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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 52,319 bioRxiv papers from 242,658 authors.

Author: Casey S. Greene

Rankings

  • All-time downloads: 90,553 (rank: 63 out of 242,658)
  • Categories:
    • bioinformatics: 81,253 (rank: 1 out of 21,501)
    • cancer biology: 1,392 (rank: 1,301 (tie) out of 13,573)
    • genetics: 1,009 (rank: 7,634 out of 23,639)
    • genomics: 1,563 (rank: 7,817 (tie) out of 28,115)
    • microbiology: 263 (rank: 11,970 (tie) out of 23,535)
    • neuroscience: 184 (rank: 29,122 (tie) out of 37,392)
    • systems biology: 4,889 (rank: 70 out of 7,231)

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 49,820 times
  • Download rankings, all-time:
    • Site-wide: 6 out of 52,319
    • In bioinformatics: 1 out of 5,482
  • Year to date:
    • Site-wide: 62 out of 52,319
  • Since beginning of last month:
    • Site-wide: 411 out of 52,319

Privacy-preserving generative deep neural networks support clinical data sharing

bioinformatics more details view paper
  • Downloaded 10,036 times
  • Download rankings, all-time:
    • Site-wide: 86 out of 52,319
    • In bioinformatics: 15 out of 5,482
  • Year to date:
    • Site-wide: 133 out of 52,319
  • Since beginning of last month:
    • Site-wide: 131 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 3,221 times
  • Download rankings, all-time:
    • Site-wide: 788 out of 52,319
    • In bioinformatics: 161 out of 5,482
  • Year to date:
    • Site-wide: 2,423 out of 52,319
  • Since beginning of last month:
    • Site-wide: 6,123 out of 52,319

Enter the matrix: factorization uncovers knowledge from omics

systems biology more details view paper
  • Downloaded 2,631 times
  • Download rankings, all-time:
    • Site-wide: 1,131 out of 52,319
    • In systems biology: 24 out of 1,528
  • Year to date:
    • Site-wide: 6,384 out of 52,319
  • Since beginning of last month:
    • Site-wide: 7,992 out of 52,319

Reproducible Computational Workflows with Continuous Analysis

bioinformatics more details view paper
  • Downloaded 2,453 times
  • Download rankings, all-time:
    • Site-wide: 1,270 out of 52,319
    • In bioinformatics: 257 out of 5,482
  • Year to date:
    • Site-wide: 24,321 out of 52,319
  • Since beginning of last month:
    • Site-wide: 21,657 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 2,333 times
  • Download rankings, all-time:
    • Site-wide: 1,424 out of 52,319
    • In bioinformatics: 286 out of 5,482
  • Year to date:
    • Site-wide: 5,480 out of 52,319
  • Since beginning of last month:
    • Site-wide: 6,002 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 2,289 times
  • Download rankings, all-time:
    • Site-wide: 1,466 out of 52,319
    • In bioinformatics: 293 out of 5,482
  • Year to date:
    • Site-wide: 17,731 out of 52,319
  • Since beginning of last month:
    • Site-wide: 18,907 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 2,055 times
  • Download rankings, all-time:
    • Site-wide: 1,763 out of 52,319
    • In bioinformatics: 369 out of 5,482
  • Year to date:
    • Site-wide: 26,173 out of 52,319
  • Since beginning of last month:
    • Site-wide: 32,522 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 1,396 times
  • Download rankings, all-time:
    • Site-wide: 3,356 out of 52,319
    • In bioinformatics: 674 out of 5,482
  • Year to date:
    • Site-wide: 1,503 out of 52,319
  • Since beginning of last month:
    • Site-wide: 2,198 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 1,346 times
  • Download rankings, all-time:
    • Site-wide: 3,558 out of 52,319
    • In bioinformatics: 717 out of 5,482
  • Year to date:
    • Site-wide: 2,359 out of 52,319
  • Since beginning of last month:
    • Site-wide: 4,382 out of 52,319

Integrative networks illuminate biological factors underlying gene-disease associations

bioinformatics more details view paper
  • Downloaded 1,211 times
  • Download rankings, all-time:
    • Site-wide: 4,202 out of 52,319
    • In bioinformatics: 849 out of 5,482
  • Year to date:
    • Site-wide: 37,050 out of 52,319
  • Since beginning of last month:
    • Site-wide: 25,993 out of 52,319

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

bioinformatics more details view paper
  • Downloaded 1,152 times
  • Download rankings, all-time:
    • Site-wide: 4,563 out of 52,319
    • In bioinformatics: 914 out of 5,482
  • Year to date:
    • Site-wide: 22,961 out of 52,319
  • Since beginning of last month:
    • Site-wide: 17,250 out of 52,319

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

systems biology more details view paper
  • Downloaded 1,143 times
  • Download rankings, all-time:
    • Site-wide: 4,616 out of 52,319
    • In systems biology: 122 out of 1,528
  • Year to date:
    • Site-wide: 27,010 out of 52,319
  • Since beginning of last month:
    • Site-wide: 28,255 out of 52,319

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

cancer biology more details view paper
  • Downloaded 1,092 times
  • Download rankings, all-time:
    • Site-wide: 4,967 out of 52,319
    • In cancer biology: 128 out of 1,669
  • Year to date:
    • Site-wide: 32,168 out of 52,319
  • Since beginning of last month:
    • Site-wide: 24,582 out of 52,319

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 951 times
  • Download rankings, all-time:
    • Site-wide: 6,227 out of 52,319
    • In systems biology: 172 out of 1,528
  • Year to date:
    • Site-wide: None out of 52,319
  • Since beginning of last month:
    • Site-wide: None out of 52,319

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

genomics more details view paper
  • Downloaded 813 times
  • Download rankings, all-time:
    • Site-wide: 7,924 out of 52,319
    • In genomics: 1,238 out of 3,745
  • Year to date:
    • Site-wide: 34,816 out of 52,319
  • Since beginning of last month:
    • Site-wide: 27,115 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 775 times
  • Download rankings, all-time:
    • Site-wide: 8,528 out of 52,319
    • In bioinformatics: 1,530 out of 5,482
  • Year to date:
    • Site-wide: 35,022 out of 52,319
  • Since beginning of last month:
    • Site-wide: 24,696 out of 52,319

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

genomics more details view paper
  • Downloaded 750 times
  • Download rankings, all-time:
    • Site-wide: 8,977 out of 52,319
    • In genomics: 1,351 out of 3,745
  • Year to date:
    • Site-wide: 1,114 out of 52,319
  • Since beginning of last month:
    • Site-wide: 2,136 out of 52,319

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

genetics more details view paper
  • Downloaded 694 times
  • Download rankings, all-time:
    • Site-wide: 9,982 out of 52,319
    • In genetics: 744 out of 3,050
  • Year to date:
    • Site-wide: 44,900 out of 52,319
  • Since beginning of last month:
    • Site-wide: 43,752 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 588 times
  • Download rankings, all-time:
    • Site-wide: 12,503 out of 52,319
    • In bioinformatics: 2,047 out of 5,482
  • Year to date:
    • Site-wide: 43,485 out of 52,319
  • Since beginning of last month:
    • Site-wide: 38,685 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 543 times
  • Download rankings, all-time:
    • Site-wide: 13,874 out of 52,319
    • In bioinformatics: 2,251 out of 5,482
  • Year to date:
    • Site-wide: 42,415 out of 52,319
  • Since beginning of last month:
    • Site-wide: 42,326 out of 52,319

Specific histone modifications associate with alternative exon selection during mammalian development

bioinformatics more details view paper
  • Downloaded 537 times
  • Download rankings, all-time:
    • Site-wide: 14,067 out of 52,319
    • In bioinformatics: 2,276 out of 5,482
  • Year to date:
    • Site-wide: 14,165 out of 52,319
  • Since beginning of last month:
    • Site-wide: 13,687 out of 52,319

Sequential compression across latent space dimensions enhances gene expression signatures

bioinformatics more details view paper
  • Downloaded 531 times
  • Download rankings, all-time:
    • Site-wide: 14,280 out of 52,319
    • In bioinformatics: 2,298 out of 5,482
  • Year to date:
    • Site-wide: 2,011 out of 52,319
  • Since beginning of last month:
    • Site-wide: 2,883 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 396 times
  • Download rankings, all-time:
    • Site-wide: 20,091 out of 52,319
    • In bioinformatics: 2,934 out of 5,482
  • Year to date:
    • Site-wide: 41,652 out of 52,319
  • Since beginning of last month:
    • Site-wide: 43,961 out of 52,319

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 324 times
  • Download rankings, all-time:
    • Site-wide: 24,466 out of 52,319
    • In bioinformatics: 3,392 out of 5,482
  • Year to date:
    • Site-wide: 4,557 out of 52,319
  • Since beginning of last month:
    • Site-wide: 556 out of 52,319

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 315 times
  • Download rankings, all-time:
    • Site-wide: 25,051 out of 52,319
    • In genetics: 1,678 out of 3,050
  • Year to date:
    • Site-wide: 46,541 out of 52,319
  • Since beginning of last month:
    • Site-wide: 41,710 out of 52,319

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

cancer biology more details view paper
  • Downloaded 300 times
  • Download rankings, all-time:
    • Site-wide: 26,268 out of 52,319
    • In cancer biology: 779 out of 1,669
  • Year to date:
    • Site-wide: 5,147 out of 52,319
  • Since beginning of last month:
    • Site-wide: 7,286 out of 52,319

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

microbiology more details view paper
  • Downloaded 263 times
  • Download rankings, all-time:
    • Site-wide: 29,194 out of 52,319
    • In microbiology: 1,789 out of 4,092
  • Year to date:
    • Site-wide: 50,068 out of 52,319
  • Since beginning of last month:
    • Site-wide: 49,681 out of 52,319

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

bioinformatics more details view paper
  • Downloaded 247 times
  • Download rankings, all-time:
    • Site-wide: 30,620 out of 52,319
    • In bioinformatics: 3,958 out of 5,482
  • Year to date:
    • Site-wide: 39,195 out of 52,319
  • Since beginning of last month:
    • Site-wide: 43,112 out of 52,319

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

neuroscience more details view paper
  • Downloaded 184 times
  • Download rankings, all-time:
    • Site-wide: 37,079 out of 52,319
    • In neuroscience: 6,427 out of 9,180
  • Year to date:
    • Site-wide: 43,028 out of 52,319
  • Since beginning of last month:
    • Site-wide: 49,909 out of 52,319

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

systems biology more details view paper
  • Downloaded 164 times
  • Download rankings, all-time:
    • Site-wide: 39,319 out of 52,319
    • In systems biology: 1,237 out of 1,528
  • Year to date:
    • Site-wide: 24,546 out of 52,319
  • Since beginning of last month:
    • Site-wide: 19,277 out of 52,319

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