Dr. Peter Meinicke

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  • 2020 | Journal Article | 
    ​ ​Wemheuer, Franziska, et al. "Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences​." ​Environmental Microbiome, vol. 15, no. 1, ​2020, , ​doi: 10.1186/s40793-020-00358-7. 
    ​Details  DOI 
  • 2018 | Preprint
    ​ ​Wemheuer, Franziska, et al. "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​." ​​2018. doi: 10.1101/490037. 
    ​Details  DOI 
  • 2017 | Journal Article | 
    ​ ​Sczyrba, Alexander, et al. "Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software​." ​Nature Methods, vol. 14, no. 11, ​2017, pp. 1063​-1071​, ​doi: 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, vol. 5, ​2017, , ​doi: 10.7717/peerj.3859. 
    ​Details  DOI  PMID  PMC 
  • 2015 | Journal Article | 
    ​ ​Kaever, Alexander, et al. "MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data​." ​Metabolomics, vol. 11, no. 3, ​2015, pp. 764​-777​, ​doi: 10.1007/s11306-014-0734-y. 
    ​Details  DOI  WoS 
  • 2015 | Journal Article | 
    ​ ​Aßhauer, Kathrin Petra, et al. "Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data​." ​Bioinformatics, vol. 31, no. 17, ​2015, pp. 2882​-2884​, ​doi: 10.1093/bioinformatics/btv287. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2015 | Journal Article | 
    ​ ​Meinicke, Peter. "UProC: tools for ultra-fast protein domain classification​." ​Bioinformatics, vol. 31, no. 9, ​2015, pp. 1382​-1388​, ​doi: 10.1093/bioinformatics/btu843. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article
    ​ ​Hoppenau, Clara E., et al. "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, vol. 108, ​2014, pp. 14​-22​, ​doi: 10.1016/j.envexpbot.2013.12.015. 
    ​Details  DOI 
  • 2014 | Journal Article
    ​ ​Nacke, Heiko, et al. "Land Use Type Significantly Affects Microbial Gene Transcription in Soil​." ​Microbial Ecology, vol. 67, no. 4, ​2014, pp. 919​-930​, ​doi: 10.1007/s00248-014-0377-6. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Asshauer, Kathrin Petra, et al. "Exploring Neighborhoods in the Metagenome Universe​." ​International Journal of Molecular Sciences, vol. 15, no. 7, ​2014, pp. 12364​-12378​, ​doi: 10.3390/ijms150712364. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Kaever, Alexander, et al. "Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets​." ​PLoS ONE, vol. 9, no. 2, ​2014, , ​doi: 10.1371/journal.pone.0089297. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Landesfeind, Manuel, et al. "Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software​." ​PeerJ, vol. 2, ​2014, , ​doi: 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, vol. 15, ​2014, , ​doi: 10.1186/1471-2164-15-1003. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2013 | Journal Article
    ​ ​Klingenberg, Heiner, et al. "Protein signature-based estimation of metagenomic abundances including all domains of life and viruses​." ​Bioinformatics, vol. 29, no. 8, ​2013, pp. 973​-980​, ​doi: 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, vol. 11, no. 1, ​2012, , ​doi: 10.2202/1544-6115.1680. 
    ​Details  DOI  WoS 
  • 2012 | Journal Article | 
    ​ ​Danielsen, Lara, et al. "Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities​." ​Ecology and Evolution, vol. 2, no. 8, ​2012, pp. 1935​-1948​, ​doi: 10.1002/ece3.305. 
    ​Details  DOI 
  • 2012 | Journal Article | 
    ​ ​Kaever, Alexander, et al. "MarVis-Filter: Ranking, Filtering, Adduct and Isotope Correction of Mass Spectrometry Data​." ​JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY, ​2012, , ​doi: 10.1155/2012/263910. 
    ​Details  DOI  WoS 
  • 2011 | Journal Article
    ​ ​Djamei, Armin, et al. "Metabolic priming by a secreted fungal effector​." ​Nature, vol. 478, no. 7369, ​2011, p. 395​, ​doi: 10.1038/nature10454. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article | 
    ​ ​Lingner, Thomas, et al. "CoMet-a web server for comparative functional profiling of metagenomes​." ​Nucleic Acids Research, vol. 39, ​2011, pp. W518​-W523​, ​doi: 10.1093/nar/gkr388. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article
    ​ ​Lingner, Thomas, et al. "Identification of Novel Plant Peroxisomal Targeting Signals by a Combination of Machine Learning Methods and in Vivo Subcellular Targeting Analyses​." ​The Plant Cell, vol. 23, no. 4, ​2011, pp. 1556​-1572​, ​doi: 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, vol. 27, no. 12, ​2011, pp. 1618​-1624​, ​doi: 10.1093/bioinformatics/btr266. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article
    ​ ​Schreiber, Fabian, et al. "Treephyler: fast taxonomic profiling of metagenomes​." ​Bioinformatics, vol. 26, no. 7, ​2010, pp. 960​-961​, ​doi: 10.1093/bioinformatics/btq070. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article
    ​ ​Nahlik, Krystyna, et al. "The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development​." ​Molecular Microbiology, vol. 78, no. 4, ​2010, pp. 964​-979​, ​doi: 10.1111/j.1365-2958.2010.07384.x. 
    ​Details  DOI  PMID  PMC 
  • 2010 | Journal Article | 
    ​ ​Subramanian, Amarendran R., et al. "DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS​." ​Nucleic Acids Research, vol. 38, ​2010, pp. W19​-W22​, ​doi: 10.1093/nar/gkq442. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article | 
    ​ ​Lingner, Thomas, et al. "Predicting phenotypic traits of prokaryotes from protein domain frequencies​." ​BMC Bioinformatics, vol. 11, ​2010, , ​doi: 10.1186/1471-2105-11-481. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2009 | Conference Abstract
    ​ ​Goebel, C., et al. "Identification of metabolic changes after wounding in Arabidopsis thaliana by an unbiased UPLC-MS approach​." ​Chemistry and Physics of Lipids, vol. 160, ​2009, . ​doi: 10.1016/j.chemphyslip.2009.06.024. 
    ​Details  DOI  WoS 
  • 2009 | Journal Article | 
    ​ ​Hoff, Katharina J., et al. "Orphelia: predicting genes in metagenomic sequencing reads​." ​Nucleic Acids Research, vol. 37, ​2009, pp. W101​-W105​, ​doi: 10.1093/nar/gkp327. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2009 | Journal Article | 
    ​ ​Kaever, Alexander, et al. "MarVis: a tool for clustering and visualization of metabolic biomarkers​." ​BMC Bioinformatics, vol. 10, ​2009, , ​doi: 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, vol. 10, ​2009, , ​doi: 10.1186/1471-2164-10-409. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Meinicke, Peter, et al. "Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps​." ​Algorithms for Molecular Biology, vol. 3, ​2008, , ​doi: 10.1186/1748-7188-3-9. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Hoff, Katharina J., et al. "Gene prediction in metagenomic fragments: A large scale machine learning approach​." ​BMC Bioinformatics, vol. 9, ​2008, , ​doi: 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, vol. 9, ​2008, , ​doi: 10.1186/1471-2105-9-259. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2007 | Journal Article
    ​ ​Igel, Christian, et al. "Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detection​." ​IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. 2, ​2007, pp. 216​-226​, ​doi: 10.1109/tcbb.2007.070208. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2007 | Journal Article
    ​ ​Mersch, Britta, et al. "Evolutionary optimization of sequence kernels for detection of bacterial gene starts​." ​International Journal of Neural Systems, vol. 17, no. 5, ​2007, pp. 369​-381​, ​doi: 10.1142/S0129065707001214. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Conference Paper
    ​ ​Mersch, Britta, et al. "Evolutionary optimization of sequence kernels for detection of bacterial gene starts​." ​Artificial neural networks - ICANN 2006, edited by Stefanos Kollias, vol. 2, ​Springer, ​2006, pp. 827​-836​. ​doi: 10.1007/11840930_86. 
    ​Details  DOI  WoS 
  • 2006 | Journal Article
    ​ ​Lingner, Thomas, and Peter Meinicke. "Remote homology detection based on oligomer distances​." ​Bioinformatics, vol. 22, no. 18, ​2006, pp. 2224​-2231​, ​doi: 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, vol. 34, ​2006, pp. W588​-W590​, ​doi: 10.1093/nar/gkl313. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Waack, Stephan, et al. "Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models​." ​BMC Bioinformatics, vol. 7, ​2006, , ​doi: 10.1186/1471-2105-7-142. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Tech, Maike, and Peter Meinicke. "An unsupervised classification scheme for improving predictions of prokaryotic TIS​." ​BMC Bioinformatics, vol. 7, ​2006, , ​doi: 10.1186/1471-2105-7-121. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Meinicke, Peter, et al. "P-value based visualization of codon usage data​." ​Algorithms for Molecular Biology, vol. 1, ​2006, , ​doi: 10.1186/1748-7188-1-10. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article
    ​ ​Meinicke, Peter, et al. "Principal surfaces from unsupervised kernel regression​." ​IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 27, no. 9, ​2005, pp. 1379​-1391​, ​doi: 10.1109/TPAMI.2005.183. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article
    ​ ​Tech, Maike, et al. "TICO: a tool for improving predictions of prokaryotic translation initiation sites​." ​Bioinformatics, vol. 21, no. 17, ​2005, pp. 3568​-3569​, ​doi: 10.1093/bioinformatics/bti563. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article
    ​ ​Kaper, M., et al. "BCI competition 2003 - Data set IIb: Support vector machines for the P300 speller paradigm​." ​IEEE Transactions on Biomedical Engineering, vol. 51, no. 6, ​2004, pp. 1073​-1076​, ​doi: 10.1109/TBME.2004.826698. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Meinicke, Peter, et al. "Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites​." ​BMC Bioinformatics, vol. 5, ​2004, , ​doi: 10.1186/1471-2105-5-169. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2001 | Journal Article
    ​ ​Meinicke, Peter, and Helge Ritter. "Resolution-Based Complexity Control for Gaussian Mixture Models​." ​Neural Computation, vol. 13, no. 2, ​2001, pp. 453​-475​, ​doi: 10.1162/089976601300014600. 
    ​Details  DOI 

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