Publications by authors named "Brian Athey"

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Health system learning achieves generalist neuroimaging models.
Akhil Kondepudi, Akshay Rao, Chenhui Zhao, Yiwei Lyu, Samir Harake, Brian Athey

Res Sq· December 2025

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A Linear Analysis Mixed Model Phenotyper (LAMP) for Bipolar Disorder: Evaluating the Impact of Medication, Substance Use Disorders, and Comorbidities on Mood Trajectories.
Qingzhi Liu, Pranjal Srivastava, Ivan Rozhkov, Gregory A Farnum, Monica J Holmes, Brian D Athey

medRxiv· September 2025

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AI-Based Computational Methods in Early Drug Discovery and Post Market Drug Assessment: A Survey.
Flora Rajaei, Cristian Minoccheri, Emily Wittrup, Richard C Wilson, Brian D Athey

IEEE Trans Comput Biol Bioinform· August 2025

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VO: The Vaccine Ontology.
Jie Zheng, Asiyah Yu Lin, Anthony Huffman, Anna Maria Masci, Rebecca Racz, Brian D Athey

bioRxiv· August 2025

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SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis.
Anthony Huffman, Feng-Yu Yeh, Junguk Hur, Jie Zheng, Anna Maria Masci, Brian Athey

bioRxiv· August 2025

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Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling.
Alexandr A Kalinin, Paula Llanos, Theresa Maria Sommer, Giovanni Sestini, Xinhai Hou, Brian D Athey

ArXiv· July 2025

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Learning neuroimaging models from health system-scale data.
Yiwei Lyu, Samir Harake, Asadur Chowdury, Soumyanil Banerjee, Rachel Gologorsky, Brian Athey

Res Sq· February 2025

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Can Machine Learning Overcome the 95% Failure Rate and Reality that Only 30% of Approved Cancer Drugs Meaningfully Extend Patient Survival?
Duxin Sun, Christian Macedonia, Zhigang Chen, Sriram Chandrasekaran, Kayvan Najarian, Brian Athey

J Med Chem· September 2024

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A new framework for host-pathogen interaction research.
Hong Yu, Li Li, Anthony Huffman, John Beverley, Junguk Hur, Brian Athey

Front Immunol· January 2023

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A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.
Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A Natale, Brian Athey

J Biomed Semantics· October 2022

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Valproic acid-induced changes of 4D nuclear morphology in astrocyte cells.
Alexandr A Kalinin, Xinhai Hou, Alex S Ade, Gordon-Victor Fon, Walter Meixner, Brian D Athey

Mol Biol Cell· August 2021

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Automated detection of acute respiratory distress syndrome from chest X-Rays using Directionality Measure and deep learning features.
Narathip Reamaroon, Michael W Sjoding, Jonathan Gryak, Brian D Athey, Kayvan Najarian

Comput Biol Med· July 2021

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Robust segmentation of lung in chest x-ray: applications in analysis of acute respiratory distress syndrome.
Narathip Reamaroon, Michael W Sjoding, Harm Derksen, Elyas Sabeti, Jonathan Gryak, Brian D Athey

BMC Med Imaging· October 2020

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CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis.
Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Brian Athey

Sci Data· June 2020

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Druggable Transcriptional Networks in the Human Neurogenic Epigenome.
Gerald A Higgins, Aaron M Williams, Alex S Ade, Hasan B Alam, Brian D Athey

Pharmacol Rev· October 2019

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Publisher Correction: 3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification.
Alexandr A Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, Brian D Athey

Sci Rep· October 2018

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3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification.
Alexandr A Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, Brian D Athey

Sci Rep· September 2018

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Deep learning in pharmacogenomics: from gene regulation to patient stratification.
Alexandr A Kalinin, Gerald A Higgins, Narathip Reamaroon, Sayedmohammadreza Soroushmehr, Ari Allyn-Feuer, Brian D Athey

Pharmacogenomics· May 2018

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Valproic acid induces prosurvival transcriptomic changes in swine subjected to traumatic injury and hemorrhagic shock.
Patrick E Georgoff, Vahagn C Nikolian, Gerald Higgins, Kiril Chtraklin, Hassan Eidy, Brian Athey

J Trauma Acute Care Surg· April 2018

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The pharmacoepigenomics informatics pipeline defines a pathway of novel and known warfarin pharmacogenomics variants.
Ari Allyn-Feuer, Alex Ade, Jasmine A Luzum, Gerald A Higgins, Brian D Athey

Pharmacogenomics· April 2018

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Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury.
Gerald A Higgins, Patrick Georgoff, Vahagn Nikolian, Ari Allyn-Feuer, Brian Pauls, Brian D Athey

Pharm Res· August 2017

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Mining the topography and dynamics of the 4D Nucleome to identify novel CNS drug pathways.
Gerald A Higgins, Ari Allyn-Feuer, Patrick Georgoff, Vahagn Nikolian, Hasan B Alam, Brian D Athey

Methods· July 2017

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Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response.
Gerald A Higgins, Ari Allyn-Feuer, Brian D Athey

Pharmacogenomics· July 2016

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A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis.
Gerald A Higgins, Ari Allyn-Feuer, Edward Barbour, Brian D Athey

Pharmacogenomics· July 2016

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Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.
Sirarat Sarntivijai, Shelley Zhang, Desikan G Jagannathan, Shadia Zaman, Keith K Burkhart, Brian D Athey

Drug Saf· July 2016

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