaded 489 times
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    • In bioinformatics: 4,652 out of 9,260
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Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells

developmental biology more details view paper
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    • Site-wide: 5,118 out of 100,856

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

bioinformatics more details view paper
  • Downloaded 459 times
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    • In bioinformatics: 4,909 out of 9,260
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    • Site-wide: 78,854 out of 100,856

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

systems biology more details view paper
  • Downloaded 456 times
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    • Site-wide: 93,394 out of 100,856

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

bioengineering more details view paper
  • Downloaded 406 times
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    • Site-wide: 28,282 out of 100,856

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

bioinformatics more details view paper
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MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data

bioinformatics more details view paper
  • Downloaded 293 times
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Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

systems biology more details view paper
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    • In systems biology: 2,022 out of 2,563
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    • Site-wide: 76,801 out of 100,856

Identification and characterization of distinct murine brown adipocyte lineages

cell biology more details view paper
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    • Site-wide: 10,247 out of 100,856

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