Casey S. Greene

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 36

Top Topics

Artificial Intelligence

Biomedical Literature

Gene Expression

Computational Biology

Top Venues

PLoS Comput. Biol.

Publications

David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti, Casey S. Greene
Changing word meanings in biomedical literature reveal pandemics and new technologies. BioData Min. 16 (1) (2023)
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodrigo Rodolpho, Ginger Tsueng, Casey S. Greene, Chunlei Wu
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes. Nucleic Acids Res. 51 (W1) (2023)
Benjamin J. Heil, Jake Crawford, Casey S. Greene
The effect of non-linear signal in classification problems using gene expression. PLoS Comput. Biol. 19 (3) (2023)
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 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
Biological research and self-driving labs in deep space supported by artificial intelligence. Nat. Mac. Intell. 5 (3) (2023)
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 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
Biomonitoring and precision health in deep space supported by artificial intelligence. Nat. Mac. Intell. 5 (3) (2023)
Ariel A. Hippen, Jake Crawford, Jacob R. Gardner, Casey S. Greene
wenda_gpu: fast domain adaptation for genomic data. Bioinform. 38 (22) (2022)
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
Ten quick tips for deep learning in biology. PLoS Comput. Biol. 18 (3) (2022)
David N. Nicholson, Daniel S. Himmelstein, Casey S. Greene
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. BioData Min. 15 (1) (2022)
Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. Genom. Proteom. Bioinform. 20 (5) (2022)
Arkarachai Fungtammasan, Alexandra Lee, Jaclyn N. Taroni, Kurt Wheeler, Chen-Shan Chin, Sean R. Davis, Casey S. Greene
Ten simple rules for large-scale data processing. PLoS Comput. Biol. 18 (2) (2022)
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
Ten Quick Tips for Deep Learning in Biology. CoRR (2021)
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 Chalk, Guillermo M. Delgado-Aparicio, Melissa 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 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
Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health. CoRR (2021)
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
An Open-Publishing Response to the COVID-19 Infodemic. CoRR (2021)
Madison Cooley, Casey S. Greene, Davis Issac, Milton Pividori, Blair D. Sullivan
Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. ACDA (2021)
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
An Open-Publishing Response to the COVID-19 Infodemic. DISCO@JCDL (2021)
Madison Cooley, Casey S. Greene, Davis Issac, Milton Pividori, Blair D. Sullivan
Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. CoRR (2021)
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
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS Comput. Biol. 17 (8) (2021)
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 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 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
Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs. CoRR (2021)
Anne E. Carpenter, Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey Finley, Kim-Anh Le Cao, Jerry S. H. Lee, Luigi Marchionni, Suzanne Sindi, Fabian J. Theis, Gregory P. Way, Jean Y. H. Yang, Elana J. Fertig
A field guide to cultivating computational biology. CoRR (2021)
Qiwen Hu, Casey S. Greene
Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. PSB (2019)
Alexander M. Crowell, Casey S. Greene, Jennifer J. Loros, Jay C. Dunlap
Learning and Imputation for Mass-spec Bias Reduction (LIMBR). Bioinform. 35 (9) (2019)
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
Open collaborative writing with Manubot. PLoS Comput. Biol. 15 (6) (2019)
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
Text Mining and Machine Learning for Precision Medicine. PSB (2019)
Gregory P. Way, Casey S. Greene
Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. PSB (2018)
Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. BioData Min. 11 (1) (2018)
Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O'Connor, Casey S. Greene, Hongfang Liu
Session Introduction. PSB (2018)
Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. PSB (2018)
Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Casey S. Greene, Jason H. Moore, Andrew J. Saykin, Li Shen
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinform. 33 (20) (2017)
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
No-Boundary Thinking in Bioinformatics. PSB (2017)
Jie Tan, Matt Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
ADAGE signature analysis: differential expression analysis with data-defined gene sets. BMC Bioinform. 18 (1) (2017)
Ailin Song, Jingwen Yan, Sungeun Kim, Shannon L. Risacher, Aaron K. Wong, Andrew J. Saykin, Li Shen, Casey S. Greene
Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. BioData Min. 9 (2016)
Brett K. Beaulieu-Jones, Casey S. Greene
Semi-supervised learning of the electronic health record for phenotype stratification. J. Biomed. Informatics 64 (2016)
Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore
Adapting bioinformatics curricula for big data. Briefings Bioinform. 17 (1) (2016)
Graciela Gonzalez, Tasnia Tahsin, Britton C. Goodale, Anna C. Greene, Casey S. Greene
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Briefings Bioinform. 17 (1) (2016)
Casey S. Greene, James A. Foster, Bruce A. Stanton, Deborah A. Hogan, Yana Bromberg
Computational Approaches to Study Microbes and Microbiomes. PSB (2016)
Daniel S. Himmelstein, Casey S. Greene, Jason H. Moore
Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology. BioData Min. 9 (2016)
J. Matthew Mahoney, Jaclyn N. Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms. PLoS Comput. Biol. 11 (1) (2015)
Jiang Gui, Casey S. Greene, Con Sullivan, Walter Taylor, Jason H. Moore, Carol Kim
Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study. BioData Min. 8 (2015)
Jie Tan, Matthew Ung, Chao Cheng, Casey S. Greene
Unsupervised Feature Construction and Knowledge Extraction from Genome-Wide Assays of Breast Cancer with Denoising Autoencoders. Pacific Symposium on Biocomputing (2015)
Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye
Session introduction. Pacific Symposium on Biocomputing (2014)
Jason H. Moore, Casey S. Greene, Douglas P. Hill
Identification of Novel Genetic Models of Glaucoma Using the "EMERGENT" Genetic Programming-Based Artificial Intelligence System. GPTP (2014)
Amanda L. Zieselman, Jonathan M. Fisher, Ting Hu, Peter C. Andrews, Casey S. Greene, Li Shen, Andrew J. Saykin, Jason H. Moore
Computational genetics analysis of grey matter density in Alzheimer's disease. BioData Min. 7 (2014)
Chao Cheng, Jason H. Moore, Casey S. Greene
Applications of Bioinformatics to Non-Coding RNAs in the Era of Next-Generation Sequencing. Pacific Symposium on Biocomputing (2014)
Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye
Session introduction. Pacific Symposium on Biocomputing (2013)
Jie Tan, Gavin D. Grant, Michael L. Whitfield, Casey S. Greene
Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments. EvoBIO (2013)
Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga G. Troyanskaya
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. PLoS Comput. Biol. 9 (3) (2013)
Casey S. Greene, Olga G. Troyanskaya
Chapter 2: Data-Driven View of Disease Biology. PLoS Comput. Biol. 8 (12) (2012)
Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars Ailo Bongo, Yuanfang Guan, Olga G. Troyanskaya
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Casey S. Greene, Olga G. Troyanskaya
PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Daniel S. Himmelstein, Casey S. Greene, Jason H. Moore
Evolving hard problems: Generating human genetics datasets with a complex etiology. BioData Min. 4 (2011)
Nadia M. Penrod, Casey S. Greene, Delaney Granizo-MacKenzie, Jason H. Moore
Artificial Immune Systems for Epistasis Analysis in Human Genetics. EvoBIO (2010)
Casey S. Greene, Nicholas A. Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, Brent T. Harris
Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. Bioinform. 26 (5) (2010)
Casey S. Greene, Daniel S. Himmelstein, Jason H. Moore
A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships. EvoBIO (2010)
Casey S. Greene, Daniel S. Himmelstein, Heather H. Nelson, Karl T. Kelsey, Scott M. Williams, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore
Enabling Personal Genomics with an Explicit Test of Epistasis. Pacific Symposium on Biocomputing (2010)
Nicholas A. Sinnott-Armstrong, Casey S. Greene, Jason H. Moore
Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units. GECCO (2010)
Casey S. Greene, Daniel S. Himmelstein, Jeff Kiralis, Jason H. Moore
The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics. EvoBIO (2010)
Jason M. Gilmore, Casey S. Greene, Peter C. Andrews, Jeff Kiralis, Jason H. Moore
An Analysis of New Expert Knowledge Scaling Methods for Biologically Inspired Computing. ECAL (2) (2009)
Casey S. Greene, Douglas P. Hill, Jason H. Moore
An Open-Ended Computational Evolution Strategy for Evolving Parsimonious Solutions to Human Genetics Problems. ECAL (1) (2009)
Casey S. Greene, Jeff Kiralis, Jason H. Moore
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 (2009)
Casey S. Greene, Bill C. White, Jason H. Moore
Sensible initialization using expert knowledge for genome-wide analysis of epistasis using genetic programming. IEEE Congress on Evolutionary Computation (2009)
Casey S. Greene, Nadia M. Penrod, Jeff Kiralis, Jason H. Moore
Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min. 2 (2009)
Casey S. Greene, Douglas P. Hill, Jason H. Moore
Environmental noise improves epistasis models of genetic data discovered using a computational evolution system. GECCO (2009)
Anna L. Tyler, Bill C. White, Casey S. Greene, Paul C. Andrews, Richard Cowper-Sallari, Jason H. Moore
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 (2009)
Casey S. Greene, Jason M. Gilmore, Jeff Kiralis, Peter C. Andrews, Jason H. Moore
Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease. EvoBIO (2009)
Casey S. Greene, Bill C. White, Jason H. Moore
Ant Colony Optimization for Genome-Wide Genetic Analysis. ANTS Conference (2008)
Casey S. Greene, Bill C. White, Jason H. Moore
Using expert knowledge in initialization for genome-wide analysis of epistasis using genetic programming. GECCO (2008)
Casey S. Greene, Bill C. White, Jason H. Moore
An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming. PRIB (2007)