Publications by authors named "Ram Samudrala"

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Deciphering bisphenol A (BPA)-elicited osteoarthritis mechanisms through network toxicology and molecular docking, then de novo generation of novel therapeutic candidates.
Sumei Xu, Liping Jiang, Zhuo Zhang, Xin Luo, Wei Wu, Ram Samudrala

BMC Pharmacol Toxicol· December 2025

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Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms.
Melissa Van Norden, William Mangione, Zackary Falls, Ram Samudrala

Bioinformatics· November 2025

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Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms.
Melissa Van Norden, William Mangione, Zackary Falls, Ram Samudrala

bioRxiv· August 2025

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Multiscale analysis and optimal glioma therapeutic candidate discovery using the CANDO platform.
Sumei Xu, William Mangione, Melissa Van Norden, Katherine Elefteriou, Yakun Hu, Ram Samudrala

bioRxiv· May 2025

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Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep.
Jeremy Horst Keeper, Jong Seto, Ersin Emre Oren, Orapin V Horst, Ling-Hong Hung, Ram Samudrala

Front Mater· December 2024

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The implications of APOBEC3-mediated C-to-U RNA editing for human disease.
Melissa Van Norden, Zackary Falls, Sapan Mandloi, Brahm H Segal, Bora E Baysal, Ram Samudrala

Commun Biol· May 2024

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The Role of C-to-U RNA Editing in Human Biodiversity.
Melissa Van Norden, Zackary Falls, Sapan Mandloi, Brahm Segal, Bora Baysal, Ram Samudrala

bioRxiv· July 2023

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Computational Grafting of Epitopes.
Manish Manish, Smriti Mishra, Monika Pahuja, Ayush Anand, Naidu Subbarao, Ram Samudrala

Methods Mol Biol· June 2023

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Effective holistic characterization of small molecule effects using heterogeneous biological networks.
William Mangione, Zackary Falls, Ram Samudrala

Front Pharmacol· April 2023

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Antiviral Approaches against Influenza Virus.
Rashmi Kumari, Suresh D Sharma, Amrita Kumar, Zachary Ende, Margarita Mishina, Ram Samudrala

Clin Microbiol Rev· March 2023

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The impact of nucleosome structure on CRISPR/Cas9 fidelity.
Christopher R Handelmann, Maria Tsompana, Ram Samudrala, Michael J Buck

Nucleic Acids Res· March 2023

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Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer.
Liana Bruggemann, Zackary Falls, William Mangione, Stanley A Schwartz, Sebastiano Battaglia, Ram Samudrala

Int J Mol Sci· January 2023

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Optimal COVID-19 therapeutic candidate discovery using the CANDO platform.
William Mangione, Zackary Falls, Ram Samudrala

Front Pharmacol· August 2022

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Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology.
Lama Moukheiber, William Mangione, Mira Moukheiber, Saeed Maleki, Zackary Falls, Ram Samudrala

Molecules· May 2022

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Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease.
Manoj J Mammen, Chengjian Tu, Matthew C Morris, Spencer Richman, William Mangione, Ram Samudrala

Pharmaceuticals (Basel)· May 2022

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Evaluating the performance of drug-repurposing technologies.
James Schuler, Zackary Falls, William Mangione, Matthew L Hudson, Liana Bruggemann, Ram Samudrala

Drug Discov Today· January 2022

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Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK.
Zackary Falls, Jonathan Fine, Gaurav Chopra, Ram Samudrala

Front Chem· January 2022

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A Deep-Learning Proteomic-Scale Approach for Drug Design.
Brennan Overhoff, Zackary Falls, William Mangione, Ram Samudrala

Pharmaceuticals (Basel)· December 2021

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A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition.
Rama Dey-Rao, George R Smith, Uddhav Timilsina, Zackary Falls, Ram Samudrala

Antiviral Res· November 2021

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A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex.
Rakesh Chatrikhi, Callen F Feeney, Mary J Pulvino, Georgios Alachouzos, Andrew J MacRae, Ram Samudrala

Cell Chem Biol· August 2021

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Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function.
L Palanikumar, Laura Karpauskaite, Mohamed Al-Sayegh, Ibrahim Chehade, Maheen Alam, Ram Samudrala

Nat Commun· June 2021

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Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform.
Matthew L Hudson, Ram Samudrala

Molecules· April 2021

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cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data.
William Mangione, Zackary Falls, Gaurav Chopra, Ram Samudrala

J Chem Inf Model· September 2020

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Association of C>U RNA Editing with Human Disease Variants.
Sapan Mandloi, Zackary Falls, Rong Deng, Ram Samudrala, Peter L Elkin

Stud Health Technol Inform· June 2020

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Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions.
Liana Bruggemann, Christopher Hawthorne, Ram Samudrala, Guillermo H Lopez-Campos

Stud Health Technol Inform· June 2020

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