Neil Saunders

Nature, Vol. 462, No. 7273. (03 December 2009), pp. 656-659. Estimates of the total number of bacterial species1, 2, 3 indicate that existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space represented by this division of life. Indeed, environmental DNA samples have been shown to encode many previously unknown classes of proteins4 and RNAs5. Bioinformatics searches6, 7, 8, 9, 10 of genomic DNA from bacteria commonly identify new noncoding RNAs (ncRNAs)10, 11, 12 such as riboswitches13, 14. In rare instances, RNAs that exhibit more extensive sequence and structural conservation across a wide range of bacteria are encountered15, 16. Given that large structured RNAs are known to carry out complex biochemical functions such as protein synthesis and RNA processing reactions, identifying more RNAs of great size and intricate structure is likely to reveal additional biochemical functions that can be achieved by RNA. We applied an updated... - Neil Saunders

Journal of proteome research (1 December 2009) Methanococcoides burtonii is a cold-adapted methanogenic archaeon from Ace Lake in Antarctica. Methanol and methylamines are the only substrates it can use for carbon and energy. We carried out quantitative proteomics using iTRAQ of M. burtonii cells grown on different substrates (methanol in defined media or trimethylamine in complex media), using techniques that enriched for secreted and membrane proteins in addition to cytoplasmic proteins. By integrating proteomic data with the complete, manually annotated genome sequence of M. burtonii, we were able to gain new insight into methylotrophic metabolism, and the effects of methanol on the cell. Metabolic processing of methanol and methylamines is initiated by methyltransferases specific for each substrate, with multiple paralogs for each of the methyltransferases (similar to other members of the Methanosarcinaceae). In M. burtonii, most methyltransferases appear to have distinct roles in... - Neil Saunders

Neil, great post. And you're right, we do make things too complicated sometimes, but do we do that at the level at which we ask questions, or at the software implementation level? My take is the latter, cause you need to ask questions the way you want to, but that doesn't mean what makes it all come together has to be one complex mess - Deepak Singh

Normalizing within your own experiments is hard enough, never mind across unrelated datasets. It's something we have to solve though, to make the most of public data. - Neil Saunders

CSIRO scientists have created ‘rogue waves’ more than 20 metres high and smashed them into virtual oil and gas production platforms to compare different mooring designs. - Neil Saunders

BMC Bioinformatics, Vol. 10, No. 1. (2009), 394. BACKGROUND:Experts in peptide:MHC binding studies are often able to estimate the impact of a single residue substitution based on a heuristic understanding of amino acid similarity in an experimental context. Our aim is to quantify this measure of similarity to improve peptide:MHC binding prediction methods. This should help compensate for holes and bias in the sequence space coverage of existing peptide binding datasets. RESULTS:Here, a novel amino acid similarity matrix (PMBEC) is directly derived from the binding affinity data of combinatorial peptide mixtures. Like BLOSUM62, this matrix captures well-known physicochemical properties of amino acid residues. However, PMBEC differs markedly from existing matrices in cases where residue substitution involves a reversal of electrostatic charge. To demonstrate its usefulness, we have developed a new peptide:MHC class I binding prediction method, using the matrix as a Bayesian prior. We... - Neil Saunders

Microbiology and molecular biology reviews : MMBR, Vol. 73, No. 4. (December 2009), pp. 775-808. Type IV secretion systems (T4SS) translocate DNA and protein substrates across prokaryotic cell envelopes generally by a mechanism requiring direct contact with a target cell. Three types of T4SS have been described: (i) conjugation systems, operationally defined as machines that translocate DNA substrates intercellularly by a contact-dependent process; (ii) effector translocator systems, functioning to deliver proteins or other macromolecules to eukaryotic target cells; and (iii) DNA release/uptake systems, which translocate DNA to or from the extracellular milieu. Studies of a few paradigmatic systems, notably the conjugation systems of plasmids F, R388, RP4, and pKM101 and the Agrobacterium tumefaciens VirB/VirD4 system, have supplied important insights into the structure, function, and mechanism of action of type IV secretion machines. Information on these systems is updated, with... - Neil Saunders

Advanced mathematical modelling is significantly improving the performance of unit operations used in the mineral processing industry. - Neil Saunders

We use BerkeleyDB here (key=snp, value=array of genotypes). Last year, Deepak suggested to use HDF5 too http://twitter.com/mndoci... - Pierre Lindenbaum

HDF is nice because scaling up is relatively straightforward, haven't tried BerkeleyDB for comparison though - Mike Chelen

@Mike I just read the doc of HDF5. I understand it is a good choice for storing structured data but it it isn't clear for me how it can be used for querying the data. e.g. find a genotype=f(sample, snp) - Pierre Lindenbaum

What about Array Express? http://www.ebi.ac.uk/microar... - Pawel Szczesny

yes, that too, although they don't import everything from geo - Neil Saunders

In this hands-on lab, you are going to build Flickr example Rails application step by step. - Neil Saunders

A new Division, CSIRO Astronomy and Space Science (CASS), has been formed today bringing together CSIRO's radio astronomy capabilities (the Australia Telescope National Facility), NASA Operations (including the Canberra Deep Space Communication Complex), CSIRO Space Sciences and Technology; and the CSIRO Boeing Advisor. - Neil Saunders