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Cellular Blood Flow Modeling with HemoCell
Many of the intriguing properties of blood originate from its cellular nature. Bulk effects, such as viscosity, depend on the local shear rates and...
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Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities
Alchemical free energy methods can be used for the efficient computation of relative binding free energies during preclinical drug discovery stages....
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HPC Framework for Performing in Silico Trials Using a 3D Virtual Human Cardiac Population as Means to Assess Drug-Induced Arrhythmic Risk
Following the 3 R’s principles of animal research—replacement, reduction, and refinement—a high-performance computational framework was produced to...
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High-Throughput Structure-Based Drug Design (HT-SBDD) Using Drug Docking, Fragment Molecular Orbital Calculations, and Molecular Dynamic Techniques
Structure-based drug design (SBDD) is rapidly evolving to be a fundamental tool for faster and more cost-effective methods of lead drug discovery....
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The Search for System’s Parameters: Statistical and Dynamical Description from Complex Network Analysis
The integration of physical and biological science styles is the key for facing the deluge of molecular level information that is becoming a real...
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Mathematical Modeling in the Study of Organisms and Their Parts
Mathematical modeling is a very powerful tool to understand natural phenomena. Such a tool carries its own assumptions and should always be used...
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From Cell States to Cell Fates: Control of Cell State Transitions
We examine the coordinated behavior of thousands of genes in cell fate transitions through genome expression as an integrated dynamical system using...
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Natural Language Processing for Drug Discovery Knowledge Graphs: Promises and Pitfalls
Building and analyzing knowledge graphs (KGs) to aid drug discovery is a topical area of research. A salient feature of KGs is their ability to...
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A Blood Flow Modeling Framework for Stroke Treatments
Circulatory models can significantly help develop new ways to alleviate the burden of stroke on society. However, it is not always easy to know what...
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Systems Biology Approaches to Understanding COVID-19 Spread in the Population
In essence, the COVID-19 pandemic can be regarded as a systems biology problem, with the entire world as the system, and the human population as the...
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Molecular Dynamics and Other HPC Simulations for Drug Discovery
High performance computing (HPC) is taking an increasingly important place in drug discovery. It makes possible the simulation of complex biochemical...
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Automated Virtual Screening
Computational methods in modern drug discovery have become ubiquitous, with methods that cover most of the discovery stages: from hit finding and...
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Teaching Medical Students to Use Supercomputers: A Personal Reflection
At the “Kick Off” meeting for CompBioMed (compbiomed.eu), which was first funded in October 2016, I had no idea that one single sentence (“I wish I...
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Identifying Key In Silico Knockout for Enhancement of Limonene Yield Through Dynamic Metabolic Modelling
Living cells display dynamic and complex behaviors. To understand their response and to infer novel insights not possible with traditional...
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Effect of Muscle Forces on Femur During Level Walking Using a Virtual Population of Older Women
Aging is associated with a greater risk of muscle and bone disorders such as sarcopenia and osteoporosis. These conditions substantially affect one’s...
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Optical Estimation of Bioelectric Patterns in Living Embryos
Fluorescent lifetime imaging (FLIM) is a powerful tool for visualizing physiological parameters in vivo. We present here a 3-dye strategy for map**...
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Systems Biology Modeling of Cancer Nonlinear Dynamics
Not unlike the climate or what holds the galaxies and planetary motions together, cancer biology has an intrinsic nonlinear dynamic. In this overview...
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Efficient and Reliable Data Management for Biomedical Applications
This chapter discusses the challenges and requirements of modern Research Data Management (RDM), particularly for biomedical applications in the...
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An Enhanced Quantitative Reverse Transcription-PCR Approach for Measuring Circulating MicroRNAs
Short (22 nt) RNAs called microRNAs (miRNAs) bind to and inhibit target messenger RNAs in gene regulatory networks. Recent study suggests that miRNAs...
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Metastasis Models: Thermodynamics and Complexity
The thermodynamic formalism of nonequilibrium systems together with the theory of complex systems and systems biology offer an appropriate...