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Visualization of omics data for systems biology

Nils Gehlenborg, Seán I O'Donoghue, Nitin S Baliga, Alexander Goesmann, Matthew A Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum, Anne-Claude Gavin
2010 Nature Methods  
Visualization has long been key in helping to understand biological systems, such as metabolism 1 , signaling 2 and the regulation of gene expression 3 . In recent years, the study of such systems has been profoundly influenced by the development of a wide range of high-throughput experimental methods (Box 1), resulting in a greatly increased volume of complex, interconnected data. Remarkably, in spite of these changes, and in spite of the development of new methods for visualizing and
more » ... these data, we still use the same primary visual metaphor to communicate ideas about biological systems: namely, pathways (graphs that show overall changes in state) or, more generally, networks (graphs that do not necessarily show state changes). As high-throughput experimental methods have become more routine, many more scientists are using network and pathway visualization to record and communicate their findings. There are now over 300 web resources 4 (see providing access to many thousands of pathways and networks that document millions of interactions between proteins, genes and small molecules. High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have many visualization methods and tools to choose from. The challenge is to create clear, meaningful and integrated visualizations that give biological insight, without being overwhelmed by the intrinsic complexity of the data. In this review, we discuss how visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data, and we highlight emerging new directions.
doi:10.1038/nmeth.1436 pmid:20195258 fatcat:ougp4zlstfevpcmepxdtm67b2y

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

Nils Hoffmann, Matthias Keck, Heiko Neuweger, Mathias Wilhelm, Petra Högy, Karsten Niehaus, Jens Stoye
2012 BMC Bioinformatics  
Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to
more » ... ow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. Results: In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CEMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CEMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum). Conclusions: We have shown that BIPACE achieves very high precision and recall and a very low number of false positive peak assignments on both evaluation datasets. CEMAPP-DTW finds a high number of true positives when executed on its own, but achieves even better results when BIPACE is used to constrain its search space. The source code of both algorithms is included in the OpenSource software framework Maltcms, which is available from http:// The evaluation scripts of the present study are available from the same source.
doi:10.1186/1471-2105-13-214 pmid:22920415 pmcid:PMC3546004 fatcat:3kjadmdqszchtju3ulwwtu3mbe

Root metabolic response of rice (Oryza sativa L.) genotypes with contrasting tolerance to zinc deficiency and bicarbonate excess

Michael T. Rose, Terry J. Rose, Juan Pariasca-Tanaka, Tadashi Yoshihashi, Heiko Neuweger, Alexander Goesmann, Michael Frei, Matthias Wissuwa
2012 Planta  
Preprocessing of GC-MS data All chromatograms were converted to netCDF format and imported into the Web-based processing platform MeltDB (Neuweger et al. 2008) .  ... 
doi:10.1007/s00425-012-1648-4 pmid:22526504 fatcat:ealldnp3ircrbeo2wifsfsaybm

MeltDB: a software platform for the analysis and integration of metabolomics experiment data

Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann
2008 Computer applications in the biosciences : CABIOS  
These findings are part of the first publication of the MeltDB system (Neuweger et al., 2008) .  ...  An alternative strategy was developed for the CoryneCenter platform Neuweger et al. (2007) for the integrated analysis of corynebacterial genome and transcriptome data.  ... 
doi:10.1093/bioinformatics/btn452 pmid:18765459 fatcat:6kraieexyvaq7hcx4fikyqg5gq

CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome data

Heiko Neuweger, Jan Baumbach, Stefan Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, Jörn Kalinowski, Sebastian Oehm, Alfred Pühler, Sven Rahmann, Jochen Weile, Alexander Goesmann
2007 BMC Systems Biology  
The introduction of high-throughput genome sequencing and post-genome analysis technologies, e.g. DNA microarray approaches, has created the potential to unravel and scrutinize complex gene-regulatory networks on a large scale. The discovery of transcriptional regulatory interactions has become a major topic in modern functional genomics. Results: To facilitate the analysis of gene-regulatory networks, we have developed CoryneCenter, a web-based resource for the systematic integration and
more » ... is of genome, transcriptome, and gene regulatory information for prokaryotes, especially corynebacteria. For this purpose, we extended and combined the following systems into a common platform: (1) GenDB, an open source genome annotation system, (2) EMMA, a MAGE compliant application for high-throughput transcriptome data storage and analysis, and (3) CoryneRegNet, an ontologybased data warehouse designed to facilitate the reconstruction and analysis of gene regulatory interactions. We demonstrate the potential of CoryneCenter by means of an application example. Using microarray hybridization data, we compare the gene expression of Corynebacterium glutamicum under acetate and glucose feeding conditions: Known regulatory networks are confirmed, but moreover CoryneCenter points out additional regulatory interactions. Conclusion: CoryneCenter provides more than the sum of its parts. Its novel analysis and visualization features significantly simplify the process of obtaining new biological insights into complex regulatory systems. Although the platform currently focusses on corynebacteria, the integrated tools are by no means restricted to these species, and the presented approach offers a general strategy for the analysis and verification of gene regulatory networks. CoryneCenter provides freely accessible projects with the underlying genome annotation, gene expression, and gene regulation data. The system is publicly available at http://www.bacterium glutamicum, is subject to regulation by RamA and RamB. J Bacteriol 2007, 189(3):1145-1149. 47. Engels V, Wendisch VF: The DeoR-type regulator SugR represses expression of ptsG in Corynebacterium glutamicum. J Bacteriol 2007, 189(8):2955-2966.
doi:10.1186/1752-0509-1-55 pmid:18034885 pmcid:PMC2212648 fatcat:f5vtl5tginb3vd64wiltwdkfvu

EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data

Michael Dondrup, Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger (+5 others)
2009 BMC Bioinformatics  
Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often
more » ... hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services.
doi:10.1186/1471-2105-10-50 pmid:19200358 pmcid:PMC2645365 fatcat:vmficlw2vnfuvggnegr4zvyp5q

Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example

Heiko Neuweger, Marcus Persicke, Stefan P Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, Jörn Winnebald, Jessica Schneider, Jörn Kalinowski, Alexander Goesmann
2009 BMC Systems Biology  
The rapid progress of post-genomic analyses, such as transcriptomics, proteomics, and metabolomics has resulted in the generation of large amounts of quantitative data covering and connecting the complete cascade from genotype to phenotype for individual organisms. Various benefits can be achieved when these "Omics" data are integrated, such as the identification of unknown gene functions or the elucidation of regulatory networks of whole organisms. In order to be able to obtain deeper insights
more » ... in the generated datasets, it is of utmost importance to present the data to the researcher in an intuitive, integrated, and knowledge-based environment. Therefore, various visualization paradigms have been established during the last years. The visualization of "Omics" data using metabolic pathway maps is intuitive and has been applied in various software tools. It has become obvious that the application of web-based and user driven software tools has great potential and benefits from the use of open and standardized formats for the description of pathways. Results: In order to combine datasets from heterogeneous "Omics" sources, we present the webbased ProMeTra system that visualizes and combines datasets from transcriptomics, proteomics, and metabolomics on user defined metabolic pathway maps. Therefore, structured exchange of data with our "Omics" applications Emma 2, Qupe and MeltDB is employed. Enriched SVG images or animations are generated and can be obtained via the user friendly web interface. To demonstrate the functionality of ProMeTra, we use quantitative data obtained during a fermentation experiment of the L-lysine producing strain Corynebacterium glutamicum DM1730. During fermentation, oxygen supply was switched off in order to perturb the system and observe
doi:10.1186/1752-0509-3-82 pmid:19698148 pmcid:PMC2744654 fatcat:mmit5eaw4jcbbfs6yvqus7xdii

Qupe—a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments

Stefan P. Albaum, Heiko Neuweger, Benjamin Fränzel, Sita Lange, Dominik Mertens, Christian Trötschel, Dirk Wolters, Jörn Kalinowski, Tim W. Nattkemper, Alexander Goesmann
2009 Computer applications in the biosciences : CABIOS  
The service has already been used to couple Qupe to ProMeTra, a web application to map expression values on biological pathways (Neuweger et al., 2009 ).  ...  ., 2009; Neuweger et al., 2008) . A second level of application-based security has been implemented The data access layer provides an object-relational mapping utilizing Hibernate.  ... 
doi:10.1093/bioinformatics/btp568 pmid:19808875 fatcat:xjvqxrxl4feglbgadliabizzki

Unravelling the Distribution of Secondary Metabolites in Olea europaea L.: Exhaustive Characterization of Eight Olive-Tree Derived Matrices by Complementary Platforms (LC-ESI/APCI-MS and GC-APCI-MS)

Lucía Olmo-García, Nikolas Kessler, Heiko Neuweger, Karin Wendt, José Olmo-Peinado, Alberto Fernández-Gutiérrez, Carsten Baessmann, Alegría Carrasco-Pancorbo
2018 Molecules  
In order to understand the distribution of the main secondary metabolites found in Olea europaea L., eight different samples (olive leaf, stem, seed, fruit skin and pulp, as well as virgin olive oil, olive oil obtained from stoned and dehydrated fruits and olive seed oil) coming from a Picudo cv. olive tree were analyzed. All the experimental conditions were selected so as to assure the maximum coverage of the metabolome of the samples under study within a single run. The use of LC and GC with
more » ... igh resolution MS (through different ionization sources, ESI and APCI) and the annotation strategies within MetaboScape 3.0 software allowed the identification of around 150 compounds in the profiles, showing great complementarity between the evaluated methodologies. The identified metabolites belonged to different chemical classes: triterpenic acids and dialcohols, tocopherols, sterols, free fatty acids, and several sub-types of phenolic compounds. The suitability of each platform and polarity (negative and positive) to determine each family of metabolites was evaluated in-depth, finding, for instance, that LC-ESI-MS (+) was the most efficient choice to ionize phenolic acids, secoiridoids, flavonoids and lignans and LC-APCI-MS was very appropriate for pentacyclic triterpenic acids (MS (−)) and sterols and tocopherols (MS (+)). Afterwards, a semi-quantitative comparison of the selected matrices was carried out, establishing their typical features (e.g., fruit skin was pointed out as the matrix with the highest relative amounts of phenolic acids, triterpenic compounds and hydroxylated fatty acids, and seed oil was distinctive for its high relative levels of acetoxypinoresinol and tocopherols).
doi:10.3390/molecules23102419 fatcat:iq47crdakvd2rgvfopla7v7qsm

Feature-based Molecular Networking in the GNPS Analysis Environment [article]

Louis Felix Nothias, Daniel Petras, Robin Schmid, Kai Duehrkop, Johannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, Madeleine Ernst, Hiroshi Tsugawa, Markus Fleischauer, Fabian Aicheler, Alexander Aksenov (+49 others)
2019 biorxiv/medrxiv   pre-print
Molecular networking has become a key method used to visualize and annotate the chemical space in non-targeted mass spectrometry-based experiments. However, distinguishing isomeric compounds and quantitative interpretation are currently limited. Therefore, we created Feature-based Molecular Networking (FBMN) as a new analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure. FBMN leverages feature detection and alignment tools to enhance quantitative
more » ... es and isomer distinction, including from ion-mobility spectrometry experiments, in molecular networks.
doi:10.1101/812404 fatcat:74xe2afpjfgynchh6py4bxki3a

Increasing arginine production in Corynebacterium glutamicum by rational strain design in combination with metabolomics and proteomics

Aiko Barsch, Frederik Walter, Marcus Persicke, Stephanie Kaspar-Schoenefeld, Heiko Neuweger, Nikolas Kessler, Jörn Kalinowski
2016 Proceedings of The 1st International Electronic Conference on Metabolomics   unpublished
doi:10.3390/iecm-1-b001 fatcat:r77z5iqk7ngshahmyx4yo7pvwm

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks

Jan Baumbach
2007 BMC Bioinformatics  
Rahmann and Andreas Tauch for supervising the whole project and providing the stimulon and regulation data, Karina Brinkrolf for helping with data standardization and performing Microarray experiments, Heiko  ...  Neuweger, Michael Dondrup and Alexander Goesmann for their help with the integration of the GenDB and EMMA web services, Jochen Weile for his help with the implementation of the COMA feature and for upgrading  ... 
doi:10.1186/1471-2105-8-429 pmid:17986320 pmcid:PMC2194740 fatcat:y6wvadow7jepjoy7vgtl5ml4ja

Wittgensteins Wink & Haslingers Hund Unsagbares im Sprechen über Literatur, während sie entsteht [chapter]

Claudia Dürr, Mohs VE
2019 Schreiben im Zwiegespräch / Writing as Dialogue  
Eine Epistemologie der künstlerischen Praxis, Wien: Passagen Verlag 2009. 4 | Hausendorf, Heiko: Vor dem Kunstwerk.  ...  Towards a Post-Critical Philosophy, London: Routledge & Kegan 1958. 17 | Vgl. etwa die Ausführungen zur Expertenforschung bei Neuweg, Georg Hans: Könnerschaft und implizites Wissen.  ... 
doi:10.14361/9783839440766-005 fatcat:emccurybujdkjpxbjxc4xq53tm

Mittelalter – Neuzeit

Die Redaktion
Im Gewann ‚Neuweg' fanden in den Jahren 1988 und 1989 durch Herrn Zimmermann intensive Aufsammlungen statt. Er machte die Funde mit dem Metallsuchgerät.  ...  Heiko Steuer -wurde durch Heiko Wagner am 20. 3. 2011 die Baugrube für das Bürgerhaus (Neue Ortsmitte) begangen.  ... 
doi:10.11588/fbbw.2015.0.44552 fatcat:i2qfwi4mlrgdrgntrynoabl7l4

Proposal for field sampling of plants and processing in the lab for environmental metabolic fingerprinting

Tanja S Maier, Jürgen Kuhn, Caroline Müller
2010 Plant Methods  
Acknowledgements We are grateful to Heiko Neuweger (Bielefeld University) for help with data analysis in the MeltDB platform.  ... 
doi:10.1186/1746-4811-6-6 pmid:20181048 pmcid:PMC2831887 fatcat:s6ooufca7va5jaqam53dbf2vcm
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