Author details

Full Name

Casey S Greene

Affiliation

ORCID

Career Start Year

2006

Papers

104

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37492101	OpenPBTA: The Open Pediatric Brain Tumor Atlas.	Cell Genom	2023
37689782	Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms.	Nat Commun	2023
36711569	The probability of edge existence due to node degree: a baseline for network-based predictions.	bioRxiv	2023
36541761	Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia.	mSystems	2023
36861991	Application of Traditional Vaccine Development Strategies to SARS-CoV-2.	mSystems	2023
36861992	The Coming of Age of Nucleic Acid Vaccines during COVID-19.	mSystems	2023
35076276	Correction for Rando et al., "Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure".	mSystems	2022
36016717	Using genome-wide expression compendia to study microorganisms.	Comput Struct Biotechnol J	2022
36193991	wenda_gpu: fast domain adaptation for genomic data.	Bioinformatics	2022
36258252	Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts.	BioData Min	2022
34890145	Human Intrigue: Meta-analysis approaches for big questions with big data while shaking up the peer review process.	Pac Symp Biocomput	2022
35104289	Examining linguistic shifts between preprints and publications.	PLoS Biol	2022
34428202	miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data.	PLoS Comput Biol	2021
33947804	Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment.	mSystems	2021
34553212	Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design.	Gigascience	2021
32554541	Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE).	Clin Cancer Res	2020
31962244	Incorporating biological structure into machine learning models in biomedicine.	Curr Opin Biotechnol	2020
32393369	Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations.	Genome Biol	2020
32098059	Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1.	Genes (Basel)	2020
31980538	<i>Pseudomonas aeruginosa lasR</i> mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin.	Proc Natl Acad Sci U S A	2020
32473302	Prognostic gene expression signature for high-grade serous ovarian cancer.	Ann Oncol	2020
33140829	Correcting for experiment-specific variability in expression compendia can remove underlying signals.	Gigascience	2020
32694666	Responsible, practical genomic data sharing that accelerates research.	Nat Rev Genet	2020
33057217	Transparency and reproducibility in artificial intelligence.	Nature	2020
31233491	Open collaborative writing with Manubot.	PLoS Comput Biol	2019
31698452	Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma.	Blood Adv	2019
31744546	The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.	Genome Biol	2019
31693904	Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.	Cell Rep	2019
30247517	Learning and Imputation for Mass-spec Bias Reduction (LIMBR).	Bioinformatics	2019
30463884	New <i>Drosophila</i> Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods.	G3 (Bethesda)	2019
29424689	Sci-Hub provides access to nearly all scholarly literature.	Elife	2018
30504887	Bayesian deep learning for single-cell analysis.	Nat Methods	2018
30395209	A parasite's perspective on data sharing.	Gigascience	2018
29988723	PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia.	BioData Min	2018
29311282	A Multimodal Strategy Used by a Large c-di-GMP Network.	J Bacteriol	2018
29625050	Oncogenic Signaling Pathways in The Cancer Genome Atlas.	Cell	2018
29618526	Opportunities and obstacles for deep learning in biology and medicine.	J R Soc Interface	2018
29617664	Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.	Cell Rep	2018
29617658	Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.	Cell Rep	2018
29218878	Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses.	Pac Symp Biocomput	2018
29218871	Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders.	Pac Symp Biocomput	2018
28166733	A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma.	BMC Genomics	2017
28889104	Machine Learning Analysis Identifies <i>Drosophila Grunge/Atrophin</i> as an Important Learning and Memory Gene Required for Memory Retention and Social Learning.	G3 (Bethesda)	2017
28330499	A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis.	Genome Med	2017
28711280	Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.	Cell Syst	2017
28575147	Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules.	Bioinformatics	2017
28792001	Implicating candidate genes at GWAS signals by leveraging topologically associating domains.	Eur J Hum Genet	2017
28358134	Celebrating parasites.	Nat Genet	2017
29226065	Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes.	Curr Epidemiol Rep	2017
29215023	A Pilot Characterization of the Human Chronobiome.	Sci Rep	2017

1 - 50 of 104

Casey S Greene

Dartmouth College Geisel School of Medicine, Princeton University, University of Colorado Anschutz Medical Campus, University of Pennsylvania Perelman School of Medicine

Co-authored papers 104

Jason H Moore

Cedars-Sinai Medical Center

Co-authored papers 19

Gregory P Way

Broad Institute of MIT and Harvard

Co-authored papers 16

Deborah A Hogan

Geisel School of Medicine at Dartmouth

Co-authored papers 11

Daniel S Himmelstein

University of Pennsylvania