Kang-Hao Lu

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 mapping between all nodes of the two networks. In this article, our aim is to improve upon existing global alignment results. Better network alignment will enable, among other things, more accurate identification of functional orthologs across species. RESULTS: We introduce IsoRankN (IsoRank-Nibble) a global multiple-network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks. Being based on spectral methods, IsoRankN is both error tolerant and computationally efficient. AVAILABILITY: Our software is available freely for non-commercial purposes on request from: http://isorank.csail.mit.edu/.

The classical and the relativistic Doppler effect for both acoustic and light waves are formulated exactly by a systematic method. This method differs only in its usage of classical and relativistic transformation laws in the formulation of the classical and relativistic Doppler effect, respectively. The method is straightforward, and much more logically rigorous than the typical demonstrations using graphical illustration. In the formulation of the classical Doppler effect, as expected, no aberration and no transverse classical Doppler effect are found. In the formulation of the relativistic Doppler effect, one important discovery is that the transverse relativistic Doppler effect depends only on the speed of the source relative to the observer, irrespective of the nonskew velocities of the source and the observer relative to the medium. PACS No.: 03.30.+p