155 Result(s)
within
English
Bioinformatics
Computer Appl. in Life Sciences
Systems Biology
**yi **a
Protocol
-
Protocol
Prediction of Protein–Protein Interactions: A Study of the Co-evolution Model
The concept of molecular co-evolution drew attention in recent years as the basis for several algorithms for the prediction of protein–protein interactions. While being successful on specific data, the concept...
-
Protocol
Microfluidics Technology for Systems Biology Research
Systems biology is a discipline seeking to understand the emergent behavior of a biological system by integrative modeling of the interactions of the molecular elements. The success of the approach relies on t...
-
Protocol
Model-Based Global Analysis of Heterogeneous Experimental Data Using gfit
Regression analysis is indispensible for quantitative understanding of biological systems and for develo** accurate computational models. By applying regression analysis, one can validate models and quantify...
-
Protocol
Prediction and Integration of Regulatory and Protein–Protein Interactions
Knowledge of transcriptional regulatory interactions (TRIs) is essential for exploring functional genomics and systems biology in any organism. While several results from genome-wide analysis of transcriptiona...
-
Protocol
Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models
Spatially realistic diffusion-reaction simulations supplement traditional experiments and provide testable hypotheses for complex physiological systems. To date, however, the creation of realistic 3D cell mode...
-
Protocol
BioLogic: A Mathematical Modeling Framework for Immunologists
The immune response to pathogens is a result of complex interactions among many cell types and a large number of molecular processes. As such it poses numerous challenges for modeling, simulation, and analysis...
-
Protocol
Methods to Reconstruct and Compare Transcriptional Regulatory Networks
The availability of completely sequenced genomes and the wealth of literature on gene regulation have enabled researchers to model the transcriptional regulation system of some organisms in the form of a netwo...
-
Protocol
Processes Parallel Execution Using Grid Wizard Enterprise
The field of high-performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete various comput...
-
Protocol
Systems Biology of Microbial Communities
Microbes exist naturally in a wide range of environments in communities where their interactions are significant, spanning the extremes of high acidity and high temperature environments to soil and the ocean. ...
-
Protocol
Enabling Public Data Sharing: Encouraging Scientific Discovery and Education
To promote scientific discovery and education, the federated Biomedical Informatics Research Network (BIRN) Data Repository (BDR) supports data storage, sharing, querying, and downloading for the biomedical co...
-
Protocol
Inferring Molecular Interactions Pathways from eQTL Data
Analysis of expression quantitative trait loci (eQTL) helps elucidate the connection between genotype, gene expression levels, and phenotype. However, standard statistical genetics can only attribute the chang...
-
Protocol
System Biology of Gene Regulation
A famous joke story that exhibits the traditionally awkward alliance between theory and experiment and showing the differences between experimental biologists and theoretical modelers is when a University send...
-
Protocol
Exploring Pathways from Gene Co-expression to Network Dynamics
One of the major challenges in post-genomic research is to understand how physiological and pathological phenotypes arise from the networks or connectivity of expressed genes. In addressing this issue, we have...
-
Protocol
Methods of Information Geometry in Computational System Biology (Consistency between Chemical and Biological Evolution)
Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological netw...
-
Protocol
Kinetic Modeling of Biological Systems
The dynamics of how the constituent components of a natural system interact defines the spatio-temporal response of the system to stimuli. Modeling the kinetics of the processes that represent a biophysical sy...
-
Protocol
Applications of Bioinformatics to Protein Structures: How Protein Structure and Bioinformatics Overlap
In this chapter, we will focus on the role of bioinformatics to analyze a protein after its protein structure has been determined. First, we present how to validate protein structures for quality assurance. Th...
-
Protocol
A Maximum Likelihood Method for Reconstruction of the Evolution of Eukaryotic Gene Structure
Spliceosomal introns are one of the principal distinctive features of eukaryotes. Nevertheless, different large-scale studies disagree about even the most basic features of their evolution. In order to come up...
-
Protocol
Effects of Functional Bias on Supervised Learning of a Gene Network Model
Gene networks have proven to be an effective approach for modeling cellular systems, capable of capturing some of the extreme complexity of cells in a formal theoretical framework. Not surprisingly, this compl...
-
Protocol
Using Evolutionary Information to Find Specificity-Determining and Co-evolving Residues
Intricate networks of protein interactions rely on the ability of a protein to recognize its targets: other proteins, ligands, and sites on DNA and RNA. To recognize other molecules, it was suggested that a pr...
-
Protocol
The Bioverse API and Web Application
The Bioverse is a framework for creating, warehousing and presenting biological information based on hierarchical levels of organisation. The framework is guided by a deeper philosophy of desiring to represent...
