相关论文: CplexA: a Mathematica package to study macromolecu…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…
Principal component analysis (PCA) is routinely used in population genetics to assess genetic structure. With chromosomal reference genomes and population-scale whole genome-sequencing becoming increasingly accessible, contemporary studies…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
CA has grown as potential classifier for addressing major problems in bioinformatics. Lot of bioinformatics problems like predicting the protein coding region, finding the promoter region, predicting the structure of protein and many other…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Background: Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…
It is well established that gene expression can be modeled as a Markovian stochastic process and hence proper observables might be subjected to large fluctuations and rare events. Since dynamics is often more than statics, one can work with…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Complexity has been a recurrent research topic in cellular automata because they represent systems where complex behaviors emerge from simple local interactions. A significant amount of previous research has been conducted proposing…
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…