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Browsing by Author "Renard, Bernhard Y."
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2018-02-02ZeitschriftenartikelComparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis Karayel, Özge; Şanal, Erdem; Giese, Sven H.; Kagıalı, Zeynep Cansu Üretmen; Polat, Ayşe Nur; Hu, Chi-Kuo; Renard, Bernhard Y.; Tuncbag, Nurcan; Özlü, NurhanThe successful completion of cytokinesis requires the coordinated activities of diverse cellular components including membranes, cytoskeletal elements and chromosomes that together form partly redundant pathways, depending ...
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2022-12-21ZeitschriftenartikelComprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly Beslic, Denis; Tscheuschner, Georg; Renard, Bernhard Y.; Weller, Michael G.; Muth, ThiloMonoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential ...
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2019-12-09ZeitschriftenartikelComputational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters Jandrasits, Christine; Kröger, Stefan; Haas, Walter; Renard, Bernhard Y.Next-generation sequencing based base-by-base distance measures have become an integral complement to epidemiological investigation of infectious disease outbreaks. This study introduces PANPASCO, a computational pan-genome ...
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2012-09-27ZeitschriftenartikelConfidence-based Somatic Mutation Evaluation and Prioritization Löwer, Martin; Renard, Bernhard Y.; Graaf, Jos de; Wagner, Meike; Paret, Claudia; Kneip, Christoph; Türeci, Özlem; Diken, Mustafa; Britten, Cedrik; Kreiter, Sebastian; Koslowski, Michael; Castle, John C.; Sahin, UgurNext generation sequencing (NGS) has enabled high throughput discovery of somatic mutations. Detection depends on experimental design, lab platforms, parameters and analysis algorithms. However, NGS-based somatic mutation ...
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2021-12-15ZeitschriftenartikelCritical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows van den Bossche, Tim; Kunath, Benoit J.; Schallert, Kay; Schäpe, Stephanie S.; Abraham, Paul E.; Armengaud, Jean; Arntzen, Magnus Ø.; Bassignani, Ariane; Benndorf, Dirk; fuchs, Stephan; Giannone, Richard J.; Griffin, Timothy J.; Hagen, Live H.; Halder, Rashi; Henry, Céline; Hettich, Robert L.; Heyer, Robert; Jagtap, Patrik; Jehmlich, Nico; Jensen, Marlene; Juste, Catherine; Kleiner, Manuel; Langella, Olivier; Lehmann, Theresa; Leith, Emma; May, Patrick; Mesuere, Patrick; Miotello, Guylaine; Peters, Samantha L.; Pible, Olivier; Queiros, Pedro T.; Reichl, Udo; Renard, Bernhard Y.; Schiebenhoefer, Henning; Sczyrba, Alexander; Tanca, Allesandro; Trappe, Kathrin; Trezzi, Jean-Pierre; Uzzau, Sergio; Verschaffelt, Pieter; von Bergen, Martin; Wilmes, Paul; Wolf, Maximilian; Martens, Lennart; Muth, ThiloMetaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, ...
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2019-10-11ZeitschriftenartikelDendritic Cells Generated From Mops condylurus, a Likely Filovirus Reservoir Host, Are Susceptible to and Activated by Zaire Ebolavirus Infection Edenborough, Kathryn M.; Bokelmann, Marcel; Lander, Angelika; Couacy-Hymann, Emmanuel; Lechner, Johanna; Drechsel, Oliver; Renard, Bernhard Y.; Radonić, Aleksandar; Feldmann, Heinz; Kurth, Andreas; Prescott, JosephEbola virus infection of human dendritic cells (DCs) induces atypical adaptive immune responses and thereby exacerbates Ebola virus disease (EVD). Human DCs, infected with Ebola virus aberrantly express low levels of the ...
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2015-09-24ZeitschriftenartikelFirst Draft Genome Sequence of Balamuthia mandrillaris, the Causative Agent of Amoebic Encephalitis Detering, H.; Aebischer, Toni; Dabrowski, Piotr Wojtek; Radonić, Aleksandar; Nitsche, Andreas; Renard, Bernhard Y.; Kiderlen, AlbrechtThe free-living amoeba Balamuthia mandrillaris is a rare but highly lethal agent of amoebic encephalitis in humans and many other mammalian species. Here, we announce the first draft genome sequence of the original 1990 ...
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2020-12-07ZeitschriftenartikelFLEXIQuant-LF to quantify protein modification extent in label-free proteomics data Schlaffner, Christoph N.; Kahnert, Konstantin; Muntel, Jan; Chauhan, Ruchi; Renard, Bernhard Y.; Steen, Judith A.; Steen, HannoImprovements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, ...
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2020-07-13Zeitschriftenartikelganon: precise metagenomics classification against large and up-to-date sets of reference sequences Piro, Victor C.; Dadi, Temesgen H.; Seiler, Enrico; Reinert, Knut; Renard, Bernhard Y.Motivation The exponential growth of assembled genome sequences greatly benefits metagenomics studies. However, currently available methods struggle to manage the increasing amount of sequences and their frequent updates. ...
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2020-01-14ZeitschriftenartikelImproving tuberculosis surveillance by detecting international transmission using publicly available whole genome sequencing data Sanchini, Andrea; Jandrasits, Christine; Tembrockhaus, Julius; Kohl, Thomas Andreas; Utpatel, Christian; Maurer, Florian P.; Niemann, Stefan; Haas, Walter; Renard, Bernhard Y.; Kröger, StefanImproving the surveillance of tuberculosis (TB) is one of the eight core activities identified by the World Health Organization (WHO) and the European Respiratory Society to achieve TB elimination, defined as less than one ...
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2021-02-01ZeitschriftenartikelInterpretable detection of novel human viruses from genome sequencing data Bartoszewicz, Jakub M.; Seidel, Anja; Renard, Bernhard Y.Viruses evolve extremely quickly, so reliable meth- ods for viral host prediction are necessary to safe- guard biosecurity and biosafety alike. Novel human- infecting viruses are difficult to detect with stan- dard ...
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2012-12-04ZeitschriftenartikeliPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations Kuhring, Mathias; Renard, Bernhard Y.Proteogenomic approaches have gained increasing popularity, however it is still difficult to integrate mass spectrometry identifications with genomic data due to differing data formats. To address this difficulty, we ...
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2015-02-26ZeitschriftenartikelIPred - integrating ab initio and evidence based gene predictions to improve prediction accuracy Zickmann, Franziska; Renard, Bernhard Y.Background: Gene prediction is a challenging but crucial part in most genome analysis pipelines. Various methods have evolved that predict genes ab initio on reference sequences or evidence based with the help of ...
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2011-09-30ZeitschriftenartikelLife cycle stage-resolved proteomic analysis of the excretome/secretome from Strongyloides ratti - identification of stage-specific proteases. Soblik, Hanns; Younis, Abuelhassan Elshazly; Mitreva, Makedonka; Renard, Bernhard Y.; Kirchner, Marc; Geisinger, Frank; Steen, Hanno; Brattig, Norbert W.A wide range of biomolecules, including proteins, are excreted and secreted from helminths and contribute to the parasite's successful establishment, survival, and reproduction in an adverse habitat. Excretory and secretory ...
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2012-08-31ZeitschriftenartikelMetagenomic abundance estimation and diagnostic testing on species level Lindner, Martin S.; Renard, Bernhard Y.One goal of sequencing-based metagenomic community analysis is the quantitative taxonomic assessment of microbial community compositions. In particular, relative quantification of taxons is of high relevance for metagenomic ...
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2015-02-02ZeitschriftenartikelMetagenomic Profiling of Known and Unknown Microbes with MicrobeGPS Lindner, Martin S.; Renard, Bernhard Y.Microbial community profiling identifies and quantifies organisms in metagenomic sequencing data using either reference based or unsupervised approaches. However, current reference based profiling methods only report the ...
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2017-12-07ZeitschriftenartikelMPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go Muth, Thilo; Kohrs, Fabian; Heyer, Robert; Benndorf, Dirk; Rapp, Erdmann; Reichl, Udo; Martens, Lennart; Renard, Bernhard Y.Metaproteomics, the mass spectrometry-based analysis of proteins from multispecies samples faces severe challenges concerning data analysis and results interpretation. To overcome these shortcomings, we here introduce ...
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2015-06-15ZeitschriftenartikelMSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms Zickmann, Franziska; Renard, Bernhard Y.Ongoing advances in high-throughput technologies have facilitated accurate proteomic measurements and provide a wealth of information on genomic and transcript level. In proteogenomics, this multi-omics data is combined ...
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2012-04-06ZeitschriftenartikelOvercoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS) Renard, Bernhard Y.; Xu, Buote; Kirchner, Marc; Zickmann, Franziska; Winter, Dominic; Korten, Simone; Brattig, Norbert W.; Tzur, Amit; Hamprecht, Fred A.; Steen, HannoCurrently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without ...
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2012-04-06ZeitschriftenartikelOvercoming species boundaries in peptide identification with BICEPS Renard, Bernhard Y.; Xu, Buote; Kirchner, Marc; Zickmann, Franziska; Winter, Dominic; Korten, Simone; Brattig, Norbert W.; Tzur, Amit; Hamprecht, Fred A.; Steen, HannoCurrently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. While sequencing capacities continue to grow, many organisms remain without ...