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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: 113,669 (rank: 683 out of 509,520)
  • Categories:
    • bioinformatics: 98,112 (rank: 2 out of 36,841)
    • cancer biology: 2,511 (rank: 1,504 out of 31,463)
    • genetic and genomic medicine: 427 (rank: 2,639 (tie) out of 6,821)
    • genetics: 1,274 (rank: 12,087 (tie) out of 38,578)
    • genomics: 2,779 (rank: 7,670 (tie) out of 45,500)
    • infectious diseases: 1,204 (rank: 14,084 (tie) out of 32,342)
    • microbiology: 529 (rank: 20,685 (tie) out of 52,210)
    • neuroscience: 282 (rank: 53,216 (tie) out of 73,597)
    • systems biology: 6,551 (rank: 367 out of 12,790)

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 54,201 times
  • Download rankings, all-time:
    • Site-wide: 88 out of 118,102
    • In bioinformatics: 3 out of 9,568
  • Year to date:
    • Site-wide: 1,853 out of 118,102
  • Since beginning of last month:
    • Site-wide: 1,585 out of 118,102

Privacy-preserving generative deep neural networks support clinical data sharing

bioinformatics more details view paper
  • Downloaded 13,019 times
  • Download rankings, all-time:
    • Site-wide: 435 out of 118,102
    • In bioinformatics: 20 out of 9,568
  • Year to date:
    • Site-wide: 3,880 out of 118,102
  • Since beginning of last month:
    • Site-wide: 4,601 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 4,061 times
  • Download rankings, all-time:
    • Site-wide: 2,139 out of 118,102
    • In bioinformatics: 210 out of 9,568
  • Year to date:
    • Site-wide: 15,160 out of 118,102
  • Since beginning of last month:
    • Site-wide: 27,073 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 3,172 times
  • Download rankings, all-time:
    • Site-wide: 3,083 out of 118,102
    • In bioinformatics: 346 out of 9,568
  • Year to date:
    • Site-wide: 11,604 out of 118,102
  • Since beginning of last month:
    • Site-wide: 19,269 out of 118,102

Enter the matrix: factorization uncovers knowledge from omics

systems biology more details view paper
  • Downloaded 3,083 times
  • Download rankings, all-time:
    • Site-wide: 3,231 out of 118,102
    • In systems biology: 54 out of 2,634
  • Year to date:
    • Site-wide: 39,304 out of 118,102
  • Since beginning of last month:
    • Site-wide: 40,385 out of 118,102

Reproducible Computational Workflows with Continuous Analysis

bioinformatics more details view paper
  • Downloaded 2,724 times
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    • Site-wide: 3,802 out of 118,102
    • In bioinformatics: 439 out of 9,568
  • Year to date:
    • Site-wide: 46,053 out of 118,102
  • Since beginning of last month:
    • Site-wide: 31,337 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 2,669 times
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    • Site-wide: 3,918 out of 118,102
    • In bioinformatics: 452 out of 9,568
  • Year to date:
    • Site-wide: 38,285 out of 118,102
  • Since beginning of last month:
    • Site-wide: 40,423 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 2,277 times
  • Download rankings, all-time:
    • Site-wide: 5,004 out of 118,102
    • In bioinformatics: 622 out of 9,568
  • Year to date:
    • Site-wide: 68,980 out of 118,102
  • Since beginning of last month:
    • Site-wide: 83,825 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 2,150 times
  • Download rankings, all-time:
    • Site-wide: 5,420 out of 118,102
    • In bioinformatics: 686 out of 9,568
  • Year to date:
    • Site-wide: 16,045 out of 118,102
  • Since beginning of last month:
    • Site-wide: 17,802 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 1,878 times
  • Download rankings, all-time:
    • Site-wide: 6,626 out of 118,102
    • In bioinformatics: 863 out of 9,568
  • Year to date:
    • Site-wide: 39,911 out of 118,102
  • Since beginning of last month:
    • Site-wide: 67,054 out of 118,102

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

genomics more details view paper
  • Downloaded 1,738 times
  • Download rankings, all-time:
    • Site-wide: 7,390 out of 118,102
    • In genomics: 873 out of 6,432
  • Year to date:
    • Site-wide: 13,999 out of 118,102
  • Since beginning of last month:
    • Site-wide: 17,416 out of 118,102

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 1,428 times
  • Download rankings, all-time:
    • Site-wide: 9,969 out of 118,102
    • In bioinformatics: 1,302 out of 9,568
  • Year to date:
    • Site-wide: 24,399 out of 118,102
  • Since beginning of last month:
    • Site-wide: 24,071 out of 118,102

Integrative networks illuminate biological factors underlying gene-disease associations

bioinformatics more details view paper
  • Downloaded 1,407 times
  • Download rankings, all-time:
    • Site-wide: 10,162 out of 118,102
    • In bioinformatics: 1,329 out of 9,568
  • Year to date:
    • Site-wide: 69,027 out of 118,102
  • Since beginning of last month:
    • Site-wide: 46,874 out of 118,102

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

systems biology more details view paper
  • Downloaded 1,402 times
  • Download rankings, all-time:
    • Site-wide: 10,219 out of 118,102
    • In systems biology: 206 out of 2,634
  • Year to date:
    • Site-wide: 57,672 out of 118,102
  • Since beginning of last month:
    • Site-wide: 76,350 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 1,400 times
  • Download rankings, all-time:
    • Site-wide: 10,239 out of 118,102
    • In bioinformatics: 1,345 out of 9,568
  • Year to date:
    • Site-wide: 20,523 out of 118,102
  • Since beginning of last month:
    • Site-wide: 21,518 out of 118,102

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

bioinformatics more details view paper
  • Downloaded 1,378 times
  • Download rankings, all-time:
    • Site-wide: 10,525 out of 118,102
    • In bioinformatics: 1,376 out of 9,568
  • Year to date:
    • Site-wide: 64,298 out of 118,102
  • Since beginning of last month:
    • Site-wide: 58,486 out of 118,102

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

cancer biology more details view paper
  • Downloaded 1,365 times
  • Download rankings, all-time:
    • Site-wide: 10,691 out of 118,102
    • In cancer biology: 224 out of 3,740
  • Year to date:
    • Site-wide: 51,372 out of 118,102
  • Since beginning of last month:
    • Site-wide: 44,832 out of 118,102

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 1,227 times
  • Download rankings, all-time:
    • Site-wide: 12,548 out of 118,102
    • In systems biology: 263 out of 2,634
  • Year to date:
    • Site-wide: 66,590 out of 118,102
  • Since beginning of last month:
    • Site-wide: 63,573 out of 118,102

Building an International Consortium for Tracking Coronavirus Health Status

infectious diseases more details view paper
  • Downloaded 1,204 times
  • Download rankings, all-time:
    • Site-wide: 12,908 out of 118,102
    • In infectious diseases: 1,149 out of 3,542
  • Year to date:
    • Site-wide: 4,804 out of 118,102
  • Since beginning of last month:
    • Site-wide: 29,393 out of 118,102

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

genomics more details view paper
  • Downloaded 1,041 times
  • Download rankings, all-time:
    • Site-wide: 16,018 out of 118,102
    • In genomics: 1,741 out of 6,432
  • Year to date:
    • Site-wide: 58,210 out of 118,102
  • Since beginning of last month:
    • Site-wide: 71,457 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 1,004 times
  • Download rankings, all-time:
    • Site-wide: 16,902 out of 118,102
    • In bioinformatics: 2,129 out of 9,568
  • Year to date:
    • Site-wide: 55,995 out of 118,102
  • Since beginning of last month:
    • Site-wide: 56,029 out of 118,102

Specific histone modifications associate with alternative exon selection during mammalian development

bioinformatics more details view paper
  • Downloaded 886 times
  • Download rankings, all-time:
    • Site-wide: 20,266 out of 118,102
    • In bioinformatics: 2,539 out of 9,568
  • Year to date:
    • Site-wide: 44,958 out of 118,102
  • Since beginning of last month:
    • Site-wide: 45,496 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 813 times
  • Download rankings, all-time:
    • Site-wide: 23,032 out of 118,102
    • In bioinformatics: 2,831 out of 9,568
  • Year to date:
    • Site-wide: 11,148 out of 118,102
  • Since beginning of last month:
    • Site-wide: 27,185 out of 118,102

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

genetics more details view paper
  • Downloaded 801 times
  • Download rankings, all-time:
    • Site-wide: 23,470 out of 118,102
    • In genetics: 1,220 out of 5,131
  • Year to date:
    • Site-wide: 104,303 out of 118,102
  • Since beginning of last month:
    • Site-wide: 105,151 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 719 times
  • Download rankings, all-time:
    • Site-wide: 27,241 out of 118,102
    • In bioinformatics: 3,233 out of 9,568
  • Year to date:
    • Site-wide: 87,452 out of 118,102
  • Since beginning of last month:
    • Site-wide: 87,836 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 671 times
  • Download rankings, all-time:
    • Site-wide: 30,013 out of 118,102
    • In bioinformatics: 3,518 out of 9,568
  • Year to date:
    • Site-wide: 99,276 out of 118,102
  • Since beginning of last month:
    • Site-wide: 103,116 out of 118,102

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

cancer biology more details view paper
  • Downloaded 658 times
  • Download rankings, all-time:
    • Site-wide: 30,752 out of 118,102
    • In cancer biology: 844 out of 3,740
  • Year to date:
    • Site-wide: 64,310 out of 118,102
  • Since beginning of last month:
    • Site-wide: 44,493 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 509 times
  • Download rankings, all-time:
    • Site-wide: 42,436 out of 118,102
    • In bioinformatics: 4,617 out of 9,568
  • Year to date:
    • Site-wide: 106,312 out of 118,102
  • Since beginning of last month:
    • Site-wide: 103,999 out of 118,102

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

cancer biology more details view paper
  • Downloaded 488 times
  • Download rankings, all-time:
    • Site-wide: 44,635 out of 118,102
    • In cancer biology: 1,258 out of 3,740
  • Year to date:
    • Site-wide: 14,424 out of 118,102
  • Since beginning of last month:
    • Site-wide: 18,178 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 475 times
  • Download rankings, all-time:
    • Site-wide: 45,935 out of 118,102
    • In bioinformatics: 4,888 out of 9,568
  • Year to date:
    • Site-wide: 14,918 out of 118,102
  • Since beginning of last month:
    • Site-wide: 41,789 out of 118,102

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 473 times
  • Download rankings, all-time:
    • Site-wide: 46,160 out of 118,102
    • In genetics: 2,299 out of 5,131
  • Year to date:
    • Site-wide: 84,051 out of 118,102
  • Since beginning of last month:
    • Site-wide: 69,618 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 452 times
  • Download rankings, all-time:
    • Site-wide: 48,571 out of 118,102
    • In bioinformatics: 5,128 out of 9,568
  • Year to date:
    • Site-wide: 70,800 out of 118,102
  • Since beginning of last month:
    • Site-wide: 79,189 out of 118,102

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 427 times
  • Download rankings, all-time:
    • Site-wide: 51,623 out of 118,102
    • In genetic and genomic medicine: 118 out of 480
  • Year to date:
    • Site-wide: 16,972 out of 118,102
  • Since beginning of last month:
    • Site-wide: 23,457 out of 118,102

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

systems biology more details view paper
  • Downloaded 420 times
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    • Site-wide: 52,573 out of 118,102
    • In systems biology: 1,314 out of 2,634
  • Year to date:
    • Site-wide: 62,536 out of 118,102
  • Since beginning of last month:
    • Site-wide: 67,066 out of 118,102

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

systems biology more details view paper
  • Downloaded 419 times
  • Download rankings, all-time:
    • Site-wide: 52,715 out of 118,102
    • In systems biology: 1,317 out of 2,634
  • Year to date:
    • Site-wide: 17,375 out of 118,102
  • Since beginning of last month:
    • Site-wide: 66,754 out of 118,102

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

microbiology more details view paper
  • Downloaded 341 times
  • Download rankings, all-time:
    • Site-wide: 64,051 out of 118,102
    • In microbiology: 4,351 out of 9,337
  • Year to date:
    • Site-wide: 114,863 out of 118,102
  • Since beginning of last month:
    • Site-wide: 110,866 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 334 times
  • Download rankings, all-time:
    • Site-wide: 65,147 out of 118,102
    • In bioinformatics: 6,381 out of 9,568
  • Year to date:
    • Site-wide: 22,983 out of 118,102
  • Since beginning of last month:
    • Site-wide: 59,733 out of 118,102

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

neuroscience more details view paper
  • Downloaded 282 times
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    • Site-wide: 74,473 out of 118,102
    • In neuroscience: 11,673 out of 18,580
  • Year to date:
    • Site-wide: 111,811 out of 118,102
  • Since beginning of last month:
    • Site-wide: 112,704 out of 118,102

Analysis of ISCB honorees and keynotes reveals disparities

bioinformatics more details view paper
  • Downloaded 262 times
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    • Site-wide: 78,242 out of 118,102
    • In bioinformatics: 7,221 out of 9,568
  • Year to date:
    • Site-wide: 30,940 out of 118,102
  • Since beginning of last month:
    • Site-wide: 48,250 out of 118,102

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

bioinformatics more details view paper
  • Downloaded 223 times
  • Download rankings, all-time:
    • Site-wide: 86,253 out of 118,102
    • In bioinformatics: 7,735 out of 9,568
  • Year to date:
    • Site-wide: 37,436 out of 118,102
  • Since beginning of last month:
    • Site-wide: 4,026 out of 118,102

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

microbiology more details view paper
  • Downloaded 188 times
  • Download rankings, all-time:
    • Site-wide: 93,167 out of 118,102
    • In microbiology: 6,871 out of 9,337
  • Year to date:
    • Site-wide: 76,082 out of 118,102
  • Since beginning of last month:
    • Site-wide: 113,567 out of 118,102

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