Manuscripts of the de.NBI special issue in Journal of Biotechnology:

 

  • Journal of Biotechnology 09/17, "The SeqAn C++ template library for efficient sequence analysis: A resource for programmers" by K. Reinert, T. H. Dadi, M. Ehrhardt, H. Hauswedell, S. Mehringer, R. Rahn, J. Kim, C. Pockrandt, J. Winkler, E. Siragusa, G. Urgese, D. Weese
  • Journal of Biotechnology 08/17, "Bioinformatics for NGS-based metagenomics and the application to biogas research" by S. Jünemann, N. Kleinbölting, S. Jaenicke, C. Henke, J. Hassa, J. Nelkner, Y. Stolze, S. P. Albaum, A. Schlüter, A. Goesmann, A. Sczyrba, J. Stoye
  • Journal of Biotechnology 08/17, "Strategies for analyzing bisulfite sequencing data" by K. Wreczycka, A. Gosdschan, D. Yusuf, B. Grüning, Y. Assenov, A. Akalin
  • Journal of Biotechnology 08/17, "Lipidomics informatics for life-science" by D. Schwudke, A. Shevchenko, N. Hoffmann, R. Ahrends
  • Journal of Biotechnology 08/17, "OTP: An automatized system for managing and processing NGS data" by E. Reisinger, L. Genthner, J. Kerssemakers, P. Kensche, S. Borufka, A. Jugold, A. Kling, M. Prinz, I. Scholz, G. Zipprich, R. Eils, C. Lawerenz, J. Eils
  • Journal of Biotechnology 08/17, "Terminology supported archiving and publication of environmental science data in PANGAEA" M. Diepenbroek, U. Schindler, R. Huber, S. Pesant, M. Stocker, J. Felden, M. Buss, M. Weinrebe
  • Journal of Biotechnology 08/17, "Workflows for microscopy image analysis and cellular phenotyping", by T. Wollmann, H. Erfle, R. Eils, K. Rohr, M. Gunkel
  • Journal of Biotechnology 08/17, "KNIME for reproducible cross-domain analysis of life science data", by A. Fillbrunn, C. Dietz, J. Pfeuffer, R. Rahn, G. A. Landrum, M. R. Berthold
  • Journal of Biotechnology 07/17, "A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies", by J. Yu, J. Blom, S.P. Glaeser, S. Jaenicke, T. Juhre, O. Rupp, O. Schwengers, S. Spänig, A. Goesmann
  • Journal of Biotechnology 07/17, "Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives", by T. Schmutzer, M. E. Bolger, S. Rudd, J. Chen, H. Gundlach, D. Arend, M. Oppermann, S. Weise, M. Lange, M. Spannagl, B. Usadel, K. F.X. Mayer, U. Scholz
  • Journal of Biotechnology 07/17, "Recent advances in RNA folding", by J. Fallmann, S. Will, J. Engelhardt, B. Grüning, R. Backofen, P. F. Stadler
  • Journal of Biotechnology 07/17, "Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments", by S. C. Lott, M. Wolfien, K. Riege, A. Bagnacani, O. Wolkenhauer, S. Hoffmann, W. R. Hess
  • Journal of Biotechnology 07/17, "Challenges and perspectives of metaproteomic data analysis", by R. Heyer, K. Schallert, R. Zoun, B. Becher, G. Saake, D. Benndorf
  • Journal of Biotechnology 07/17, "Phenotype databases for genetic screens in human cells", by B. Rauscher, E. Valentini, U. Hardeland, M. Boutros
  • Journal of Biotechnology 07/17, "From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library", by S. Bietz, T. Inhester, F. Lauck, K. Sommer, M. M. von Behren, R. Fährrolfes, F. Flachsenberg, A. Meyder, E. Nittinger, T. Otto, M. Hilbig, K. T. Schomburg, A. Volkamer, M. Rarey
  • Journal of Biotechnology 07/17, "RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation", by R. Backofen, J. Engelhardt, A. Erxleben, J. Fallmann, B. Grüning, U. Ohler, N. Rajewsky, P. F. Stadler
  • Journal of Biotechnology 07/17, "25 years of serving the community with ribosomal RNA gene reference databases and tools", by F. O. Glöckner, P. Yilmaz, C. Quast, J. Gerken, A. Beccati, A. Ciuprina, G. Bruns, P. Yarzac, J. Peplies, R. Westram, W. Ludwig
  • Journal of Biotechnology 07/17, "COPASI and its applications in biotechnology", by F. T. Bergmann, S. Hoops, B. Klahn, U. Kummer, P. Mendes, J. Pahle, S. Sahle
  • Journal of Biotechnology 07/17, "Computational proteomics tools for identification and quality control", by D. Kopczynski, A. Sickmann, R. Ahrends
  • Journal of Biotechnology 07/17, "Data management and data enrichment for systems biology projects", by U. Wittig, M. Rey, A. Weidemann, W. Müller
  • Journal of Biotechnology 06/17, "OpenMS – A platform for reproducible analysis of mass spectrometry data", by J. Pfeuffer, T. Sachsenberg, O. Alka, M. Walzer, A. Fillbrunn, L. Nilse, O. Schilling, K. Reinert, O. Kohlbacher
  • Journal of Biotechnology 06/17, "BioInfra.Prot: A Comprehensive Proteomics Workflow Including Data Standardization, Protein Inference, Expression Analysis and Data Publication", by M. Turewicz, M. Kohl, M. Ahrens, G. Mayer, J. Uszkoreit, W. Naboulsi, T. Bracht, D.A. Megger, B. Sitek, K. Marcus, M. Eisenacher
  • Journal of Biotechnology 06/17, "From Plant Genomes to Phenotypes", by M. Bolger M, R. Schwacke, H. Gundlach, T. Schmutzer, J. Chen, D. Arend, M. Oppermann, S. Weise, M. Lange, F. Fiorani, M. Spannagl, U. Scholz, K. Mayer, B. Usadel
  • Journal of Biotechnology 05/17, "Bioinformatics can boost metabolomics research", by R. Meier, C. Ruttkies, H. Treutler, S. Neumann
  • Journal of Biotechnology 05/17, "Use of CellNetAnalyzer in biotechnology and metabolic engineering", by von A. von Kamp, S. Thiele, O. Hädicke, S. Klamt
  • Journal of Biotechnology 05/17, "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase", by L. C. Reimer, C. Söhngen, A. Vetcininova, J. Overmann
  • Journal of Biotechnology 04/17, "The BRENDA enzyme information system–From a database to an expert system", by I. Schomburg, L. Jeske, M. Ulbrich, S. Placzek, A. Chang, D. Schomburg