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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 65,351 bioRxiv papers from 289,483 authors.

Author: Casey S. Greene

Rankings

  • All-time downloads: 96,473 (rank: 73 out of 289,483)
  • Categories:
    • bioinformatics: 85,789 (rank: 1 out of 25,218)
    • cancer biology: 1,667 (rank: 1,311 (tie) out of 18,052)
    • genetics: 1,094 (rank: 9,701 (tie) out of 28,760)
    • genomics: 1,998 (rank: 7,062 (tie) out of 32,919)
    • microbiology: 345 (rank: 13,168 (tie) out of 29,708)
    • neuroscience: 218 (rank: 35,534 (tie) out of 48,166)
    • systems biology: 5,362 (rank: 127 out of 8,770)

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 51,122 times
  • Download rankings, all-time:
    • Site-wide: 7 out of 65,351
    • In bioinformatics: 1 out of 6,471
  • Year to date:
    • Site-wide: 103 out of 65,351
  • Since beginning of last month:
    • Site-wide: 511 out of 65,351

Privacy-preserving generative deep neural networks support clinical data sharing

bioinformatics more details view paper
  • Downloaded 11,340 times
  • Download rankings, all-time:
    • Site-wide: 87 out of 65,351
    • In bioinformatics: 15 out of 6,471
  • Year to date:
    • Site-wide: 155 out of 65,351
  • Since beginning of last month:
    • Site-wide: 713 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 3,458 times
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    • Site-wide: 867 out of 65,351
    • In bioinformatics: 172 out of 6,471
  • Year to date:
    • Site-wide: 3,156 out of 65,351
  • Since beginning of last month:
    • Site-wide: 5,808 out of 65,351

Enter the matrix: factorization uncovers knowledge from omics

systems biology more details view paper
  • Downloaded 2,813 times
  • Download rankings, all-time:
    • Site-wide: 1,288 out of 65,351
    • In systems biology: 28 out of 1,835
  • Year to date:
    • Site-wide: 7,050 out of 65,351
  • Since beginning of last month:
    • Site-wide: 12,034 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 2,551 times
  • Download rankings, all-time:
    • Site-wide: 1,511 out of 65,351
    • In bioinformatics: 297 out of 6,471
  • Year to date:
    • Site-wide: 5,680 out of 65,351
  • Since beginning of last month:
    • Site-wide: 10,163 out of 65,351

Reproducible Computational Workflows with Continuous Analysis

bioinformatics more details view paper
  • Downloaded 2,513 times
  • Download rankings, all-time:
    • Site-wide: 1,554 out of 65,351
    • In bioinformatics: 307 out of 6,471
  • Year to date:
    • Site-wide: 32,121 out of 65,351
  • Since beginning of last month:
    • Site-wide: 28,840 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 2,417 times
  • Download rankings, all-time:
    • Site-wide: 1,677 out of 65,351
    • In bioinformatics: 336 out of 6,471
  • Year to date:
    • Site-wide: 17,119 out of 65,351
  • Since beginning of last month:
    • Site-wide: 15,985 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 2,128 times
  • Download rankings, all-time:
    • Site-wide: 2,120 out of 65,351
    • In bioinformatics: 429 out of 6,471
  • Year to date:
    • Site-wide: 30,801 out of 65,351
  • Since beginning of last month:
    • Site-wide: 39,622 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 1,669 times
  • Download rankings, all-time:
    • Site-wide: 3,196 out of 65,351
    • In bioinformatics: 639 out of 6,471
  • Year to date:
    • Site-wide: 2,514 out of 65,351
  • Since beginning of last month:
    • Site-wide: 5,181 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 1,606 times
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    • Site-wide: 3,397 out of 65,351
    • In bioinformatics: 679 out of 6,471
  • Year to date:
    • Site-wide: 2,344 out of 65,351
  • Since beginning of last month:
    • Site-wide: 7,065 out of 65,351

Integrative networks illuminate biological factors underlying gene-disease associations

bioinformatics more details view paper
  • Downloaded 1,258 times
  • Download rankings, all-time:
    • Site-wide: 5,102 out of 65,351
    • In bioinformatics: 990 out of 6,471
  • Year to date:
    • Site-wide: 46,726 out of 65,351
  • Since beginning of last month:
    • Site-wide: 51,277 out of 65,351

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

bioinformatics more details view paper
  • Downloaded 1,215 times
  • Download rankings, all-time:
    • Site-wide: 5,413 out of 65,351
    • In bioinformatics: 1,035 out of 6,471
  • Year to date:
    • Site-wide: 30,345 out of 65,351
  • Since beginning of last month:
    • Site-wide: 26,806 out of 65,351

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

systems biology more details view paper
  • Downloaded 1,213 times
  • Download rankings, all-time:
    • Site-wide: 5,431 out of 65,351
    • In systems biology: 140 out of 1,835
  • Year to date:
    • Site-wide: 32,050 out of 65,351
  • Since beginning of last month:
    • Site-wide: 26,955 out of 65,351

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

cancer biology more details view paper
  • Downloaded 1,179 times
  • Download rankings, all-time:
    • Site-wide: 5,704 out of 65,351
    • In cancer biology: 153 out of 2,178
  • Year to date:
    • Site-wide: 32,228 out of 65,351
  • Since beginning of last month:
    • Site-wide: 20,436 out of 65,351

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

genomics more details view paper
  • Downloaded 1,121 times
  • Download rankings, all-time:
    • Site-wide: 6,207 out of 65,351
    • In genomics: 1,023 out of 4,459
  • Year to date:
    • Site-wide: 1,432 out of 65,351
  • Since beginning of last month:
    • Site-wide: 5,009 out of 65,351

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 1,080 times
  • Download rankings, all-time:
    • Site-wide: 6,623 out of 65,351
    • In systems biology: 189 out of 1,835
  • Year to date:
    • Site-wide: 41,369 out of 65,351
  • Since beginning of last month:
    • Site-wide: 27,824 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 915 times
  • Download rankings, all-time:
    • Site-wide: 8,640 out of 65,351
    • In bioinformatics: 1,510 out of 6,471
  • Year to date:
    • Site-wide: 2,047 out of 65,351
  • Since beginning of last month:
    • Site-wide: 1,896 out of 65,351

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

genomics more details view paper
  • Downloaded 877 times
  • Download rankings, all-time:
    • Site-wide: 9,195 out of 65,351
    • In genomics: 1,393 out of 4,459
  • Year to date:
    • Site-wide: 39,697 out of 65,351
  • Since beginning of last month:
    • Site-wide: 40,426 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 834 times
  • Download rankings, all-time:
    • Site-wide: 9,931 out of 65,351
    • In bioinformatics: 1,724 out of 6,471
  • Year to date:
    • Site-wide: 41,144 out of 65,351
  • Since beginning of last month:
    • Site-wide: 33,212 out of 65,351

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

genetics more details view paper
  • Downloaded 726 times
  • Download rankings, all-time:
    • Site-wide: 12,235 out of 65,351
    • In genetics: 855 out of 3,696
  • Year to date:
    • Site-wide: 58,036 out of 65,351
  • Since beginning of last month:
    • Site-wide: 63,403 out of 65,351

Specific histone modifications associate with alternative exon selection during mammalian development

bioinformatics more details view paper
  • Downloaded 655 times
  • Download rankings, all-time:
    • Site-wide: 14,153 out of 65,351
    • In bioinformatics: 2,264 out of 6,471
  • Year to date:
    • Site-wide: 15,690 out of 65,351
  • Since beginning of last month:
    • Site-wide: 18,859 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 621 times
  • Download rankings, all-time:
    • Site-wide: 15,225 out of 65,351
    • In bioinformatics: 2,397 out of 6,471
  • Year to date:
    • Site-wide: 57,184 out of 65,351
  • Since beginning of last month:
    • Site-wide: 53,328 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 588 times
  • Download rankings, all-time:
    • Site-wide: 16,445 out of 65,351
    • In bioinformatics: 2,543 out of 6,471
  • Year to date:
    • Site-wide: 51,621 out of 65,351
  • Since beginning of last month:
    • Site-wide: 40,609 out of 65,351

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

cancer biology more details view paper
  • Downloaded 488 times
  • Download rankings, all-time:
    • Site-wide: 20,929 out of 65,351
    • In cancer biology: 632 out of 2,178
  • Year to date:
    • Site-wide: 6,047 out of 65,351
  • Since beginning of last month:
    • Site-wide: 9,872 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 428 times
  • Download rankings, all-time:
    • Site-wide: 24,418 out of 65,351
    • In bioinformatics: 3,408 out of 6,471
  • Year to date:
    • Site-wide: 55,834 out of 65,351
  • Since beginning of last month:
    • Site-wide: 48,108 out of 65,351

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 368 times
  • Download rankings, all-time:
    • Site-wide: 28,687 out of 65,351
    • In genetics: 1,837 out of 3,696
  • Year to date:
    • Site-wide: 51,983 out of 65,351
  • Since beginning of last month:
    • Site-wide: 42,199 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 311 times
  • Download rankings, all-time:
    • Site-wide: 33,833 out of 65,351
    • In bioinformatics: 4,239 out of 6,471
  • Year to date:
    • Site-wide: 42,849 out of 65,351
  • Since beginning of last month:
    • Site-wide: 43,762 out of 65,351

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

microbiology more details view paper
  • Downloaded 286 times
  • Download rankings, all-time:
    • Site-wide: 36,277 out of 65,351
    • In microbiology: 2,336 out of 5,254
  • Year to date:
    • Site-wide: 63,562 out of 65,351
  • Since beginning of last month:
    • Site-wide: 61,208 out of 65,351

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

systems biology more details view paper
  • Downloaded 256 times
  • Download rankings, all-time:
    • Site-wide: 39,534 out of 65,351
    • In systems biology: 1,234 out of 1,835
  • Year to date:
    • Site-wide: 26,153 out of 65,351
  • Since beginning of last month:
    • Site-wide: 20,959 out of 65,351

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

neuroscience more details view paper
  • Downloaded 218 times
  • Download rankings, all-time:
    • Site-wide: 44,126 out of 65,351
    • In neuroscience: 7,768 out of 11,706
  • Year to date:
    • Site-wide: 56,213 out of 65,351
  • Since beginning of last month:
    • Site-wide: 60,556 out of 65,351

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

bioinformatics more details view paper
  • Downloaded 160 times
  • Download rankings, all-time:
    • Site-wide: 52,053 out of 65,351
    • In bioinformatics: 5,629 out of 6,471
  • Year to date:
    • Site-wide: 29,885 out of 65,351
  • Since beginning of last month:
    • Site-wide: 22,924 out of 65,351

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

microbiology more details view paper
  • Downloaded 59 times
  • Download rankings, all-time:
    • Site-wide: 63,333 out of 65,351
    • In microbiology: 5,022 out of 5,254
  • Year to date:
    • Site-wide: 59,592 out of 65,351
  • Since beginning of last month:
    • Site-wide: 8,278 out of 65,351

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