MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Briefings in Bioinformatics' source. Thu, 09 Feb 2012 22:12:26 +0100 http://www.medworm.com/index.php?rid=5657923&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22287794%26dopt%3DAbstract Authors: Wang J, Zhang Y, Marian C, Ressom HW Abstract Many complex diseases such as cancer are associated with changes in biological pathways and molecular networks rather than being caused by single gene alterations. A major challenge in the diagnosis and treatment of such diseases is to identify characteristic aberrancies in the biological pathways and molecular network activities and elucidate their relationship to the disease. This review presents recent progress in using high-throughput biological assays to decipher aberrant pathways and network activities. In particular, this review provides specific examples in which high-throughput data have been applied to identify relationships between diseases and aberrant pathways and network activities. The achievements in this field ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5657923 Fri, 27 Jan 2012 05:00:00 +0100 5657923 http://www.medworm.com/index.php?rid=5620106&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22253280%26dopt%3DAbstract Authors: Carver T, Harris SR, Otto TD, Berriman M, Parkhill J, McQuillan JA Abstract So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence. It is a desktop application for browsing the aligned or mapped reads [Ruffalo, M, LaFramboise, T, Koyutürk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27:2790-6] at different levels of magnification, from nucleotide level, where the base qualities can be seen, to genome or chromosome level where ove... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5620106 Mon, 16 Jan 2012 05:00:00 +0100 5620106 http://www.medworm.com/index.php?rid=5598285&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22247263%26dopt%3DAbstract Authors: Capriotti E, Nehrt NL, Kann MG, Bromberg Y Abstract An international consortium released the first draft sequence of the human genome 10 years ago. Although the analysis of this data has suggested the genetic underpinnings of many diseases, we have not yet been able to fully quantify the relationship between genotype and phenotype. Thus, a major current effort of the scientific community focuses on evaluating individual predispositions to specific phenotypic traits given their genetic backgrounds. Many resources aim to identify and annotate the specific genes responsible for the observed phenotypes. Some of these use intra-species genetic variability as a means for better understanding this relationship. In addition, several online resources are now dedicated to collecting... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5598285 Fri, 13 Jan 2012 05:00:00 +0100 5598285 http://www.medworm.com/index.php?rid=5577827&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22228511%26dopt%3DAbstract Authors: Flores SC, Bernauer J, Shin S, Zhou R, Huang X Abstract In this article, we review the recent progress in multiresolution modeling of structure and dynamics of protein, RNA and their complexes. Many approaches using both physics-based and knowledge-based potentials have been developed at multiple granularities to model both protein and RNA. Coarse graining can be achieved not only in the length, but also in the time domain using discrete time and discrete state kinetic network models. Models with different resolutions can be combined either in a sequential or parallel fashion. Similarly, the modeling of assemblies is also often achieved using multiple granularities. The progress shows that a multiresolution approach has considerable potential to continue extending the leng... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5577827 Fri, 06 Jan 2012 05:00:00 +0100 5577827 http://www.medworm.com/index.php?rid=5577828&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22223742%26dopt%3DAbstract We present an update to the Bio2RDF Linked Data Network, which now comprises ∼30 billion statements across 30 data sets. Significant changes to the framework include the accommodation of global mirrors, offline data processing and new search and integration services. The utility of this new network of knowledge is illustrated through a Bio2RDF-based mashup with microarray gene expression results and interaction data obtained from the HIV-1, Human Protein Interaction Database (HHPID) with respect to the infection of human macrophages with the human immunodeficiency virus type 1 (HIV-1). PMID: 22223742 [PubMed - in process] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5577828 Sun, 01 Jan 2012 05:00:00 +0100 5577828 http://www.medworm.com/index.php?rid=5559362&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22210854%26dopt%3DAbstract Authors: McCall MN, Almudevar A Abstract Affymetrix GeneChip microarrays are the most widely used high-throughput technology to measure gene expression, and a wide variety of preprocessing methods have been developed to transform probe intensities reported by a microarray scanner into gene expression estimates. There have been numerous comparisons of these preprocessing methods, focusing on the most common analyses-detection of differential expression and gene or sample clustering. Recently, more complex multivariate analyses, such as gene co-expression, differential co-expression, gene set analysis and network modeling, are becoming more common; however, the same preprocessing methods are typically applied. In this article, we examine the effect of preprocessing methods on some of... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5559362 Fri, 30 Dec 2011 05:00:00 +0100 5559362 http://www.medworm.com/index.php?rid=5548169&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22199378%26dopt%3DAbstract We present the framework both in matrix algebra as well as in more insightful geometrical terms. We show the workings of the different special cases of our framework with a real-life metabolomics example from nutritional research and a gene-expression example from the field of virology. PMID: 22199378 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5548169 Fri, 23 Dec 2011 05:00:00 +0100 5548169 http://www.medworm.com/index.php?rid=5548168&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22199379%26dopt%3DAbstract Authors: Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M Abstract Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative genome assembler. These applications have been used to assemble and analyze dozens of genomes ranging in complexity from simple microbial species through mammalian genomes. Recent efforts have been focused on enhancing support for new data characteristics brought on by second- and now third-generation sequencing. This review ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5548168 Fri, 23 Dec 2011 05:00:00 +0100 5548168 http://www.medworm.com/index.php?rid=5548167&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22199380%26dopt%3DAbstract Authors: Allen JD, Wang S, Chen M, Girard L, Minna JD, Xie Y, Xiao G Abstract Access to gene expression data has become increasingly common in recent years; however, analysis has become more difficult as it is often desirable to integrate data from different platforms. Probe mapping across microarray platforms is the first and most crucial step for data integration. In this article, we systematically review and compare different approaches to map probes across seven platforms from different vendors: U95A, U133A and U133 Plus 2.0 from Affymetrix, Inc.; HT-12 v1, HT-12v2 and HT-12v3 from Illumina, Inc.; and 4112A from Agilent, Inc. We use a unique data set, which contains 56 lung cancer cell line samples-each of which has been measured by two different microarray platforms-to evaluat... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5548167 Fri, 23 Dec 2011 05:00:00 +0100 5548167 http://www.medworm.com/index.php?rid=5531748&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155641%26dopt%3DAbstract Authors: Krzywinski M, Birol I, Jones SJ, Marra MA Abstract Networks are typically visualized with force-based or spectral layouts. These algorithms lack reproducibility and perceptual uniformity because they do not use a node coordinate system. The layouts can be difficult to interpret and are unsuitable for assessing differences in networks. To address these issues, we introduce hive plots (http://www.hiveplot.com) for generating informative, quantitative and comparable network layouts. Hive plots depict network structure transparently, are simple to understand and can be easily tuned to identify patterns of interest. The method is computationally straightforward, scales well and is amenable to a plugin for existing tools. PMID: 22155641 [PubMed - as supplied by publisher] (S... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5531748 Fri, 09 Dec 2011 05:00:00 +0100 5531748 http://www.medworm.com/index.php?rid=5492756&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22138322%26dopt%3DAbstract Authors: Guzzi PH, Mina M, Guerra C, Cannataro M Abstract The integration of proteomics data with biological knowledge is a recent trend in bioinformatics. A lot of biological information is available and is spread on different sources and encoded in different ontologies (e.g. Gene Ontology). Annotating existing protein data with biological information may enable the use (and the development) of algorithms that use biological ontologies as framework to mine annotated data. Recently many methodologies and algorithms that use ontologies to extract knowledge from data, as well as to analyse ontologies themselves have been proposed and applied to other fields. Conversely, the use of such annotations for the analysis of protein data is a relatively novel research area that is currently ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5492756 Fri, 02 Dec 2011 05:00:00 +0100 5492756 http://www.medworm.com/index.php?rid=5492755&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22138323%26dopt%3DAbstract Authors: Duverle DA, Mamitsuka H Abstract A fundamental component of systems biology, proteolytic cleavage is involved in nearly all aspects of cellular activities: from gene regulation to cell lifecycle regulation. Current sequencing technologies have made it possible to compile large amount of cleavage data and brought greater understanding of the underlying protein interactions. However, the practical impossibility to exhaustively retrieve substrate sequences through experimentation alone has long highlighted the need for efficient computational prediction methods. Such methods must be able to quickly mark substrate candidates and putative cleavage sites for further analysis. Available methods and expected reliability depend heavily on the type and complexity of proteolytic acti... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5492755 Fri, 02 Dec 2011 05:00:00 +0100 5492755 http://www.medworm.com/index.php?rid=5492754&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22138324%26dopt%3DAbstract Authors: Zhao X, Tong C, Pang X, Wang Z, Guo Y, Du F, Wu R Abstract All organisms face the problem of how to perform a sequence of developmental changes and transitions during ontogeny. We revise functional mapping, a statistical model originally derived to map genes that determine developmental dynamics, to take into account the entire process of ontogenetic growth from embryo to adult and from the vegetative to reproductive phase. The revised model provides a framework that reconciles the genetic architecture of development at different stages and elucidates a comprehensive picture of the genetic control mechanisms of growth that change gradually from a simple to a more complex level. We use an annual flowering plant, as an example, to demonstrate our model by which to map genes ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5492754 Fri, 02 Dec 2011 05:00:00 +0100 5492754 http://www.medworm.com/index.php?rid=5474177&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22110242%26dopt%3DAbstract Authors: Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C Abstract Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes a... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5474177 Tue, 22 Nov 2011 05:00:00 +0100 5474177 http://www.medworm.com/index.php?rid=5439055&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22101028%26dopt%3DAbstract Authors: Romano P, Giugno R, Pulvirenti A PMID: 22101028 [PubMed - in process] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5439055 Tue, 01 Nov 2011 04:00:00 +0100 5439055 http://www.medworm.com/index.php?rid=5439054&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22101029%26dopt%3DAbstract Authors: Mayne SL, Patterton HG Abstract Multi-subunit protein complexes are involved in many essential biochemical processes including signal transduction, protein synthesis, RNA synthesis, DNA replication and protein degradation. An accurate description of the relative structural arrangement of the constituent subunits in such complexes is crucial for an understanding of the molecular mechanism of the complex as a whole. Many complexes, however, lie in the mega-Dalton range, and are not amenable to X-ray crystallographic or nuclear magnetic resonance analysis. Techniques that are suited to structural studies of such large complexes, such as cryo-electron microscopy, do not provide the resolution required for a mechanistic insight. Mass spectrometry (MS) has increasingly been appl... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5439054 Tue, 01 Nov 2011 04:00:00 +0100 5439054 http://www.medworm.com/index.php?rid=5360845&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22021901%26dopt%3DAbstract Authors: Corrada D, Viti F, Merelli I, Battaglia C, Milanesi L Abstract miRNA target genes prediction represents a crucial step in miRNAs functional characterization. In this context, the challenging issue remains predictions accuracy and recognition of false positive results. In this article myMIR, a web based system for increasing reliability of miRNAs predicted targets lists, is presented. myMIR implements an integrated pipeline for computing ranked miRNA::target lists and provides annotations for narrowing them down. The system relies on knowledge base data, suitably integrated in order to extend the functional characterization of targeted genes to miRNAs, by highlighting the search on over-represented annotation terms. Validation results show a dramatic reduction in the quanti... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5360845 Sat, 22 Oct 2011 04:00:00 +0100 5360845 http://www.medworm.com/index.php?rid=5360846&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22021898%26dopt%3DAbstract Authors: Finotello F, Lavezzo E, Fontana P, Peruzzo D, Albiero A, Barzon L, Falda M, Di Camillo B, Toppo S Abstract Next-generation sequencing technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. In this context, an important issue is the need of a careful assessment of the accuracy of the assembly process. Here, we review the efficiency of a panel of assemblers, specifically designed to handle data from GS FLX 454 platform, on three bacterial data sets with different characteristics in terms of reads coverage and repeats content. Our aim is to investigate their strengths and weaknesses in the reconstruction of the reference genomes. In our benchmarking, we... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5360846 Fri, 21 Oct 2011 04:00:00 +0100 5360846 http://www.medworm.com/index.php?rid=5360847&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22016404%26dopt%3DAbstract Authors: Schlatter R, Philippi N, Wangorsch G, Pick R, Sawodny O, Borner C, Timmer J, Ederer M, Dandekar T Abstract The number of mathematical models for biological pathways is rapidly growing. In particular, Boolean modelling proved to be suited to describe large cellular signalling networks. Systems biology is at the threshold to holistic understanding of comprehensive networks. In order to reach this goal, connection and integration of existing models of parts of cellular networks into more comprehensive network models is necessary. We discuss model combination approaches for Boolean models. Boolean modelling is qualitative rather than quantitative and does not require detailed kinetic information. We show that these models are useful precursors for large-scale quantitative mode... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5360847 Thu, 20 Oct 2011 04:00:00 +0100 5360847 http://www.medworm.com/index.php?rid=5360848&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21984743%26dopt%3DAbstract In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies. PMID: 21984743 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5360848 Fri, 07 Oct 2011 04:00:00 +0100 5360848 http://www.medworm.com/index.php?rid=5296166&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21969471%26dopt%3DAbstract We present how the use of metadata and Semantic Web technologies can effectively help to organize the knowledge generated by modern collaborative research, how these technologies can enable effective data management solutions during and beyond the project lifecycle, and how resources such as the DC-THERA Directory fit into the larger context of e-science. PMID: 21969471 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5296166 Mon, 03 Oct 2011 04:00:00 +0100 5296166 http://www.medworm.com/index.php?rid=5276548&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21949241%26dopt%3DAbstract Authors: Dutheil JY Abstract Positions in a molecule that share a common constraint do not evolve independently, and therefore leave a signature in the patterns of homologous sequences. Exhibiting such positions with a coevolution pattern from a sequence alignment has great potential for predicting functional and structural properties of molecules through comparative analysis. This task is complicated by the existence of additional correlation sources, leading to false predictions. The nature of the data is a major source of noise correlation: sequences are taken from individuals with different degrees of relatedness, and who therefore are intrinsically correlated. This has led to several method developments in different fields that are potentially confusing for non-expert users in... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5276548 Sat, 24 Sep 2011 04:00:00 +0100 5276548 http://www.medworm.com/index.php?rid=5276550&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21949216%26dopt%3DAbstract Authors: Huang N, Shah PK, Li C Abstract Over the last decade, multiple functional genomic datasets studying chromosomal aberrations and their downstream effects on gene expression have accumulated for several cancer types. A vast majority of them are in the form of paired gene expression profiles and somatic copy number alterations (CNA) information on the same patients identified using microarray platforms. In response, many algorithms and software packages are available for integrating these paired data. Surprisingly, there has been no serious attempt to review the currently available methodologies or the novel insights brought using them. In this work, we discuss the quantitative relationships observed between CNA and gene expression in multiple cancer types and biological mile... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5276550 Fri, 23 Sep 2011 04:00:00 +0100 5276550 http://www.medworm.com/index.php?rid=5276549&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21949217%26dopt%3DAbstract Authors: Wang J, Li ZX, Qiu CX, Wang D, Cui QH Abstract Previous analysis of systems pharmacology has revealed a tendency of rational drug design in the pharmaceutical industry. The targets of new drugs tend to be close with the corresponding disease genes in the biological networks. However, it remains unclear whether the rational drug design introduces disadvantages, i.e. side effects. Therefore, it is important to dissect the relationship between rational drug design and drug side effects. Based on a recently released drug side effect database, SIDER, here we analyzed the relationship between drug side effects and the rational drug design. We revealed that the incidence drug side effect is significantly associated with the network distance of drug targets and diseases genes. Dru... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5276549 Fri, 23 Sep 2011 04:00:00 +0100 5276549 http://www.medworm.com/index.php?rid=5276551&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21949215%26dopt%3DAbstract Authors: Zhang L, Udaka K, Mamitsuka H, Zhu S Abstract Binding of short antigenic peptides to major histocompatibility complex (MHC) molecules is a core step in adaptive immune response. Precise identification of MHC-restricted peptides is of great significance for understanding the mechanism of immune response and promoting the discovery of immunogenic epitopes. However, due to the extremely high MHC polymorphism and huge cost of biochemical experiments, there is no experimentally measured binding data for most MHC molecules. To address the problem of predicting peptides binding to these MHC molecules, recently computational approaches, called pan-specific methods, have received keen interest. Pan-specific methods make use of experimentally obtained binding data of multiple allele... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5276551 Thu, 22 Sep 2011 04:00:00 +0100 5276551 http://www.medworm.com/index.php?rid=5245978&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21930656%26dopt%3DAbstract Authors: Benítez-Páez A, Cárdenas-Brito S, Gutiérrez AJ Abstract In recent years, numerous biocomputational tools have been designed to extract functional and evolutionary information from multiple sequence alignments (MSAs) of proteins and genes. Most biologists working actively on the characterization of proteins from a single or family perspective use the MSA analysis to retrieve valuable information about amino acid conservation and the functional role of residues in query protein(s). In MSAs, adjustment of alignment parameters is a key point to improve the quality of MSA output. However, this issue is frequently underestimated and/or misunderstood by scientists and there is no in-depth knowledge available in this field. This brief review focuses on biocomputational approac... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5245978 Mon, 19 Sep 2011 04:00:00 +0100 5245978 http://www.medworm.com/index.php?rid=5218223&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21908864%26dopt%3DAbstract Authors: Li X, Jiang W, Li W, Lian B, Wang S, Liao M, Chen X, Wang Y, Lv Y, Wang S, Yang L Abstract The global insight into the relationships between miRNAs and their regulatory influences remains poorly understood. And most of complex diseases may be attributed to certain local areas of pathway (subpathway) instead of the entire pathway. Here, we reviewed the studies on miRNA regulations to pathways and constructed a bipartite miRNAs and subpathways network for systematic analyzing the miRNA regulatory influences to subpathways. We found that a small fraction of miRNAs were global regulators, environmental information processing pathways were preferentially regulated by miRNAs, and miRNAs had synergistic effect on regulating group of subpathways with similar function. Integrating ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5218223 Sat, 10 Sep 2011 04:00:00 +0100 5218223 http://www.medworm.com/index.php?rid=5218222&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21908865%26dopt%3DAbstract Authors: Boulesteix AL, Bender A, Lorenzo Bermejo J, Strobl C Abstract The use of random forests is increasingly common in genetic association studies. The variable importance measure (VIM) that is automatically calculated as a by-product of the algorithm is often used to rank polymorphisms with respect to their ability to predict the investigated phenotype. Here, we investigate a characteristic of this methodology that may be considered as an important pitfall, namely that common variants are systematically favoured by the widely used Gini VIM. As a consequence, researchers may overlook rare variants that contribute to the missing heritability. The goal of the present article is 3-fold: (i) to assess this effect quantitatively using simulation studies for different types of random... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5218222 Sat, 10 Sep 2011 04:00:00 +0100 5218222 http://www.medworm.com/index.php?rid=5218224&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21900207%26dopt%3DAbstract Authors: Hung JH, Yang TH, Hu Z, Weng Z, Delisi C Abstract A central goal of biology is understanding and describing the molecular basis of plasticity: the sets of genes that are combinatorially selected by exogenous and endogenous environmental changes, and the relations among the genes. The most viable current approach to this problem consists of determining whether sets of genes are connected by some common theme, e.g. genes from the same pathway are overrepresented among those whose differential expression in response to a perturbation is most pronounced. There are many approaches to this problem, and the results they produce show a fair amount of dispersion, but they all fall within a common framework consisting of a few basic components. We critically review these components,... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5218224 Wed, 07 Sep 2011 04:00:00 +0100 5218224 http://www.medworm.com/index.php?rid=5218227&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21896613%26dopt%3DAbstract We describe the choice of a template structure, preparation of input files, and explore three possible modeling strategies. In the end, we evaluate the resulting models using six alternative benchmarks. The ModeRNA software can be freely downloaded from http://iimcb.genesilico.pl/moderna/ under the conditions of the General Public License. It runs under LINUX, Windows and Mac OS. It is also available as a server at http://iimcb.genesilico.pl/modernaserver/. The models and the script to reproduce the study from this article are available at http://www.genesilico.pl/moderna/examples/. PMID: 21896613 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5218227 Tue, 06 Sep 2011 04:00:00 +0100 5218227 http://www.medworm.com/index.php?rid=5192450&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21873635%26dopt%3DAbstract Authors: Gaudet P, Livstone MS, Lewis SE, Thomas PD Abstract The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5192450 Fri, 26 Aug 2011 23:00:00 +0100 5192450 http://www.medworm.com/index.php?rid=5097457&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21803786%26dopt%3DAbstract This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/) and discusses the production and distribution of high-quality tutorial videos, which would be useful to viewer, with examples. This article intends to stimulate and encourage researchers who develop and use databases and tools to distribute how-to videos as a tool to enhance product usability. PMID: 21803786 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5097457 Thu, 28 Jul 2011 23:00:00 +0100 5097457 http://www.medworm.com/index.php?rid=5097444&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21803787%26dopt%3DAbstract This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers. PMID: 21803787 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5097444 Thu, 28 Jul 2011 23:00:00 +0100 5097444 http://www.medworm.com/index.php?rid=5097490&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21798956%26dopt%3DAbstract Authors: Wittek A, Miller K A recent review article on 'Current progress in patient-specific modeling' in Briefings in Bioinformatics contains the statement summarizing the results of our previous study 'On the unimportance of constitutive models in computing brain deformation for image-guided surgery' published in Biomechanics and Modeling in Mechanobiology as confirmation of adequacy of linear elastic model for such computation. The purpose of this Letter to the Editor is to clarify this statement by informing the Readers of Briefings in Bioinformatics that our study indicates the following: (i) a simple linear elastic constitutive model for the brain tissue is sufficient when used with an appropriate finite deformation solution (i.e. geometrically non-linear analysis); and (ii) Line... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5097490 Wed, 27 Jul 2011 23:00:00 +0100 5097490 http://www.medworm.com/index.php?rid=5051353&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21746694%26dopt%3DAbstract We describe a computational framework for clustering the dynamics of gene expression in distinct environments through Gaussian mixture fitting to the expression data measured at a set of discrete time points. We outline a number of quantitative testable hypotheses about the patterns of dynamic gene expression in changing environments and gene-environment interactions causing developmental differentiation. The future directions of gene clustering in terms of incorporations of the latest biological discoveries and statistical innovations are discussed. We provide a set of computational tools that are applicable to modeling and analysis of dynamic gene expression data measured in multiple environments. PMID: 21746694 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5051353 Sat, 09 Jul 2011 23:00:00 +0100 5051353 http://www.medworm.com/index.php?rid=5051354&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21737420%26dopt%3DAbstract Authors: Boeckmann B, Robinson-Rechavi M, Xenarios I, Dessimoz C Phylogenomic databases provide orthology predictions for species with fully sequenced genomes. Although the goal seems well-defined, the content of these databases differs greatly. Seven ortholog databases (Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, Panther) were compared on the basis of reference trees. For three well-conserved protein families, we observed a generally high specificity of orthology assignments for these databases. We show that differences in the completeness of predicted gene relationships and in the phylogenetic information are, for the great majority, not due to the methods used, but to differences in the underlying database concepts. According to our metrics, none of the databases pro... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5051354 Wed, 06 Jul 2011 23:00:00 +0100 5051354 http://www.medworm.com/index.php?rid=5051355&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21737419%26dopt%3DAbstract Authors: Teif VB, Rippe K Current high-throughput experiments already generate enough data for retrieving the DNA sequence-dependent binding affinities of transcription factors (TF) and other chromosomal proteins throughout the complete genome. However, the reverse task of calculating binding maps in a chromatin context for a given set of concentrations and TF affinities appears to be even more challenging and computationally demanding. The problem can be addressed by considering the DNA sequence as a one-dimensional lattice with units of one or more base pairs. To calculate protein occupancies in chromatin, one needs to consider the competition of TF and histone octamers for binding sites as well as the partial unwrapping of nucleosomal DNA. Here, we consider five different classes of... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5051355 Tue, 05 Jul 2011 23:00:00 +0100 5051355 http://www.medworm.com/index.php?rid=5051352&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21768130%26dopt%3DAbstract Authors: Sanseau P, Koehler J PMID: 21768130 [PubMed - in process] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5051352 Thu, 30 Jun 2011 23:00:00 +0100 5051352 http://www.medworm.com/index.php?rid=5051351&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21768131%26dopt%3DAbstract Authors: Moriaud F, Richard SB, Adcock SA, Chanas-Martin L, Surgand JS, Ben Jelloul M, Delfaud F Predicting off-targets by computational methods is gaining increasing interest in early-stage drug discovery. Here, we present a computational method based on full 3D comparisons of 3D structures. When a similar binding site is detected in the Protein Data Bank (PDB) (or any protein structure database), it is possible that the corresponding ligand also binds to that similar site. On one hand, this target hopping case is probably rare because it requires a high similarity between the binding sites. On the other hand, it could be a strong rational evidence to highlight possible off-target reactions and possibly a potential undesired side effect. This target-based drug repurposing can be exten... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5051351 Thu, 30 Jun 2011 23:00:00 +0100 5051351 http://www.medworm.com/index.php?rid=5000810&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21712341%26dopt%3DAbstract In this study, using the genome of a cartilaginous fish, Callorhinchus milii, as test case, we performed gene prediction using a model specifically trained for this genome. We implemented an algorithm, designated ESPRIT, to identify possible linkages between multiple protein-coding portions derived from a single genomic locus split into multiple unassembled genomic segments. We developed a validation framework based on an artificially fragmented human genome, improvements between early and recent mouse genome assemblies, comparison with experimentally validated sequences from GenBank, and phylogenetic analyses. Our strategy provided insights into practical solutions for efficient annotation of only partially sequenced (low-coverage) genomes. To our knowledge, our study is the first formula... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5000810 Tue, 28 Jun 2011 23:00:00 +0100 5000810 http://www.medworm.com/index.php?rid=5000807&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21715466%26dopt%3DAbstract Authors: Swamidass SJ Repurposing and repositioning drugs-discovering new uses for existing and experimental medicines-is an attractive strategy for rescuing stalled pharmaceutical projects, finding treatments for neglected diseases, and reducing the time, cost and risk of drug development. As this strategy emerged, academic researchers began performing high-throughput screens (HTS) of small molecules-the type of experiments once exclusively conducted in industry-and making the data from these screens available to all. Several methods can mine this data to inform repurposing and repositioning efforts. Despite these methods' limitations, it is hopeful that they will accelerate the discovery of new uses for known drugs, but this hope has not yet been realized. PMID: 21715466 [PubMed ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5000807 Tue, 28 Jun 2011 23:00:00 +0100 5000807 http://www.medworm.com/index.php?rid=5000809&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21712342%26dopt%3DAbstract Authors: Andronis C, Sharma A, Virvilis V, Deftereos S, Persidis A The immense growth of MEDLINE coupled with the realization that a vast amount of biomedical knowledge is recorded in free-text format, has led to the appearance of a large number of literature mining techniques aiming to extract biomedical terms and their inter-relations from the scientific literature. Ontologies have been extensively utilized in the biomedical domain either as controlled vocabularies or to provide the framework for mapping relations between concepts in biology and medicine. Literature-based approaches and ontologies have been used in the past for the purpose of hypothesis generation in connection with drug discovery. Here, we review the application of literature mining and ontology modeling and travers... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5000809 Mon, 27 Jun 2011 23:00:00 +0100 5000809 http://www.medworm.com/index.php?rid=5000808&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21712343%26dopt%3DAbstract Authors: Sjölander K, Datta RS, Shen Y, Shoffner GM Ortholog identification is used in gene functional annotation, species phylogeny estimation, phylogenetic profile construction and many other analyses. Bioinformatics methods for ortholog identification are commonly based on pairwise protein sequence comparisons between whole genomes. Phylogenetic methods of ortholog identification have also been developed; these methods can be applied to protein data sets sharing a common domain architecture or which share a single functional domain but differ outside this region of homology. While promiscuous domains represent a challenge to all orthology prediction methods, overall structural similarity is highly correlated with proximity in a phylogenetic tree, conferring a degree of robustness t... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5000808 Mon, 27 Jun 2011 23:00:00 +0100 5000808 http://www.medworm.com/index.php?rid=5000812&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21705405%26dopt%3DAbstract Authors: Wang J, Zhou X, Zhu J, Gu Y, Zhao W, Zou J, Guo Z In high-throughput studies of diseases, terms enriched with disease-related genes based on Gene Ontology (GO) are routinely found. However, most current algorithms used to find significant GO terms cannot handle the redundancy that results from the dependencies of GO terms. Simply based on some numerical considerations, current algorithms developed for reducing this redundancy may produce results that do not account for biologically interesting cases. In this article, we present several rules used to design a tool called GO-function for extracting biologically relevant terms from statistically significant GO terms for a disease. Using one gene expression profile for colorectal cancer, we compared GO-function with four algorithm... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5000812 Thu, 23 Jun 2011 23:00:00 +0100 5000812 http://www.medworm.com/index.php?rid=5000811&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21705766%26dopt%3DAbstract Authors: Dewey CN Orthology is a powerful refinement of homology that allows us to describe more precisely the evolution of genomes and understand the function of the genes they contain. However, because orthology is not concerned with genomic position, it is limited in its ability to describe genes that are likely to have equivalent roles in different genomes. Because of this limitation, the concept of 'positional orthology' has emerged, which describes the relation between orthologous genes that retain their ancestral genomic positions. In this review, we formally define this concept, for which we introduce the shorter term 'toporthology', with respect to the evolutionary events experienced by a gene's ancestors. Through a discussion of recent studies on the role of genomic context i... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5000811 Thu, 23 Jun 2011 23:00:00 +0100 5000811 http://www.medworm.com/index.php?rid=4954607&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21690101%26dopt%3DAbstract Authors: Dudley JT, Deshpande T, Butte AJ Finding new uses for existing drugs, or drug repositioning, has been used as a strategy for decades to get drugs to more patients. As the ability to measure molecules in high-throughput ways has improved over the past decade, it is logical that such data might be useful for enabling drug repositioning through computational methods. Many computational predictions for new indications have been borne out in cellular model systems, though extensive animal model and clinical trial-based validation are still pending. In this review, we show that computational methods for drug repositioning can be classified in two axes: drug based, where discovery initiates from the chemical perspective, or disease based, where discovery initiates from the clinical p... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4954607 Sun, 19 Jun 2011 23:00:00 +0100 4954607 http://www.medworm.com/index.php?rid=4954608&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21690100%26dopt%3DAbstract Authors: Kristensen DM, Wolf YI, Mushegian AR, Koonin EV Accurate inference of orthologous genes is a pre-requisite for most comparative genomics studies, and is also important for functional annotation of new genomes. Identification of orthologous gene sets typically involves phylogenetic tree analysis, heuristic algorithms based on sequence conservation, synteny analysis, or some combination of these approaches. The most direct tree-based methods typically rely on the comparison of an individual gene tree with a species tree. Once the two trees are accurately constructed, orthologs are straightforwardly identified by the definition of orthology as those homologs that are related by speciation, rather than gene duplication, at their most recent point of origin. Although ideal for the ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4954608 Sat, 18 Jun 2011 23:00:00 +0100 4954608 http://www.medworm.com/index.php?rid=4954609&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21677033%26dopt%3DAbstract Authors: Gharib WH, Robinson-Rechavi M Despite the common assumption that orthologs usually share the same function, there have been various reports of divergence between orthologs, even among species as close as mammals. The comparison of mouse and human is of special interest, because mouse is often used as a model organism to understand human biology. We review the literature on evidence for divergence between human and mouse orthologous genes, and discuss it in the context of biomedical research. PMID: 21677033 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4954609 Wed, 15 Jun 2011 23:00:00 +0100 4954609 http://www.medworm.com/index.php?rid=4954612&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21677032%26dopt%3DAbstract Authors: Faro A, Giordano D, Spampinato C A huge amount of important biomedical information is hidden in the bulk of research articles in biomedical fields. At the same time, the publication of databases of biological information and of experimental datasets generated by high-throughput methods is in great expansion, and a wealth of annotated gene databases, chemical, genomic (including microarray datasets), clinical and other types of data repositories are now available on the Web. Thus a current challenge of bioinformatics is to develop targeted methods and tools that integrate scientific literature, biological databases and experimental data for reducing the time of database curation and for accessing evidence, either in the literature or in the datasets, useful for the analysis at ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4954612 Tue, 14 Jun 2011 23:00:00 +0100 4954612 http://www.medworm.com/index.php?rid=4954613&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21666252%26dopt%3DAbstract Authors: Schmitt T, Messina DN, Schreiber F, Sonnhammer EL There is a great need for standards in the orthology field. Users must contend with different ortholog data representations from each provider, and the providers themselves must independently gather and parse the input sequence data. These burdensome and redundant procedures make data comparison and integration difficult. We have designed two XML-based formats, SeqXML and OrthoXML, to solve these problems. SeqXML is a lightweight format for sequence records-the input for orthology prediction. It stores the same sequence and metadata as typical FASTA format records, but overcomes common problems such as unstructured metadata in the header and erroneous sequence content. XML provides validation to prevent data integrity problems ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4954613 Fri, 10 Jun 2011 23:00:00 +0100 4954613 http://www.medworm.com/index.php?rid=4905687&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21622543%26dopt%3DAbstract Authors: Wu M, Chan C The recent advent of high-throughput microarray data has enabled the global analysis of the transcriptome, driving the development and application of computational approaches to study transcriptional regulation on the genome scale, by reconstructing in silico the regulatory interactions of the gene network. Although there are many in-depth reviews of such 'reverse-engineering' methodologies, most have focused on the practical aspect of data mining, and few on the biological problem and the biological relevance of the methodology. Therefore, in this review, from a biological perspective, we used a set of yeast microarray data as a working example, to evaluate the fundamental assumptions implicit in associating transcription factor (TF)-target gene expression levels... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4905687 Wed, 25 May 2011 23:00:00 +0100 4905687 http://www.medworm.com/index.php?rid=4855857&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21565935%26dopt%3DAbstract Authors: Forslund K, Schreiber F, Thanintorn N, Sonnhammer EL Orthology is one of the most important tools available to modern biology, as it allows making inferences from easily studied model systems to much less tractable systems of interest, such as ourselves. This becomes important not least in the study of genetic diseases. We here review work on the orthology of disease-associated genes and also present an updated version of the InParanoid-based disease orthology database and web site OrthoDisease, with 14-fold increased species coverage since the previous version. Using this resource, we survey the taxonomic distribution of orthologs of human genes involved in different disease categories. The hypothesis that paralogs can mask the effect of deleterious mutations predicts that kn... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4855857 Wed, 11 May 2011 23:00:00 +0100 4855857 http://www.medworm.com/index.php?rid=4855856&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21565936%26dopt%3DAbstract Authors: Wang C, Wang Z, Prows DR, Wu R Genetic imprinting, by which the expression of a gene depends on the parental origin of its alleles, may be subjected to reprogramming through each generation. Currently, such reprogramming is limited to qualitative description only, lacking more precise quantitative estimation for its extent, pattern and mechanism. Here, we present a computational framework for analyzing the magnitude of genetic imprinting and its transgenerational inheritance mode. This quantitative model is based on the breeding scheme of reciprocal backcrosses between reciprocal F(1) hybrids and original inbred parents, in which the transmission of genetic imprinting across generations can be tracked. We define a series of quantitative genetic parameters that describe the ext... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4855856 Wed, 11 May 2011 23:00:00 +0100 4855856 http://www.medworm.com/index.php?rid=4803894&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21546447%26dopt%3DAbstract Authors: Boulesteix AL PMID: 21546447 [PubMed - in process] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4803894 Sat, 30 Apr 2011 23:00:00 +0100 4803894 http://www.medworm.com/index.php?rid=4803893&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21546448%26dopt%3DAbstract Authors: König IR Validation of genetic associations is understood to be a cornerstone for the scientific credibility of the results. To approach this topic, the general concept of genetic association studies is introduced briefly, followed by how the term 'validation' is used in the context of genetic association studies. As a central issue, reasons for the importance of validation and for failure of validation will be described. PMID: 21546448 [PubMed - in process] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4803893 Sat, 30 Apr 2011 23:00:00 +0100 4803893 http://www.medworm.com/index.php?rid=4803892&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21546449%26dopt%3DAbstract Authors: Thompson JR, Attia J, Minelli C The pressure to publish novel genetic associations has meant that meta-analysis has been applied to genome-wide association studies without the time for a careful consideration of the methods that are used. This review distinguishes between the use of meta-analysis to validate previously reported genetic associations and its use for gene discovery, and advocates viewing gene discovery as an exploratory screen that requires independent replication instead of treating it as the application of hundreds of thousands of statistical tests. The review considers the use of fixed and random effects meta-analyses, the investigation of between-study heterogeneity, adjustment for confounding, assessing the combined evidence and genomic control, and comments... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4803892 Sat, 30 Apr 2011 23:00:00 +0100 4803892 http://www.medworm.com/index.php?rid=4803895&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21525143%26dopt%3DAbstract Authors: Sun Y, Cai Y, Huse SM, Knight R, Farmerie WG, Wang X, Mai V Recent advances in massively parallel sequencing technology have created new opportunities to probe the hidden world of microbes. Taxonomy-independent clustering of the 16S rRNA gene is usually the first step in analyzing microbial communities. Dozens of algorithms have been developed in the last decade, but a comprehensive benchmark study is lacking. Here, we survey algorithms currently used by microbiologists, and compare seven representative methods in a large-scale benchmark study that addresses several issues of concern. A new experimental protocol was developed that allows different algorithms to be compared using the same platform, and several criteria were introduced to facilitate a quantitative evaluation of ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4803895 Tue, 26 Apr 2011 23:00:00 +0100 4803895 http://www.medworm.com/index.php?rid=4750383&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21515902%26dopt%3DAbstract Authors: Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T Gene duplication is one of the main mechanisms by which genomes can acquire novel functions. It has been proposed that the retention of gene duplicates can be associated to processes of tissue expression divergence. These models predict that acquisition of divergent expression patterns should be acquired shortly after the duplication, and that larger divergence in tissue expression would be expected for paralogs, as compared to orthologs of a similar age. Many studies have shown that gene duplicates tend to have divergent expression patterns and that gene family expansions are associated with high levels of tissue specificity. However, the timeframe in which these processes occur have rarely been investigated in detail, particul... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750383 Thu, 21 Apr 2011 23:00:00 +0100 4750383 http://www.medworm.com/index.php?rid=4750385&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21504985%26dopt%3DAbstract In this study, we will review some of these issues and the current methodologies adopted or proposed to overcome them and translate chemical and biological discoveries into safe and effective orphan disease therapeutics. PMID: 21504985 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750385 Sun, 17 Apr 2011 23:00:00 +0100 4750385 http://www.medworm.com/index.php?rid=4750384&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21504986%26dopt%3DAbstract Authors: Ribeca P, Valiente G Next-generation sequencing technologies have opened up an unprecedented opportunity for microbiology by enabling the culture-independent genetic study of complex microbial communities, which were so far largely unknown. The analysis of metagenomic data is challenging: potentially, one is faced with a sample containing a mixture of many different bacterial species, whose genome has not necessarily been sequenced beforehand. In the simpler case of the analysis of 16S ribosomal RNA metagenomic data, for which databases of reference sequences are known, we survey the computational challenges to be solved in order to be able to characterize and quantify a sample. In particular, we examine two aspects: how the necessary adoption of new tools geared towards high-... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750384 Sun, 17 Apr 2011 23:00:00 +0100 4750384 http://www.medworm.com/index.php?rid=4750395&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21498549%26dopt%3DAbstract Authors: Mansmann U, Jurinovic V Gene expression is a dynamic process where thousands of components interact dynamically in a complex way. A major goal in systems biology/medicine is to reconstruct the network of components from microarray data. Here, we address two key aspects of network reconstruction: (i) ergodicity supports the interpretation of the measured data as time averages and (ii) confounding is an important aspect of network reconstruction. To elucidate these aspects, we explore a data set of 214 lymphoma patients with translocated or normal MYC gene. MYC (c-Myc) translocations to immunoglobulin heavy-chain (IGH@) or light-chain (IGK@, IGL@) loci lead to c-Myc overexpression and are widely believed to be the crucial initiating oncogenic events. There is a rich body of know... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750395 Thu, 14 Apr 2011 23:00:00 +0100 4750395 http://www.medworm.com/index.php?rid=4750394&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21498550%26dopt%3DAbstract Authors: Lockstone HE The use of microarray technology to measure gene expression on a genome-wide scale has been well established for more than a decade. Methods to process and analyse the vast quantity of expression data generated by a typical microarray experiment are similarly well-established. The Affymetrix Exon 1.0 ST array is a relatively new type of array, which has the capability to assess expression at the individual exon level. This allows a more comprehensive analysis of the transcriptome, and in particular enables the study of alternative splicing, a gene regulation mechanism important in both normal conditions and in diseases. Some aspects of exon array data analysis are shared with those for standard gene expression data but others present new challenges that have requi... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750394 Thu, 14 Apr 2011 23:00:00 +0100 4750394 http://www.medworm.com/index.php?rid=4750393&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21498551%26dopt%3DAbstract Authors: Fang Z, Cui X The next-generation sequencing technologies are being rapidly applied in biological research. Tens of millions of short sequences generated in a single experiment provide us enormous information on genome composition, genetic variants, gene expression levels and protein binding sites depending on the applications. Various methods are being developed for analyzing the data generated by these technologies. However, the relevant experimental design issues have rarely been discussed. In this review, we use RNA-seq as an example to bring this topic into focus and to discuss experimental design and validation issues pertaining to next-generation sequencing in the quantification of transcripts. PMID: 21498551 [PubMed - as supplied by publisher] (Source: Briefings in... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750393 Thu, 14 Apr 2011 23:00:00 +0100 4750393 http://www.medworm.com/index.php?rid=4750386&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21498552%26dopt%3DAbstract Authors: Nicodemus KK A recent study examined the stability of rankings from random forests using two variable importance measures (mean decrease accuracy (MDA) and mean decrease Gini (MDG)) and concluded that rankings based on the MDG were more robust than MDA. However, studies examining data-specific characteristics on ranking stability have been few. Rankings based on the MDG measure showed sensitivity to within-predictor correlation and differences in category frequencies, even when the number of categories was held constant, and thus may produce spurious results. The MDA measure was robust to these data characteristics. Further, under strong within-predictor correlation, MDG rankings were less stable than those using MDA. PMID: 21498552 [PubMed - as supplied by publisher] (Sou... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750386 Thu, 14 Apr 2011 23:00:00 +0100 4750386 http://www.medworm.com/index.php?rid=4750396&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21450805%26dopt%3DAbstract Authors: Mourad R, Sinoquet C, Leray P Probabilistic graphical models have been widely recognized as a powerful formalism in the bioinformatics field, especially in gene expression studies and linkage analysis. Although less well known in association genetics, many successful methods have recently emerged to dissect the genetic architecture of complex diseases. In this review article, we cover the applications of these models to the population association studies' context, such as linkage disequilibrium modeling, fine mapping and candidate gene studies, and genome-scale association studies. Significant breakthroughs of the corresponding methods are highlighted, but emphasis is also given to their current limitations, in particular, to the issue of scalability. Finally, we give promisin... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750396 Tue, 29 Mar 2011 23:00:00 +0100 4750396 http://www.medworm.com/index.php?rid=4750398&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441561%26dopt%3DAbstract Authors: Van Steen K Over the last few years, main effect genetic association analysis has proven to be a successful tool to unravel genetic risk components to a variety of complex diseases. In the quest for disease susceptibility factors and the search for the 'missing heritability', supplementary and complementary efforts have been undertaken. These include the inclusion of several genetic inheritance assumptions in model development, the consideration of different sources of information, and the acknowledgement of disease underlying pathways of networks. The search for epistasis or gene-gene interaction effects on traits of interest is marked by an exponential growth, not only in terms of methodological development, but also in terms of practical applications, translation of statist... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750398 Sat, 26 Mar 2011 00:00:00 +0100 4750398 http://www.medworm.com/index.php?rid=4750397&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441562%26dopt%3DAbstract Authors: Haupt VJ, Schroeder M Developing a drug de novo is a laborious and costly endeavor. Thus, the repositioning of already approved drugs for the treatment of new diseases is promising and valuable. One computational approach to repositioning exploits the structural similarity of binding sites of known and new targets. Here, we review computational methods to represent and align binding sites. We review available tools, present success stories and discuss limits of the approach. PMID: 21441562 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4750397 Sat, 26 Mar 2011 00:00:00 +0100 4750397 http://www.medworm.com/index.php?rid=4637987&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21436145%26dopt%3DAbstract Authors: Nabhan AR, Sarkar IN Over the past two decades, there has been a long-standing debate about the impact of taxon sampling on phylogenetic inference. Studies have been based on both real and simulated data sets, within actual and theoretical contexts, and using different inference methods, to study the impact of taxon sampling. In some cases, conflicting conclusions have been drawn for the same data set. The main questions explored in studies to date have been about the effects of using sparse data, adding new taxa, including more characters from genome sequences and using different (or concatenated) locus regions. These questions can be reduced to more fundamental ones about the assessment of data quality and the design guidelines of taxon sampling in phylogenetic inference exp... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4637987 Wed, 23 Mar 2011 00:00:00 +0100 4637987 http://www.medworm.com/index.php?rid=4637991&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21422065%26dopt%3DAbstract We report on the results of a survey encompassing 78 of such tools, of which 22 were inspected in detail and seven were tested hands-on. We report on our experiences with a focus on completeness of functionality, ease-of-use, and necessary effort for installation and maintenance. Thereby, our survey provides a valuable guideline for any project considering the use of a microarray data management system. It reveals which tasks are covered by mature tools and also shows that important requirements, especially in the area of integrated analysis of different experimental data, are not yet met satisfyingly by existing systems. PMID: 21422065 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4637991 Mon, 21 Mar 2011 00:00:00 +0100 4637991 http://www.medworm.com/index.php?rid=4637990&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21422066%26dopt%3DAbstract This article discusses the caveats and pitfalls of ROC analysis in clinical microarray research, particularly in relation to (i) the interpretation of AUC (especially a value close to 0.5); (ii) model comparisons based on AUC; (iii) the differences between ranking and classification; (iv) effects due to multiple hypotheses testing; (v) the importance of confidence intervals for AUC; and (vi) the choice of the appropriate performance metric. With a discussion of illustrative examples and concrete real-world studies, this article highlights critical misconceptions that can profoundly impact the conclusions about the observed performance. PMID: 21422066 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4637990 Mon, 21 Mar 2011 00:00:00 +0100 4637990 http://www.medworm.com/index.php?rid=4637989&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21422070%26dopt%3DAbstract Authors: Barash D, Churkin A Programs for RNA mutational analysis that are structure-based and rely on secondary structure prediction have been developed and expanded in the past several years. They can be used for a variety of purposes, such as in suggesting point mutations that will alter RNA virus replication or translation initiation, investigating the effect of deleterious and compensatory mutations in allosteric ribozymes and riboswitches, computing an optimal path of mutations to get from one ribozyme fold to another, or analyzing regulatory RNA sequences by their mutational profile. This review describes three different freeware programs (RNAMute, RDMAS and RNAmutants) that have been developed for such purposes. RNAMute and RDMAS in principle perform energy minimization predict... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4637989 Tue, 01 Mar 2011 00:00:00 +0100 4637989 http://www.medworm.com/index.php?rid=4637988&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21422071%26dopt%3DAbstract Authors: Kalaimathy S, Sowdhamini R, Kanagarajadurai K Accurate sequence alignments are crucial for modelling and to provide an evolutionary picture of related proteins. It is well-known that alignments are hard to obtain during distant relationships. Three thousand and fifty-two alignments of 218 pairs of protein domain structural entries, with <40% sequence identity, belonging to different structural classes, of diverse domain sizes and length-rigid/variable domains were performed using 12 programs. Structural parameters such as root mean square deviation, secondary-structural content and equivalences were considered for critical assessment. Methods that compare fragments and permit twists and translations align well during distant relationships and length variations. PMID: 21... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4637988 Tue, 01 Mar 2011 00:00:00 +0100 4637988 http://www.medworm.com/index.php?rid=4578630&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21357612%26dopt%3DAbstract Authors: Xu K, Coté TR Facing substantial obstacles to developing new therapies for rare diseases, some sponsors are looking to 'repurpose' drugs already approved for other conditions and use those therapies to treat rare diseases. In an effort to facilitate such repurposing and speed the delivery of new therapies to people who need them, we have established a new resource, the Rare Disease Repurposing Database (RDRD). The advantages of repurposed compounds include their demonstrated efficacy (in some clinical contexts), their observed toxicity profiles and their clearly described manufacturing controls. To create the RDRD, we matched the US Food and Drug Administration (FDA) orphan designation database to FDA drug and biological product approval lists. The RDRD lists 236 products tha... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4578630 Sat, 26 Feb 2011 00:00:00 +0100 4578630 http://www.medworm.com/index.php?rid=4525286&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21330331%26dopt%3DAbstract Authors: du Plessis L, Skunca N, Dessimoz C With high-throughput technologies providing vast amounts of data, it has become more important to provide systematic, quality annotations. The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use is not yet ubiquitous and is still fraught with pitfalls. In this review, we provide a short primer to the GO for bioinformaticians. We summarize important aspects of the structure of the ontology, describe sources and types of functional annotations, survey measures of GO annotation similarity, review typical uses of GO and discuss other important considerations pertaining to the use of GO in bioinformatics applications. PMID: 21330331 [PubMed - as supplied by publisher] (Source: Briefings in Bio... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4525286 Thu, 17 Feb 2011 00:00:00 +0100 4525286 http://www.medworm.com/index.php?rid=4525287&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21324971%26dopt%3DAbstract Authors: Simon RM, Subramanian J, Li MC, Menezes S Developments in whole genome biotechnology have stimulated statistical focus on prediction methods. We review here methodology for classifying patients into survival risk groups and for using cross-validation to evaluate such classifications. Measures of discrimination for survival risk models include separation of survival curves, time-dependent ROC curves and Harrell's concordance index. For high-dimensional data applications, however, computing these measures as re-substitution statistics on the same data used for model development results in highly biased estimates. Most developments in methodology for survival risk modeling with high-dimensional data have utilized separate test data sets for model evaluation. Cross-validation has ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4525287 Tue, 15 Feb 2011 00:00:00 +0100 4525287 http://www.medworm.com/index.php?rid=4470635&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21310717%26dopt%3DAbstract Authors: Chavent M, Lévy B, Krone M, Bidmon K, Nominé JP, Ertl T, Baaden M Recent advances in experimental structure determination provide a wealth of structural data on huge macromolecular assemblies such as the ribosome or viral capsids, available in public databases. Further structural models arise from reconstructions using symmetry orders or fitting crystal structures into low-resolution maps obtained by electron-microscopy or small angle X-ray scattering experiments. Visual inspection of these huge structures remains an important way of unravelling some of their secrets. However, such visualization cannot conveniently be carried out using conventional rendering approaches, either due to performance limitations or due to lack of realism. Recent developments, in particular drawin... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4470635 Wed, 09 Feb 2011 00:00:00 +0100 4470635 http://www.medworm.com/index.php?rid=4470636&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21300697%26dopt%3DAbstract In conclusion, these results document that many cross-validation practices employed in the literature are potentially biased and genuine progress in this field will require adoption of routine external validation of molecular classifiers, preferably in much larger studies than in current practice. PMID: 21300697 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4470636 Mon, 07 Feb 2011 00:00:00 +0100 4470636 http://www.medworm.com/index.php?rid=4470637&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21278369%26dopt%3DAbstract We report results of a survey comprising 100 papers recently published in Bioinformatics. The main finding is that authors of this journal share a culture of making data available. However, the number of papers where source code for simulation studies or analyzes is available is still rather limited. PMID: 21278369 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4470637 Fri, 28 Jan 2011 00:00:00 +0100 4470637 http://www.medworm.com/index.php?rid=4400202&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21262742%26dopt%3DAbstract Authors: Meng Y, Shao C, Chen M Current achievements in plant microRNA (miRNA) research area are inspiring. Molecular cloning and functional elucidation have greatly advanced our understanding of this small RNA species. As one of the ultimate goals, many research efforts devoted to draw a comprehensive view of miRNA-mediated gene regulatory networks in plants. Numerous bioinformatics tools competent for network analysis have been available. However, the most important point for network construction is to obtain reliable analytical results based on sufficient experimental data. Here, we introduced a general workflow to retrieve and analyze the desired data sets that serve as the cornerstones for network construction. For the upstream analyses of miRNA genes, the sequence feature of miRN... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4400202 Sun, 23 Jan 2011 00:00:00 +0100 4400202 http://www.medworm.com/index.php?rid=4400203&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21257650%26dopt%3DAbstract Authors: Stamatakis A, Izquierdo-Carrasco F Verification in phylogenetics represents an extremely difficult subject. Phylogenetic analysis deals with the reconstruction of evolutionary histories of species, and as long as mankind is not able to travel in time, it will not be possible to verify deep evolutionary histories reconstructed with modern computational methods. Here, we focus on two more tangible issues that are related to verification in phylogenetics (i) the inference of support values on trees that provide some notion about the 'correctness' of the tree within narrow limits and, more importantly; (ii) issues pertaining to program verification, especially with respect to codes that rely heavily on floating-point arithmetics. Program verification represents a largely underesti... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4400203 Fri, 21 Jan 2011 00:00:00 +0100 4400203 http://www.medworm.com/index.php?rid=4400204&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21252072%26dopt%3DAbstract Authors: Zhang H, Zhang T, Chen K, Kedarisetti KD, Mizianty MJ, Bao Q, Stach W, Kurgan L Sequence-based prediction of protein secondary structure (SS) enjoys wide-spread and increasing use for the analysis and prediction of numerous structural and functional characteristics of proteins. The lack of a recent comprehensive and large-scale comparison of the numerous prediction methods results in an often arbitrary selection of a SS predictor. To address this void, we compare and analyze 12 popular, standalone and high-throughput predictors on a large set of 1975 proteins to provide in-depth, novel and practical insights. We show that there is no universally best predictor and thus detailed comparative studies are needed to support informed selection of SS predictors for a given applicatio... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4400204 Thu, 20 Jan 2011 00:00:00 +0100 4400204 http://www.medworm.com/index.php?rid=4400206&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21245078%26dopt%3DAbstract This article reviews procedures that assess and validate the added predictive value of high-dimensional molecular data. It critically surveys various approaches for the construction of combined prediction models using both clinical and molecular data, for validating added predictive value based on independent data, and for assessing added predictive value using a single data set. PMID: 21245078 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4400206 Tue, 18 Jan 2011 00:00:00 +0100 4400206 http://www.medworm.com/index.php?rid=4400205&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21245079%26dopt%3DAbstract Authors: Ledergerber C, Dessimoz C Next-generation sequencing platforms are dramatically reducing the cost of DNA sequencing. With these technologies, bases are inferred from light intensity signals, a process commonly referred to as base-calling. Thus, understanding and improving the quality of sequence data generated using these approaches are of high interest. Recently, a number of papers have characterized the biases associated with base-calling and proposed methodological improvements. In this review, we summarize recent development of base-calling approaches for the Illumina and Roche 454 sequencing platforms. PMID: 21245079 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4400205 Tue, 18 Jan 2011 00:00:00 +0100 4400205 http://www.medworm.com/index.php?rid=4400207&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21242203%26dopt%3DAbstract This article consists of the following parts. First, we review the standard PCA technique and their applications in bioinformatics data analysis. Second, we describe recent 'non-standard' applications of PCA, including accommodating interactions among genes, pathways and network modules and conducting PCA with estimating equations as opposed to gene expressions. Third, we introduce several recently proposed PCA-based techniques, including the supervised PCA, sparse PCA and functional PCA. The supervised PCA and sparse PCA have been shown to have better empirical performance than the standard PCA. The functional PCA can analyze time-course gene expression data. Last, we raise the awareness of several critical but unsolved problems related to PCA. The goal of this article is to make bioinfor... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4400207 Mon, 17 Jan 2011 00:00:00 +0100 4400207 http://www.medworm.com/index.php?rid=4334135&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21183477%26dopt%3DAbstract This article examines both perspectives in the framework of a distance function between two networks. It considers some of the obstacles to validation and provides examples of both validation paradigms. PMID: 21183477 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4334135 Wed, 22 Dec 2010 00:00:00 +0100 4334135 http://www.medworm.com/index.php?rid=4334134&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21183478%26dopt%3DAbstract Authors: Jelier R, Goeman JJ, Hettne KM, Schuemie MJ, den Dunnen JT, 't Hoen PA Most methods for the interpretation of gene expression profiling experiments rely on the categorization of genes, as provided by the Gene Ontology (GO) and pathway databases. Due to the manual curation process, such databases are never up-to-date and tend to be limited in focus and coverage. Automated literature mining tools provide an attractive, alternative approach. We review how they can be employed for the interpretation of gene expression profiling experiments. We illustrate that their comprehensive scope aids the interpretation of data from domains poorly covered by GO or alternative databases, and allows for the linking of gene expression with diseases, drugs, tissues and other types of concepts. A ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4334134 Wed, 22 Dec 2010 00:00:00 +0100 4334134 http://www.medworm.com/index.php?rid=4275758&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21156727%26dopt%3DAbstract Authors: Liew AW, Law NF, Yan H Microarray gene expression data generally suffers from missing value problem due to a variety of experimental reasons. Since the missing data points can adversely affect downstream analysis, many algorithms have been proposed to impute missing values. In this survey, we provide a comprehensive review of existing missing value imputation algorithms, focusing on their underlying algorithmic techniques and how they utilize local or global information from within the data, or their use of domain knowledge during imputation. In addition, we describe how the imputation results can be validated and the different ways to assess the performance of different imputation algorithms, as well as a discussion on some possible future research directions. It is hoped tha... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4275758 Tue, 14 Dec 2010 00:00:00 +0100 4275758 http://www.medworm.com/index.php?rid=4200909&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21087949%26dopt%3DAbstract The objectives of this study are 2-fold. First, we investigate ranking markers under three commonly adopted semiparametric models, namely the Cox, accelerated failure time and additive risk models. Data analysis shows that the ranking may vary significantly under different models. Second, we describe a nonparametric concordance measure, which has roots in the time-dependent ROC (receiver operating characteristic) framework and relies on much weaker assumptions than the semiparametric models. In simulation, it is shown that ranking using the concordance measure is not sensitive to model specification whereas ranking under the semiparametric models is. In data analysis, the concordance measure generates rankings significantly different from those under the semiparametric models. PMID: 21... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4200909 Thu, 18 Nov 2010 00:00:00 +0100 4200909 http://www.medworm.com/index.php?rid=4166016&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21059603%26dopt%3DAbstract Authors: Szalkowski AM, Schmid CD The current understanding of the regulation of transcription does not keep the pace with the spectacular advances in the determination of genomic sequences. Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) promises to give better insight into transcription regulation by locating sites of protein-DNA interactions. Such loci of putative interactions can be inferred from the genome-wide distributions of ChIP-seq data by peak-calling software. The analysis of ChIP-seq data critically depends on this step and a multitude of these peak-callers have been deployed in the recent years. A recent study reported severe variation among peak-calling results. Yet, peak-calling still lacks systematic quantitative benchmarking. Here, w... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4166016 Mon, 08 Nov 2010 00:00:00 +0100 4166016 http://www.medworm.com/index.php?rid=4166015&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21059604%26dopt%3DAbstract Authors: Lourenço A, Carneiro S, Rocha M, Ferreira EC, Rocha I One key challenge in Systems Biology is to provide mechanisms to collect and integrate the necessary data to be able to meet multiple analysis requirements. Typically, biological contents are scattered over multiple data sources and there is no easy way of comparing heterogeneous data contents. This work discusses ongoing standardisation and interoperability efforts and exposes integration challenges for the model organism Escherichia coli K-12. The goal is to analyse the major obstacles faced by integration processes, suggest ways to systematically identify them, and whenever possible, propose solutions or means to assist manual curation. Integration of gene, protein and compound data was evaluated by performing compariso... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4166015 Sun, 07 Nov 2010 00:00:00 +0100 4166015 http://www.medworm.com/index.php?rid=4139536&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21036947%26dopt%3DAbstract Authors: Jungck JR, Donovan SS, Weisstein AE, Khiripet N, Everse SJ Bioinformatics is central to biology education in the 21st century. With the generation of terabytes of data per day, the application of computer-based tools to stored and distributed data is fundamentally changing research and its application to problems in medicine, agriculture, conservation and forensics. In light of this 'information revolution,' undergraduate biology curricula must be redesigned to prepare the next generation of informed citizens as well as those who will pursue careers in the life sciences. The BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting together) has fostered an international community of bioinformatics educators. The initiative's goals are t... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4139536 Fri, 29 Oct 2010 00:00:00 +0100 4139536 http://www.medworm.com/index.php?rid=4107865&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20965999%26dopt%3DAbstract Authors: Navas-Delgado I, Real-Chicharro A, Medina MA, Sánchez-Jiménez F, Aldana-Montes JF High-throughput experiments have produced large amounts of heterogeneous data in the life sciences. These data are usually represented in different formats (and sometimes in technical documents) on the Web. Inevitably, life science researchers have to deal with all these data and different formats to perform their daily research, but it is simply not possible for a single human mind to analyse all these data. The integration of data in the life sciences is a key component in the analysis of biological processes. These data may contain errors, but the curation of the vast amount of data generated in the 'omic' era cannot be done by individual researchers. To address this problem, community-drive... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4107865 Wed, 20 Oct 2010 23:00:00 +0100 4107865 http://www.medworm.com/index.php?rid=4107864&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20966000%26dopt%3DAbstract This article is a review of its functional organization and evolution. We aim to share our experience with people considering setting-up similar training facilities elsewhere. More than 1600 course attendees, so far, have attended our courses. Their experiences have helped us to know how to satisfy their training requirements and what is feasible with very limited resources. PMID: 20966000 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4107864 Wed, 20 Oct 2010 23:00:00 +0100 4107864 http://www.medworm.com/index.php?rid=4003610&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20858738%26dopt%3DAbstract Authors: Dai X, Zhuang Z, Zhao PX Plant microRNAs (miRNA) target recognition mechanism was once thought to be simple and straightforward, i.e. through perfect reverse complementary matching; therefore, very few target prediction tools and algorithms were developed for plants as compared to those for animals. However, the discovery of transcription suppression and the more recent observation of widespread translational regulation by miRNAs highlight the enormous diversity and complexity of gene regulation in plant systems. This, in turn, necessitates the need for advanced computational tools/algorithms for comprehensive miRNA target analysis to help understand miRNA regulatory mechanisms. Yet, advanced/comprehensive plant miRNA target analysis tools are still lacking despite the desirab... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4003610 Mon, 20 Sep 2010 23:00:00 +0100 4003610 http://www.medworm.com/index.php?rid=3988014&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20851835%26dopt%3DAbstract Authors: Klingström T, Plewczynski D The amount of information regarding protein-protein interactions (PPI) at a proteomic scale is constantly increasing. This is paralleled with an increase of databases making information available. Consequently there are diverse ways of delivering information about not only PPIs but also regarding the databases themselves. This creates a time consuming obstacle for many researchers working in the field. Our survey provides a valuable tool for researchers to reduce the time necessary to gain a broad overview of PPI-databases and is supported by a graphical representation of data exchange. The graphical representation is made available in cooperation with the team maintaining www.pathguide.org and can be accessed at http://www.pathguide.org/interact... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3988014 Thu, 16 Sep 2010 23:00:00 +0100 3988014 http://www.medworm.com/index.php?rid=3912165&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20798181%26dopt%3DAbstract Authors: Williams JM, Mangan ME, Perreault-Micale C, Lathe S, Sirohi N, Lathe WC The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explo... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3912165 Wed, 25 Aug 2010 23:00:00 +0100 3912165 http://www.medworm.com/index.php?rid=3912164&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20798182%26dopt%3DAbstract Authors: Cummings MP, Temple GG The major opportunities for broader incorporation of bioinformatics in education can be placed into three general categories: general applicability of bioinformatics in life science and related curricula; inherent fit of bioinformatics for promoting student learning in most biology programs; and the general experience and associated comfort students have with computers and technology. Conversely, the major challenges for broader incorporation of bioinformatics in education can be placed into three general categories: required infrastructure and logistics; instructor knowledge of bioinformatics and continuing education; and the breadth of bioinformatics, and the diversity of students and educational objectives. Broader incorporation of bioinformatics at a... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3912164 Wed, 25 Aug 2010 23:00:00 +0100 3912164 http://www.medworm.com/index.php?rid=3890799&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20724457%26dopt%3DAbstract Authors: Buttigieg PL Using live presentation to communicate the interdisciplinary and abstract content of bioinformatics to its educationally diverse studentship is a sizeable challenge. This review collects a number of perspectives on multimedia presentation, visual communication and pedagogy. The aim is to encourage educators to reflect on the great potential of live presentation in facilitating bioinformatics education. PMID: 20724457 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3890799 Wed, 18 Aug 2010 23:00:00 +0100 3890799 http://www.medworm.com/index.php?rid=3890798&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20724458%26dopt%3DAbstract Authors: Paszkiewicz K, Studholme DJ A new generation of sequencing technologies is revolutionizing molecular biology. Illumina's Solexa and Applied Biosystems' SOLiD generate gigabases of nucleotide sequence per week. However, a perceived limitation of these ultra-high-throughput technologies is their short read-lengths. De novo assembly of sequence reads generated by classical Sanger capillary sequencing is a mature field of research. Unfortunately, the existing sequence assembly programs were not effective for short sequence reads generated by Illumina and SOLiD platforms. Early studies suggested that, in principle, sequence reads as short as 20-30 nucleotides could be used to generate useful assemblies of both prokaryotic and eukaryotic genome sequences, albeit containing many gaps... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3890798 Wed, 18 Aug 2010 23:00:00 +0100 3890798 http://www.medworm.com/index.php?rid=3865546&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20705754%26dopt%3DAbstract Authors: Kulkarni-Kale U, Sawant S, Chavan V An account of bioinformatics education in India is presented along with future prospects. Establishment of BTIS network by Department of Biotechnology (DBT), Government of India in the 1980s had been a systematic effort in the development of bioinformatics infrastructure in India to provide services to scientific community. Advances in the field of bioinformatics underpinned the need for well-trained professionals with skills in information technology and biotechnology. As a result, programmes for capacity building in terms of human resource development were initiated. Educational programmes gradually evolved from the organisation of short-term workshops to the institution of formal diploma/degree programmes. A case study of the Master's deg... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3865546 Wed, 11 Aug 2010 23:00:00 +0100 3865546 http://www.medworm.com/index.php?rid=3865547&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20702596%26dopt%3DAbstract Authors: Fuellen G If fragments of DNA are transcribed (expressed), they deserve to be called (parts of) a gene. Whether transcription takes place depends on the 'gene regulatory network'. This network is defined as the complex interplay of the sequence, biochemical modifications and structure of the chromosomal DNA with the regulatory proteins/RNA (transcription factors, co-factors, regulating RNA and the transcriptional apparatus itself). Gene regulatory networks play a role in various stages of development as well as in the maintenance of the organism; in this review we will concentrate on the former. Their evolutionary reconstruction is daunting (to say the least), and bioinformatics tools are in their infancy. However, gain of understanding offers a reward beyond itself, since evo... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3865547 Tue, 10 Aug 2010 23:00:00 +0100 3865547 http://www.medworm.com/index.php?rid=3795208&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20660497%26dopt%3DAbstract Authors: Yamashita G, Miller H, Goddard A, Norton C Many areas of science such as biology, medicine and oceanography are becoming increasingly data-rich and most programs that train scientists do not address informatics techniques or technologies that are necessary for managing and analysing large amounts of data. Educational resources for scientists in informatics are scarce, yet scientists need the skills and knowledge to work with informaticians and manage graduate students and post-docs in informatics projects. The Marine Biological Laboratory houses a world-renowned library and is involved in a number of informatics projects in the sciences. The MBL has been home to the National Library of Medicine's BioMedical Informatics Course for nearly two decades and is committed to educatin... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3795208 Sat, 24 Jul 2010 23:00:00 +0100 3795208 http://www.medworm.com/index.php?rid=3795209&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20656749%26dopt%3DAbstract Authors: Rother K, Rother M, Pleus A, Upmeier Zu Belzen A Delivering hands-on tutorials on bioinformatics software and web applications is a challenging didactic scenario. The main reason is that trainees have heterogeneous backgrounds, different previous knowledge and vary in learning speed. In this article, we demonstrate how multi-stage learning aids can be used to allow all trainees to progress at a similar speed. In this technique, the trainees can utilize cards with hints and answers to guide themselves self-dependently through a complex task. We have successfully conducted a tutorial for the molecular viewer PyMOL using two sets of learning aid cards. The trainees responded positively, were able to complete the task, and the trainer had spare time to respond to individual questi... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3795209 Thu, 22 Jul 2010 23:00:00 +0100 3795209 http://www.medworm.com/index.php?rid=3734067&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20601435%26dopt%3DAbstract Authors: Wright VA, Vaughan BW, Laurent T, Lopez R, Brooksbank C, Schneider MV Today's molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the world's most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBI's mission. We have evaluated eLearning, in parallel with face-to-... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3734067 Thu, 01 Jul 2010 23:00:00 +0100 3734067 http://www.medworm.com/index.php?rid=3691705&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20570844%26dopt%3DAbstract Authors: Cooper PS, Lipshultz D, Matten WT, McGinnis SD, Pechous S, Romiti ML, Tao T, Valjavec-Gratian M, Sayers EW The National Center for Biotechnology Information (NCBI) hosts 39 literature and molecular biology databases containing almost half a billion records. As the complexity of these data and associated resources and tools continues to expand, so does the need for educational resources to help investigators, clinicians, information specialists and the general public make use of the wealth of public data available at the NCBI. This review describes the educational resources available at NCBI via the NCBI Education page (www.ncbi.nlm.nih.gov/Education/). These resources include materials designed for new users, such as About NCBI and the NCBI Guide, as well as documentation, Fre... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3691705 Mon, 21 Jun 2010 23:00:00 +0100 3691705 http://www.medworm.com/index.php?rid=3691706&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20562256%26dopt%3DAbstract Authors: Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Phillip Judge D, van der Gool W, Brooksbank C As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3691706 Thu, 17 Jun 2010 23:00:00 +0100 3691706 http://www.medworm.com/index.php?rid=3673432&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20534688%26dopt%3DAbstract Authors: Roy P, Truntzer C, Maucort-Boulch D, Jouve T, Molinari N The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. In recent years there has been a growing interest in using high throughput technologies for the detection of such biomarkers. In particular, mass spectrometry appears as an exciting tool with great potential. However, to extract any benefit from the massive potential of clinical proteomic studies, appropriate methods, improvement and validation are required. To better understand the key statistical points involved with such studies, this review presents the main data analysis steps of protein mass spectra data analysis, from the pre-processing of the data to the identification and validation of biomarkers. ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3673432 Tue, 08 Jun 2010 23:00:00 +0100 3673432 http://www.medworm.com/index.php?rid=3633804&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20519329%26dopt%3DAbstract Authors: Koboldt DC Massively parallel sequencing technologies continue to alter the study of human genetics. As the cost of sequencing declines, next-generation sequencing (NGS) instruments and datasets will become increasingly accessible to the wider research community. Newcomers are understandably eager to harness the power of these new technologies. Sequencing human genomes on these platforms, however, presents numerous production and bioinformatics challenges. Production issues like sample contamination, library chimaeras and variable run quality have become increasingly problematic in the transition from technology development lab to production floor. Analysis of NGS data, too, remains challenging, particularly given the short-read lengths (35-250 bp) and sheer volume of data. Th... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3633804 Tue, 01 Jun 2010 23:00:00 +0100 3633804 http://www.medworm.com/index.php?rid=3626413&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20513669%26dopt%3DAbstract This article reviews the application of algorithmic discrete models, with a focus on tissue growth and regeneration phenomena in the context of health and disease. The review begins with an overview of basic concepts, problems and approaches of computational discrete models. This will include a discussion of basic assumptions and design principles. An overview of key cell-driven approaches and examples of applications in tissue growth and regeneration is provided. The specification, implementation and analysis of a model are illustrated with a hypothetical example, which mimics the branching and sprouting patterns observed in blood vessel network development. The article concludes with a discussion of current challenges and recommendations. PMID: 20513669 [PubMed - as supplied by publi... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3626413 Sat, 29 May 2010 23:00:00 +0100 3626413 http://www.medworm.com/index.php?rid=3609243&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20501549%26dopt%3DAbstract Authors: Werner T Genome-wide sequencing has enabled modern biomedical research to relate more and more events in healthy as well as disease-affected cells and tissues to the genomic sequence. Now next generation sequencing (NGS) extends that reach into multiple almost complete genomes of the same species, revealing more and more details about how individual genomes as well as individual aspects of their regulation differ from each other. The inclusion of NGS-based transcriptome sequencing, chromatin-immunoprecipitation (ChIP) of transcription factor binding and epigenetic analyses (usually based on DNA methylation or histone modification ChIP) completes the picture with unprecedented resolution enabling the detection of even subtle differences such as alternative splicing of individua... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3609243 Mon, 24 May 2010 23:00:00 +0100 3609243 http://www.medworm.com/index.php?rid=3564545&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20460430%26dopt%3DAbstract Authors: Li H, Homer N Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. A wide variety of alignment algorithms and software have been subsequently developed over the past two years. In this article, we will systematically review the current development of these algorithms and introduce their practical applications on different types of experimental data. We come to the conclusion that short-read alignment is no longer the bottleneck of data analyses. We also consider future development of alignment algorithms with respect to emerging long sequence reads and the prospect of cloud computing. PMID: 20460430 [PubMed - as supplied... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3564545 Mon, 10 May 2010 23:00:00 +0100 3564545 http://www.medworm.com/index.php?rid=3556671&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20457755%26dopt%3DAbstract Authors: Huss M Sequencing-based approaches now allow high-resolution, genome-scale investigation of cellular epigenetic landscapes. For example, mapping of open chromatin regions, post-translational histone modifications and DNA methylation across a whole genome is now feasible, and new non-coding regulatory RNAs can be sensitively identified via RNA sequencing. The resulting large-scale data sets promise to contribute towards a more precise and complete understanding of gene regulation and to yield insights into the interplay between genomes and the environment. In this article, I review some of the conceptual issues and currently available software tools for the analysis of sequencing-based whole-genome epigenetics data. PMID: 20457755 [PubMed - as supplied by publisher] (Source... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3556671 Sun, 09 May 2010 23:00:00 +0100 3556671 http://www.medworm.com/index.php?rid=3521975&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20427421%26dopt%3DAbstract Authors: Robison K New generations of DNA sequencing technologies are enabling the systematic study of genetic derangement in cancers. Sequencing of cancer exomes or transcriptomes or even entire cancer genomes are now possible, though technical and economic challenges remain. Cancer samples are inherently heterogeneous and are often contaminated with normal DNA, placing additional demands on informatics tools for detecting genetic variation. However, even low coverage sequencing data can provide valuable information on genetic rearrangements, amplifications and losses in tumor genomes. Novel recurrent oncogenic mutations and fusion transcripts have been discovered with these technologies. In some sequenced cancer genomes, tens of thousands of genetic alterations have been discovered. ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3521975 Tue, 27 Apr 2010 23:00:00 +0100 3521975 http://www.medworm.com/index.php?rid=3433666&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20360022%26dopt%3DAbstract Authors: Calle ML, Urrea V The goal of this article (letter to the editor) is to emphasize the value of exploring ranking stability when using the importance measures, mean decrease accuracy (MDA) and mean decrease Gini (MDG), provided by Random Forest. We illustrate with a real and a simulated example that ranks based on the MDA are unstable to small perturbations of the dataset and ranks based on the MDG provide more robust results. PMID: 20360022 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3433666 Tue, 30 Mar 2010 23:00:00 +0100 3433666 http://www.medworm.com/index.php?rid=3427321&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20353961%26dopt%3DAbstract Authors: Pinzón A, Rodriguez-R LM, González A, Bernal A, Restrepo S Genome-scale metabolic reconstruction (GEMR), along with flux balance analysis, has been widely used to study complex metabolic networks in several microbial organisms. This approach is of particular applicability in biological systems where the lack of kinetics data is typical. This is the case of plant-pathogen interactions, where these methods open the possibility of studying host metabolic network phenotype during the interaction with pathogens. Since GEMRs are based on sequenced genomes, its applicability to organisms where genomic information is lacking is limited. Here we describe an alternative approach to GEMR: targeted metabolic reconstruction, where network reconstruction is guided by transcriptomi... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3427321 Sun, 28 Mar 2010 23:00:00 +0100 3427321 http://www.medworm.com/index.php?rid=3420868&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20348133%26dopt%3DAbstract This article will introduce some of these efforts, the interoperable cancer data-mining resources and repositories, from a user-perspective. Some of the considerations to be addressed when building interoperable, sustainable cancer resources will be discussed with case studies-hoping this will prove useful for researchers designing their own cancer databases. PMID: 20348133 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3420868 Thu, 25 Mar 2010 00:00:00 +0100 3420868 http://www.medworm.com/index.php?rid=3354918&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20211843%26dopt%3DAbstract Authors: Dematté L, Prandi D The development of detailed, coherent, models of complex biological systems is recognized as a key requirement for integrating the increasing amount of experimental data. In addition, in-silico simulation of bio-chemical models provides an easy way to test different experimental conditions, helping in the discovery of the dynamics that regulate biological systems. However, the computational power required by these simulations often exceeds that available on common desktop computers and thus expensive high performance computing solutions are required. An emerging alternative is represented by general-purpose scientific computing on graphics processing units (GPGPU), which offers the power of a small computer cluster at a cost of approximately $400. Comp... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3354918 Sun, 07 Mar 2010 00:00:00 +0100 3354918 http://www.medworm.com/index.php?rid=3340110&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20203074%26dopt%3DAbstract Authors: Wong C, Li Y, Lee C, Huang CH Classification of mitochondrial DNA (mtDNA) into their respective haplogroups allows the addressing of various anthropologic and forensic issues. Unique to mtDNA is its abundance and non-recombining uni-parental mode of inheritance; consequently, mutations are the only changes observed in the genetic material. These individual mutations are classified into their cladistic haplogroups allowing the tracing of different genetic branch points in human (and other organisms) evolution. Due to the large number of samples, it becomes necessary to automate the classification process. Using 5-fold cross-validation, we investigated two classification techniques on the consented database of 21 141 samples published by the Genographic project. The support vect... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3340110 Thu, 04 Mar 2010 00:00:00 +0100 3340110 http://www.medworm.com/index.php?rid=3303182&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20172948%26dopt%3DAbstract Authors: van de Wiel MA, Picard F, van Wieringen WN, Ylstra B Analysis of DNA copy number profiles requires methods tailored to the specific nature of these data. The number of available data analysis methods has grown enormously in the last 5 years. We discuss the typical characteristics of DNA copy number data, as measured by microarray technology and review the extensive literature on preprocessing methods such as segmentation and calling. Subsequently, the focus narrows to applications of DNA copy number in cancer, in particular, several downstream analyses of multi-sample data sets such as testing, clustering and classification. Finally, we look ahead: what should we prepare for and which methodology-related topics may deserve attention in the near future? PMID: 20172948 [PubM... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3303182 Fri, 19 Feb 2010 00:00:00 +0100 3303182 http://www.medworm.com/index.php?rid=3276973&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156987%26dopt%3DAbstract Authors: Casiraghi M, Labra M, Ferri E, Galimberti A, De Mattia F DNA barcoding is a recent and widely used molecular-based identification system that aims to identify biological specimens, and to assign them to a given species. However, DNA barcoding is even more than this, and besides many practical uses, it can be considered the core of an integrated taxonomic system, where bioinformatics plays a key role. DNA barcoding data could be interpreted in different ways depending on the examined taxa but the technique relies on standardized approaches, methods and analyses. The existing reference towards a common way to treat DNA barcoding data, analyses and results is the Barcode of Life Data Systems. However, the scientific community has produced in the recent years a number of alternati... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3276973 Mon, 15 Feb 2010 00:00:00 +0100 3276973 http://www.medworm.com/index.php?rid=3269972&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20150321%26dopt%3DAbstract Authors: Valentin F, Squizzato S, Goujon M, McWilliam H, Paern J, Lopez R The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI. Currently, users can access information from more than 62 distinct datasets covering some 400 million entries. The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property. The EB... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3269972 Thu, 11 Feb 2010 00:00:00 +0100 3269972 http://www.medworm.com/index.php?rid=3236789&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20123941%26dopt%3DAbstract Authors: Richmond P, Walker D, Coakley S, Romano D Driven by the availability of experimental data and ability to simulate a biological scale which is of immediate interest, the cellular scale is fast emerging as an ideal candidate for middle-out modelling. As with 'bottom-up' simulation approaches, cellular level simulations demand a high degree of computational power, which in large-scale simulations can only be achieved through parallel computing. The flexible large-scale agent modelling environment (FLAME) is a template driven framework for agent-based modelling (ABM) on parallel architectures ideally suited to the simulation of cellular systems. It is available for both high performance computing clusters (www.flame.ac.uk) and GPU hardware (www.flamegpu.com) and uses a formal spec... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3236789 Mon, 01 Feb 2010 00:00:00 +0100 3236789 http://www.medworm.com/index.php?rid=3236788&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20123942%26dopt%3DAbstract Authors: Ma S, Huang J, Shi M, Li Y, Shia BC Development of high-throughput technologies makes it possible to survey the whole genome. Genomic studies have been extensively conducted, searching for markers with predictive power for prognosis of complex diseases such as cancer, diabetes and obesity. Most existing statistical analyses are focused on developing marker selection techniques, while little attention is paid to the underlying prognosis models. In this article, we review three commonly used prognosis models, namely the Cox, additive risk and accelerated failure time models. We conduct simulation and show that gene identification can be unsatisfactory under model misspecification. We analyze three cancer prognosis studies under the three models, and show that the gene identifica... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3236788 Mon, 01 Feb 2010 00:00:00 +0100 3236788 http://www.medworm.com/index.php?rid=3229833&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20118105%26dopt%3DAbstract Authors: Ewald R, Himmelspach J, Jeschke M, Leye S, Uhrmacher AM Dry-lab experimentation is being increasingly used to complement wet-lab experimentation. However, conducting dry-lab experiments is a challenging endeavor that requires the combination of diverse techniques. JAMES II, a plug-in-based open source modeling and simulation framework, facilitates the exploitation and configuration of these techniques. The different aspects that form an experiment are made explicit to facilitate repeatability and reuse. Each of those influences the performance and the quality of the simulation experiment. Common experimentation pitfalls and current challenges are discussed along the way. PMID: 20118105 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3229833 Thu, 28 Jan 2010 00:00:00 +0100 3229833 http://www.medworm.com/index.php?rid=3172523&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20064873%26dopt%3DAbstract Authors: Mazza T, Romanel A, Jordán F In order to understand the complex relationships among the components of biological systems, network models have been used for a long time. Although they have been extensively used for visualization, data storage, structural analysis and simulation, some computational processes are still very inefficient when applied on complex networks. In particular, any parallel simulation technique requires a network previously divided into a number of clusters in numbers equal to that of the available processors. At the same time, let maximally disconnected clusters be chosen in order to minimize extra-communication overhead and to optimize the overall computational efficiency. Obtaining such a disconnection becomes a computationally hard problem when dis... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3172523 Mon, 11 Jan 2010 00:00:00 +0100 3172523 http://www.medworm.com/index.php?rid=3164483&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20061351%26dopt%3DAbstract Authors: Przytycka TM, Singh M, Slonim DK Dynamic molecular interactions play a central role in regulating the functioning of cells and organisms. The availability of experimentally determined large-scale cellular networks, along with other high-throughput experimental data sets that provide snapshots of biological systems at different times and conditions, is increasingly helpful in elucidating interaction dynamics. Here we review the beginnings of a new subfield within computational biology, one focused on the global inference and analysis of the dynamic interactome. This burgeoning research area, which entails a shift from static to dynamic network analysis, promises to be a major step forward in our ability to model and reason about cellular function and behavior. PMID: 2006135... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3164483 Fri, 08 Jan 2010 00:00:00 +0100 3164483 http://www.medworm.com/index.php?rid=3153991&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20053732%26dopt%3DAbstract This article demonstrates that artificial spiking neural networks-built to resemble the biological model-encoding information in the timing of single spikes, are capable of computing and learning clusters from realistic data. It shows how a spiking neural network based on spike-time coding can successfully perform unsupervised and supervised clustering on real-world data. A temporal encoding procedure of continuously valued data is developed, together with a hardware implementation oriented new learning rule set. Solutions that make use of embedded soft-core microcontrollers are investigated, to implement some of the most resource-consuming components of the artificial neural network. Details of the implementations are given, with benchmark application evaluation and test bench description... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3153991 Wed, 06 Jan 2010 00:00:00 +0100 3153991 http://www.medworm.com/index.php?rid=3153990&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20053733%26dopt%3DAbstract Authors: Dalca AV, Brudno M The advent of high-throughput sequencing (HTS) technologies is enabling sequencing of human genomes at a significantly lower cost. The availability of these genomes is hoped to enable novel medical diagnostics and treatment, specific to the individual, thus launching the era of personalized medicine. The data currently generated by HTS machines require extensive computational analysis in order to identify genomic variants present in the sequenced individual. In this paper, we overview HTS technologies and discuss several of the plethora of algorithms and tools designed to analyze HTS data, including algorithms for read mapping, as well as methods for identification of single-nucleotide polymorphisms, insertions/deletions and large-scale structural variants a... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3153990 Wed, 06 Jan 2010 00:00:00 +0100 3153990 http://www.medworm.com/index.php?rid=3130105&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20038567%26dopt%3DAbstract Authors: Zhao J, Jiang P, Zhang W To target complex, multi-factorial diseases more effectively, there has been an emerging trend of multi-target drug development based on network biology, as well as an increasing interest in traditional Chinese medicine (TCM) that applies a more holistic treatment to diseases. Thousands of years' clinic practices in TCM have accumulated a considerable number of formulae that exhibit reliable in vivo efficacy and safety. However, the molecular mechanisms responsible for their therapeutic effectiveness are still unclear. The development of network-based systems biology has provided considerable support for the understanding of the holistic, complementary and synergic essence of TCM in the context of molecular networks. This review introduces available so... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3130105 Mon, 28 Dec 2009 00:00:00 +0100 3130105 http://www.medworm.com/index.php?rid=3130104&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20038568%26dopt%3DAbstract Authors: Cecilia JM, García JM, Guerrero GD, Martínez-Del-Amor MA, Pérez-Hurtado I, Pérez-Jiménez MJ P systems or Membrane Systems provide a high-level computational modelling framework that combines the structure and dynamic aspects of biological systems in a relevant and understandable way. They are inherently parallel and non-deterministic computing devices. In this article, we discuss the motivation, design principles and key of the implementation of a simulator for the class of recognizer P systems with active membranes running on a (GPU). We compare our parallel simulator for GPUs to the simulator developed for a single central processing unit (CPU), showing that GPUs are better suited than CPUs to simulate P systems due to their highly parallel nature. ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3130104 Mon, 28 Dec 2009 00:00:00 +0100 3130104 http://www.medworm.com/index.php?rid=3119512&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20028713%26dopt%3DAbstract This article reviews the currently emerging field of multi-scale modelling in computational biomedicine. Many exciting multi-scale models exist or are under development. However, an underpinning multi-scale modelling methodology seems to be missing. We propose a direction that complements the classic dynamical systems approach and introduce two distinct case studies, transmission of resistance in human immunodeficiency virus spreading and in-stent restenosis in coronary artery disease. PMID: 20028713 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3119512 Tue, 22 Dec 2009 00:00:00 +0100 3119512 http://www.medworm.com/index.php?rid=3067513&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19965979%26dopt%3DAbstract Authors: Aittokallio T High-throughput biotechnologies, such as gene expression microarrays or mass-spectrometry-based proteomic assays, suffer from frequent missing values due to various experimental reasons. Since the missing data points can hinder downstream analyses, there exists a wide variety of ways in which to deal with missing values in large-scale data sets. Nowadays, it has become routine to estimate (or impute) the missing values prior to the actual data analysis. After nearly a decade since the publication of the first missing value imputation methods for gene expression microarray data, new imputation approaches are still being developed at an increasing rate. However, what is lagging behind is a systematic and objective evaluation of the strengths and weaknesses of the d... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3067513 Fri, 04 Dec 2009 00:00:00 +0100 3067513 http://www.medworm.com/index.php?rid=3057355&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19955235%26dopt%3DAbstract Authors: Herai RH, Yamagishi ME Trans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, 'Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3057355 Wed, 02 Dec 2009 00:00:00 +0100 3057355 http://www.medworm.com/index.php?rid=3057354&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19955236%26dopt%3DAbstract We present a survey of recent advancements in the emerging field of patient-specific modeling (PSM). Researchers in this field are currently simulating a wide variety of tissue and organ dynamics to address challenges in various clinical domains. The majority of this research employs three-dimensional, image-based modeling techniques. Recent PSM publications mostly represent feasibility or preliminary validation studies on modeling technologies, and these systems will require further clinical validation and usability testing before they can become a standard of care. We anticipate that with further testing and research, PSM-derived technologies will eventually become valuable, versatile clinical tools. PMID: 19955236 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformat... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3057354 Wed, 02 Dec 2009 00:00:00 +0100 3057354 http://www.medworm.com/index.php?rid=3057353&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19955237%26dopt%3DAbstract This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be ex... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3057353 Wed, 02 Dec 2009 00:00:00 +0100 3057353 http://www.medworm.com/index.php?rid=3033883&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19939940%26dopt%3DAbstract Authors: Li C, Courtot M, Le Novère N, Laibe C Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, pub... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3033883 Wed, 25 Nov 2009 00:00:00 +0100 3033883 http://www.medworm.com/index.php?rid=3033882&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19939941%26dopt%3DAbstract We examined the performance of these detection call algorithms and default parameters by applying the methods to two spike-in datasets. We show that the default parameters for qualitative detection calls yield few absent calls for high spike-in concentrations. When genes of interest are expected to be present at very low concentrations, spike-in datasets can be useful for appropriately adjusting the tuning parameters for qualitative detection calls. PMID: 19939941 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3033882 Wed, 25 Nov 2009 00:00:00 +0100 3033882 http://www.medworm.com/index.php?rid=2992897&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19906839%26dopt%3DAbstract Authors: Alterovitz G, Muso T, Ramoni MF The field of synthetic biology holds an inspiring vision for the future; it integrates computational analysis, biological data and the systems engineering paradigm in the design of new biological machines and systems. These biological machines are built from basic biomolecular components analogous to electrical devices, and the information flow among these components requires the augmentation of biological insight with the power of a formal approach to information management. Here we review the informatics challenges in synthetic biology along three dimensions: in silico, in vitro and in vivo. First, we describe state of the art of the in silico support of synthetic biology, from the specific data exchange formats, to the most popular software p... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2992897 Wed, 11 Nov 2009 00:00:00 +0100 2992897 http://www.medworm.com/index.php?rid=2944377&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19864250%26dopt%3DAbstract Authors: Horner DS, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called 'next-generation' sequencing platforms, with several others anticipated to become available shortly. The previously unimaginable scale and economy of these methods, coupled with their enthusiastic uptake by the scientific community and the potential for further improvements in accuracy and read length, suggest that these technologies are destined to make a huge and ongoing impact upon genomic and post-genomic biol... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2944377 Tue, 27 Oct 2009 00:00:00 +0100 2944377 http://www.medworm.com/index.php?rid=2935549&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19854753%26dopt%3DAbstract Authors: Ochs MF The emergence of high-throughput technologies for measuring biological systems has introduced problems for data interpretation that must be addressed for proper inference. First, analysis techniques need to be matched to the biological system, reflecting in their mathematical structure the underlying behavior being studied. When this is not done, mathematical techniques will generate answers, but the values and reliability estimates may not accurately reflect the biology. Second, analysis approaches must address the vast excess in variables measured (e.g. transcript levels of genes) over the number of samples (e.g. tumors, time points), known as the 'large-p, small-n' problem. In large-p, small-n paradigms, standard statistical techniques generally fail, and computatio... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2935549 Fri, 23 Oct 2009 00:00:00 +0100 2935549 http://www.medworm.com/index.php?rid=2877329&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19815645%26dopt%3DAbstract Authors: Alves R, Rodriguez-Baena DS, Aguilar-Ruiz JS Establishing an association between variables is always of interest in genomic studies. Generation of DNA microarray gene expression data introduces a variety of data analysis issues not encountered in traditional molecular biology or medicine. Frequent pattern mining (FPM) has been applied successfully in business and scientific data for discovering interesting association patterns, and is becoming a promising strategy in microarray gene expression analysis. We review the most relevant FPM strategies, as well as surrounding main issues when devising efficient and practical methods for gene association analysis (GAA). We observed that, so far, scalability achieved by efficient methods does not imply biological soundness of the disco... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2877329 Wed, 07 Oct 2009 23:00:00 +0100 2877329 http://www.medworm.com/index.php?rid=2856111&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19789265%26dopt%3DAbstract Authors: Duval B, Hao JK Gene selection aims at identifying a (small) subset of informative genes from the initial data in order to obtain high predictive accuracy for classification. Gene selection can be considered as a combinatorial search problem and thus be conveniently handled with optimization methods. In this article, we summarize some recent developments of using metaheuristic-based methods within an embedded approach for gene selection. In particular, we put forward the importance and usefulness of integrating problem-specific knowledge into the search operators of such a method. To illustrate the point, we explain how ranking coefficients of a linear classifier such as support vector machine (SVM) can be profitably used to reinforce the search efficiency of Local Search and ... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2856111 Mon, 28 Sep 2009 23:00:00 +0100 2856111 http://www.medworm.com/index.php?rid=2775297&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19734255%26dopt%3DAbstract Authors: Armstead I, Huang L, Ravagnani A, Robson P, Ougham H Orphan crops are those which are grown as food, animal feed or other crops of some importance in agriculture, but which have not yet received the investment of research effort or funding required to develop significant public bioinformatics resources. Where an orphan crop is related to a well-characterised model plant species, comparative genomics and bioinformatics can often, though not always, be exploited to assist research and crop improvement. This review addresses some challenges and opportunities presented by bioinformatics in the orphan crops, using three examples: forage grasses from the genera Lolium and Festuca, forage legumes and the second generation energy crop Miscanthus. PMID: 19734255 [PubMed - as suppli... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2775297 Thu, 03 Sep 2009 23:00:00 +0100 2775297 http://www.medworm.com/index.php?rid=2703206&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19679825%26dopt%3DAbstract Authors: Boulesteix AL, Slawski M Ranked gene lists are highly instable in the sense that similar measures of differential gene expression may yield very different rankings, and that a small change of the data set usually affects the obtained gene list considerably. Stability issues have long been under-considered in the literature, but they have grown to a hot topic in the last few years, perhaps as a consequence of the increasing skepticism on the reproducibility and clinical applicability of molecular research findings. In this article, we review existing approaches for the assessment of stability of ranked gene lists and the related problem of aggregation, give some practical recommendations, and warn against potential misuse of these methods. This overview is illustrated through a... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2703206 Sun, 16 Aug 2009 08:12:04 +0100 2703206 http://www.medworm.com/index.php?rid=2473126&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19457869%26dopt%3DAbstract Authors: Antezana E, Kuiper M, Mironov V New knowledge is produced at a continuously increasing speed, and the list of papers, databases and other knowledge sources that a researcher in the life sciences needs to cope with is actually turning into a problem rather than an asset. The adequate management of knowledge is therefore becoming fundamentally important for life scientists, especially if they work with approaches that thoroughly depend on knowledge integration, such as systems biology. Several initiatives to organize biological knowledge sources into a readily exploitable resourceome are presently being carried out. Ontologies and Semantic Web technologies revolutionize these efforts. Here, we review the benefits, trends, current possibilities, and the potential this holds for t... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2473126 Sat, 13 Jun 2009 15:19:55 +0100 2473126 http://www.medworm.com/index.php?rid=2473124&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19482960%26dopt%3DAbstract Authors: Pop M Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological landscape leads to the need for continued research. In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings. For example, the new field of metagenomics relies on large-scale sequencing of entire microbial communities instead of isolate genomes, leading to new computational challenges. In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in t... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2473124 Sat, 13 Jun 2009 15:19:42 +0100 2473124 http://www.medworm.com/index.php?rid=2473120&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19505887%26dopt%3DAbstract Authors: Dubitzky W PMID: 19505887 [PubMed - in process] (Source: Briefings in Bioinformatics) Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2473120 Sat, 13 Jun 2009 15:14:06 +0100 2473120 http://www.medworm.com/index.php?rid=2473096&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19505888%26dopt%3DAbstract Authors: Cheung KH, Lim E, Samwald M, Chen H, Marenco L, Holford ME, Morse TM, Mutalik P, Shepherd GM, Miller PL As the number of neuroscience databases increases, the need for neuroscience data integration grows. This paper reviews and compares several approaches, including the Neuroscience Database Gateway (NDG), Neuroscience Information Framework (NIF) and Entrez Neuron, which enable neuroscience database annotation and integration. These approaches cover a range of activities spanning from registry, discovery and integration of a wide variety of neuroscience data sources. They also provide different user interfaces for browsing, querying and displaying query results. In Entrez Neuron, for example, four different facets or tree views (neuron, neuronal property, gene and drug) are us... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2473096 Sat, 13 Jun 2009 14:46:15 +0100 2473096 http://www.medworm.com/index.php?rid=2473094&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19505889%26dopt%3DAbstract Authors: Lee WP, Tzou WS Designing and conducting experiments are routine practices for modern biologists. The real challenge, especially in the post-genome era, usually comes not from acquiring data, but from subsequent activities such as data processing, analysis, knowledge generation and gaining insight into the research question of interest. The approach of inferring gene regulatory networks (GRNs) has been flourishing for many years, and new methods from mathematics, information science, engineering and social sciences have been applied. We review different kinds of computational methods biologists use to infer networks of varying levels of accuracy and complexity. The primary concern of biologists is how to translate the inferred network into hypotheses that can be tested with re... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2473094 Sat, 13 Jun 2009 14:22:00 +0100 2473094 http://www.medworm.com/index.php?rid=2473122&cid=s_37630_79_f&fid=37630&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19498042%26dopt%3DAbstract Authors: Loo PV, Marynen P Metazoan transcription regulation occurs through the concerted action of multiple transcription factors that bind co-operatively to cis-regulatory modules (CRMs). The annotation of these key regulators of transcription is lagging far behind the annotation of the transcriptome itself. Here, we give an overview of existing computational methods to detect these CRMs in metazoan genomes. We subdivide these methods into three classes: CRM scanners screen sequences for CRMs based on predefined models that often consist of multiple position weight matrices (PWMs). CRM builders construct models of similar CRMs controlling a set of co-regulated or co-expressed genes. CRM genome screeners screen sequences or complete genomes for CRMs as homotypic or heterotypic cluster... Briefings in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2473122 Thu, 04 Jun 2009 04:00:00 +0100 2473122