Casey S. Greene

71 papers A 3B 3Misc 12Journal 40Unranked 12

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. PLoS Comput. Biol. Natalie R. Davidson, Fan Zhang, Casey S. Greene
2024	J	`jnl`	A publishing infrastructure for Artificial Intelligence (AI)-assisted academic authoring. J. Am. Medical Informatics Assoc. Milton Pividori, Casey S. Greene
2024	J	`jnl`	Best holdout assessment is sufficient for cancer transcriptomic model selection. Patterns Jake Crawford, Maria Chikina, Casey S. Greene
2023	J	`jnl`	Biological research and self-driving labs in deep space supported by artificial intelligence. Nat. Mac. Intell. Lauren M. Sanders, Ryan T. Scott, Jason H. Yang, Amina Ann Qutub, Héctor García Martín, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart J. Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Seung-Min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes
2023	J	`jnl`	Biomonitoring and precision health in deep space supported by artificial intelligence. Nat. Mac. Intell. Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-Min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart J. Chalk, Guillermo M. Delgado-Aparicio, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Héctor García Martín, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes
2023	J	`jnl`	Changing word meanings in biomedical literature reveal pandemics and new technologies. BioData Min. David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti, Casey S. Greene
2023	J	`jnl`	MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes. Nucleic Acids Res. Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodrigo Rodolpho, Ginger Tsueng, Casey S. Greene, Chunlei Wu
2023	J	`jnl`	The effect of non-linear signal in classification problems using gene expression. PLoS Comput. Biol. Benjamin J. Heil, Jake Crawford, Casey S. Greene
2022	J	`jnl`	Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. BioData Min. David N. Nicholson, Daniel S. Himmelstein, Casey S. Greene
2022	J	`jnl`	SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. Genom. Proteom. Bioinform. Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene
2022	J	`jnl`	Ten quick tips for deep learning in biology. PLoS Comput. Biol. Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus, Michael D. Kessler, Alexandra J. Lee, Marc G. Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M. Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J. Fertig, Alexandr A. Kalinin, Brandon Signal, Benjamin J. Lengerich, Timothy J. Triche Jr., Simina M. Boca
2022	J	`jnl`	Ten simple rules for large-scale data processing. PLoS Comput. Biol. Arkarachai Fungtammasan, Alexandra Lee, Jaclyn N. Taroni, Kurt Wheeler, Chen-Shan Chin, Sean Davis, Casey S. Greene
2022	J	`jnl`	wenda_gpu: fast domain adaptation for genomic data. Bioinform. Ariel A. Hippen, Jake Crawford, Jacob R. Gardner, Casey S. Greene
2021	J	`jnl`	A field guide to cultivating computational biology. CoRR Anne E. Carpenter, Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley, Kim-Anh Lê Cao, Jerry S. H. Lee, Luigi Marchionni, Suzanne Sindi, Fabian J. Theis, Gregory P. Way, Jean Y. H. Yang, Elana J. Fertig
2021	—	`conf`	An Open-Publishing Response to the COVID-19 Infodemic. DISCO@JCDL Halie M. Rando, Simina M. Boca, Lucy D'Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, Anthony Gitter
2021	J	`jnl`	An Open-Publishing Response to the COVID-19 Infodemic. CoRR Halie M. Rando, Simina M. Boca, Lucy D'Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, Anthony Gitter
2021	J	`jnl`	Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs. CoRR Lauren M. Sanders, Jason H. Yang, Ryan T. Scott, Amina Ann Qutub, Héctor García Martín, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart J. Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Seung-Min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes
2021	J	`jnl`	Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health. CoRR Ryan T. Scott, Erik L. Antonsen, Lauren M. Sanders, Jaden J. A. Hastings, Seung-Min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart J. Chalk, Guillermo M. Delgado-Aparicio, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Héctor García Martín, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes
2021	—	`conf`	Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. ACDA Madison Cooley, Casey S. Greene, Davis Issac, Milton Pividori, Blair D. Sullivan
2021	J	`jnl`	Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. CoRR Madison Cooley, Casey S. Greene, Davis Issac, Milton Pividori, Blair D. Sullivan
2021	J	`jnl`	Ten Quick Tips for Deep Learning in Biology. CoRR Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus, Michael D. Kessler, Alexandra J. Lee, Marc G. Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M. Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J. Fertig, Alexandr A. Kalinin, Beth Signal, Benjamin J. Lengerich, Timothy J. Triche Jr., Simina M. Boca
2021	J	`jnl`	miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS Comput. Biol. Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks
2019	J	`jnl`	Learning and Imputation for Mass-spec Bias Reduction (LIMBR). Bioinform. Alexander M. Crowell, Casey S. Greene, Jennifer J. Loros, Jay C. Dunlap
2019	J	`jnl`	Open collaborative writing with Manubot. PLoS Comput. Biol. Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
2019	Misc	`conf`	Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. PSB Qiwen Hu, Casey S. Greene
2019	Misc	`conf`	Text Mining and Machine Learning for Precision Medicine. PSB Graciela Gonzalez, Zhiyong Lu, Robert Leaman, Davy Weissenbacher, Mary Regina Boland, Yong Chen, Jingcheng Du, Juliane Fluck, Casey S. Greene, John H. Holmes, Aditya Kashyap, Rikke Linnemann Nielsen, Zhengqing Ouyang, Sebastian Schaaf, Jaclyn N. Taroni, Cui Tao, Yuping Zhang, Hongfang Liu
2018	Misc	`conf`	Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. PSB Gregory P. Way, Casey S. Greene
2018	Misc	`conf`	Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. PSB Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene
2018	J	`jnl`	PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. BioData Min. Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene
2018	Misc	`conf`	Session Introduction. PSB Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O'Connor, Casey S. Greene, Hongfang Liu
2017	J	`jnl`	ADAGE signature analysis: differential expression analysis with data-defined gene sets. BMC Bioinform. Jie Tan, Matt Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
2017	Misc	`conf`	No-Boundary Thinking in Bioinformatics. PSB Jason H. Moore, Steven F. Jennings, Casey S. Greene, Lawrence E. Hunter, Andy D. Perkins, ClarLynda R. Williams-DeVane, Donald C. Wunsch, Zhongming Zhao, Xiuzhen Huang
2017	J	`jnl`	Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinform. Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Casey S. Greene, Jason H. Moore, Andrew J. Saykin, Li Shen
2016	J	`jnl`	Adapting bioinformatics curricula for big data. Briefings Bioinform. Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore
2016	Misc	`conf`	Computational Approaches to Study Microbes and Microbiomes. PSB Casey S. Greene, James A. Foster, Bruce A. Stanton, Deborah A. Hogan, Yana Bromberg
2016	J	`jnl`	Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology. BioData Min. Daniel S. Himmelstein, Casey S. Greene, Jason H. Moore
2016	J	`jnl`	Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. BioData Min. Ailin Song, Jingwen Yan, Sungeun Kim, Shannon L. Risacher, Aaron K. Wong, Andrew J. Saykin, Li Shen, Casey S. Greene
2016	J	`jnl`	Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Briefings Bioinform. Graciela Gonzalez, Tasnia Tahsin, Britton C. Goodale, Anna C. Greene, Casey S. Greene
2016	J	`jnl`	Semi-supervised learning of the electronic health record for phenotype stratification. J. Biomed. Informatics Brett K. Beaulieu-Jones, Casey S. Greene
2015	J	`jnl`	Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms. PLoS Comput. Biol. J. Matthew Mahoney, Jaclyn N. Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield
2015	J	`jnl`	Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study. BioData Min. Jiang Gui, Casey S. Greene, Con Sullivan, Walter Taylor, Jason H. Moore, Carol Kim
2015	Misc	`conf`	Unsupervised Feature Construction and Knowledge Extraction from Genome-Wide Assays of Breast Cancer with Denoising Autoencoders. Pacific Symposium on Biocomputing Jie Tan, Matthew Ung, Chao Cheng, Casey S. Greene
2014	Misc	`conf`	Applications of Bioinformatics to Non-Coding RNAs in the Era of Next-Generation Sequencing. Pacific Symposium on Biocomputing Chao Cheng, Jason H. Moore, Casey S. Greene
2014	J	`jnl`	Computational genetics analysis of grey matter density in Alzheimer's disease. BioData Min. Amanda L. Zieselman, Jonathan M. Fisher, Ting Hu, Peter C. Andrews, Casey S. Greene, Li Shen, Andrew J. Saykin, Jason H. Moore
2014	—	`conf`	Identification of Novel Genetic Models of Glaucoma Using the "EMERGENT" Genetic Programming-Based Artificial Intelligence System. GPTP Jason H. Moore, Casey S. Greene, Douglas P. Hill
2014	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye
2013	J	`jnl`	Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. PLoS Comput. Biol. Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga G. Troyanskaya
2013	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye
2013	—	`conf`	Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments. EvoBIO Jie Tan, Gavin D. Grant, Michael L. Whitfield, Casey S. Greene
2012	J	`jnl`	Chapter 2: Data-Driven View of Disease Biology. PLoS Comput. Biol. Casey S. Greene, Olga G. Troyanskaya
2012	J	`jnl`	IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars Ailo Bongo, Yuanfang Guan, Olga G. Troyanskaya
2011	J	`jnl`	Evolving hard problems: Generating human genetics datasets with a complex etiology. BioData Min. Daniel S. Himmelstein, Casey S. Greene, Jason H. Moore
2011	J	`jnl`	PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res. Casey S. Greene, Olga G. Troyanskaya
2010	—	`conf`	A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships. EvoBIO Casey S. Greene, Daniel S. Himmelstein, Jason H. Moore
2010	—	`conf`	Artificial Immune Systems for Epistasis Analysis in Human Genetics. EvoBIO Nadia M. Penrod, Casey S. Greene, Delaney Granizo-MacKenzie, Jason H. Moore
2010	Misc	`conf`	Enabling Personal Genomics with an Explicit Test of Epistasis. Pacific Symposium on Biocomputing Casey S. Greene, Daniel S. Himmelstein, Heather H. Nelson, Karl T. Kelsey, Scott M. Williams, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore
2010	A	`conf`	Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units. GECCO Nicholas A. Sinnott-Armstrong, Casey S. Greene, Jason H. Moore
2010	J	`jnl`	Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. Bioinform. Casey S. Greene, Nicholas A. Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, Brent T. Harris
2010	—	`ch.`	Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms Requires Strategies which Exploit Domain-Specific Knowledge. Nature-Inspired Informatics for Intelligent Applications and Knowledge Discovery Casey S. Greene, Jason H. Moore
2010	—	`conf`	The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics. EvoBIO Casey S. Greene, Daniel S. Himmelstein, Jeff Kiralis, Jason H. Moore
2009	—	`conf`	An Analysis of New Expert Knowledge Scaling Methods for Biologically Inspired Computing. ECAL (2) Jason M. Gilmore, Casey S. Greene, Peter C. Andrews, Jeff Kiralis, Jason H. Moore
2009	—	`conf`	An Open-Ended Computational Evolution Strategy for Evolving Parsimonious Solutions to Human Genetics Problems. ECAL (1) Casey S. Greene, Douglas P. Hill, Jason H. Moore
2009	B	`conf`	Development and evaluation of an open-ended computational evolution system for the creation of digital organisms with complex genetic architecture. IEEE Congress on Evolutionary Computation Anna L. Tyler, Bill C. White, Casey S. Greene, Paul C. Andrews, Richard Cowper-Sallari, Jason H. Moore
2009	A	`conf`	Environmental noise improves epistasis models of genetic data discovered using a computational evolution system. GECCO Casey S. Greene, Douglas P. Hill, Jason H. Moore
2009	B	`conf`	Nature-inspired algorithms for the genetic analysis of epistasis in common human diseases: Theoretical assessment of wrapper vs. filter approaches. IEEE Congress on Evolutionary Computation Casey S. Greene, Jeff Kiralis, Jason H. Moore
2009	—	`conf`	Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease. EvoBIO Casey S. Greene, Jason M. Gilmore, Jeff Kiralis, Peter C. Andrews, Jason H. Moore
2009	B	`conf`	Sensible initialization using expert knowledge for genome-wide analysis of epistasis using genetic programming. IEEE Congress on Evolutionary Computation Casey S. Greene, Bill C. White, Jason H. Moore
2009	J	`jnl`	Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min. Casey S. Greene, Nadia M. Penrod, Jeff Kiralis, Jason H. Moore
2008	—	`conf`	Ant Colony Optimization for Genome-Wide Genetic Analysis. ANTS Conference Casey S. Greene, Bill C. White, Jason H. Moore
2008	A	`conf`	Using expert knowledge in initialization for genome-wide analysis of epistasis using genetic programming. GECCO Casey S. Greene, Bill C. White, Jason H. Moore
2007	—	`conf`	An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming. PRIB Casey S. Greene, Bill C. White, Jason H. Moore