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Introduction to High-Performance Computing
Since the first general-purpose computing machines came up in the middle of the twentieth century, computer science’s popularity has been growing...
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Prediction and Analysis of Transcription Factor Binding Sites: Practical Examples and Case Studies Using R Programming
Transcription factors (TFs) bind to specific regions of DNA known as transcription factor binding sites (TFBSs) and modulate gene expression by...
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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...
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Understanding Cell Differentiation Through Single-Cell Approaches: Conceptual Challenges of the Systemic Approach
The cells of a multicellular organism are derived from a single zygote and genetically almost identical. Yet, they are phenotypically very different....
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Expanding the Landscape of Amyloid Sequences with CARs-DB: A Database of Polar Amyloidogenic Peptides from Disordered Proteins
Several databases collecting amyloidogenic regions have been released to provide information on protein sequences able to form amyloid fibrils....
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Antiviral Drug Target Identification and Ligand Discovery
This chapter intends to provide a general overview of web-based resources available for antiviral drug discovery studies. First, we explain how the...
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Bayesian Optimization in Drug Discovery
Drug discovery deals with the search for initial hits and their optimization toward a targeted clinical profile. Throughout the discovery pipeline,...
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Deep Learning for Predicting Gene Regulatory Networks: A Step-by-Step Protocol in R
Deep learning has emerged as a powerful tool for solving complex problems, including reconstruction of gene regulatory networks within the realm...
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GRAMM Web Server for Protein Docking
Prediction of the structure of protein complexes by docking methods is a well-established research field. The intermolecular energy landscapes in...
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Molecular Dynamics Simulation-Based Prediction of Glycosaminoglycan Interactions with Drug Molecules
Glycosaminoglycans (GAGs) are a class of long linear anionic periodic polysaccharides. Their biological activities are very broad including tissue...
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Accelerating COVID-19 Drug Discovery with High-Performance Computing
The recent COVID-19 pandemic has served as a timely reminder that the existing drug discovery is a laborious, expensive, and slow process. Never has...
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Interpreting Gene Ontology Annotations Derived from Sequence Homology Methods
The Gene Ontology (GO) project describes the functions of the gene products of organisms from all kingdoms of life in a standardized way, enabling...
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The Future of Drug Development with Quantum Computing
Novel medication development is a time-consuming and expensive multistage procedure. Recent technology developments have lowered timeframes,...
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Implementation of Exome Sequencing to Identify Rare Genetic Diseases
Modern high-throughput genomic testing using next-generation sequencing (NGS) has led to a significant increase in the successful diagnosis of rare...
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A Review of Computational Approach for S-system-based Modeling of Gene Regulatory Network
Inference of gene regulatory network (GRN) from time series microarray data remains as a fascinating task for computer science researchers to...
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Mining Chemogenomic Spaces for Prediction of Drug–Target Interactions
The pipeline of drug discovery consists of a number of processes; drug–target interaction determination is one of the salient steps among them....
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Artificial Intelligence in ADME Property Prediction
Absorption, distribution, metabolism, excretion (ADME) are key properties of a small molecule that govern pharmacokinetic profiles and impact its...
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Introduction to Computational Biomedicine
The domain of computational biomedicine is a new and burgeoning one. Its areas of concern cover all scales of human biology, physiology, and...
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Knowledge Graphs and Their Applications in Drug Discovery
Knowledge graphs represent information in the form of entities and relationships between those entities. Such a representation has multiple potential...