Feb 19, 2008
From Shiu Lab
Contents |
Bioinformatics
1) Choosing BLAST options for better detection of orthologs as reciprocal best hits Using E.coli vs RefSeq sequences, looked at two parameters - low complexity segments (stringent vs relaxed) and alignment method (BLAST vs Smith Waterman) and found significant differences. Compared results against reciprocal shortest distances (RSD) and looked at error rates. Found highest error rates in RSD. Suggest using soft filtering and smith waterman.
2) Structural systems identification of genetic regulatory networks Use some variant of Expectation Maximization (EM) to determine the structure of the SOS regulatory network in E.coli.
3) NetworkBLAST: comparative analysis of protein networksComparison of Protein-Protein interaction networks. Web based server.
4) A hybrid model for robust detection of transcription factor binding sitesAn ab-initio predictor for TF binding sites. They say that there is a difference between di-nucleotide content of the TF binding sites and the background DNA, and they make use of that fact.
5) Prediction of both conserved and nonconserved microRNA targets in animalsUsed microarray datasets to train Support Vector Machines (SVMs) to look for patterns of miRNA-based regulation, and used this information to predict downstream targets of miRNAs.
Evolution
1) EVOLUTION OF THE GENOMIC RATE OF RECOMBINATION IN MAMMALS The recombination rate in mammals is similar in closely related clades. Also, they propose that the differences observed within mammals is a result of neutral mutations.
TiPS
1) Unexpected silencing effects from T-DNA tags in Arabidopsis Suggest that there is some complex effect in T-DNA insertional mutants which inhibits expression of the 35S promoter probably by siRNA based effects.
Mol. Biology and Evolution
1) Natural Variation in Arabidopsis lyrata Vernalization Requirement Conferred by a FRIGIDA Indel Polymorphism Was earlier known in Arabidopsis thaliana. Now they have shown the same thing has happened in lyrata too.
2) Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis They show that between 3 species of Caenorhabditis that diverged 100MYA there is >92% similarity between the alternatively spliced exons. This is much higher than the figure of 21.3% between 2 Drosophila species separated about 25 MYA. They discuss its immplications.
COGD
1) The evolution of resistance genes in multi-protein plant resistance systems Review on evolution of R-genes in plants.
2) Inherited variation at the epigenetic level: paramutation from the plant to the mouseReview on the role of RNA elements in hereditary transmission of characters.
Nature Genetics
1) Epigenetic regulation and the variability of gene expressionAs the name suggests. Extensive analysis.
2) Genome-wide analysis of transcript isoform variation in humans Analysed HapMap data and performed tiling array experiments. Showed a statistical correlation between SNPs/other structural variation and transcript abundance in some 324 genes.
3) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegansLooked at data from various sources to make a functional network prediction and tested it using RNAi *IMPORTANT*
4) Ultraconservation identifies a small subset of extremely constrained developmental enhancersPropose that many of the highly conserved non-coding elements between humans and mouse have remained so because of their role in development.
