Seminars

Wednesday 4th November, 3-4pm in Mac 1 (Old Biology Building)

Kay Nieselt - University of Tuebingen

Title: "Characterisation of non-coding RNAs and RNA-RNA interactions in Streptomyces coelicolor"

Abstract:Several studies of non-coding RNAs (ncRNAs) have shown that they are involved in a wide spectrum of different processes and almost daily the list of processes is enlarged. Nevertheless, the functions of most ncRNA transcripts are still unknown. There is by now a number of tools published for the genomewide prediction of ncRNA regions. However, most such programs produce an unknown number of false positives. Furthermore, the locus prediction does not provide information about functional ncRNAs that might be contained in the corresponnding region. We present an approach to annotate ncRNAs predicted by programs such as RNAz (Washietl et al., 2005). Loci containing predicted ncRNAs are compared to known ncRNA families. In addition, we compute features related to the transcription process which allows us to distingush putative ncRNA transcripts from ncRNA regulatory motifs. In addition, we can predict interactions between putative ncRNA transcripts and mRNAs. These methods are applied to the antibiotic-producing soil bacterium Streptomyces coelicolor. Almost 4000 ncRNA elements were predicted, most of them overlapping with protein coding genes. First results show that several key proteins in S. coelicolor are regulated by ncRNA transcripts. This is supported by genomewide high resolution time series expression data using a custom-designed microarray targeting all protein coding genes as well as our predicted ncRNAs.


Wednesday 18th November

Steffen Klaere - Department of Mathematics

Title: “MISFITS: assigning extra mutations to a phylogenetic treeâ€


Tuesday 8th December

Dr Naryttza Díaz - Ludwig Institute for Cancer Research, Swiss Institute of Bioinformatics

Title: "Taxonomic classification of environmental genomic fragments: From whole genomes to genomic fragments"

Abstract:Understanding the species composition of natural microbial communities is a milestone to gain access to the beneficial aspects of these microbial collectives. The dropping sequencing costs allow to sequence entire microbial communities without previous culturing. Metagenomics is the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment. The metagenomics approach promises to be a gateway to access the estimated 99% of species that still resist cultivation. However, due to the complexity and amount of data generated in metagenomic projects the prediction of the taxonomic origin of the genomic fragments composing a metagenomic sample is still a challenging issue in computational biology. In this talk, a novel strategy for the taxonomic classification of metagenomic sequence data will be presented.


Wednesday 9th December

Greg Gamble - Department of Medicine

Title: “Workflows I have metâ€



Scott Family trust PhD Scholarship

26th August 2009

Title: Mapping ocean biogeography for ecosystem assessments, MPA network planning, and predicting climate change effect.

Full description of the scholarship can be download here

News

4th August 2009

Bioinformatics Summer Studentships - Closed!


The Bioinformatics Institute is once again offering summer studentships to undergraduate students who are enrolled in a BSc (Bioinformatics) and BSc (Hons). The scholarships provide funding over the summer break and a chance to experience real applications of Bioinformatics data. Students are invited to submit an academic CV (non-official) and to nominate the project they would be interested in undertaking (email Emma Marks at e.marks@auckland.ac.nz). Applications close on the 4th of Sept at 5pm. Notification of acceptance will be made via email in late September.

List of summer pojects can be download here Summer Studentship Projects 2009


4th August 2009

Here are some recent publications from members of the Bioinformatics Institute!

- Abbott, W. G. H.,Tsai, P.,Leung, E., Trevarton, A., ‘Ofanoa, M., Hornell, J., Gane, E. J., Munn, S.R., andRodrigo, A. G.(In press) Associations between HLA Class I Alleles and Escape Mutations in the Hepatitis B Virus Core Gene in New Zealand-Resident Tongans. Journal of Virology

- Rambaut, A; Ho, SYW;Drummond, AJ.Accommodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories. MOLECULAR BIOLOGY AND EVOLUTION, 26 (2): 245-248 FEB 2009. Full text

- Atkinson, QD; Gray, RD;Drummond, AJ.Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 276 (1655): 367-373 JAN 22 2009. Full text

- Gray, RD;Drummond, AJ;Greenhill, SJ. Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement. SCIENCE, 323 (5913): 479-483 JAN 23 2009. Full text

-Marks E. J., Rodrigo A. G.& Brunton D. H (In press). Ecstatic Display Calls of the Adélie penguin honestly predict male condition and breeding success. Behaviour.

-Wu, S.H.,Black, M.A., North, R. A., Atkinson, K.,R. andRodrigo, A. G.(In press). A statistical model to identify differentially expressed proteins in 2D PAGE gels. PLoS Comp. Biol.

- Marion Blumenstein1, Michael T. McMaster, Michael A. Black,Steven Wu,Roneel Prakash, Janine Cooney, Lesley M. E. McCowan, Garth J. S. Cooper and Robyn A. North. A proteomic approach identifies early pregnancy biomarkers for preeclampsia: Novel linkages between a predisposition to preeclampsia and cardiovascular disease. Proteomic

-Hayward, J. H.andRodrigo, A. G.(In press). Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus). Veterinary Immunology and Immunopathology

-Rodrigo, A. G.(2009) The coalescent. In The Phylogenetics Handbook 2nd Edition (eds. Salemi, M., Vandamme A.M, and Lemey, P). Cambridge University Press.

-Langhoff, P.,Authier, A., Buckley, T. R., Dugdale, J. S.,Rodrigo, A., and Newcomb, R.D. (In press). DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix. Molecular Ecology Notes. Full text

-Rodrigo, A. G., Tsai, P.,andShearman, H.2009. On the Use of Bootstrapped Topologies in Coalescent-Based Bayesian McMc Inference: A Comparison of Estimation and Computational Efficiencies. Evolutionary Bioinformatics 5:97-105. Full text

- Gillman, L. N., D. J. Keeling,H. A. Ross,and S. D. Wright. (In press). Latitude, elevation and the tempo of molecular evolution in mammals. Proceedings of the Royal Society B-Biological Sciences.

- Wright, S. D., L. N. Gillman,H. A. Ross,and D. J. Keeling. (In press). Slower tempo of microevolution in island birds: implications for conservation biology. Evolution.

- Anderson, M. G.,H. A. Ross,D. H. Brunton, and M. E. Hauber. (In press). Begging call matching between a specialist brood parasite and its host: A comparative approach to detect co-evolution. Biological Journal of the Linnean Society.

 Featured Research
Wai Lok, Sibon LiWai Lok, Sibon Li

My research focuses on the application of between-species genome comparisons, phylogenetics (the study of organism relationships using trees) and evolutionary concepts to solving common biological problems. The focus is in developing methods of computation biology that facilitate and reduce the need for costly, exhaustive laboratory procedures. Our study also includes finding correlations and patterns amongst genome comparisons, in order to further understand the dynamics of evolutionary divergence. Computer software is developed so biologists can apply our methods to their own genome datasets.

The identification of selection in different regions of the genome may indicate important functional constraints. Detecting lineage-specific and gene-specific selection provides a picture of the adaptive evolutionary history of the species in question. We have defined a method of detecting lineage-specific selection on a genomic scale using phylogenetic analysis and demonstrate its use through its application to a set of vertebrate sequences.

Rates of DNA substitution vary across sites, genes and lineages. The evolutionary rate experienced by a protein-coding gene may be increased through bursts of adaptive change or decreased by strong structural or functional constraints on the coded protein. We investigated the hypothesis that the patterns of variation of evolutionary divergence correlate to the biological processes in which the genes are involved. Given this assumption is true, characteristics of the divergence can provide us information to classify genes to their underlying biological processes. We outlined a novel procedure for identifying the biological pathways to which a gene belongs based on profiling the pattern of lineage-specific rate variation from gene sequence data. We demonstrated that the pattern of lineage-specific substitution rates can be used to identify the biological processes that a gene is involved in.
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