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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 73,249 bioRxiv papers from 318,847 authors.

Author: Casey S. Greene

Rankings

  • All-time downloads: 101,076 (rank: 104 out of 318,928)
  • Categories:
    • bioinformatics: 89,438 (rank: 2 out of 27,654)
    • cancer biology: 1,772 (rank: 1,505 (tie) out of 20,978)
    • genetics: 1,140 (rank: 10,478 (tie) out of 31,247)
    • genomics: 2,244 (rank: 7,030 (tie) out of 35,528)
    • microbiology: 399 (rank: 13,744 (tie) out of 33,259)
    • neuroscience: 238 (rank: 39,669 (tie) out of 53,863)
    • systems biology: 5,845 (rank: 131 out of 9,613)

Downloads per author, site-wide

Preprints

Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment

cancer biology more details view paper

No bioRxiv download data for this paper yet.

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 51,723 times
  • Download rankings, all-time:
    • Site-wide: 8 out of 73,279
    • In bioinformatics: 1 out of 7,144
  • Year to date:
    • Site-wide: 987 out of 73,279
  • Since beginning of last month:
    • Site-wide: 987 out of 73,279

Privacy-preserving generative deep neural networks support clinical data sharing

bioinformatics more details view paper
  • Downloaded 11,728 times
  • Download rankings, all-time:
    • Site-wide: 103 out of 73,279
    • In bioinformatics: 16 out of 7,144
  • Year to date:
    • Site-wide: 2,240 out of 73,279
  • Since beginning of last month:
    • Site-wide: 2,240 out of 73,279

Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders

bioinformatics more details view paper
  • Downloaded 3,648 times
  • Download rankings, all-time:
    • Site-wide: 920 out of 73,279
    • In bioinformatics: 180 out of 7,144
  • Year to date:
    • Site-wide: 10,013 out of 73,279
  • Since beginning of last month:
    • Site-wide: 10,013 out of 73,279

Enter the matrix: factorization uncovers knowledge from omics

systems biology more details view paper
  • Downloaded 2,898 times
  • Download rankings, all-time:
    • Site-wide: 1,404 out of 73,279
    • In systems biology: 32 out of 2,008
  • Year to date:
    • Site-wide: 22,230 out of 73,279
  • Since beginning of last month:
    • Site-wide: 22,230 out of 73,279

Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously

bioinformatics more details view paper
  • Downloaded 2,663 times
  • Download rankings, all-time:
    • Site-wide: 1,619 out of 73,279
    • In bioinformatics: 321 out of 7,144
  • Year to date:
    • Site-wide: 7,665 out of 73,279
  • Since beginning of last month:
    • Site-wide: 7,665 out of 73,279

Reproducible Computational Workflows with Continuous Analysis

bioinformatics more details view paper
  • Downloaded 2,563 times
  • Download rankings, all-time:
    • Site-wide: 1,741 out of 73,279
    • In bioinformatics: 343 out of 7,144
  • Year to date:
    • Site-wide: 27,947 out of 73,279
  • Since beginning of last month:
    • Site-wide: 27,947 out of 73,279

Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification

bioinformatics more details view paper
  • Downloaded 2,469 times
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    • Site-wide: 1,872 out of 73,279
    • In bioinformatics: 374 out of 7,144
  • Year to date:
    • Site-wide: 38,198 out of 73,279
  • Since beginning of last month:
    • Site-wide: 38,198 out of 73,279

ADAGE analysis of publicly available gene expression data collections illuminates Pseudomonas aeruginosa-host interactions

bioinformatics more details view paper
  • Downloaded 2,171 times
  • Download rankings, all-time:
    • Site-wide: 2,339 out of 73,279
    • In bioinformatics: 463 out of 7,144
  • Year to date:
    • Site-wide: 41,101 out of 73,279
  • Since beginning of last month:
    • Site-wide: 41,101 out of 73,279

Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics

bioinformatics more details view paper
  • Downloaded 1,732 times
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    • Site-wide: 3,454 out of 73,279
    • In bioinformatics: 678 out of 7,144
  • Year to date:
    • Site-wide: 21,917 out of 73,279
  • Since beginning of last month:
    • Site-wide: 21,917 out of 73,279

MultiPLIER: a transfer learning framework for transcriptomics reveals systemic features of rare disease

bioinformatics more details view paper
  • Downloaded 1,719 times
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    • Site-wide: 3,494 out of 73,279
    • In bioinformatics: 688 out of 7,144
  • Year to date:
    • Site-wide: 10,725 out of 73,279
  • Since beginning of last month:
    • Site-wide: 10,725 out of 73,279

Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design

genomics more details view paper
  • Downloaded 1,334 times
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    • Site-wide: 5,369 out of 73,279
    • In genomics: 921 out of 4,867
  • Year to date:
    • Site-wide: 4,939 out of 73,279
  • Since beginning of last month:
    • Site-wide: 4,939 out of 73,279

Integrative networks illuminate biological factors underlying gene-disease associations

bioinformatics more details view paper
  • Downloaded 1,299 times
  • Download rankings, all-time:
    • Site-wide: 5,603 out of 73,279
    • In bioinformatics: 1,058 out of 7,144
  • Year to date:
    • Site-wide: 45,777 out of 73,279
  • Since beginning of last month:
    • Site-wide: 45,777 out of 73,279

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

systems biology more details view paper
  • Downloaded 1,283 times
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    • Site-wide: 5,719 out of 73,279
    • In systems biology: 153 out of 2,008
  • Year to date:
    • Site-wide: 21,604 out of 73,279
  • Since beginning of last month:
    • Site-wide: 21,604 out of 73,279

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

bioinformatics more details view paper
  • Downloaded 1,264 times
  • Download rankings, all-time:
    • Site-wide: 5,860 out of 73,279
    • In bioinformatics: 1,110 out of 7,144
  • Year to date:
    • Site-wide: 37,694 out of 73,279
  • Since beginning of last month:
    • Site-wide: 37,694 out of 73,279

Comprehensive cross-population analysis of high-grade serous ovarian cancer supports no more than three subtypes

cancer biology more details view paper
  • Downloaded 1,224 times
  • Download rankings, all-time:
    • Site-wide: 6,185 out of 73,279
    • In cancer biology: 166 out of 2,510
  • Year to date:
    • Site-wide: 25,254 out of 73,279
  • Since beginning of last month:
    • Site-wide: 25,254 out of 73,279

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

bioinformatics more details view paper
  • Downloaded 1,191 times
  • Download rankings, all-time:
    • Site-wide: 6,489 out of 73,279
    • In bioinformatics: 1,205 out of 7,144
  • Year to date:
    • Site-wide: 5,975 out of 73,279
  • Since beginning of last month:
    • Site-wide: 5,975 out of 73,279

A Novel Multi-network Approach Reveals Tissue-specific Cellular Modulators of Fibrosis in Systemic Sclerosis, Pulmonary Fibrosis and Pulmonary Arterial Hypertension

systems biology more details view paper
  • Downloaded 1,114 times
  • Download rankings, all-time:
    • Site-wide: 7,267 out of 73,279
    • In systems biology: 211 out of 2,008
  • Year to date:
    • Site-wide: 47,615 out of 73,279
  • Since beginning of last month:
    • Site-wide: 47,615 out of 73,279

Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality

bioinformatics more details view paper
  • Downloaded 1,095 times
  • Download rankings, all-time:
    • Site-wide: 7,446 out of 73,279
    • In bioinformatics: 1,323 out of 7,144
  • Year to date:
    • Site-wide: 8,585 out of 73,279
  • Since beginning of last month:
    • Site-wide: 8,585 out of 73,279

A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma

genomics more details view paper
  • Downloaded 910 times
  • Download rankings, all-time:
    • Site-wide: 10,097 out of 73,279
    • In genomics: 1,494 out of 4,867
  • Year to date:
    • Site-wide: 41,801 out of 73,279
  • Since beginning of last month:
    • Site-wide: 41,801 out of 73,279

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

bioinformatics more details view paper
  • Downloaded 868 times
  • Download rankings, all-time:
    • Site-wide: 10,901 out of 73,279
    • In bioinformatics: 1,831 out of 7,144
  • Year to date:
    • Site-wide: 38,217 out of 73,279
  • Since beginning of last month:
    • Site-wide: 38,217 out of 73,279

Pathway and network-based strategies to translate genetic discoveries into effective therapies

genetics more details view paper
  • Downloaded 748 times
  • Download rankings, all-time:
    • Site-wide: 13,598 out of 73,279
    • In genetics: 926 out of 4,026
  • Year to date:
    • Site-wide: 48,854 out of 73,279
  • Since beginning of last month:
    • Site-wide: 48,854 out of 73,279

Specific histone modifications associate with alternative exon selection during mammalian development

bioinformatics more details view paper
  • Downloaded 726 times
  • Download rankings, all-time:
    • Site-wide: 14,246 out of 73,279
    • In bioinformatics: 2,278 out of 7,144
  • Year to date:
    • Site-wide: 22,389 out of 73,279
  • Since beginning of last month:
    • Site-wide: 22,389 out of 73,279

Tribe: The collaborative platform for reproducible web-based analysis of gene sets

bioinformatics more details view paper
  • Downloaded 638 times
  • Download rankings, all-time:
    • Site-wide: 17,166 out of 73,279
    • In bioinformatics: 2,622 out of 7,144
  • Year to date:
    • Site-wide: 62,490 out of 73,279
  • Since beginning of last month:
    • Site-wide: 62,490 out of 73,279

ADAGE signature analysis: differential expression analysis with data-defined gene sets

bioinformatics more details view paper
  • Downloaded 608 times
  • Download rankings, all-time:
    • Site-wide: 18,404 out of 73,279
    • In bioinformatics: 2,766 out of 7,144
  • Year to date:
    • Site-wide: 58,339 out of 73,279
  • Since beginning of last month:
    • Site-wide: 58,339 out of 73,279

Integrated Phosphoproteomics and Transcriptional Classifiers Reveal Hidden RAS Signaling Dynamics in Multiple Myeloma

cancer biology more details view paper
  • Downloaded 548 times
  • Download rankings, all-time:
    • Site-wide: 21,233 out of 73,279
    • In cancer biology: 659 out of 2,510
  • Year to date:
    • Site-wide: 30,268 out of 73,279
  • Since beginning of last month:
    • Site-wide: 30,268 out of 73,279

Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses

bioinformatics more details view paper
  • Downloaded 456 times
  • Download rankings, all-time:
    • Site-wide: 26,677 out of 73,279
    • In bioinformatics: 3,611 out of 7,144
  • Year to date:
    • Site-wide: 59,518 out of 73,279
  • Since beginning of last month:
    • Site-wide: 59,518 out of 73,279

Machine learning analysis identifies Drosophila Grunge/Atrophin as an important learning and memory gene required for memory retention and social learning.

genetics more details view paper
  • Downloaded 392 times
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    • Site-wide: 31,627 out of 73,279
    • In genetics: 1,974 out of 4,026
  • Year to date:
    • Site-wide: 47,965 out of 73,279
  • Since beginning of last month:
    • Site-wide: 47,965 out of 73,279

Learning and Imputation for Mass-spec Bias Reduction (LIMBR)

bioinformatics more details view paper
  • Downloaded 348 times
  • Download rankings, all-time:
    • Site-wide: 35,769 out of 73,279
    • In bioinformatics: 4,428 out of 7,144
  • Year to date:
    • Site-wide: 47,546 out of 73,279
  • Since beginning of last month:
    • Site-wide: 47,546 out of 73,279

Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts

bioinformatics more details view paper
  • Downloaded 334 times
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    • Site-wide: 37,217 out of 73,279
    • In bioinformatics: 4,555 out of 7,144
  • Year to date:
    • Site-wide: 3,651 out of 73,279
  • Since beginning of last month:
    • Site-wide: 3,651 out of 73,279

Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome

systems biology more details view paper
  • Downloaded 308 times
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    • Site-wide: 39,922 out of 73,279
    • In systems biology: 1,213 out of 2,008
  • Year to date:
    • Site-wide: 26,811 out of 73,279
  • Since beginning of last month:
    • Site-wide: 26,811 out of 73,279

A Multimodal Strategy Used By A Large c-di-GMP Network

microbiology more details view paper
  • Downloaded 303 times
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    • Site-wide: 40,459 out of 73,279
    • In microbiology: 2,642 out of 5,964
  • Year to date:
    • Site-wide: 71,456 out of 73,279
  • Since beginning of last month:
    • Site-wide: 71,456 out of 73,279

Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1

systems biology more details view paper
  • Downloaded 242 times
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    • Site-wide: 48,370 out of 73,279
    • In systems biology: 1,477 out of 2,008
  • Year to date:
    • Site-wide: 1,092 out of 73,279
  • Since beginning of last month:
    • Site-wide: 1,092 out of 73,279

New Drosophila long-term memory genes revealed by assessing computational function prediction methods.

neuroscience more details view paper
  • Downloaded 238 times
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    • Site-wide: 48,801 out of 73,279
    • In neuroscience: 8,664 out of 13,178
  • Year to date:
    • Site-wide: 58,485 out of 73,279
  • Since beginning of last month:
    • Site-wide: 58,485 out of 73,279

Graph biased feature selection of genes is better than random for many genes

bioinformatics more details view paper
  • Downloaded 195 times
  • Download rankings, all-time:
    • Site-wide: 55,125 out of 73,279
    • In bioinformatics: 5,957 out of 7,144
  • Year to date:
    • Site-wide: 1,583 out of 73,279
  • Since beginning of last month:
    • Site-wide: 1,583 out of 73,279

Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin

microbiology more details view paper
  • Downloaded 96 times
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    • Site-wide: 69,267 out of 73,279
    • In microbiology: 5,480 out of 5,964
  • Year to date:
    • Site-wide: 39,852 out of 73,279
  • Since beginning of last month:
    • Site-wide: 39,852 out of 73,279

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