Accurate systems biology modeling requires a complete catalog of protein complexes and their constituent proteins. We discuss a graph-theoretic/statistical algorithm for local dynamic modeling of protein complexes using data from affinity purification-mass spectrometry experiments. The algorithm...

Because haplotypes may parsimoniously summarize the effect of genes on disease, there is great interest in using haplotypes in case-control studies of unphased genotype data. Previous methods for investigating haplotypes effects in case-control studies have not allowed for both of the following...

We describe a method for the generation of knowledge-based potentials and apply it to the observed torsional angles of known protein structures. The potential is derived using Bayesian reasoning, and is useful as a prior for further such reasoning in the presence of additional data. The...

Analysis of viral strand sequence data and viral replication capacity could potentially lead to biological insights regarding the replication ability of HIV-1. Determining specific target codons on the viral strand will facilitate the manufacturing of target-specific antiretrovirals. Various...

We present a new instance of Laplace's second Law of Errors and show how it can be used in the analysis of data from microarray experiments. This error distribution is shown to fit microarray expression data much better than a normal distribution. The use of this distribution in a parametric...

Transcription factors and many other DNA-binding proteins recognize more than one specific sequence. Among sequences recognized by a given DNA-binding protein, different positions exhibit varying degrees of conservation. The reason is that base pairs that are more extensively contacted by the...

Approaches based upon sequence weights, to construct a position weight matrix of nucleotides from aligned inputs, are popular but little effort has been expended to measure their quality.We derive optimal sequence weights that minimize the sum of the variances of the estimators of base frequency...

Motivation: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are...

We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding statistical significance. Based on gene expression data alone, only local structures of genetic networks...

We present a mathematical model to extend the dynamic range of gene expression data measured by laser scanners. The strategy is based on the rather simple but novel idea of producing two images with different scanner sensitivities, obtaining two different sets of expression values: the first is...