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Author: Casey S Greene

  • ORCiD: http://orcid.org/0000-0001-8713-9213
  • Most recently observed institution: Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania

Rankings

  • All-time downloads: 114,456 (rank: 711 )
  • Categories:
    • bioinformatics: 98,607 (rank: 2 )
    • cancer biology: 2,637 (rank: 1,507 )
    • genetic and genomic medicine: 453 (rank: 3,041 (tie) )
    • genetics: 1,288 (rank: 12,305 (tie) )
    • genomics: 2,813 (rank: 7,773 (tie) )
    • infectious diseases: 1,208 (rank: 15,102 (tie) )
    • microbiology: 548 (rank: 21,190 (tie) )
    • neuroscience: 285 (rank: 55,066 (tie) )
    • systems biology: 6,617 (rank: 378 )

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 54,274 times
  • Download rankings, all-time:
    • Site-wide: 89
    • In bioinformatics: 3
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 12,179

Privacy-preserving generative deep neural networks support clinical data sharing

bioinformatics more details view paper
  • Downloaded 13,064 times
  • Download rankings, all-time:
    • Site-wide: 458
    • In bioinformatics: 20
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 55,487

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

bioinformatics more details view paper
  • Downloaded 4,078 times
  • Download rankings, all-time:
    • Site-wide: 2,258
    • In bioinformatics: 211
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 82,297

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

bioinformatics more details view paper
  • Downloaded 3,212 times
  • Download rankings, all-time:
    • Site-wide: 3,234
    • In bioinformatics: 355
  • Year to date:
    • Site-wide: 18,442
  • Since beginning of last month:
    • Site-wide: 21,680

Enter the matrix: factorization uncovers knowledge from omics

systems biology more details view paper
  • Downloaded 3,096 times
  • Download rankings, all-time:
    • Site-wide: 3,418
    • In systems biology: 56
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 88,105

Reproducible Computational Workflows with Continuous Analysis

bioinformatics more details view paper
  • Downloaded 2,743 times
  • Download rankings, all-time:
    • Site-wide: 3,987
    • In bioinformatics: 448
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 42,655

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

bioinformatics more details view paper
  • Downloaded 2,675 times
  • Download rankings, all-time:
    • Site-wide: 4,148
    • In bioinformatics: 468
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 81,993

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

bioinformatics more details view paper
  • Downloaded 2,280 times
  • Download rankings, all-time:
    • Site-wide: 5,288
    • In bioinformatics: 641
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 91,658

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

bioinformatics more details view paper
  • Downloaded 2,164 times
  • Download rankings, all-time:
    • Site-wide: 5,704
    • In bioinformatics: 702
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 96,357

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

bioinformatics more details view paper
  • Downloaded 1,897 times
  • Download rankings, all-time:
    • Site-wide: 6,920
    • In bioinformatics: 876
  • Year to date:
    • Site-wide: 67,473
  • Since beginning of last month:
    • Site-wide: 55,357

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

genomics more details view paper
  • Downloaded 1,762 times
  • Download rankings, all-time:
    • Site-wide: 7,707
    • In genomics: 887
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 77,992

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 1,462 times
  • Download rankings, all-time:
    • Site-wide: 10,220
    • In bioinformatics: 1,298
  • Year to date:
    • Site-wide: 31,643
  • Since beginning of last month:
    • Site-wide: 25,437

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

bioinformatics more details view paper
  • Downloaded 1,412 times
  • Download rankings, all-time:
    • Site-wide: 10,793
    • In bioinformatics: 1,380
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 40,502

Integrative networks illuminate biological factors underlying gene-disease associations

bioinformatics more details view paper
  • Downloaded 1,411 times
  • Download rankings, all-time:
    • Site-wide: 10,817
    • In bioinformatics: 1,386
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 114,630

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

systems biology more details view paper
  • Downloaded 1,406 times
  • Download rankings, all-time:
    • Site-wide: 10,868
    • In systems biology: 219
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 114,786

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

cancer biology more details view paper
  • Downloaded 1,395 times
  • Download rankings, all-time:
    • Site-wide: 10,999
    • In cancer biology: 231
  • Year to date:
    • Site-wide: 55,525
  • Since beginning of last month:
    • Site-wide: 20,597

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

bioinformatics more details view paper
  • Downloaded 1,385 times
  • Download rankings, all-time:
    • Site-wide: 11,113
    • In bioinformatics: 1,418
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 76,416

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 1,250 times
  • Download rankings, all-time:
    • Site-wide: 12,966
    • In systems biology: 267
  • Year to date:
    • Site-wide: 40,956
  • Since beginning of last month:
    • Site-wide: 59,537

Building an International Consortium for Tracking Coronavirus Health Status

infectious diseases more details view paper
  • Downloaded 1,208 times
  • Download rankings, all-time:
    • Site-wide: 13,638
    • In infectious diseases: 1,219
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 110,784

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

genomics more details view paper
  • Downloaded 1,051 times
  • Download rankings, all-time:
    • Site-wide: 16,808
    • In genomics: 1,789
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 73,398

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

bioinformatics more details view paper
  • Downloaded 1,011 times
  • Download rankings, all-time:
    • Site-wide: 17,814
    • In bioinformatics: 2,199
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 116,311

Specific histone modifications associate with alternative exon selection during mammalian development

bioinformatics more details view paper
  • Downloaded 895 times
  • Download rankings, all-time:
    • Site-wide: 21,287
    • In bioinformatics: 2,605
  • Year to date:
    • Site-wide: 53,834
  • Since beginning of last month:
    • Site-wide: 73,849

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

bioinformatics more details view paper
  • Downloaded 880 times
  • Download rankings, all-time:
    • Site-wide: 21,831
    • In bioinformatics: 2,660
  • Year to date:
    • Site-wide: 17,490
  • Since beginning of last month:
    • Site-wide: 15,221

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

genetics more details view paper
  • Downloaded 811 times
  • Download rankings, all-time:
    • Site-wide: 24,508
    • In genetics: 1,244
  • Year to date:
    • Site-wide: 59,136
  • Since beginning of last month:
    • Site-wide: 69,386

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

bioinformatics more details view paper
  • Downloaded 743 times
  • Download rankings, all-time:
    • Site-wide: 27,704
    • In bioinformatics: 3,255
  • Year to date:
    • Site-wide: 48,397
  • Since beginning of last month:
    • Site-wide: 41,098

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

bioinformatics more details view paper
  • Downloaded 684 times
  • Download rankings, all-time:
    • Site-wide: 31,045
    • In bioinformatics: 3,585
  • Year to date:
    • Site-wide: 64,154
  • Since beginning of last month:
    • Site-wide: 78,534

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

cancer biology more details view paper
  • Downloaded 672 times
  • Download rankings, all-time:
    • Site-wide: 31,809
    • In cancer biology: 870
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 57,074

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

cancer biology more details view paper
  • Downloaded 570 times
  • Download rankings, all-time:
    • Site-wide: 39,226
    • In cancer biology: 1,095
  • Year to date:
    • Site-wide: 4,653
  • Since beginning of last month:
    • Site-wide: 11,079

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

bioinformatics more details view paper
  • Downloaded 518 times
  • Download rankings, all-time:
    • Site-wide: 44,231
    • In bioinformatics: 4,730
  • Year to date:
    • Site-wide: 46,976
  • Since beginning of last month:
    • Site-wide: 88,042

Correcting for experiment-specific variability in expression compendia can remove underlying signals

bioinformatics more details view paper
  • Downloaded 495 times
  • Download rankings, all-time:
    • Site-wide: 46,598
    • In bioinformatics: 4,926
  • Year to date:
    • Site-wide: 41,496
  • Since beginning of last month:
    • Site-wide: 87,238

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 477 times
  • Download rankings, all-time:
    • Site-wide: 48,547
    • In genetics: 2,372
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 107,770

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

bioinformatics more details view paper
  • Downloaded 460 times
  • Download rankings, all-time:
    • Site-wide: 50,603
    • In bioinformatics: 5,262
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 93,184

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping

genetic and genomic medicine more details view paper
  • Downloaded 453 times
  • Download rankings, all-time:
    • Site-wide: 51,457
    • In genetic and genomic medicine: 133
  • Year to date:
    • Site-wide: 36,656
  • Since beginning of last month:
    • Site-wide: 41,390

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

systems biology more details view paper
  • Downloaded 435 times
  • Download rankings, all-time:
    • Site-wide: 53,758
    • In systems biology: 1,335
  • Year to date:
    • Site-wide: 24,023
  • Since beginning of last month:
    • Site-wide: 54,285

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

systems biology more details view paper
  • Downloaded 430 times
  • Download rankings, all-time:
    • Site-wide: 54,339
    • In systems biology: 1,343
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 96,999

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

microbiology more details view paper
  • Downloaded 345 times
  • Download rankings, all-time:
    • Site-wide: 67,232
    • In microbiology: 4,537
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 89,486

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

bioinformatics more details view paper
  • Downloaded 338 times
  • Download rankings, all-time:
    • Site-wide: 68,360
    • In bioinformatics: 6,572
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 114,503

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

neuroscience more details view paper
  • Downloaded 285 times
  • Download rankings, all-time:
    • Site-wide: 78,123
    • In neuroscience: 12,106
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 109,279

Analysis of ISCB honorees and keynotes reveals disparities

bioinformatics more details view paper
  • Downloaded 269 times
  • Download rankings, all-time:
    • Site-wide: 81,216
    • In bioinformatics: 7,391
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 106,366

Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

bioinformatics more details view paper
  • Downloaded 257 times
  • Download rankings, all-time:
    • Site-wide: 83,714
    • In bioinformatics: 7,549
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 27,123

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

microbiology more details view paper
  • Downloaded 203 times
  • Download rankings, all-time:
    • Site-wide: 95,039
    • In microbiology: 6,940
  • Year to date:
    • Site-wide: 51,420
  • Since beginning of last month:
    • Site-wide: 68,020

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