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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 62,747 bioRxiv papers from 278,434 authors.

Author: Casey S. Greene

Rankings

  • All-time downloads: 95,126 (rank: 70 out of 278,434)
  • Categories:
    • bioinformatics: 84,747 (rank: 1 out of 24,395)
    • cancer biology: 1,606 (rank: 1,296 (tie) out of 17,227)
    • genetics: 1,078 (rank: 9,526 (tie) out of 27,725)
    • genomics: 1,922 (rank: 7,082 (tie) out of 31,945)
    • microbiology: 280 (rank: 14,861 (tie) out of 28,540)
    • neuroscience: 212 (rank: 33,997 (tie) out of 45,895)
    • systems biology: 5,281 (rank: 127 out of 8,440)

Downloads per author, site-wide

Preprints

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

microbiology 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 50,811 times
  • Download rankings, all-time:
    • Site-wide: 7 out of 62,747
    • In bioinformatics: 1 out of 6,251
  • Year to date:
    • Site-wide: 95 out of 62,747
  • Since beginning of last month:
    • Site-wide: 649 out of 62,747

Privacy-preserving generative deep neural networks support clinical data sharing

bioinformatics more details view paper
  • Downloaded 11,117 times
  • Download rankings, all-time:
    • Site-wide: 85 out of 62,747
    • In bioinformatics: 15 out of 6,251
  • Year to date:
    • Site-wide: 143 out of 62,747
  • Since beginning of last month:
    • Site-wide: 708 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 3,386 times
  • Download rankings, all-time:
    • Site-wide: 864 out of 62,747
    • In bioinformatics: 173 out of 6,251
  • Year to date:
    • Site-wide: 3,195 out of 62,747
  • Since beginning of last month:
    • Site-wide: 15,019 out of 62,747

Enter the matrix: factorization uncovers knowledge from omics

systems biology more details view paper
  • Downloaded 2,781 times
  • Download rankings, all-time:
    • Site-wide: 1,256 out of 62,747
    • In systems biology: 25 out of 1,783
  • Year to date:
    • Site-wide: 6,729 out of 62,747
  • Since beginning of last month:
    • Site-wide: 9,116 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 2,514 times
  • Download rankings, all-time:
    • Site-wide: 1,474 out of 62,747
    • In bioinformatics: 292 out of 6,251
  • Year to date:
    • Site-wide: 5,476 out of 62,747
  • Since beginning of last month:
    • Site-wide: 7,430 out of 62,747

Reproducible Computational Workflows with Continuous Analysis

bioinformatics more details view paper
  • Downloaded 2,495 times
  • Download rankings, all-time:
    • Site-wide: 1,496 out of 62,747
    • In bioinformatics: 297 out of 6,251
  • Year to date:
    • Site-wide: 31,983 out of 62,747
  • Since beginning of last month:
    • Site-wide: 35,169 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 2,393 times
  • Download rankings, all-time:
    • Site-wide: 1,629 out of 62,747
    • In bioinformatics: 328 out of 6,251
  • Year to date:
    • Site-wide: 16,978 out of 62,747
  • Since beginning of last month:
    • Site-wide: 17,409 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 2,116 times
  • Download rankings, all-time:
    • Site-wide: 2,018 out of 62,747
    • In bioinformatics: 415 out of 6,251
  • Year to date:
    • Site-wide: 29,254 out of 62,747
  • Since beginning of last month:
    • Site-wide: 48,632 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 1,610 times
  • Download rankings, all-time:
    • Site-wide: 3,221 out of 62,747
    • In bioinformatics: 653 out of 6,251
  • Year to date:
    • Site-wide: 2,435 out of 62,747
  • Since beginning of last month:
    • Site-wide: 4,674 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 1,553 times
  • Download rankings, all-time:
    • Site-wide: 3,425 out of 62,747
    • In bioinformatics: 695 out of 6,251
  • Year to date:
    • Site-wide: 2,228 out of 62,747
  • Since beginning of last month:
    • Site-wide: 8,292 out of 62,747

Integrative networks illuminate biological factors underlying gene-disease associations

bioinformatics more details view paper
  • Downloaded 1,254 times
  • Download rankings, all-time:
    • Site-wide: 4,869 out of 62,747
    • In bioinformatics: 949 out of 6,251
  • Year to date:
    • Site-wide: 42,877 out of 62,747
  • Since beginning of last month:
    • Site-wide: 30,338 out of 62,747

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

systems biology more details view paper
  • Downloaded 1,202 times
  • Download rankings, all-time:
    • Site-wide: 5,232 out of 62,747
    • In systems biology: 136 out of 1,783
  • Year to date:
    • Site-wide: 30,541 out of 62,747
  • Since beginning of last month:
    • Site-wide: 26,327 out of 62,747

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

bioinformatics more details view paper
  • Downloaded 1,198 times
  • Download rankings, all-time:
    • Site-wide: 5,249 out of 62,747
    • In bioinformatics: 1,016 out of 6,251
  • Year to date:
    • Site-wide: 29,656 out of 62,747
  • Since beginning of last month:
    • Site-wide: 28,427 out of 62,747

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

cancer biology more details view paper
  • Downloaded 1,157 times
  • Download rankings, all-time:
    • Site-wide: 5,581 out of 62,747
    • In cancer biology: 148 out of 2,061
  • Year to date:
    • Site-wide: 33,034 out of 62,747
  • Since beginning of last month:
    • Site-wide: 26,185 out of 62,747

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 1,063 times
  • Download rankings, all-time:
    • Site-wide: 6,431 out of 62,747
    • In systems biology: 179 out of 1,783
  • Year to date:
    • Site-wide: 41,579 out of 62,747
  • Since beginning of last month:
    • Site-wide: 39,155 out of 62,747

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

genomics more details view paper
  • Downloaded 1,054 times
  • Download rankings, all-time:
    • Site-wide: 6,517 out of 62,747
    • In genomics: 1,066 out of 4,316
  • Year to date:
    • Site-wide: 1,354 out of 62,747
  • Since beginning of last month:
    • Site-wide: 3,944 out of 62,747

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

genomics more details view paper
  • Downloaded 868 times
  • Download rankings, all-time:
    • Site-wide: 8,870 out of 62,747
    • In genomics: 1,349 out of 4,316
  • Year to date:
    • Site-wide: 37,641 out of 62,747
  • Since beginning of last month:
    • Site-wide: 43,565 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 820 times
  • Download rankings, all-time:
    • Site-wide: 9,669 out of 62,747
    • In bioinformatics: 1,687 out of 6,251
  • Year to date:
    • Site-wide: 40,470 out of 62,747
  • Since beginning of last month:
    • Site-wide: 45,300 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 793 times
  • Download rankings, all-time:
    • Site-wide: 10,186 out of 62,747
    • In bioinformatics: 1,759 out of 6,251
  • Year to date:
    • Site-wide: 2,197 out of 62,747
  • Since beginning of last month:
    • Site-wide: 2,347 out of 62,747

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

genetics more details view paper
  • Downloaded 722 times
  • Download rankings, all-time:
    • Site-wide: 11,647 out of 62,747
    • In genetics: 824 out of 3,562
  • Year to date:
    • Site-wide: 54,693 out of 62,747
  • Since beginning of last month:
    • Site-wide: 57,252 out of 62,747

Specific histone modifications associate with alternative exon selection during mammalian development

bioinformatics more details view paper
  • Downloaded 631 times
  • Download rankings, all-time:
    • Site-wide: 14,104 out of 62,747
    • In bioinformatics: 2,258 out of 6,251
  • Year to date:
    • Site-wide: 15,440 out of 62,747
  • Since beginning of last month:
    • Site-wide: 18,859 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 612 times
  • Download rankings, all-time:
    • Site-wide: 14,708 out of 62,747
    • In bioinformatics: 2,336 out of 6,251
  • Year to date:
    • Site-wide: 55,300 out of 62,747
  • Since beginning of last month:
    • Site-wide: 60,645 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 577 times
  • Download rankings, all-time:
    • Site-wide: 15,954 out of 62,747
    • In bioinformatics: 2,489 out of 6,251
  • Year to date:
    • Site-wide: 50,349 out of 62,747
  • Since beginning of last month:
    • Site-wide: 43,981 out of 62,747

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

cancer biology more details view paper
  • Downloaded 449 times
  • Download rankings, all-time:
    • Site-wide: 21,866 out of 62,747
    • In cancer biology: 673 out of 2,061
  • Year to date:
    • Site-wide: 5,874 out of 62,747
  • Since beginning of last month:
    • Site-wide: 10,116 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 420 times
  • Download rankings, all-time:
    • Site-wide: 23,568 out of 62,747
    • In bioinformatics: 3,325 out of 6,251
  • Year to date:
    • Site-wide: 53,758 out of 62,747
  • Since beginning of last month:
    • Site-wide: 48,923 out of 62,747

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 356 times
  • Download rankings, all-time:
    • Site-wide: 27,960 out of 62,747
    • In genetics: 1,802 out of 3,562
  • Year to date:
    • Site-wide: 51,057 out of 62,747
  • Since beginning of last month:
    • Site-wide: 60,983 out of 62,747

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

bioinformatics more details view paper
  • Downloaded 300 times
  • Download rankings, all-time:
    • Site-wide: 32,926 out of 62,747
    • In bioinformatics: 4,167 out of 6,251
  • Year to date:
    • Site-wide: 41,338 out of 62,747
  • Since beginning of last month:
    • Site-wide: 39,995 out of 62,747

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

microbiology more details view paper
  • Downloaded 280 times
  • Download rankings, all-time:
    • Site-wide: 34,859 out of 62,747
    • In microbiology: 2,238 out of 5,025
  • Year to date:
    • Site-wide: 60,798 out of 62,747
  • Since beginning of last month:
    • Site-wide: 60,291 out of 62,747

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

systems biology more details view paper
  • Downloaded 235 times
  • Download rankings, all-time:
    • Site-wide: 39,728 out of 62,747
    • In systems biology: 1,250 out of 1,783
  • Year to date:
    • Site-wide: 26,236 out of 62,747
  • Since beginning of last month:
    • Site-wide: 27,061 out of 62,747

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

neuroscience more details view paper
  • Downloaded 212 times
  • Download rankings, all-time:
    • Site-wide: 42,609 out of 62,747
    • In neuroscience: 7,443 out of 11,207
  • Year to date:
    • Site-wide: 53,456 out of 62,747
  • Since beginning of last month:
    • Site-wide: 51,800 out of 62,747

Reusing label functions to extract multiple types of biomedical relationships from biomedical abstracts at scale

bioinformatics more details view paper
  • Downloaded 147 times
  • Download rankings, all-time:
    • Site-wide: 51,133 out of 62,747
    • In bioinformatics: 5,562 out of 6,251
  • Year to date:
    • Site-wide: 28,543 out of 62,747
  • Since beginning of last month:
    • Site-wide: 6,450 out of 62,747

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