Dr. Peter Meinicke

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  • 2020 | Journal Article | 
    ​ ​Wemheuer, Franziska, Jessica A. Taylor, Rolf Daniel, Emma Johnston, Peter Meinicke, Torsten Thomas, and Bernd Wemheuer. "Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences​." ​Environmental Microbiome ​15, no. 1 (2020): . ​https://doi.org/10.1186/s40793-020-00358-7.
    ​Details  DOI 
  • 2018 | Preprint
    ​ ​Wemheuer, Franziska, Jessica A. Taylor, Rolf Daniel, Emma Johnston, Peter Meinicke, Torsten Thomas, and Bernd Wemheuer​. "Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences​." ​Preprint, submitted ​​2018. https://doi.org/10.1101/490037.
    ​Details  DOI 
  • 2017 | Journal Article | 
    ​ ​Sczyrba, Alexander, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor et al. "Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software​." ​Nature Methods ​14, no. 11 (2017): ​1063​-1071​. ​https://doi.org/10.1038/nmeth.4458.
    ​Details  DOI 
  • 2017 | Journal Article | 
    ​ ​Klingenberg, Heiner, and Peter Meinicke. "How to normalize metatranscriptomic count data for differential expression analysis.​." ​PeerJ ​5 (2017): ​e3859​. ​https://doi.org/10.7717/peerj.3859.
    ​Details  DOI  PMID  PMC 
  • 2015 | Journal Article | 
    ​ ​Kaever, Alexander, Manuel Landesfeind, Kirstin Feussner, Alina Mosblech, Ingo Heilmann, Burkhard Morgenstern, Ivo Feussner, and Peter Meinicke. "MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data​." ​Metabolomics ​11, no. 3 (2015): ​764​-777​. ​https://doi.org/10.1007/s11306-014-0734-y.
    ​Details  DOI  WoS 
  • 2015 | Journal Article | 
    ​ ​Aßhauer, Kathrin Petra, Bernd Wemheuer, Rolf Daniel, and Peter Meinicke. "Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data​." ​Bioinformatics ​31, no. 17 (2015): ​2882​-2884​. ​https://doi.org/10.1093/bioinformatics/btv287.
    ​Details  DOI  PMID  PMC  WoS 
  • 2015 | Journal Article | 
    ​ ​Meinicke, Peter. "UProC: tools for ultra-fast protein domain classification​." ​Bioinformatics ​31, no. 9 (2015): ​1382​-1388​. ​https://doi.org/10.1093/bioinformatics/btu843.
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article
    ​ ​Hoppenau, Clara E., Van-Tuan Tran, Harald Kusch, Kathrin P. Aßhauer, Manuel Landesfeind, Peter Meinicke, Blagovesta Popova, Susanna A. Braus-Stromeyer, and Gerhard H. Braus. "Verticillium dahliae VdTHI4, involved in thiazole biosynthesis, stress response and DNA repair functions, is required for vascular disease induction in tomato​." ​Environmental and Experimental Botany ​108 (2014): ​14​-22​. ​https://doi.org/10.1016/j.envexpbot.2013.12.015.
    ​Details  DOI 
  • 2014 | Journal Article
    ​ ​Nacke, Heiko, Christiane Fischer, Andrea Thuermer, Peter Meinicke, and Rolf Daniel. "Land Use Type Significantly Affects Microbial Gene Transcription in Soil​." ​Microbial Ecology ​67, no. 4 (2014): ​919​-930​. ​https://doi.org/10.1007/s00248-014-0377-6.
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Asshauer, Kathrin Petra, Heiner Klingenberg, Thomas Lingner, and Peter Meinicke. "Exploring Neighborhoods in the Metagenome Universe​." ​International Journal of Molecular Sciences ​15, no. 7 (2014): ​12364​-12378​. ​https://doi.org/10.3390/ijms150712364.
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Kaever, Alexander, Manuel Landesfeind, Kirstin Feussner, Burkhard Morgenstern, Ivo Feussner, and Peter Meinicke. "Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets​." ​PLoS ONE ​9, no. 2 (2014): ​e89297​. ​https://doi.org/10.1371/journal.pone.0089297.
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Landesfeind, Manuel, Alexander Kaever, Kirstin Feussner, Corinna Thurow, Christiane Gatz, Ivo Feussner, and Peter Meinicke. "Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software​." ​PeerJ ​2 (2014): ​e239​. ​https://doi.org/10.7717/peerj.239.
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Landesfeind, Manuel, and Peter Meinicke. "Predicting the functional repertoire of an organism from unassembled RNA-seq data​." ​BMC Genomics ​15 (2014): ​1003​. ​https://doi.org/10.1186/1471-2164-15-1003.
    ​Details  DOI  PMID  PMC  WoS 
  • 2013 | Journal Article
    ​ ​Klingenberg, Heiner, Kathrin Petra Assauer, Thomas Lingner, and Peter Meinicke. "Protein signature-based estimation of metagenomic abundances including all domains of life and viruses​." ​Bioinformatics ​29, no. 8 (2013): ​973​-980​. ​https://doi.org/10.1093/bioinformatics/btt077.
    ​Details  DOI  PMID  PMC  WoS 
  • 2012 | Journal Article
    ​ ​Bulla, Ingo, Anne-Kathrin Schultz, and Peter Meinicke. "Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 Subtypes through Linear Classifier Learning​." ​Statistical Applications in Genetics and Molecular Biology ​11, no. 1 (2012): ​1​. ​https://doi.org/10.2202/1544-6115.1680.
    ​Details  DOI  WoS 
  • 2012 | Journal Article | 
    ​ ​Danielsen, Lara, A. Thürmer, P. Meinicke, Marc Buée, E. Morin, Francis Martin, Gilles Pilate, Rolf Daniel, Andrea Polle, and M. Reich. "Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities​." ​Ecology and Evolution ​2, no. 8 (2012): ​1935​-1948​. ​https://doi.org/10.1002/ece3.305.
    ​Details  DOI 
  • 2012 | Journal Article | 
    ​ ​Kaever, Alexander, Manuel Landesfeind, Mareike Possienke, Kirstin Feussner, Ivo Feussner, and Peter Meinicke. "MarVis-Filter: Ranking, Filtering, Adduct and Isotope Correction of Mass Spectrometry Data​." ​JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY (2012): ​263910​. ​https://doi.org/10.1155/2012/263910.
    ​Details  DOI  WoS 
  • 2011 | Journal Article
    ​ ​Djamei, Armin, Kerstin Schipper, Franziska Rabe, Anupama Ghosh, Volker Vincon, Joerg Kahnt, Sonia Osorio et al. "Metabolic priming by a secreted fungal effector​." ​Nature ​478, no. 7369 (2011): ​395​. ​https://doi.org/10.1038/nature10454.
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article | 
    ​ ​Lingner, Thomas, Kathrin Petra Asshauer, Fabian Schreiber, and Peter Meinicke. "CoMet-a web server for comparative functional profiling of metagenomes​." ​Nucleic Acids Research ​39 (2011): ​W518​-W523​. ​https://doi.org/10.1093/nar/gkr388.
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  • 2011 | Journal Article
    ​ ​Lingner, Thomas, Amr R. Kataya, Gerardo E. Antonicelli, Aline Benichou, Kjersti Nilssen, Xiong-Yan Chen, Tanja Siemsen, Burkhard Morgenstern, Peter Meinicke, and Sigrun Reumann. "Identification of Novel Plant Peroxisomal Targeting Signals by a Combination of Machine Learning Methods and in Vivo Subcellular Targeting Analyses​." ​The Plant Cell ​23, no. 4 (2011): ​1556​-1572​. ​https://doi.org/10.1105/tpc.111.084095.
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article
    ​ ​Meinicke, Peter, Kathrin Petra Asshauer, and Thomas Lingner. "Mixture models for analysis of the taxonomic composition of metagenomes​." ​Bioinformatics ​27, no. 12 (2011): ​1618​-1624​. ​https://doi.org/10.1093/bioinformatics/btr266.
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article
    ​ ​Schreiber, Fabian, Peter Gumrich, Rolf Daniel, and Peter Meinicke. "Treephyler: fast taxonomic profiling of metagenomes​." ​Bioinformatics ​26, no. 7 (2010): ​960​-961​. ​https://doi.org/10.1093/bioinformatics/btq070.
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article
    ​ ​Nahlik, Krystyna, Marc Dumkow, Ozgür Bayram, Kerstin Helmstaedt, Silke Busch, Oliver Valerius, Jennifer Gerke et al. "The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development​." ​Molecular Microbiology ​78, no. 4 (2010): ​964​-979​. ​https://doi.org/10.1111/j.1365-2958.2010.07384.x.
    ​Details  DOI  PMID  PMC 
  • 2010 | Journal Article | 
    ​ ​Subramanian, Amarendran R., Suvrat Hiran, Rasmus Steinkamp, Peter Meinicke, Eduardo Corel, and Burkhard Morgenstern. "DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS​." ​Nucleic Acids Research ​38 (2010): ​W19​-W22​. ​https://doi.org/10.1093/nar/gkq442.
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article | 
    ​ ​Lingner, Thomas, Stefanie Muehlhausen, Toni Gabaldon, Cedric Notredame, and Peter Meinicke. "Predicting phenotypic traits of prokaryotes from protein domain frequencies​." ​BMC Bioinformatics ​11 (2010): ​481​. ​https://doi.org/10.1186/1471-2105-11-481.
    ​Details  DOI  PMID  PMC  WoS 
  • 2009 | Conference Abstract
    ​ ​Goebel, C., Kristin Feussner, Alexander Kaever, Peter Meinicke, Burkhard Morgenstern, and Ivo Feussner. "Identification of metabolic changes after wounding in Arabidopsis thaliana by an unbiased UPLC-MS approach​." ​Chemistry and Physics of Lipids ​160​ ​(2009): https://doi.org/10.1016/j.chemphyslip.2009.06.024.
    ​Details  DOI  WoS 
  • 2009 | Journal Article | 
    ​ ​Hoff, Katharina J., Thomas Lingner, Peter Meinicke, and Maike Tech. "Orphelia: predicting genes in metagenomic sequencing reads​." ​Nucleic Acids Research ​37 (2009): ​W101​-W105​. ​https://doi.org/10.1093/nar/gkp327.
    ​Details  DOI  PMID  PMC  WoS 
  • 2009 | Journal Article | 
    ​ ​Kaever, Alexander, Thomas Lingner, Kirstin Feussner, Cornelia Goebel, Ivo Feussner, and Peter Meinicke. "MarVis: a tool for clustering and visualization of metabolic biomarkers​." ​BMC Bioinformatics ​10 (2009): ​92​. ​https://doi.org/10.1186/1471-2105-10-92.
    ​Details  DOI  PMID  PMC  WoS 
  • 2009 | Review | 
    ​ ​Meinicke, Peter. "UFO: a web server for ultra-fast functional profiling of whole genome protein sequences​." BMC Genomics ​10​ (2009): ​409​. ​https://doi.org/10.1186/1471-2164-10-409.
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Meinicke, Peter, Thomas Lingner, Alexander Kaever, Kirstin Feussner, Cornelia Goebel, Ivo Feussner, Petr Karlovsky, and Burkhard Morgenstern. "Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps​." ​Algorithms for Molecular Biology ​3 (2008): ​9​. ​https://doi.org/10.1186/1748-7188-3-9.
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Hoff, Katharina J., Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, and Peter Meinicke. "Gene prediction in metagenomic fragments: A large scale machine learning approach​." ​BMC Bioinformatics ​9 (2008): ​217​. ​https://doi.org/10.1186/1471-2105-9-217.
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Lingner, Thomas, and Peter Meinicke. "Word correlation matrices for protein sequence analysis and remote homology detection​." ​BMC Bioinformatics ​9 (2008): ​259​. ​https://doi.org/10.1186/1471-2105-9-259.
    ​Details  DOI  PMID  PMC  WoS 
  • 2007 | Journal Article
    ​ ​Igel, Christian, Tobias Glasmachers, Britta Mersch, Nico Pfeifer, and Peter Meinicke. "Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detection​." ​IEEE/ACM Transactions on Computational Biology and Bioinformatics ​4, no. 2 (2007): ​216​-226​. ​https://doi.org/10.1109/tcbb.2007.070208.
    ​Details  DOI  PMID  PMC  WoS 
  • 2007 | Journal Article
    ​ ​Mersch, Britta, Tobias Glasmachers, Peter Meinicke, and Christian Igel. "Evolutionary optimization of sequence kernels for detection of bacterial gene starts​." ​International Journal of Neural Systems ​17, no. 5 (2007): ​369​-381​. ​https://doi.org/10.1142/S0129065707001214.
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Conference Paper
    ​ ​Mersch, Britta, Tobias Glasmachers, Peter Meinicke, and Christian Igel. "Evolutionary optimization of sequence kernels for detection of bacterial gene starts​." ​In Artificial neural networks - ICANN 2006, edited by Stefanos Kollias. ​827​-836. Vol. 2. ​Berlin, Heidelberg: ​Springer, ​2006. https://doi.org/10.1007/11840930_86.
    ​Details  DOI  WoS 
  • 2006 | Journal Article
    ​ ​Lingner, Thomas, and Peter Meinicke. "Remote homology detection based on oligomer distances​." ​Bioinformatics ​22, no. 18 (2006): ​2224​-2231​. ​https://doi.org/10.1093/bioinformatics/btl376.
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Tech, Maike, Burkhard Morgenstern, and Peter Meinicke. "TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites​." ​Nucleic Acids Research ​34 (2006): ​W588​-W590​. ​https://doi.org/10.1093/nar/gkl313.
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Waack, Stephan, Oliver Keller, Roman Asper, Thomas Brodag, Carsten Damm, Wolfgang Florian Fricke, Katharina Surovcik, Peter Meinicke, and Rainer Merkl. "Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models​." ​BMC Bioinformatics ​7 (2006): ​142​. ​https://doi.org/10.1186/1471-2105-7-142.
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  • 2006 | Journal Article | 
    ​ ​Tech, Maike, and Peter Meinicke. "An unsupervised classification scheme for improving predictions of prokaryotic TIS​." ​BMC Bioinformatics ​7 (2006): ​121​. ​https://doi.org/10.1186/1471-2105-7-121.
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Meinicke, Peter, Thomas Brodag, Wolfgang Florian Fricke, and Stephan Waack. "P-value based visualization of codon usage data​." ​Algorithms for Molecular Biology ​1 (2006): ​10​. ​https://doi.org/10.1186/1748-7188-1-10.
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article
    ​ ​Meinicke, Peter, S. Klanke, R. Memisevic, and H. Ritter. "Principal surfaces from unsupervised kernel regression​." ​IEEE Transactions on Pattern Analysis and Machine Intelligence ​27, no. 9 (2005): ​1379​-1391​. ​https://doi.org/10.1109/TPAMI.2005.183.
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article
    ​ ​Tech, Maike, N. Pfeifer, Burkhard Morgenstern, and Peter Meinicke. "TICO: a tool for improving predictions of prokaryotic translation initiation sites​." ​Bioinformatics ​21, no. 17 (2005): ​3568​-3569​. ​https://doi.org/10.1093/bioinformatics/bti563.
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article
    ​ ​Kaper, M., Peter Meinicke, U. Grossekathoefer, Thomas Lingner, and H. Ritter. "BCI competition 2003 - Data set IIb: Support vector machines for the P300 speller paradigm​." ​IEEE Transactions on Biomedical Engineering ​51, no. 6 (2004): ​1073​-1076​. ​https://doi.org/10.1109/TBME.2004.826698.
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  • 2004 | Journal Article | 
    ​ ​Meinicke, Peter, Maike Tech, Burkhard Morgenstern, and R. Merkl. "Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites​." ​BMC Bioinformatics ​5 (2004): ​169​. ​https://doi.org/10.1186/1471-2105-5-169.
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  • 2001 | Journal Article
    ​ ​Meinicke, Peter, and Helge Ritter. "Resolution-Based Complexity Control for Gaussian Mixture Models​." ​Neural Computation ​13, no. 2 (2001): ​453​-475​. ​https://doi.org/10.1162/089976601300014600.
    ​Details  DOI 

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