WorldCat Identities

Albert-Ludwigs-Universität Freiburg Professur für Bioinformatik

Overview
Works: 8 works in 8 publications in 1 language and 47 library holdings
Roles: Contributor
Publication Timeline
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Most widely held works by Albert-Ludwigs-Universität Freiburg
Modelling binding preferences of RNA-binding proteins by Daniel Maticzka( )

1 edition published in 2017 in English and held by 17 WorldCat member libraries worldwide

Computational characterisation of genomic CRISPR-Cas systems in archaea and bacteria by Omer S Alkhnbashi( )

1 edition published in 2017 in English and held by 16 WorldCat member libraries worldwide

Disseminating metaproteomic informatics capabilities and knowledge using the Galaxy-P framework by Clemens Blank( )

1 edition published in 2018 in English and held by 3 WorldCat member libraries worldwide

Abstract: The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software
MICA: multiple interval-based curve alignment by Martin Raden( )

1 edition published in 2018 in English and held by 3 WorldCat member libraries worldwide

Abstract: MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments.<br>Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data.<br>The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA
Mechanism of [beta]-actin mRNA Recognition by ZBP1 by Giuseppe Nicastro( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs by Viktoria Reimann( )

1 edition published in 2016 in English and held by 2 WorldCat member libraries worldwide

Abstract: A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Based on genetic and transcriptomic evidence, two associated endoribonucleases, Cas6-1 and Cas6-2a, were postulated to be involved in crRNA maturation from CRISPR1 or CRISPR2, respectively. Here, we report a promiscuity of both enzymes to process in vitro not only their cognate transcripts, but also the respective non-cognate precursors, whereas they are specific in vivo. Moreover, while most of the repeats serving as substrates were cleaved in vitro, some were not. RNA structure predictions suggested that the context sequence surrounding a repeat can interfere with its stable folding. Indeed, structure accuracy calculations of the hairpin motifs within the repeat sequences explained the majority of analyzed cleavage reactions, making this a good measure for predicting successful cleavage events. We conclude that the cleavage of CRISPR1 and CRISPR2 repeat instances requires a stable formation of the characteristic hairpin motif, which is similar between the two types of repeats. The influence of surrounding sequences might partially explain variations in crRNA abundances and should be considered when designing artificial CRISPR arrays
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains by Patrick R Wright( )

1 edition published in 2014 in English and held by 2 WorldCat member libraries worldwide

Abstract: CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool IntaRNA (Interacting RNAs) in order to predict tar- gets, interaction domains and consequently the regulatory networks of bacterial small RNA molecules. The CopraRNA prediction results are accompanied by extensive postprocessing methods such as functional enrichment analysis and visualization of interacting regions. Here, we introduce the functionality of the CopraRNA and IntaRNA webservers and give detailed explanations on their postprocessing functionalities. Both tools are freely accessible at http://rna.informatik.uni-freiburg.de
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems by Sita Johanna Saunders( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Abstract: Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein-binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik.uni-freiburg.de/CRISPRmap
 
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Audience level: 0.93 (from 0.92 for Modelling ... to 0.97 for Modelling ...)

Alternative Names
Albert-Ludwigs-Universität Freiburg Bioinformatics

Albert-Ludwigs-Universität Freiburg Bioinformatics Group

Albert-Ludwigs-Universität Freiburg Chair of Bioinformatics

Albert-Ludwigs-Universität Freiburg Technische Fakultät Institut für Informatik Professur für Bioinformatik

Albert-Ludwigs-Universität Freiburg Technische Fakultät Professur für Bioinformatik

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