Spatially or chemically isolated modules that carry out discrete functions are considered fundamental building blocks of cellular organization. However, detecting them in highly integrated biological networks requires a thorough understanding of the organization of the ...
In this chapter, we discuss a number of approaches to network inference from large-scale functional genomics data. Our goal is to describe current methods that can be used to infer predictive networks. At present, one of the most effective methods to produce networks with predictive value is the B ...
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 changes in expression levels to loci on the genome, not specific genes. Each ...
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 network. In order to reconstruct such networks in non-model organisms, three prin ...
Organisms must continually adapt to changing cellular and environmental factors (e.g., oxygen levels) by altering their gene expression patterns. At the same time, all organisms must have stable gene expression patterns that are robust to small fluctuations in environmental factors ...
Probably one of the most characteristic features of a living system is its continual propensity to change as it juggles the demands of survival with the need to replicate. Internally these adjustments are manifest as changes in metabolite, protein, and gene activities. Such changes have beco ...
Many model regulatory networks are approaching the depth of characterisation of bacteriophage λ, wherein the vast majority of individual components and interactions are identified, and research can focus on understanding whole network function and the role of interactions with ...
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 system has long been pursued with the aim of improving our understanding of the stud ...
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 with a more reliable reconstruction of intron evolution, we developed a mo ...
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 protein uses a small set of specificity-determining residues (SDRs). How can one find these r ...
Enzymes play central roles in metabolic pathways, and the prediction of metabolic pathways in newly sequenced genomes usually starts with the assignment of genes to enzymatic reactions. However, genes with similar catalytic activity are not necessarily similar in sequence, and ther ...
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 complexity, combined with our still-limited amount of experimental data measur ...
Understanding how mutations lead to changes in protein function and/or protein interaction is critical to understanding the molecular causes of clinical phenotypes. In this method, we present a path toward integration of protein interaction data and mutation data and then demonstr ...
Clustering is a popular technique commonly used to search for groups of similarly expressed genes using mRNA expression data. There are many different clustering algorithms and the application of each one will usually produce different results. Without additional evaluation, it is d ...
Here we describe a statistically based partitioning method called median partitioning (MP), which involves the transformation of value distributions of molecular property descriptors into a binary classification scheme. The MP approach fundamentally differs from other pa ...
The concepts of diversity and similarity of molecules are widely used in quantitative methods for designing (selecting) a representative set of molecules and for analyzing the relationship between chemical structure and biological activity. We review methods and algorithms for d ...
The recent emphasis in combinatorial library design has shifted from the design of very large diverse libraries to the design of smaller more focused libraries. Typically the aim is to incorporate as much knowledge into the design as possible. This knowledge may relate to the target protein its ...
The design and analysis of a screening set for high throughput screening is complex. We examine three statistical strategies for compound selection, random, clustering, and space-filling. We examine two types of chemical descriptors, BCUTs and principal components of Dragon Consti ...
The wealth of information available from the solution of the human genome has dramatically altered the nature of combinatorial library design. While single-target-focused library design remains an important objective, creation of libraries directed toward families of recept ...
We describe here a stochastic optimization protocol for computational library design based on the principle of simulated annealing (SA). We also demonstrate via computer simulation studies that the SA-guided diversity sampling affords higher information content than random s ...
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