Rxivist logo

Author: Fabian J. Theis

Rankings

  • All-time downloads: 87,274 (rank: 424 out of 396,059)
  • Categories:
    • bioengineering: 345 (rank: 6,395 (tie) out of 11,641)
    • bioinformatics: 67,031 (rank: 11 out of 33,591)
    • cell biology: 246 (rank: 22,102 (tie) out of 29,606)
    • genetics: 1,025 (rank: 12,982 (tie) out of 36,261)
    • genomics: 2,837 (rank: 6,942 (tie) out of 42,054)
    • immunology: 1,383 (rank: 3,050 (tie) out of 22,144)
    • neuroscience: 606 (rank: 27,315 (tie) out of 66,107)
    • systems biology: 13,801 (rank: 160 out of 11,557)

Downloads per author, site-wide

Preprints

Generalizing RNA velocity to transient cell states through dynamical modeling

bioinformatics more details view paper
  • Downloaded 7,527 times
  • Download rankings, all-time:
    • Site-wide: 400 out of 92,755
    • In bioinformatics: 53 out of 8,680
  • Year to date:
    • Site-wide: 265 out of 92,755
  • Since beginning of last month:
    • Site-wide: 329 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 6,949 times
  • Download rankings, all-time:
    • Site-wide: 448 out of 92,755
    • In bioinformatics: 62 out of 8,680
  • Year to date:
    • Site-wide: 2,774 out of 92,755
  • Since beginning of last month:
    • Site-wide: 7,749 out of 92,755

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

bioinformatics more details view paper
  • Downloaded 5,958 times
  • Download rankings, all-time:
    • Site-wide: 578 out of 92,755
    • In bioinformatics: 88 out of 8,680
  • Year to date:
    • Site-wide: 1,906 out of 92,755
  • Since beginning of last month:
    • Site-wide: 2,915 out of 92,755

Reconstructing cell cycle and disease progression using deep learning

bioinformatics more details view paper
  • Downloaded 5,848 times
  • Download rankings, all-time:
    • Site-wide: 593 out of 92,755
    • In bioinformatics: 91 out of 8,680
  • Year to date:
    • Site-wide: 6,654 out of 92,755
  • Since beginning of last month:
    • Site-wide: 8,370 out of 92,755

Single cell RNA-seq denoising using a deep count autoencoder

bioinformatics more details view paper
  • Downloaded 5,803 times
  • Download rankings, all-time:
    • Site-wide: 600 out of 92,755
    • In bioinformatics: 94 out of 8,680
  • Year to date:
    • Site-wide: 10,110 out of 92,755
  • Since beginning of last month:
    • Site-wide: 19,213 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 5,496 times
  • Download rankings, all-time:
    • Site-wide: 661 out of 92,755
    • In bioinformatics: 105 out of 8,680
  • Year to date:
    • Site-wide: 2,312 out of 92,755
  • Since beginning of last month:
    • Site-wide: 2,843 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 4,654 times
  • Download rankings, all-time:
    • Site-wide: 894 out of 92,755
    • In bioinformatics: 150 out of 8,680
  • Year to date:
    • Site-wide: 2,797 out of 92,755
  • Since beginning of last month:
    • Site-wide: 4,273 out of 92,755

Benchmarking atlas-level data integration in single-cell genomics

bioinformatics more details view paper
  • Downloaded 4,003 times
  • Download rankings, all-time:
    • Site-wide: 1,164 out of 92,755
    • In bioinformatics: 197 out of 8,680
  • Year to date:
    • Site-wide: 284 out of 92,755
  • Since beginning of last month:
    • Site-wide: 295 out of 92,755

Diffusion pseudotime robustly reconstructs lineage branching

bioinformatics more details view paper
  • Downloaded 3,807 times
  • Download rankings, all-time:
    • Site-wide: 1,280 out of 92,755
    • In bioinformatics: 213 out of 8,680
  • Year to date:
    • Site-wide: 5,115 out of 92,755
  • Since beginning of last month:
    • Site-wide: 5,825 out of 92,755

Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration

systems biology more details view paper
  • Downloaded 3,458 times
  • Download rankings, all-time:
    • Site-wide: 1,496 out of 92,755
    • In systems biology: 34 out of 2,374
  • Year to date:
    • Site-wide: 1,106 out of 92,755
  • Since beginning of last month:
    • Site-wide: 1,392 out of 92,755

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

genomics more details view paper
  • Downloaded 2,837 times
  • Download rankings, all-time:
    • Site-wide: 2,111 out of 92,755
    • In genomics: 411 out of 5,845
  • Year to date:
    • Site-wide: 5,441 out of 92,755
  • Since beginning of last month:
    • Site-wide: 6,779 out of 92,755

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

systems biology more details view paper
  • Downloaded 2,639 times
  • Download rankings, all-time:
    • Site-wide: 2,391 out of 92,755
    • In systems biology: 59 out of 2,374
  • Year to date:
    • Site-wide: 8,907 out of 92,755
  • Since beginning of last month:
    • Site-wide: 16,463 out of 92,755

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

systems biology more details view paper
  • Downloaded 2,615 times
  • Download rankings, all-time:
    • Site-wide: 2,433 out of 92,755
    • In systems biology: 64 out of 2,374
  • Year to date:
    • Site-wide: 36,451 out of 92,755
  • Since beginning of last month:
    • Site-wide: 45,703 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 2,497 times
  • Download rankings, all-time:
    • Site-wide: 2,637 out of 92,755
    • In bioinformatics: 472 out of 8,680
  • Year to date:
    • Site-wide: 19,695 out of 92,755
  • Since beginning of last month:
    • Site-wide: 35,037 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 2,199 times
  • Download rankings, all-time:
    • Site-wide: 3,253 out of 92,755
    • In bioinformatics: 583 out of 8,680
  • Year to date:
    • Site-wide: 26,746 out of 92,755
  • Since beginning of last month:
    • Site-wide: 16,724 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 2,054 times
  • Download rankings, all-time:
    • Site-wide: 3,628 out of 92,755
    • In bioinformatics: 659 out of 8,680
  • Year to date:
    • Site-wide: 6,453 out of 92,755
  • Since beginning of last month:
    • Site-wide: 4,774 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 1,845 times
  • Download rankings, all-time:
    • Site-wide: 4,347 out of 92,755
    • In bioinformatics: 794 out of 8,680
  • Year to date:
    • Site-wide: 2,706 out of 92,755
  • Since beginning of last month:
    • Site-wide: 3,993 out of 92,755

epiScanpy: integrated single-cell epigenomic analysis

bioinformatics more details view paper
  • Downloaded 1,439 times
  • Download rankings, all-time:
    • Site-wide: 6,536 out of 92,755
    • In bioinformatics: 1,144 out of 8,680
  • Year to date:
    • Site-wide: 7,487 out of 92,755
  • Since beginning of last month:
    • Site-wide: 5,847 out of 92,755

Meeting the challenges of high-dimensional data analysis in immunology

immunology more details view paper
  • Downloaded 1,383 times
  • Download rankings, all-time:
    • Site-wide: 6,987 out of 92,755
    • In immunology: 184 out of 2,738
  • Year to date:
    • Site-wide: 15,072 out of 92,755
  • Since beginning of last month:
    • Site-wide: 39,590 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 1,346 times
  • Download rankings, all-time:
    • Site-wide: 7,316 out of 92,755
    • In bioinformatics: 1,279 out of 8,680
  • Year to date:
    • Site-wide: 19,071 out of 92,755
  • Since beginning of last month:
    • Site-wide: 9,467 out of 92,755

Query to reference single-cell integration with transfer learning

bioinformatics more details view paper
  • Downloaded 1,150 times
  • Download rankings, all-time:
    • Site-wide: 9,532 out of 92,755
    • In bioinformatics: 1,578 out of 8,680
  • Year to date:
    • Site-wide: 1,389 out of 92,755
  • Since beginning of last month:
    • Site-wide: 73 out of 92,755

Deep learning the collisional cross sections of the peptide universe from a million training samples

systems biology more details view paper
  • Downloaded 1,020 times
  • Download rankings, all-time:
    • Site-wide: 11,631 out of 92,755
    • In systems biology: 310 out of 2,374
  • Year to date:
    • Site-wide: 1,697 out of 92,755
  • Since beginning of last month:
    • Site-wide: 3,143 out of 92,755

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

systems biology more details view paper
  • Downloaded 953 times
  • Download rankings, all-time:
    • Site-wide: 12,884 out of 92,755
    • In systems biology: 344 out of 2,374
  • Year to date:
    • Site-wide: 44,088 out of 92,755
  • Since beginning of last month:
    • Site-wide: 35,458 out of 92,755

Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

systems biology more details view paper
  • Downloaded 932 times
  • Download rankings, all-time:
    • Site-wide: 13,356 out of 92,755
    • In systems biology: 358 out of 2,374
  • Year to date:
    • Site-wide: 1,926 out of 92,755
  • Since beginning of last month:
    • Site-wide: 3,161 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 901 times
  • Download rankings, all-time:
    • Site-wide: 14,101 out of 92,755
    • In bioinformatics: 2,200 out of 8,680
  • Year to date:
    • Site-wide: 58,080 out of 92,755
  • Since beginning of last month:
    • Site-wide: 77,952 out of 92,755

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

systems biology more details view paper
  • Downloaded 823 times
  • Download rankings, all-time:
    • Site-wide: 16,243 out of 92,755
    • In systems biology: 439 out of 2,374
  • Year to date:
    • Site-wide: 77,465 out of 92,755
  • Since beginning of last month:
    • Site-wide: 60,387 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 771 times
  • Download rankings, all-time:
    • Site-wide: 17,933 out of 92,755
    • In bioinformatics: 2,680 out of 8,680
  • Year to date:
    • Site-wide: 2,520 out of 92,755
  • Since beginning of last month:
    • Site-wide: 449 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 673 times
  • Download rankings, all-time:
    • Site-wide: 21,942 out of 92,755
    • In bioinformatics: 3,142 out of 8,680
  • Year to date:
    • Site-wide: 72,406 out of 92,755
  • Since beginning of last month:
    • Site-wide: 56,003 out of 92,755

Design and power analysis for multi-sample single cell genomics experiments

bioinformatics more details view paper
  • Downloaded 610 times
  • Download rankings, all-time:
    • Site-wide: 25,260 out of 92,755
    • In bioinformatics: 3,487 out of 8,680
  • Year to date:
    • Site-wide: 3,579 out of 92,755
  • Since beginning of last month:
    • Site-wide: 5,552 out of 92,755

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

neuroscience more details view paper
  • Downloaded 606 times
  • Download rankings, all-time:
    • Site-wide: 25,470 out of 92,755
    • In neuroscience: 4,248 out of 16,496
  • Year to date:
    • Site-wide: 3,610 out of 92,755
  • Since beginning of last month:
    • Site-wide: 6,716 out of 92,755

Network-based metabolite ratios for an improved functional characterization of genome-wide association study results

genetics more details view paper
  • Downloaded 574 times
  • Download rankings, all-time:
    • Site-wide: 27,371 out of 92,755
    • In genetics: 1,676 out of 4,748
  • Year to date:
    • Site-wide: 63,592 out of 92,755
  • Since beginning of last month:
    • Site-wide: 27,319 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 489 times
  • Download rankings, all-time:
    • Site-wide: 33,571 out of 92,755
    • In bioinformatics: 4,284 out of 8,680
  • Year to date:
    • Site-wide: 6,951 out of 92,755
  • Since beginning of last month:
    • Site-wide: 19,522 out of 92,755

Variably methylated regions in the newborn epigenome: environmental, genetic and combined influences

genetics more details view paper
  • Downloaded 451 times
  • Download rankings, all-time:
    • Site-wide: 36,878 out of 92,755
    • In genetics: 2,158 out of 4,748
  • Year to date:
    • Site-wide: 59,118 out of 92,755
  • Since beginning of last month:
    • Site-wide: 55,943 out of 92,755

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

systems biology more details view paper
  • Downloaded 446 times
  • Download rankings, all-time:
    • Site-wide: 37,449 out of 92,755
    • In systems biology: 1,065 out of 2,374
  • Year to date:
    • Site-wide: 84,235 out of 92,755
  • Since beginning of last month:
    • Site-wide: 79,741 out of 92,755

Scalable parameter estimation for genome-scale biochemical reaction networks

systems biology more details view paper
  • Downloaded 406 times
  • Download rankings, all-time:
    • Site-wide: 41,524 out of 92,755
    • In systems biology: 1,208 out of 2,374
  • Year to date:
    • Site-wide: 88,611 out of 92,755
  • Since beginning of last month:
    • Site-wide: 85,552 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 396 times
  • Download rankings, all-time:
    • Site-wide: 42,599 out of 92,755
    • In bioinformatics: 5,101 out of 8,680
  • Year to date:
    • Site-wide: 6,956 out of 92,755
  • Since beginning of last month:
    • Site-wide: 10,248 out of 92,755

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

bioengineering more details view paper
  • Downloaded 345 times
  • Download rankings, all-time:
    • Site-wide: 48,838 out of 92,755
    • In bioengineering: 948 out of 2,100
  • Year to date:
    • Site-wide: 17,479 out of 92,755
  • Since beginning of last month:
    • Site-wide: 18,111 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 344 times
  • Download rankings, all-time:
    • Site-wide: 49,011 out of 92,755
    • In bioinformatics: 5,615 out of 8,680
  • Year to date:
    • Site-wide: 8,706 out of 92,755
  • Since beginning of last month:
    • Site-wide: 25,534 out of 92,755

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines

systems biology more details view paper
  • Downloaded 289 times
  • Download rankings, all-time:
    • Site-wide: 56,900 out of 92,755
    • In systems biology: 1,665 out of 2,374
  • Year to date:
    • Site-wide: 68,851 out of 92,755
  • Since beginning of last month:
    • Site-wide: 68,825 out of 92,755

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

bioinformatics more details view paper
  • Downloaded 272 times
  • Download rankings, all-time:
    • Site-wide: 59,367 out of 92,755
    • In bioinformatics: 6,401 out of 8,680
  • Year to date:
    • Site-wide: 79,346 out of 92,755
  • Since beginning of last month:
    • Site-wide: 67,527 out of 92,755

In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning

cell biology more details view paper
  • Downloaded 246 times
  • Download rankings, all-time:
    • Site-wide: 63,681 out of 92,755
    • In cell biology: 3,266 out of 4,776
  • Year to date:
    • Site-wide: 14,415 out of 92,755
  • Since beginning of last month:
    • Site-wide: 10,953 out of 92,755

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

systems biology more details view paper
  • Downloaded 220 times
  • Download rankings, all-time:
    • Site-wide: 68,262 out of 92,755
    • In systems biology: 1,939 out of 2,374
  • Year to date:
    • Site-wide: 82,626 out of 92,755
  • Since beginning of last month:
    • Site-wide: 68,550 out of 92,755

PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News