http://en.redtram.com/ News on "Science & Education"  everywhere Copyright (c) 2009 RedTram. All rights reserved. webmaster@redtram.com (RedTram) en Sat, 07 Nov 2009 15:11:11 GMT 300 100 50 http://en.redtram.com/ http://img.en.redtram.com/rsslogo.gif 50445 | MLwiN 2.15 and MLwiN Forum http://en.redtram.com/go/229209969/top100/ 229209969 We have now released MLwiN 2.15. Some bugs have been fixed, e.g. we have fixed a potential error when reading worksheets containing column descriptions. Further details about MLwiN 2.1 bug fixes go to our bugs page www.cmm.bristol.ac.uk/MLwiN/bugs/fixes.shtmlAlso! We are delighted Sat, 07 Nov 2009 14:21:17 GMT http://en.redtram.com/go/229209969/top100/ 55357 | Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways http://en.redtram.com/go/229209705/top100/ 229209705 Motivation: Systematic analysis of connection between proteins, their cellular function and phenotypic manifestations in disease is a central problem of biological and clinical research. The solution to this problem requires the development of new approaches to link the rapidly growing Sat, 07 Nov 2009 14:13:03 GMT http://en.redtram.com/go/229209705/top100/ 55357 | De novo computational prediction of non-coding RNA genes in prokaryotic genomes http://en.redtram.com/go/229209704/top100/ 229209704 Motivation: The computational identification of non-coding RNA (ncRNA) genes represents one of the most important and challenging problems in computational biology. Existing methods for ncRNA gene prediction rely mostly on homology information, thus limiting their applications to ncRNA genes with Sat, 07 Nov 2009 14:12:58 GMT http://en.redtram.com/go/229209704/top100/ 55357 | Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer http://en.redtram.com/go/229209703/top100/ 229209703 Motivation: The molecular complexity of a tumor manifests itself at the genomic, epigenomic, transcriptomic and proteomic levels. Genomic profiling at these multiple levels should allow an integrated characterization of tumor etiology. However, there is a shortage of effective statistical and Sat, 07 Nov 2009 14:12:53 GMT http://en.redtram.com/go/229209703/top100/ 55357 | Predicting homologous signaling pathways using machine learning http://en.redtram.com/go/229209702/top100/ 229209702 Motivation: In general, each cell signaling pathway involves many proteins, each with one or more specific roles. As they are essential components of cell activity, it is important to understand how these proteins work—and in particular, to determine which of Sat, 07 Nov 2009 14:12:50 GMT http://en.redtram.com/go/229209702/top100/ 55357 | Understanding hydrogen-bond patterns in proteins using network motifs http://en.redtram.com/go/229209701/top100/ 229209701 Summary: Protein structures can be viewed as networks of contacts (edges) between amino-acid residues (nodes). Here we dissect proteins into sub-graphs consisting of six nodes and their corresponding edges, with an edge being either a backbone hydrogen bond (H-bond) or Sat, 07 Nov 2009 14:12:46 GMT http://en.redtram.com/go/229209701/top100/ 55357 | A boosting approach to structure learning of graphs with and without prior knowledge http://en.redtram.com/go/229209700/top100/ 229209700 Motivation: Identifying the network structure through which genes and their products interact can help to elucidate normal cell physiology as well as the genetic architecture of pathological phenotypes. Recently, a number of gene network inference tools have appeared based on Sat, 07 Nov 2009 14:12:43 GMT http://en.redtram.com/go/229209700/top100/ 55357 | Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics http://en.redtram.com/go/229209699/top100/ 229209699 Motivation: Regulation of gene expression is fundamental to the operation of a cell. Revealing the structure and dynamics of a gene regulatory network (GRN) is of great interest and represents a considerably challenging computational problem. The GRN estimation problem is Sat, 07 Nov 2009 14:12:38 GMT http://en.redtram.com/go/229209699/top100/ 55357 | Identification of genes involved in the same pathways using a Hidden Markov Model-based approach http://en.redtram.com/go/229209698/top100/ 229209698 Motivation: The sequencing of whole genomes from various species has provided us with a wealth of genetic information. To make use of the vast amounts of data available today it is necessary to devise computer-based analysis techniques. Sat, 07 Nov 2009 14:12:35 GMT http://en.redtram.com/go/229209698/top100/ 55357 | Mining gene functional networks to improve mass-spectrometry-based protein identification http://en.redtram.com/go/229209697/top100/ 229209697 Motivation: High-throughput protein identification experiments based on tandem mass spectrometry (MS/MS) often suffer from low sensitivity and low-confidence protein identifications. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there Sat, 07 Nov 2009 14:12:32 GMT http://en.redtram.com/go/229209697/top100/ 55357 | Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach http://en.redtram.com/go/229209696/top100/ 229209696 Motivation: The existing supervised methods for biological network inference work on each of the networks individually based only on intra-species information such as gene expression data. We believe that it will be more effective to use genomic data and cross-species Sat, 07 Nov 2009 14:12:26 GMT http://en.redtram.com/go/229209696/top100/ 55357 | Improving peptide identification with single-stage mass spectrum peaks http://en.redtram.com/go/229209693/top100/ 229209693 Motivation: Database searching is the major peptide identification method in shotgun proteomics. It searches tandem mass spectrometry (MS/MS) spectra against a protein database to identify target peptides. The success of such a database searching method relies on a scoring algorithm Sat, 07 Nov 2009 14:12:20 GMT http://en.redtram.com/go/229209693/top100/ 55357 | Metabolite and reaction inference based on enzyme specificities http://en.redtram.com/go/229209691/top100/ 229209691 Motivation: Many enzymes are not absolutely specific, or even promiscuous: they can catalyze transformations of more compounds than the traditional ones as listed in, e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity Sat, 07 Nov 2009 14:12:18 GMT http://en.redtram.com/go/229209691/top100/ 55357 | A dictionary to identify small molecules and drugs in free text http://en.redtram.com/go/229209688/top100/ 229209688 Motivation: From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has Sat, 07 Nov 2009 14:12:15 GMT http://en.redtram.com/go/229209688/top100/ 55357 | Characterization of 1H NMR spectroscopic data and the generation of synthetic validation sets http://en.redtram.com/go/229209685/top100/ 229209685 Motivation: Common contemporary practice within the nuclear magnetic resonance (NMR) metabolomics community is to evaluate and validate novel algorithms on empirical data or simplified simulated data. Empirical data captures the complex characteristics of experimental data, but the optimal or most Sat, 07 Nov 2009 14:12:11 GMT http://en.redtram.com/go/229209685/top100/ 55357 | Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks http://en.redtram.com/go/229209683/top100/ 229209683 Motivation: The highly coordinated expression of thousands of genes in an organism is regulated by the concerted action of transcription factors, chromatin proteins and epigenetic mechanisms. High-throughput experimental data for genome wide in vivo protein-DNA interactions and epigenetic marks are Sat, 07 Nov 2009 14:12:08 GMT http://en.redtram.com/go/229209683/top100/ 55357 | Mobyle: a new full web bioinformatics framework http://en.redtram.com/go/229209681/top100/ 229209681 Motivation: For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using Sat, 07 Nov 2009 14:12:05 GMT http://en.redtram.com/go/229209681/top100/ 55357 | A method for visualizing CellML models http://en.redtram.com/go/229209675/top100/ 229209675 Motivation: The Physiome Project was established in 1997 to develop tools to facilitate international collaboration in the physiological sciences and the sharing of biological models and experimental data. The CellML language was developed to represent and exchange mathematical models of Sat, 07 Nov 2009 14:11:59 GMT http://en.redtram.com/go/229209675/top100/ 55357 | Comparative analysis and unification of domain-domain interaction networks http://en.redtram.com/go/229209672/top100/ 229209672 Motivation: Certain protein domains are known to preferentially interact with other domains. Several approaches have been proposed to predict domain-domain interactions, and over nine datasets are available. Our aim is to analyse the coverage and quality of the existing resources, Sat, 07 Nov 2009 14:11:57 GMT http://en.redtram.com/go/229209672/top100/ 55357 | Saint: a lightweight integration environment for model annotation http://en.redtram.com/go/229209668/top100/ 229209668 Summary: Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources. Sat, 07 Nov 2009 14:11:54 GMT http://en.redtram.com/go/229209668/top100/