Elizabeth Brunk

Publications

• A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism
• ssbio: A Python Framework for Structural Systems Biology
• iML1515, a knowledgebase that computes Escherichia coli traits
• Recon3D enables a three-dimensional view of gene variation in human metabolism
• Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
• A Standardized Protocol for Sample Preparation for Scanning Electron Microscopy (SEM) to Visualize Extrachromosomal DNA (ecDNA)
• Machine learning of three-dimensional protein structures to predict the functional impacts of genome variation
• Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation
• Kinase Plasticity in Response to Vandetanib Enhances Sensitivity to Tamoxifen and Identifies Co-Treatment Strategies in Estrogen Receptor Positive Breast Cancer
• CytoCellDB: a comprehensive resource for exploring extrachromosomal DNA in cancer cell lines
• A standardized protocol for sample preparation for scanning electron microscopy to visualize extrachromosomal DNA
• Advances in the Management of Early-Stage Triple-Negative Breast Cancer
• Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism
• Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System
• Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework
• Multi-omic data integration enables discovery of hidden biological regularities
• Lessons from Nature: Computational Design of Biomimetic Compounds and Processes
• Mechanism to Trigger Unfolding in O6‐Alkylguanine‐DNA Alkyltransferase
• Leveraging AI to Automate Detection and Quantification of Extrachromosomal DNA (ecDNA) to Decode Drug Responses
• Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions
• Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes
• Machine learning in computational biology to accelerate high-throughput protein expression
• NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling
• Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome
• Genetic‐Algorithm‐Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2
• The Need for Integrated Approaches in Metabolic Engineering
• Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow
• Systems biology of the structural proteome
• Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC
• Model-driven discovery of underground metabolic functions in Escherichia coli
• Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
• Free-Energy Landscape and Characteristic Forces for the Initiation of DNA Unzipping
• A Streamlined Ribosome Profiling Protocol for the Characterization of Microorganisms
• A Mechanochemical Switch to Control Radical Intermediates
• Integrating computational methods to retrofit enzymes to synthetic pathways
• Computational, Structural, and Kinetic Evidence That Vibrio vulnificus FrsA Is Not a Cofactor-Independent Pyruvate Decarboxylase
• Role of Environment for Catalysis of the DNA Repair Enzyme MutY
• Directed Evolution of the Suicide Protein O6-Alkylguanine-DNA Alkyltransferase for Increased Reactivity Results in an Alkylated Protein with Exceptional Stability
• Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems
• AI-Driven Variant Annotation for Precision Oncology in Breast Cancer