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List of works by Casey S. Greene

A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships

article

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

scientific article published on 8 January 2018

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

A Parasite's Perspective on Data Sharing

scientific article published on 01 November 2018

A Pilot Characterization of the Human Chronobiome

scientific article published on 7 December 2017

A field guide to cultivating computational biology

scientific article published on 08 October 2021

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

scientific article

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

scholarly article published 15 September 2016

A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis.

scientific article published on 23 March 2017

A stromal focus reveals tumor immune signatures

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

article

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

scientific article published on 22 November 2017

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

article

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

scientific article

Ability of epistatic interactions of cytokine single‐nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patients

scientific article published on 01 July 2008

Abstract 1928: High-grade serous ovarian cancer subtypes are similar across diverse populations

Abstract 2171: Leveraging global gene expression patterns to identify gene sets that predict expression of large numbers of unmeasured genes

article

Abstract 815: Patterns of metagene activation in ovarian cancer subtypes

Accelerating epistasis analysis in human genetics with consumer graphics hardware

scientific article

Accurate evaluation and analysis of functional genomics data and methods ⬇️

scientific article published on January 23, 2012

Adapting bioinformatics curricula for big data

scientific article

Advances in Text Mining and Visualization for Precision Medicine

scientific article published in January 2018

An Analysis of New Expert Knowledge Scaling Methods for Biologically Inspired Computing

An Open-Ended Computational Evolution Strategy for Evolving Parsimonious Solutions to Human Genetics Problems

article

An Open-Publishing Response to the COVID-19 Infodemic ⬇️

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

Ant Colony Optimization for Genome-Wide Genetic Analysis

article

Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing

scientific article published on January 2014

Bayesian deep learning for single-cell analysis

scientific article published on 01 December 2018

Big data bioinformatics.

scientific article

Biologically Informed Neural Networks Predict Drug Responses

scientific article published on 21 October 2020

Building an International Consortium for Tracking Coronavirus Health Status

scientific article published on 06 April 2020

Building an international consortium for tracking coronavirus health status

scientific article published on 02 June 2020

COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES.

scientific article published in January 2016

Celebrating parasites

scientific article published on March 2017

Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes.

scientific article published on 10 July 2017

Chapter 2: Data-Driven View of Disease Biology ⬇️

scientific article published on December 27, 2012

Characterizing Long COVID: Deep Phenotype of a Complex Condition

scientific article published on 25 November 2021

Cheap-seq

scientific article published on 01 December 2016

CoINcIDE: All together now

Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes

scientific article published on 11 October 2016

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

Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

scientific article published on 11 May 2020

Computational audits combat disparities in recognition

scientific article published in 2022

Computational genetics analysis of grey matter density in Alzheimer's disease

scientific article

Constructing knowledge graphs and their biomedical applications

scientific article published on 02 June 2020

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

scientific article published on 01 November 2020

Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research

scientific article published on 01 September 2020

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

article

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

scientific article

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

scholarly article published 30 October 2015

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

scholarly article published 30 October 2015

Data-Sharing Models

scientific article published on June 2017

Defining cell-type specificity at the transcriptional level in human disease

scientific article published on 15 August 2013

Development and evaluation of an open-ended computational evolution system for the creation of digital organisms with complex genetic architecture

article

Development and validation of the gene-expression Predictor of high-grade-serous Ovarian carcinoma molecular subTYPE (PrOTYPE)

scientific article published on 17 June 2020

Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning

scholarly article published 20 September 2018

Embracing study heterogeneity for finding genetic interactions in large-scale research consortia

scientific article published on 04 October 2019

Enabling personal genomics with an explicit test of epistasis

scientific article published on January 2010

Enter the Matrix: Factorization Uncovers Knowledge from Omics

scientific article published on 22 August 2018

Enter the matrix: factorization uncovers knowledge from omics

Environmental noise improves epistasis models of genetic data discovered using a computational evolution system

Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology

scientific article published on 3 February 2016

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression

scientific article

Evolving hard problems: Generating human genetics datasets with a complex etiology ⬇️

scientific article (publication date: 7 July 2011)

Examining linguistic shifts between preprints and publications

scientific article published on 01 February 2022

Expanding and Remixing the Metadata Landscape

scientific article published on 20 November 2020

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

Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders

scientific article published in January 2018

Failure to replicate a genetic association may provide important clues about genetic architecture

scientific article

Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes

scientific article

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

scientific article published in January 2018

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

Genetic Association-Guided Analysis of Gene Networks for the Study of Complex Traits

scientific article published on April 2016

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

scientific article published on 23 September 2021

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

scientific article published on 01 November 2019

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

scientific article published in April 2018

Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites

scientific article published on 25 February 2016

Gut check

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

scientific article

Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions

scientific article

Immune landscapes associated with different glioblastoma molecular subtypes

scientific article published on 29 November 2019

Implicating candidate genes at GWAS signals by leveraging topologically associating domains.

scientific article published on 09 August 2017

Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay.

scientific article published on 6 April 2018

Incorporating biological structure into machine learning models in biomedicine

scientific article published on 18 January 2020

Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

publication published on 01 February 2021

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

Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma

scientific article published on 01 November 2019

Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1

scientific article published on 21 February 2020

Integrative networks illuminate biological factors underlying gene-disease associations

Integrative systems biology for data-driven knowledge discovery ⬇️

scientific article published on September 1, 2010

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

scientific article

LT-IIb(T13I), a non-toxic type II heat-labile enterotoxin, augments the capacity of a ricin toxin subunit vaccine to evoke neutralizing antibodies and protective immunity

scientific article published on 02 August 2013

LTR retrotransposon-gene associations in Drosophila melanogaster

scientific article published on 11 January 2006

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

scholarly article by Alexander M Crowell published in September 2018

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

scholarly article published 14 April 2018

Leveraging global gene expression patterns to predict expression of unmeasured genes

scientific article published on 15 December 2015

Machine Learning Analysis Identifies Drosophila Grunge/Atrophin as an Important Learning and Memory Gene Required for Memory Retention and Social Learning.

scientific article published on 9 September 2017

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

scientific article published in April 2018

Machine learning analysis identifies Drosophila Grunge/Atrophin as an important learning and memory gene required for memory retention and social learning

article

Metabolic pathways and immunometabolism in rare kidney diseases

scientific article published on 03 May 2018

MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease

scientific article published on 01 May 2019

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

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS.

scientific article

MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes

scientific article published on 18 April 2023

NO-BOUNDARY THINKING IN BIOINFORMATICS.

scientific article

Nature-inspired algorithms for the genetic analysis of epistasis in common human diseases: Theoretical assessment of wrapper vs. filter approaches

Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts

scientific article

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

article

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

article

Nothing but a hound dog

Oncogenic Signaling Pathways in The Cancer Genome Atlas

scientific article published in April 2018

Open collaborative writing with Manubot

scientific article published in June 2019

Opportunities And Obstacles For Deep Learning In Biology And Medicine

scholarly article published 28 May 2017

Opportunities and obstacles for deep learning in biology and medicine.

scientific article published in April 2018

Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease

article

PILGRM: an interactive data-driven discovery platform for expert biologists ⬇️

scientific article published on June 7, 2011

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

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

scientific article published on 01 January 2019

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

scholarly article published 8 June 2017

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

scientific article

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

scientific article published on 23 June 2016

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

Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States

scientific article published on 11 June 2020

Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing

scientific article published on 26 August 2020

Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity

scientific article

Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing

scientific article published on 09 July 2019

Privacy-preserving generative deep neural networks support clinical data sharing

scholarly article published 5 July 2017

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

scientific article published on 24 January 2020

Publisher Correction: Building an international consortium for tracking coronavirus health status

scientific article published on 26 June 2020

Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery

scientific article

Recommendations to enhance rigor and reproducibility in biomedical research

scientific article published on 01 June 2020

Relief-based bioinformatics methods for the analysis of epistasis in genetic association studies

Reproducibility of computational workflows is automated using continuous analysis ⬇️

scientific article (publication date: 13 March 2017)

Reproducibility standards for machine learning in the life sciences

scientific article

Reproducible Computational Workflows with Continuous Analysis

Reproducible Computational Workflows with Continuous Analysis [preprint] ⬇️

journal article from 'bioRxiv' published in 2016

Responsible, practical genomic data sharing that accelerates research

scientific article published on 21 July 2020

Sci-Hub provides access to nearly all scholarly literature

article

Sci-Hub provides access to nearly all scholarly literature

Sci-Hub provides access to nearly all scholarly literature

Sci-Hub provides access to nearly all scholarly literature

Sci-Hub provides access to nearly all scholarly literature.

scientific article published on 9 February 2018

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

article

Semi-supervised learning of the electronic health record for phenotype stratification

scientific article

Sensible Initialization Using Expert Knowledge for Genome-Wide Analysis of Epistasis Using Genetic Programming

article

Sequential compression across latent space dimensions enhances gene expression signatures

article

Show me the models

scientific article published on 01 June 2019

Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms Requires Strategies which Exploit Domain-Specific Knowledge

article

Solving complex problems in human genetics using GP

article

Spatially uniform relieff (SURF) for computationally-efficient filtering of gene-gene interactions

scientific article published on 22 September 2009

Specific histone modifications associate with alternative exon selection during mammalian development

article

Specific histone modifications associate with alternative exon selection during mammalian development

scientific article published on 22 April 2020

Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms.

scientific article

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

scientific article published on 12 January 2015

Tell me your neighbors, and I will tell you what you are

scientific article published on 01 February 2017

Ten quick tips for deep learning in biology

scientific article published on 24 March 2022

Ten simple rules for large-scale data processing

scientific article published on 10 February 2022

Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study

scientific article published on 17 June 2015

Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study

Text and data mining for biomedical discovery ⬇️

scientific article published on 01 January 2013

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

scientific article published on 19 November 2019

The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics

article

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

scientific article published on 28 March 2019

The future is unsupervised

ThinkLab as a vetting system for traditional grants

Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments

Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules.

scientific article published on 29 May 2017

Transparency and reproducibility in artificial intelligence

scientific article published on 14 October 2020

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

article

Understanding multicellular function and disease with human tissue-specific networks

scientific article published on 27 April 2015

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

scientific article published on 11 July 2017

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders

scientific article

Voices in methods development

scientific article published on 01 October 2019

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

scientific article published on 24 August 2021

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