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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 60,222 bioRxiv papers from 267,720 authors.

Author: Casey S. Greene

Rankings

  • All-time downloads: 94,218 (rank: 71 out of 267,720)
  • Categories:
    • bioinformatics: 84,025 (rank: 1 out of 23,843)
    • cancer biology: 1,564 (rank: 1,292 (tie) out of 16,249)
    • genetics: 1,071 (rank: 9,096 (tie) out of 27,065)
    • genomics: 1,859 (rank: 7,177 (tie) out of 31,247)
    • microbiology: 277 (rank: 14,230 (tie) out of 27,365)
    • neuroscience: 207 (rank: 32,950 (tie) out of 43,945)
    • systems biology: 5,215 (rank: 127 out of 8,141)

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 50,610 times
  • Download rankings, all-time:
    • Site-wide: 7 out of 60,222
    • In bioinformatics: 1 out of 6,078
  • Year to date:
    • Site-wide: 91 out of 60,222
  • Since beginning of last month:
    • Site-wide: 480 out of 60,222

Privacy-preserving generative deep neural networks support clinical data sharing

bioinformatics more details view paper
  • Downloaded 10,970 times
  • Download rankings, all-time:
    • Site-wide: 85 out of 60,222
    • In bioinformatics: 14 out of 6,078
  • Year to date:
    • Site-wide: 135 out of 60,222
  • Since beginning of last month:
    • Site-wide: 424 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 3,362 times
  • Download rankings, all-time:
    • Site-wide: 851 out of 60,222
    • In bioinformatics: 171 out of 6,078
  • Year to date:
    • Site-wide: 2,997 out of 60,222
  • Since beginning of last month:
    • Site-wide: 8,180 out of 60,222

Enter the matrix: factorization uncovers knowledge from omics

systems biology more details view paper
  • Downloaded 2,753 times
  • Download rankings, all-time:
    • Site-wide: 1,233 out of 60,222
    • In systems biology: 24 out of 1,707
  • Year to date:
    • Site-wide: 6,611 out of 60,222
  • Since beginning of last month:
    • Site-wide: 10,171 out of 60,222

Reproducible Computational Workflows with Continuous Analysis

bioinformatics more details view paper
  • Downloaded 2,483 times
  • Download rankings, all-time:
    • Site-wide: 1,450 out of 60,222
    • In bioinformatics: 287 out of 6,078
  • Year to date:
    • Site-wide: 31,441 out of 60,222
  • Since beginning of last month:
    • Site-wide: 51,842 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 2,475 times
  • Download rankings, all-time:
    • Site-wide: 1,463 out of 60,222
    • In bioinformatics: 288 out of 6,078
  • Year to date:
    • Site-wide: 5,522 out of 60,222
  • Since beginning of last month:
    • Site-wide: 9,131 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 2,368 times
  • Download rankings, all-time:
    • Site-wide: 1,596 out of 60,222
    • In bioinformatics: 316 out of 6,078
  • Year to date:
    • Site-wide: 17,473 out of 60,222
  • Since beginning of last month:
    • Site-wide: 31,912 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 2,109 times
  • Download rankings, all-time:
    • Site-wide: 1,945 out of 60,222
    • In bioinformatics: 403 out of 6,078
  • Year to date:
    • Site-wide: 27,617 out of 60,222
  • Since beginning of last month:
    • Site-wide: 38,515 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 1,574 times
  • Download rankings, all-time:
    • Site-wide: 3,214 out of 60,222
    • In bioinformatics: 650 out of 6,078
  • Year to date:
    • Site-wide: 2,311 out of 60,222
  • Since beginning of last month:
    • Site-wide: 4,339 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 1,526 times
  • Download rankings, all-time:
    • Site-wide: 3,390 out of 60,222
    • In bioinformatics: 688 out of 6,078
  • Year to date:
    • Site-wide: 2,092 out of 60,222
  • Since beginning of last month:
    • Site-wide: 9,440 out of 60,222

Integrative networks illuminate biological factors underlying gene-disease associations

bioinformatics more details view paper
  • Downloaded 1,243 times
  • Download rankings, all-time:
    • Site-wide: 4,754 out of 60,222
    • In bioinformatics: 937 out of 6,078
  • Year to date:
    • Site-wide: 42,634 out of 60,222
  • Since beginning of last month:
    • Site-wide: 44,072 out of 60,222

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

systems biology more details view paper
  • Downloaded 1,188 times
  • Download rankings, all-time:
    • Site-wide: 5,109 out of 60,222
    • In systems biology: 136 out of 1,707
  • Year to date:
    • Site-wide: 30,460 out of 60,222
  • Since beginning of last month:
    • Site-wide: 40,458 out of 60,222

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

bioinformatics more details view paper
  • Downloaded 1,188 times
  • Download rankings, all-time:
    • Site-wide: 5,102 out of 60,222
    • In bioinformatics: 992 out of 6,078
  • Year to date:
    • Site-wide: 28,831 out of 60,222
  • Since beginning of last month:
    • Site-wide: 28,191 out of 60,222

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

cancer biology more details view paper
  • Downloaded 1,143 times
  • Download rankings, all-time:
    • Site-wide: 5,474 out of 60,222
    • In cancer biology: 140 out of 1,975
  • Year to date:
    • Site-wide: 33,070 out of 60,222
  • Since beginning of last month:
    • Site-wide: 28,162 out of 60,222

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 1,052 times
  • Download rankings, all-time:
    • Site-wide: 6,291 out of 60,222
    • In systems biology: 178 out of 1,707
  • Year to date:
    • Site-wide: 41,349 out of 60,222
  • Since beginning of last month:
    • Site-wide: 48,870 out of 60,222

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

genomics more details view paper
  • Downloaded 999 times
  • Download rankings, all-time:
    • Site-wide: 6,840 out of 60,222
    • In genomics: 1,117 out of 4,168
  • Year to date:
    • Site-wide: 1,305 out of 60,222
  • Since beginning of last month:
    • Site-wide: 2,625 out of 60,222

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

genomics more details view paper
  • Downloaded 860 times
  • Download rankings, all-time:
    • Site-wide: 8,645 out of 60,222
    • In genomics: 1,325 out of 4,168
  • Year to date:
    • Site-wide: 36,290 out of 60,222
  • Since beginning of last month:
    • Site-wide: 46,457 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 812 times
  • Download rankings, all-time:
    • Site-wide: 9,465 out of 60,222
    • In bioinformatics: 1,654 out of 6,078
  • Year to date:
    • Site-wide: 39,497 out of 60,222
  • Since beginning of last month:
    • Site-wide: 51,652 out of 60,222

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

genetics more details view paper
  • Downloaded 717 times
  • Download rankings, all-time:
    • Site-wide: 11,318 out of 60,222
    • In genetics: 812 out of 3,432
  • Year to date:
    • Site-wide: 52,467 out of 60,222
  • Since beginning of last month:
    • Site-wide: 58,030 out of 60,222

Sequential compression across latent space dimensions enhances gene expression signatures

bioinformatics more details view paper
  • Downloaded 687 times
  • Download rankings, all-time:
    • Site-wide: 12,042 out of 60,222
    • In bioinformatics: 2,002 out of 6,078
  • Year to date:
    • Site-wide: 2,476 out of 60,222
  • Since beginning of last month:
    • Site-wide: 6,977 out of 60,222

Specific histone modifications associate with alternative exon selection during mammalian development

bioinformatics more details view paper
  • Downloaded 611 times
  • Download rankings, all-time:
    • Site-wide: 14,148 out of 60,222
    • In bioinformatics: 2,259 out of 6,078
  • Year to date:
    • Site-wide: 15,405 out of 60,222
  • Since beginning of last month:
    • Site-wide: 15,033 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 609 times
  • Download rankings, all-time:
    • Site-wide: 14,194 out of 60,222
    • In bioinformatics: 2,269 out of 6,078
  • Year to date:
    • Site-wide: 52,599 out of 60,222
  • Since beginning of last month:
    • Site-wide: 58,649 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 568 times
  • Download rankings, all-time:
    • Site-wide: 15,637 out of 60,222
    • In bioinformatics: 2,455 out of 6,078
  • Year to date:
    • Site-wide: 49,854 out of 60,222
  • Since beginning of last month:
    • Site-wide: 42,205 out of 60,222

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

cancer biology more details view paper
  • Downloaded 421 times
  • Download rankings, all-time:
    • Site-wide: 22,483 out of 60,222
    • In cancer biology: 687 out of 1,975
  • Year to date:
    • Site-wide: 5,701 out of 60,222
  • Since beginning of last month:
    • Site-wide: 12,109 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 414 times
  • Download rankings, all-time:
    • Site-wide: 22,940 out of 60,222
    • In bioinformatics: 3,248 out of 6,078
  • Year to date:
    • Site-wide: 52,246 out of 60,222
  • Since beginning of last month:
    • Site-wide: 52,886 out of 60,222

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 354 times
  • Download rankings, all-time:
    • Site-wide: 26,951 out of 60,222
    • In genetics: 1,752 out of 3,432
  • Year to date:
    • Site-wide: 47,723 out of 60,222
  • Since beginning of last month:
    • Site-wide: 45,741 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 289 times
  • Download rankings, all-time:
    • Site-wide: 32,559 out of 60,222
    • In bioinformatics: 4,147 out of 6,078
  • Year to date:
    • Site-wide: 40,918 out of 60,222
  • Since beginning of last month:
    • Site-wide: 30,552 out of 60,222

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

microbiology more details view paper
  • Downloaded 277 times
  • Download rankings, all-time:
    • Site-wide: 33,695 out of 60,222
    • In microbiology: 2,151 out of 4,799
  • Year to date:
    • Site-wide: 58,459 out of 60,222
  • Since beginning of last month:
    • Site-wide: 56,595 out of 60,222

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

systems biology more details view paper
  • Downloaded 222 times
  • Download rankings, all-time:
    • Site-wide: 39,625 out of 60,222
    • In systems biology: 1,258 out of 1,707
  • Year to date:
    • Site-wide: 25,716 out of 60,222
  • Since beginning of last month:
    • Site-wide: 20,310 out of 60,222

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

neuroscience more details view paper
  • Downloaded 207 times
  • Download rankings, all-time:
    • Site-wide: 41,389 out of 60,222
    • In neuroscience: 7,205 out of 10,621
  • Year to date:
    • Site-wide: 51,299 out of 60,222
  • Since beginning of last month:
    • Site-wide: 57,051 out of 60,222

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

bioinformatics more details view paper
  • Downloaded 127 times
  • Download rankings, all-time:
    • Site-wide: 51,698 out of 60,222
    • In bioinformatics: 5,573 out of 6,078
  • Year to date:
    • Site-wide: 29,664 out of 60,222
  • Since beginning of last month:
    • Site-wide: 2,590 out of 60,222

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