Publication Date: 2008 Dec 2 PMID: 19050036br/Authors: Kuk, A. Y. - Zhang, H. - Yang, Y.br/Journal: Bioinformaticsbr/br/MOTIVATION: Pooling large number of DNA samples is a common practice in association study, especially for initial screening. However, the use of EM type algorithms in estimating haplotype distributions for even moderate pool sizes is hampered by the computational complexity involved. A novel constrained EM algorithm called PoooL has been proposed recently to bypass the difficulty via the use of asymptotic normality of the pooled allele frequencies. The resulting estimates are, however, not maximum likelihood estimates and hence not optimal. Furthermore, the assumption of Hardy-Weinberg equilibrium (HWE) made may not be realistic in practice. METHODS: Rather than carrying out constrained maximization as in PoooL, we revert to the usual EM algorithm but make it computationally feasible by using normal approximations. The resulting algorithm is much simpler to implement than PoooL because there is no need to invoke sophisticated iterative scaling methods as in PoooL. We also develop an estimating equation analogue of the EM algorithm for the case of Hardy-Weinberg disequilbrium (HWD) by conditioning on the haplotypes of both chromosomes of the same individual. Incorporated into the method is a way of estimating the inbreeding coefficient by relating it to overdispersion. RESULTS: Simulation study assuming HWE shows that our simplified implementation of the EM algorithm leads to estimates with substantially smaller standard deviations than PoooL estimates. Further simulations show that ignoring HWD will induce biases in the estimates. Our extended method with estimation of inbreeding coefficient incorporated is able to reduce the bias leading to estimates with substantially smaller mean square errors. We also present results to suggest that our method can cope with a certain degree of locus specific inbreeding as well as additional overdispersion not caused by inbreeding. AVAILABILITY: http://staff.ustc.edu.cn/~ynyang/aem-aes CONTACT: stakuka@nus.edu.sg, ynyang@ustc.edu.cn.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19050036title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Nov 27 PMID: 19051389br/Authors: Sanderson, K.br/Journal: Naturebr/br/br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19051389title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 3 PMID: 19050713br/Authors: Kretzschmar, H.br/Journal: Nat Rev Neuroscibr/br/Brain banks collect post-mortem human brains to foster research into human CNS function and disease. They have been indispensable for uncovering the secrets of many diseases, including Alzheimer's and Parkinson's. At a time when there are so many open questions in neuroscience and the incidence of brain diseases continues to increase in parallel with the aging of the population, brain banking remains at the heart of brain research. However, the major source of brain banks, the clinical autopsy, is rapidly falling into limbo. New strategies, including donor programmes, medico-legal autopsies and banking in networks, as well as fresh considerations of the ethics and public relations, are required.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19050713title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 2 PMID: 19050035br/Authors: Wabnik, K. - Hvidsten, T. R. - Kedzierska, A. - Van Leene, J. - De Jaeger, G. - Beemster, G. T. - Komorowski, J. - Kuiper, M. T.br/Journal: Bioinformaticsbr/br/MOTIVATION: Genome-scale 'omics' data constitutes a potentially rich source of information about biological systems and their function. There is a plethora of tools and methods available to mine omics data. However, the diversity and complexity of different omics data types is a stumbling block for multi-data integration, hence there is a dire need for additional methods to exploit potential synergy from integrated orthogonal data. Rough Sets provide an efficient means to use complex information in classification approaches. Here, we set out to explore the possibilities of Rough Sets to incorporate diverse information sources in a functional classification of unknown genes. RESULTS: We explored the use of Rough Sets for a novel data integration strategy where gene expression data, protein features, and GO annotations were combined to describe general and biologically relevant patterns represented by If-Then rules. The descriptive rules were used to predict the function of unknown genes in Arabidopsis thaliana and Schizosaccharomyces pombe. The If-Then rule models showed success rates of up to 0.89 (discriminative and predictive power for both modeled organisms) whereas models built solely of one data type (protein features or gene expression data) yielded success rates varying from 0.68 to 0.78. Our models were applied to generate classifications for many unknown genes, of which a sizeable number were confirmed either by PubMed literature reports or electronically interfered annotations. Finally, we studied cell cycle protein-protein interactions derived from both tandem affinity purification (TAP) experiments and in silico experiments in the BioGRID interactome database and found strong experimental evidence for the predictions generated by our models. The results show that our approach can be used to build very robust models that create synergy from integrating gene expression data and protein fea-tures. AVAILABILITY: The Rough Set-based method is implemented in the Rosetta toolkit kernel version 1.0.1 available at: http://rosetta.lcb.uu.se/ CONTACT: kuiper@nt.ntnu.no; krwab@psb.ugent.be SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19050035title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 3 PMID: 19050712br/Authors: Fletcher, P. C. - Frith, C. D.br/Journal: Nat Rev Neuroscibr/br/Advances in cognitive neuroscience offer us new ways to understand the symptoms of mental illness by uniting basic neurochemical and neurophysiological observations with the conscious experiences that characterize these symptoms. Cognitive theories about the positive symptoms of schizophrenia - hallucinations and delusions - have tended to treat perception and belief formation as distinct processes. However, recent advances in computational neuroscience have led us to consider the unusual perceptual experiences of patients and their sometimes bizarre beliefs as part of the same core abnormality - a disturbance in error-dependent updating of inferences and beliefs about the world. We suggest that it is possible to understand these symptoms in terms of a disturbed hierarchical Bayesian framework, without recourse to separate considerations of experience and belief.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19050712title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 3 PMID: 19050711br/Authors: Leppanen, J. M. - Nelson, C. A.br/Journal: Nat Rev Neuroscibr/br/Humans in different cultures develop a similar capacity to recognize the emotional signals of diverse facial expressions. This capacity is mediated by a brain network that involves emotion-related brain circuits and higher-level visual-representation areas. Recent studies suggest that the key components of this network begin to emerge early in life. The studies also suggest that initial biases in emotion-related brain circuits and the early coupling of these circuits and cortical perceptual areas provide a foundation for a rapid acquisition of representations of those facial features that denote specific emotions.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19050711title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Nov 20 PMID: 19046974br/Authors: Pathuri, P. - Nguyen, E. T. - Ozorowski, G. - Svard, S. G. - Luecke, H.br/Journal: J Mol Biolbr/br/Alpha-14 giardin (annexin E1), a member of the alpha giardin family of annexins, has been shown to localize to the flagella of the intestinal protozoan parasite Giardia lamblia. Alpha giardins show a common ancestry with the annexins, a family of proteins most of which bind to phospholipids and cellular membranes in a Ca(2+)-dependent manner and are implicated in numerous membrane-related processes including cytoskeletal rearrangements and membrane organization. It has been proposed that alpha-14 giardin may play a significant role during the cytoskeletal rearrangement during differentiation of Giardia. To gain a better understanding of alpha-14 giardin's mode of action and its biological role, we have determined the three-dimensional structure of alpha-14 giardin and its phospholipid-binding properties. Here, we report the apo crystal structure of alpha-14 giardin determined in two different crystal forms as well as the Ca(2+)-bound crystal structure of alpha-14 giardin, refined to 1.9, 1.6 and 1.65 A, respectively. Although the overall fold of alpha-14 giardin is similar to that of alpha-11 giardin, multiwavelength anomalous dispersion phasing was required to solve the alpha-14 giardin structure, indicating significant structural differences between these two members of the alpha giardin family. Unlike most annexin structures, which typically possess N-terminal domains, alpha-14 giardin is composed of only a core domain, followed by a C-terminal extension that may serve as a ligand for binding to cytoskeletal protein partners in Giardia. In the Ca(2+)-bound structure we detected five bound calcium ions, one of which is a novel, highly coordinated calcium-binding site not previously observed in annexin structures. This novel high-affinity calcium-binding site is composed of seven protein donor groups, a feature rarely observed in crystal structures. In addition, phospholipid-binding assays suggest that alpha-14 giardin exhibits calcium-dependent binding to phospholipids that coordinate cytoskeletal disassembly/assembly during differentiation of the parasite.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046974title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 1 PMID: 19046436br/Authors: Su, S. Y. - White, J. - Balding, D. J. - Coin, L. J.br/Journal: BMC Bioinformaticsbr/br/ABSTRACT: BACKGROUND: The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals. Partial polyploidy is sometimes observed in humans (e.g. trisomy 21; Down's syndrome), and it arises more frequently in some human tissues. Local changes in ploidy, known as copy number variations (CNV), arise throughout the genome. Here we present a method, implemented in the software polyHap, for the inference of haplotype phase and missing observations from polyploid genotypes. RESULTS: PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences. In the simulation study, we combine real haplotype data to create artificial diploid, triploid, and tetraploid genotypes, and use these to demonstrate that polyHap performs well, in terms of both switch error rate in recovering phase and imputation error rate for missing genotypes. To our knowledge, there is no comparable software for phasing a large, densely genotyped region of chromosome from triploids and tetraploids, while for diploids we found polyHap to be more accurate than fastPhase. We also compare the results of polyHap to SATlotyper on an experimentally haplotyped tetraploid dataset of 12 SNPs, and show polyHap is more accurate. With the availability of large SNP data in polyploids and CNV regions, CONCLUSIONS: We believe that polyHap, our proposed method for inferring haplotypic phase from genotype data, will be useful in enabling researchers analysing such data to exploit the power of haplotype-based analyses.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046436title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Nov 20 PMID: 19046973br/Authors: Synowsky, S. A. - van Wijk, M. - Raijmakers, R. - Heck, A. J.br/Journal: J Mol Biolbr/br/Here we combined tandem affinity purification with several mass-spectrometry-based approaches to gain more insight into the composition and structure of the yeast nuclear-cytoplasmic exosome protein complex. The yeast exosome fulfills several different functions in RNA metabolism and can be localized in both the cytoplasm and the nucleus. These two exosome complexes differ in protein composition, although they share several constituents. We focused on these differences in composition by selecting a nuclear-specific exosome protein (Rrp6) and a cytoplasmic-specific protein (Ski7) as the tandem-affinity-purification-tagged affinity bait protein. First, we investigated both these purified exosome assemblies by macromolecular mass spectrometry (MS) to determine the stability and mass of the intact protein complexes and to obtain information on composition and core constituents. We used tandem MS on these intact protein complexes to further probe the composition and to obtain insight into the peripheral nature of some of the constituents. Finally, we combine stable isotope labeling with MS to quantitate differences in exosome composition and their posttranslational modifications. We identified a few phosphorylation sites that are differentially regulated between the cytoplasmic exosome and the nuclear exosome. From all of these data, we conclude that the yeast nuclear exosome and the cytoplasmic exosome share a common stable core complex, but are decorated with quite a few differing peripheral proteins. We show that the nuclear exosome selectively copurifies with the alpha/beta importin heterodimer, which is known to be involved in the transport of proteins across the nuclear membrane.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046973title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 1 PMID: 19046434br/Authors: Blangiardo, M. - Richardson, S.br/Journal: BMC Bioinformaticsbr/br/ABSTRACT: BACKGROUND: In gene expression studies a key role is played by the so called ;;pre-processing'', a series of steps designed to extract the signal and account for the sources of variability due to the technology used rather than to biological differences between the RNA samples. At the moment there is no commonly agreed gold standard pre-processing method and each researcher has the responsibility to choose one method, incurring the risk of false positive and false negative features arising from the particular method chosen. RESULTS: We propose a Bayesian calibration model that makes use of the information provided by several pre-processing methods and we show that this model gives a better assessment of the ;true' unknown differential expression between two conditions. We demonstrate how to estimate the posterior distribution of the differential expression values of interest from the combined information. CONCLUSIONS: On simulated data and on the spike-in Latin Square dataset from Affymetrix the Bayesian calibration model proves to have more power than each pre-processing method. Its biological interest is demonstrated through an experimental example on publicly available data.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046434title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 1 PMID: 19046431br/Authors: Oscamou, M. - McDonald, D. - Yap, V. B. - Huttley, G. A. - Lladser, M. E. - Knight, R.br/Journal: BMC Bioinformaticsbr/br/ABSTRACT: BACKGROUND: The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include counting sequence differences and taking the log of the resulting probability matrices, methods based on Markov triples, and maximum likelihood methods that infer the substitution probabilities that lead to the most likely model of evolution. However, the speed and accuracy of these methods has not been compared. RESULTS: Different methods differ in performance by orders of magnitude (ranging from 1 ms to 10 s per matrix), but differences in accuracy of rate matrix reconstruction appear to be relatively small. Encouragingly, relatively simple and fast methods can provide results at least as accurate as far more complex and computationally intensive methods, especially when the sequences to be compared are relatively short. CONCLUSIONS: Based on the conditions tested, we recommend the use of method of Gojobori et al. (1982) for long sequences (300 nucleotides), and the method of Goldman et al. (1996) for shorter sequences (300 nucleotides). The method of Barry and Hartigan (1987) can provide somewhat more accuracy, measured as the Euclidean distance between the true and inferred matrices, on long sequences (2000 nucleotides) at the expense of substantially longer computation time. The availability of methods that are both fast and accurate will allow us to gain a global picture of change in the nucleotide substitution rate matrix on a genomewide scale across the tree of life.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046431title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 1 PMID: 19046430br/Authors: Liu, B. - Wang, X. - Lin, L. - Dong, Q. - Wang, X.br/Journal: BMC Bioinformaticsbr/br/ABSTRACT: BACKGROUND: Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences. RESULTS: In this paper, a novel building block of proteins called Top-n-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-n-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-n-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-n-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-n-grams and LSA gives significantly better results compared to related methods. CONCLUSIONS: The method based on Top-n-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-n-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046430title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 1 PMID: 19046422br/Authors: Naiser, T. - Kayser, J. - Mai, T. - Michel, W. - Ott, A.br/Journal: BMC Bioinformaticsbr/br/ABSTRACT: BACKGROUND: The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study. RESULTS: We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results. CONCLUSIONS: Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046422title=Entrez+PubmedCiteULike/a