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Casey S. Greene
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2020 – today
- 2024
- [j32]Milton Pividori
, Casey S. Greene
A publishing infrastructure for Artificial Intelligence (AI)-assisted academic authoring. J. Am. Medical Informatics Assoc. 31(9): 2103-2113 (2024) - 2023
- [j31]David N. Nicholson
Changing word meanings in biomedical literature reveal pandemics and new technologies. BioData Min. 16(1) (2023) - [j30]Ricardo Avila
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes. Nucleic Acids Res. 51(W1): 350-356 (2023) - [j29]Ryan T. Scott
Biomonitoring and precision health in deep space supported by artificial intelligence. Nat. Mac. Intell. 5(3): 196-207 (2023) - [j28]Lauren M. Sanders
Biological research and self-driving labs in deep space supported by artificial intelligence. Nat. Mac. Intell. 5(3): 208-219 (2023) - [j27]Benjamin J. Heil
The effect of non-linear signal in classification problems using gene expression. PLoS Comput. Biol. 19(3) (2023) - 2022
- [j26]David N. Nicholson
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. BioData Min. 15(1) (2022) - [j25]Ariel A. Hippen, Jake Crawford, Jacob R. Gardner, Casey S. Greene
wenda_gpu: fast domain adaptation for genomic data. Bioinform. 38(22): 5129-5130 (2022) - [j24]Alexandra J. Lee
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. Genom. Proteom. Bioinform. 20(5): 912-927 (2022) - [j23]Arkarachai Fungtammasan
Ten simple rules for large-scale data processing. PLoS Comput. Biol. 18(2) (2022) - [j22]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) - 2021
- [j21]Ariel A. Hippen
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS Comput. Biol. 17(8) (2021) - [c30]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: 111-122 - [c29]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: 29-38 - [i6]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:
A field guide to cultivating computational biology. CoRR abs/2104.11364 (2021) - [i5]Benjamin D. Lee, Anthony Gitter
Ten Quick Tips for Deep Learning in Biology. CoRR abs/2105.14372 (2021) - [i4]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 abs/2106.00657 (2021) - [i3]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 abs/2109.08633 (2021) - [i2]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
Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health. CoRR abs/2112.12554 (2021) - [i1]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
Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs. CoRR abs/2112.12582 (2021)
2010 – 2019
- 2019
- [j20]Alexander M. Crowell
Learning and Imputation for Mass-spec Bias Reduction (LIMBR). Bioinform. 35(9): 1518-1526 (2019) - [j19]Daniel S. Himmelstein
Open collaborative writing with Manubot. PLoS Comput. Biol. 15(6) (2019) - [c28]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: 362-373 - [c27]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: 449-454 - 2018
- [j18]Kathleen M. Chen
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. BioData Min. 11(1): 14:1-14:20 (2018) - [c26]Gregory P. Way, Casey S. Greene:
Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. PSB 2018: 80-91 - [c25]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: 157-167 - [c24]Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O'Connor, Casey S. Greene, Hongfang Liu:
Session Introduction. PSB 2018: 559-565 - 2017
- [j17]Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinform. 33(20): 3250-3257 (2017) - [j16]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): 512 (2017) - [c23]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: 646-648 - 2016
- [j15]Graciela Gonzalez
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Briefings Bioinform. 17(1): 33-42 (2016) - [j14]Anna C. Greene
Adapting bioinformatics curricula for big data. Briefings Bioinform. 17(1): 43-50 (2016) - [j13]Ailin Song, Jingwen Yan, Sungeun Kim, Shannon L. Risacher
Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. BioData Min. 9: 3 (2016) - [j12]Daniel S. Himmelstein, Casey S. Greene
Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology. BioData Min. 9: 9 (2016) - [j11]Brett K. Beaulieu-Jones
Semi-supervised learning of the electronic health record for phenotype stratification. J. Biomed. Informatics 64: 168-178 (2016) - [c22]Casey S. Greene, James A. Foster, Bruce A. Stanton, Deborah A. Hogan, Yana Bromberg:
Computational Approaches to Study Microbes and Microbiomes. PSB 2016: 557-565 - 2015
- [j10]Jiang Gui, Casey S. Greene
Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study. BioData Min. 8: 17 (2015) - [j9]J. Matthew Mahoney, Jaclyn N. Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms. PLoS Comput. Biol. 11(1) (2015) - [c21]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: 132-143 - 2014
- [j8]Amanda L. Zieselman, Jonathan M. Fisher, Ting Hu, Peter C. Andrews, Casey S. Greene
Computational genetics analysis of grey matter density in Alzheimer's disease. BioData Min. 7: 17 (2014) - [c20]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: 17-35 - [c19]Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye:
Session introduction. Pacific Symposium on Biocomputing 2014: 312-315 - [c18]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: 412-416 - 2013
- [j7]Christopher Y. Park, Aaron K. Wong
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. PLoS Comput. Biol. 9(3) (2013) - [c17]Jie Tan, Gavin D. Grant, Michael L. Whitfield, Casey S. Greene
Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments. EvoBIO 2013: 11-22 - [c16]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: 368-372 - 2012
- [j6]Aaron K. Wong
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 40(Web-Server-Issue): 484-490 (2012) - [j5]Casey S. Greene
Chapter 2: Data-Driven View of Disease Biology. PLoS Comput. Biol. 8(12) (2012) - 2011
- [j4]Daniel S. Himmelstein
Evolving hard problems: Generating human genetics datasets with a complex etiology. BioData Min. 4: 21 (2011) - [j3]Casey S. Greene
PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res. 39(Web-Server-Issue): 368-374 (2011) - 2010
- [j2]Casey S. Greene
Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. Bioinform. 26(5): 694-695 (2010) - [c15]Casey S. Greene
A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships. EvoBIO 2010: 74-85 - [c14]Casey S. Greene
The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics. EvoBIO 2010: 182-193 - [c13]Nadia M. Penrod, Casey S. Greene
Artificial Immune Systems for Epistasis Analysis in Human Genetics. EvoBIO 2010: 194-204 - [c12]Nicholas A. Sinnott-Armstrong, Casey S. Greene
Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units. GECCO 2010: 215-216 - [c11]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: 327-336 - [p1]Casey S. Greene
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 2010: 166-180
2000 – 2009
- 2009
- [j1]Casey S. Greene
Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min. 2: 5 (2009) - [c10]Casey S. Greene
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: 800-807 - [c9]Casey S. Greene
Sensible initialization using expert knowledge for genome-wide analysis of epistasis using genetic programming. IEEE Congress on Evolutionary Computation 2009: 1289-1296 - [c8]Anna L. Tyler, Bill C. White, Casey S. Greene
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: 2907-2912 - [c7]Jason M. Gilmore, Casey S. Greene
An Analysis of New Expert Knowledge Scaling Methods for Biologically Inspired Computing. ECAL (2) 2009: 286-293 - [c6]Casey S. Greene
An Open-Ended Computational Evolution Strategy for Evolving Parsimonious Solutions to Human Genetics Problems. ECAL (1) 2009: 313-320 - [c5]Casey S. Greene
Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease. EvoBIO 2009: 92-103 - [c4]Casey S. Greene
Environmental noise improves epistasis models of genetic data discovered using a computational evolution system. GECCO 2009: 1785-1786 - 2008
- [c3]Casey S. Greene
Ant Colony Optimization for Genome-Wide Genetic Analysis. ANTS Conference 2008: 37-47 - [c2]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: 351-352 - 2007
- [c1]Casey S. Greene
An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming. PRIB 2007: 30-40
Coauthor Index
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