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Author: Casey S Greene

Rankings

  • All-time downloads: 105,840 (rank: 247 out of 361,769)
  • Categories:
    • bioinformatics: 93,204 (rank: 2 out of 31,271)
    • cancer biology: 2,119 (rank: 1,422 out of 24,619)
    • genetics: 1,200 (rank: 11,024 (tie) out of 33,967)
    • genomics: 2,449 (rank: 7,392 (tie) out of 39,128)
    • microbiology: 470 (rank: 15,898 (tie) out of 39,953)
    • neuroscience: 260 (rank: 45,066 (tie) out of 60,770)
    • systems biology: 6,138 (rank: 309 out of 10,792)

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Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

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Privacy-preserving generative deep neural networks support clinical data sharing

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

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Enter the matrix: factorization uncovers knowledge from omics

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

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Reproducible Computational Workflows with Continuous Analysis

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

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

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

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

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

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Unsupervised extraction of stable expression signatures from public compendia with eADAGE

systems biology more details view paper
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    • In systems biology: 181 out of 2,222
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Integrative networks illuminate biological factors underlying gene-disease associations

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    • In bioinformatics: 1,189 out of 8,053
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Implicating candidate genes at GWAS signals by leveraging topologically associating domains

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    • In bioinformatics: 1,229 out of 8,053
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

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

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

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A Novel Multi-network Approach Reveals Tissue-specific Cellular Modulators of Fibrosis in Systemic Sclerosis, Pulmonary Fibrosis and Pulmonary Arterial Hypertension

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    • Site-wide: 42,695 out of 84,017

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

genomics more details view paper
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    • In genomics: 1,606 out of 5,423
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PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

bioinformatics more details view paper
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Specific histone modifications associate with alternative exon selection during mammalian development

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    • In bioinformatics: 2,289 out of 8,053
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Pathway and network-based strategies to translate genetic discoveries into effective therapies

genetics more details view paper
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    • In genetics: 1,029 out of 4,416
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    • Site-wide: 76,563 out of 84,017

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

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    • In bioinformatics: 2,880 out of 8,053
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ADAGE signature analysis: differential expression analysis with data-defined gene sets

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

cancer biology more details view paper
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Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts

bioinformatics more details view paper
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Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses

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    • In bioinformatics: 3,994 out of 8,053
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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
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    • Site-wide: 71,668 out of 84,017

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

bioinformatics more details view paper
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    • In bioinformatics: 4,654 out of 8,053
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Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome

systems biology more details view paper
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A Multimodal Strategy Used By A Large c-di-GMP Network

microbiology more details view paper
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    • Site-wide: 76,124 out of 84,017

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

systems biology more details view paper
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    • Site-wide: 45,809 out of 84,017

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

bioinformatics more details view paper
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New Drosophila long-term memory genes revealed by assessing computational function prediction methods.

neuroscience more details view paper
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Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment

cancer biology more details view paper
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Graph biased feature selection of genes is better than random for many genes

bioinformatics more details view paper
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Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin

microbiology more details view paper
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Analysis of ISCB honorees and keynotes reveals disparities

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