New cytotoxic ergosterols from a plant-associated fungus .

Three new ergosterols, colletosterols A-C (-), together with two known analogues and , were isolated from the endophytic fungus associated with the leaves of by a bioassay-guided fractionation method. The new structures were elucidated on the basis of extensive spectroscopic analyses and electronic circular dichroism (ECD) calculations. All the ergosterols were evaluated for their cytotoxic activities against A549 and HeLa cell lines.

Trichodestruxins A-D: Cytotoxic Cyclodepsipeptides from the Endophytic Fungus .

Four new cyclodepsipeptides, trichodestruxins A-D (-), together with destruxin E2 chlorohydrin () and destruxin A2 (), were isolated from the plant endophytic fungus by a bioassay-guided fractionation method. Their planar structures were elucidated on the basis of 1D and 2D NMR and MS/MS spectroscopic analyses. The stereochemical configuration was established by application of the advanced Marfey's method, -based configuration analysis, Mosher's method, and chemical derivatizations.

Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins.

Alternative splicing acts on transcripts from almost all human multi-exon genes. Notwithstanding its ubiquity, fundamental ramifications of splicing on protein expression remain unresolved. The number and identity of spliced transcripts that form stably folded proteins remain the sources of considerable debate, due largely to low coverage of experimental methods and the resulting absence of negative data.

Towards a practical O(nlogn) phylogeny algorithm.

: Recently, we have identified a randomized quartet phylogeny algorithm that has O(nlogn) runtime with high probability, which is asymptotically optimal. Our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O(loglogn) taxa that is correct with high probability. In practice, none of these assumptions is correct: quartet errors are positively correlated and occur with unknown probability, and the guide tree is often error prone.

OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.

Motivation: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays protein-protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows PPI networks derived from experiments to be overlaid on networks extracted from public databases, supporting the identification and verification of new interactors.