235 Result(s)
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Life Sciences
Bioinformatics
Systems Biology
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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. ...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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Computational Modeling of Biochemical Networks Using COPASI
Computational modeling and simulation of biochemical networks is at the core of systems biology and this includes many types of analyses that can aid understanding of how these systems work. COPASI is a generi...
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Biological Network Inference and Analysis Using SEBINI and CABIN
Attaining a detailed understanding of the various biological networks in an organism lies at the core of the emerging discipline of systems biology. A precise description of the relationships formed between genes...
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Identification of cis-Regulatory Elements in Gene Co-expression Networks Using A-GLAM
Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. The sophistication of transcriptional regulation in higher eukaryotes, particularly in me...
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Modeling Molecular Regulatory Networks with JigCell and PET
We demonstrate how to model macromolecular regulatory networks with JigCell and the Parameter Estimation Toolkit (PET). These software tools are designed specifically to support the process typically used by s...
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Inferring Protein–Protein Interactions from Multiple Protein Domain Combinations
The ever accumulating wealth of knowledge about protein interactions and the domain architecture of involved proteins in different organisms offers ways to understand the intricate interplay between interactom...
