The dynamics of biological processes are often modeled as systems of nonlinear ordinary differential equations (ODE). An important feature of nonlinear ODEs is that seemingly minor...
Abstract. Hierarchical clustering is a popular method for grouping together similar elements based on a distance measure between them. In many cases, annotation information for som...
Saket Navlakha, James Robert White, Niranjan Nagar...
A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Example...
Phylogenetic Bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of th...
Nicholas D. Pattengale, Masoud Alipour, Olaf R. P....
Abstract. Between-Pathway Models (BPMs) are network motifs consisting of pairs of putative redundant pathways. In this paper, we show how adding another source of high-throughput d...
Benjamin J. Hescott, Mark D. M. Leiserson, Lenore ...
Finding similar structures from 3-D structure databases of proteins is becoming more and more important issue in the post-genomic molecular biology. To compare 3-D structures of tw...
Reconciliation between a set of gene trees and a species tree is the most commonly used approach to infer the duplication and loss events in the evolution of gene families, given a...
The combination of fully sequence genomes and new technologies for high density arrays and ultra-rapid sequencing enables the mapping of generegulatory and epigenetics marks on a g...