Publications by authors named "Geoffrey Fox"

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FAIR for AI: An interdisciplinary and international community building perspective.
E A Huerta, Ben Blaiszik, L Catherine Brinson, Kristofer E Bouchard, Daniel Diaz, Caterina Doglioni, Javier M Duarte, Murali Emani, Ian Foster, Geoffrey Fox

Sci Data· July 2023

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Generative diffusion model surrogates for mechanistic agent-based biological models.
Tien Comlekoglu, J Quetzalcoatl Toledo-Marín, Douglas W DeSimone, Shayn M Peirce, Geoffrey Fox

Mach Learn Sci Technol· December 2025

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Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture.
Tien Comlekoglu, J Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W DeSimone, Shayn M Peirce, Geoffrey Fox

PLoS Comput Biol· November 2025

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SETD2 suppresses tumorigenesis in a KRAS-driven lung cancer model, and its catalytic activity is regulated by histone acetylation.
Ricardo J Mack, Natasha M Flores, Geoffrey C Fox, Hanyang Dong, Metehan Cebeci

Elife· September 2025

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Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture.
Tien Comlekoglu, J Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W Desimone, Shayn M Peirce, Geoffrey Fox

ArXiv· July 2025

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SETD2 suppresses tumorigenesis in a KRAS-driven lung cancer model and its catalytic activity is regulated by histone acetylation.
Ricardo J Mack, Natasha M Flores, Geoffrey C Fox, Hanyang Dong, Metehan Cebeci

bioRxiv· July 2025

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Conditioned quantum-assisted deep generative surrogate for particle-binary vector indicating thecalorimeter interactions.
J Quetzalcóatl Toledo-Marín, Sebastian Gonzalez, Hao Jia, Ian Lu, Deniz Sogutlu, Geoffrey C Fox

npj Quantum Inf· July 2025

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Generative diffusion model surrogates for mechanistic agent-based biological models.
Tien Comlekoglu, J Quetzalcoatl Toledo-Marín, Douglas W DeSimone, Shayn M Peirce, Geoffrey Fox

ArXiv· June 2025

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Evidence for dual roles of histone H3 lysine 4 in antagonizing Polycomb group function and promoting target gene expression.
Cyril S Anyetei-Anum, Mary P Leatham-Jensen, Geoffrey C Fox, B Rutledge Smith, Venkat R Chirasani

Genes Dev· November 2024

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Histone H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation.
Geoffrey C Fox, Karl F Poncha, B Rutledge Smith, Lara N van der Maas, Nathaniel N Robbins

J Biol Chem· August 2024

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Dual roles of histone H3 lysine-4 in antagonizing Polycomb group function and promoting target gene expression.
Cyril S Anyetei-Anum, Mary P Leatham-Jensen, Geoffrey C Fox, B Rutledge Smith, Krzysztof Krajewski

bioRxiv· June 2024

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H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation.
Geoffrey C Fox, Karl F Poncha, B Rutledge Smith, Lara N van der Maas, Nathaniel N Robbins

bioRxiv· May 2024

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An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability.
Kanishk Jain, Matthew R Marunde, Jonathan M Burg, Susan L Gloor, Faith M Joseph, Geoffrey C Fox

Elife· May 2023

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Optimizing Earthquake Nowcasting With Machine Learning: The Role of Strain Hardening in the Earthquake Cycle.
John B Rundle, Joe Yazbeck, Andrea Donnellan, Geoffrey Fox, Lisa Grant Ludwig

Earth Space Sci· November 2022

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Parallel Operators for High Performance Data Science and Data Engineering.
Vibhatha Abeykoon, Supun Kamburugamuve, Chathura Widanage, Niranda Perera, Ahmet Uyar, Geoffrey Fox

Front Big Data· February 2022

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Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations.
J Quetzalcóatl Toledo-Marín, Geoffrey Fox, James P Sluka, James A Glazier

Front Physiol· June 2021

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Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams.
Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao

BMC Med Inform Decis Mak· February 2021

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MGEScan: a Galaxy-based system for identifying retrotransposons in genomes.
Hyungro Lee, Minsu Lee, Wazim Mohammed Ismail, Mina Rho, Geoffrey C Fox

Bioinformatics· August 2016

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Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering.
Geoffrey L House, Saliya Ekanayake, Yang Ruan, Ursel M E Schütte, Wittaya Kaonongbua, Geoffrey Fox

Appl Environ Microbiol· August 2016

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Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.
Eugene Kolker, Vural Özdemir, Lennart Martens, William Hancock, Gordon Anderson, Geoffrey Fox

OMICS· January 2014

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Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.
Eugene Kolker, Vural Özdemir, Lennart Martens, William Hancock, Gordon Anderson, Geoffrey Fox

Big Data· December 2013

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Reproducibility: In praise of open research measures.
Eugene Kolker, Ilkay Altintas, Philip Bourne, Jack Faris, Geoffrey Fox

Nature· June 2013

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Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education.
Rajarshi Guha, Gary D Wiggins, David J Wild, Mu-Hyun Baik, Marlon E Pierce And, Geoffrey C Fox

In Silico Biol· July 2012

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Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets.
Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Geoffrey Fox

BMC Bioinformatics· March 2012

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Hybrid cloud and cluster computing paradigms for life science applications.
Judy Qiu, Jaliya Ekanayake, Thilina Gunarathne, Jong Youl Choi, Seung-Hee Bae, Geoffrey Fox

BMC Bioinformatics· December 2010

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