Learn More
Protein-protein interactions (PPIs) and their networks play a central role in all biological processes. Akin to the complete sequencing of genomes and their comparative analysis, complete descriptions of interactomes and their comparative analysis is fundamental to a deeper understanding of biological processes. A first step in such an analysis is to align(More)
MOTIVATION With the increasing availability of large protein-protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across networks, and global alignment, which attempts to find a best(More)
We describe an algorithm, IsoRank, for global alignment of two protein-protein interaction (PPI) networks. IsoRank aims to maximize the overall match between the two networks; in contrast, much of previous work has focused on the local alignment problem— identifying many possible alignments, each corresponding to a local region of similarity. IsoRank is(More)
UNLABELLED We describe an algorithm for global alignment of multiple protein-protein interaction (PPI) networks, the goal being to maximize the overall match across the input networks. The intuition behind our algorithm is that a protein in one PPI network is a good match for a protein in another network if the former's neighbors are good matches for the(More)
We describe IsoBase, a database identifying functionally related proteins, across five major eukaryotic model organisms: Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus and Homo Sapiens. Nearly all existing algorithms for orthology detection are based on sequence comparison. Although these have been successful in(More)
Many time-series experiments seek to estimate some signal as a continuous function of time. In this paper, we address the <i>sampling problem</i> for such experiments: determining which time-points ought to be sampled in order to minimize the cost of data collection. We restrict our attention to a growing class of experiments which measure multiple signals(More)
Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein-protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of the PPI interactome remains inadequate.(More)
Characterizing the extent and logic of signaling networks is essential to understanding specificity in such physiological and pathophysiological contexts as cell fate decisions and mechanisms of oncogenesis and resistance to chemotherapy. Cell-based RNA interference (RNAi) screens enable the inference of large numbers of genes that regulate signaling(More)
UNLABELLED This paper presents a framework for predicting protein-protein interactions (PPI) that integrates structure-based information with other functional annotations, e.g. GO, co-expression and co-localization, etc., Given two protein sequences, the structure-based interaction prediction technique threads these two sequences to all the protein(More)