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  • 1
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    Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-14
    Description: Motivation: The combination of liquid chromatography and mass spectrometry (LC/MS) has been widely used for large-scale comparative studies in systems biology, including proteomics, glycomics and metabolomics. In almost all experimental design, it is necessary to compare chromatograms across biological or technical replicates and across sample groups. Central to this is the peak alignment step, which is one of the most important but challenging preprocessing steps. Existing alignment tools do not take into account the structural dependencies between related peaks that coelute and are derived from the same metabolite or peptide. We propose a direct matching peak alignment method for LC/MS data that incorporates related peaks information (within each LC/MS run) and investigate its effect on alignment performance (across runs). The groupings of related peaks necessary for our method can be obtained from any peak clustering method and are built into a pair-wise peak similarity score function. The similarity score matrix produced is used by an approximation algorithm for the weighted matching problem to produce the actual alignment result. Results: We demonstrate that related peak information can improve alignment performance. The performance is evaluated on a set of benchmark datasets, where our method performs competitively compared to other popular alignment tools. Availability: The proposed alignment method has been implemented as a stand-alone application in Python, available for download at http://github.com/joewandy/peak-grouping-alignment . Contact: Simon.Rogers@glasgow.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Judging synthetic biology risks (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-01-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breitling, Rainer -- Takano, Eriko -- Gardner, Timothy S -- New York, N.Y. -- Science. 2015 Jan 9;347(6218):107. doi: 10.1126/science.aaa5253.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rainer Breitling is a Professor of Systems Biology at the University of Manchester, Manchester, UK, and an external expert to the European Commission Scientific Committees. rainer.breitling@manchester.ac.uk. ; Eriko Takano is a Professor of Synthetic Biology and Co-Director of the Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), University of Manchester, Manchester, UK, and an external expert to the European Commission Scientific Committees. eriko.takano@manchester.ac.uk. ; Timothy S. Gardner is Chief Executive Officer of Riffyn, Inc., in Oakland, CA, USA, and an external expert to the European Commission Scientific Committees. tg@riffyn.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25573995" target="_blank"〉PubMed〈/a〉
    Keywords: Europe ; European Union ; Risk Assessment/methods/standards ; Synthetic Biology/*trends ; United States
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
    Electronic Resource
    Electronic Resource
    Expression and secretion of Interferon-α1 by Streptomyces lividans: use of staphylokinase signals and amplification of a neo gene
    Amsterdam : Elsevier
    Gene 68 (1988), S. 53-62 
    Details
    ISSN: 0378-1119
    Keywords: Recombinant DNA ; direct and inverted repeats ; long-term chemostat cultivation ; plasmid vector pIJ487 ; protein export
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0378-1119(88)90598-7
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    Temperature-inducible gene expression in Bacillus subtilis mediated by the c1857-encoded repressor of bacteriophage lambda
    Amsterdam : Elsevier
    Gene 93 (1990), S. 35-40 
    Details
    ISSN: 0378-1119
    Keywords: Recombinant DNA ; heterologous expression signals ; site-directed mutagenesis ; staphylokinase ; α-amylase
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0378-1119(90)90132-B
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  • 5
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    antiSMASH 3.0--a comprehensive resource for the genome mining of biosynthetic gene clusters (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-02
    Description: Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org . Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-01-17
    Description: Motivation: Stable isotope - labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here , we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R. Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono - isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab - delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13 C - labelled metabolome dataset from trypanosomal parasites. Availability: mzMatch.R and mzMatch–ISO are available free of charge from http://mzmatch.sourceforge.net and can be used on Linux and Windows platforms running the latest version of R. Contact: rainer.breitling@manchester.ac.uk . Supplementary information: Supplementary data are available at Bioinformatics online
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-31
    Description: : The application of emerging metabolomics technologies to the comprehensive investigation of cellular biochemistry has been limited by bottlenecks in data processing, particularly noise filtering and metabolite identification. IDEOM provides a user-friendly data processing application that automates filtering and identification of metabolite peaks, paying particular attention to common sources of noise and false identifications generated by liquid chromatography–mass spectrometry (LC–MS) platforms. Building on advanced processing tools such as mzMatch and XCMS, it allows users to run a comprehensive pipeline for data analysis and visualization from a graphical user interface within Microsoft Excel, a familiar program for most biological scientists. Availability and implementation: IDEOM is provided free of charge at http://mzmatch.sourceforge.net/ideom.html , as a macro-enabled spreadsheet (.xlsb). Implementation requires Microsoft Excel (2007 or later). R is also required for full functionality. Contact: michael.barrett@glasgow.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 8
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    TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc ( http://www.metexplore.fr/trypanocyc/ ), which describes the generic and condition-specific metabolic network of Trypanosoma brucei , a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-25
    Description: Motivation: The use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metabolites are present in a sample. This article looks at the dual problem of annotating peaks in a sample with a metabolite, together with putatively annotating whether a metabolite is present in the sample. The starting point of the approach is a Bayesian clustering of peaks into groups, each corresponding to putative adducts and isotopes of a single metabolite. Results: The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade-off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations. Availability and implementation : The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http://mzmatch.sourceforge.net/ . Contact: Ronan.Daly@glasgow.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-16
    Description: The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. The contextualization offered by MultiGeneBlast allows users to get a better understanding of the function, evolutionary history, and practical applications of such genomic regions. The tool is fully equipped with applications to generate search databases from GenBank or from the user’s own sequence data. Finally, an architecture search mode allows searching for gene clusters with novel configurations, by detecting genomic regions with any user-specified combination of genes. Sources, precompiled binaries, and a graphical tutorial of MultiGeneBlast are freely available from http://multigeneblast.sourceforge.net/ .
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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