Dr. Peter Meinicke

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  • 2020 | Journal Article | 
    ​ ​Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences​
    Wemheuer, F. ; Taylor, J. A.; Daniel, R. ; Johnston, E.; Meinicke, P. ; Thomas, T. & Wemheuer, B. ​ (2020) 
    Environmental Microbiome, 15(1).​ DOI: https://doi.org/10.1186/s40793-020-00358-7 
    ​Details  DOI 
  • 2018 | Preprint
    ​ ​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​
    Wemheuer, F. ; Taylor, J. A.; Daniel, R. ; Johnston, E.; Meinicke, P. ; Thomas, T.& Wemheuer, B. ​ (2018). DOI: https://doi.org/10.1101/490037 
    ​Details  DOI 
  • 2017 | Journal Article | 
    ​ ​Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software​
    Sczyrba, A.; Hofmann, P.; Belmann, P.; Koslicki, D.; Janssen, S.; Dröge, J. & Gregor, I. et al.​ (2017) 
    Nature Methods, 14(11) pp. 1063​-1071​.​ DOI: https://doi.org/10.1038/nmeth.4458 
    ​Details  DOI 
  • 2017 | Journal Article | 
    ​ ​How to normalize metatranscriptomic count data for differential expression analysis.​
    Klingenberg, H. & Meinicke, P. ​ (2017) 
    PeerJ, 5 art. e3859​.​ DOI: https://doi.org/10.7717/peerj.3859 
    ​Details  DOI  PMID  PMC 
  • 2015 | Journal Article | 
    ​ ​MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data​
    Kaever, A.; Landesfeind, M.; Feussner, K.; Mosblech, A.; Heilmann, I.; Morgenstern, B.   & Feussner, I. et al.​ (2015) 
    Metabolomics, 11(3) pp. 764​-777​.​ DOI: https://doi.org/10.1007/s11306-014-0734-y 
    ​Details  DOI  WoS 
  • 2015 | Journal Article | 
    ​ ​UProC: tools for ultra-fast protein domain classification​
    Meinicke, P. ​ (2015) 
    Bioinformatics, 31(9) pp. 1382​-1388​.​ DOI: https://doi.org/10.1093/bioinformatics/btu843 
    ​Details  DOI  PMID  PMC  WoS 
  • 2015 | Journal Article | 
    ​ ​Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data​
    Aßhauer, K. P.; Wemheuer, B. ; Daniel, R.   & Meinicke, P. ​ (2015) 
    Bioinformatics, 31(17) pp. 2882​-2884​.​ DOI: https://doi.org/10.1093/bioinformatics/btv287 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article
    ​ ​Verticillium dahliae VdTHI4, involved in thiazole biosynthesis, stress response and DNA repair functions, is required for vascular disease induction in tomato​
    Hoppenau, C. E.; Tran, V.-T.; Kusch, H. ; Aßhauer, K. P.; Landesfeind, M.; Meinicke, P.   & Popova, B.  et al.​ (2014) 
    Environmental and Experimental Botany, 108 pp. 14​-22​.​ DOI: https://doi.org/10.1016/j.envexpbot.2013.12.015 
    ​Details  DOI 
  • 2014 | Journal Article | 
    ​ ​Predicting the functional repertoire of an organism from unassembled RNA-seq data​
    Landesfeind, M. & Meinicke, P. ​ (2014) 
    BMC Genomics, 15 art. 1003​.​ DOI: https://doi.org/10.1186/1471-2164-15-1003 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article
    ​ ​Land Use Type Significantly Affects Microbial Gene Transcription in Soil​
    Nacke, H.; Fischer, C.; Thuermer, A.; Meinicke, P.   & Daniel, R.​ (2014) 
    Microbial Ecology, 67(4) pp. 919​-930​.​ DOI: https://doi.org/10.1007/s00248-014-0377-6 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Exploring Neighborhoods in the Metagenome Universe​
    Asshauer, K. P.; Klingenberg, H.; Lingner, T. & Meinicke, P. ​ (2014) 
    International Journal of Molecular Sciences, 15(7) pp. 12364​-12378​.​ DOI: https://doi.org/10.3390/ijms150712364 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets​
    Kaever, A.; Landesfeind, M.; Feussner, K.; Morgenstern, B. ; Feussner, I. & Meinicke, P. ​ (2014) 
    PLoS ONE, 9(2) art. e89297​.​ DOI: https://doi.org/10.1371/journal.pone.0089297 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software​
    Landesfeind, M.; Kaever, A.; Feussner, K.; Thurow, C.; Gatz, C.; Feussner, I. & Meinicke, P. ​ (2014) 
    PeerJ, 2 art. e239​.​ DOI: https://doi.org/10.7717/peerj.239 
    ​Details  DOI  PMID  PMC  WoS 
  • 2013 | Journal Article
    ​ ​Protein signature-based estimation of metagenomic abundances including all domains of life and viruses​
    Klingenberg, H.; Assauer, K. P.; Lingner, T. & Meinicke, P. ​ (2013) 
    Bioinformatics, 29(8) pp. 973​-980​.​ DOI: https://doi.org/10.1093/bioinformatics/btt077 
    ​Details  DOI  PMID  PMC  WoS 
  • 2012 | Journal Article
    ​ ​Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 Subtypes through Linear Classifier Learning​
    Bulla, I.; Schultz, A.-K. & Meinicke, P. ​ (2012) 
    Statistical Applications in Genetics and Molecular Biology, 11(1) art. 1​.​ DOI: https://doi.org/10.2202/1544-6115.1680 
    ​Details  DOI  WoS 
  • 2012 | Journal Article | 
    ​ ​Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities​
    Danielsen, L.; Thürmer, A.; Meinicke, P. ; Buée, M.; Morin, E.; Martin, F. & Pilate, G. et al.​ (2012) 
    Ecology and Evolution, 2(8) pp. 1935​-1948​.​ DOI: https://doi.org/10.1002/ece3.305 
    ​Details  DOI 
  • 2012 | Journal Article | 
    ​ ​MarVis-Filter: Ranking, Filtering, Adduct and Isotope Correction of Mass Spectrometry Data​
    Kaever, A.; Landesfeind, M.; Possienke, M.; Feussner, K.; Feussner, I. & Meinicke, P. ​ (2012) 
    JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY, art. 263910​.​ DOI: https://doi.org/10.1155/2012/263910 
    ​Details  DOI  WoS 
  • 2011 | Journal Article
    ​ ​Metabolic priming by a secreted fungal effector​
    Djamei, A.; Schipper, K.; Rabe, F.; Ghosh, A.; Vincon, V.; Kahnt, J. & Osorio, S. et al.​ (2011) 
    Nature, 478(7369) pp. 395​.​ DOI: https://doi.org/10.1038/nature10454 
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article | 
    ​ ​CoMet-a web server for comparative functional profiling of metagenomes​
    Lingner, T.; Asshauer, K. P.; Schreiber, F. & Meinicke, P. ​ (2011) 
    Nucleic Acids Research, 39 pp. W518​-W523​.​ DOI: https://doi.org/10.1093/nar/gkr388 
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article
    ​ ​Identification of Novel Plant Peroxisomal Targeting Signals by a Combination of Machine Learning Methods and in Vivo Subcellular Targeting Analyses​
    Lingner, T.; Kataya, A. R.; Antonicelli, G. E.; Benichou, A.; Nilssen, K.; Chen, X.-Y. & Siemsen, T. et al.​ (2011) 
    The Plant Cell, 23(4) pp. 1556​-1572​.​ DOI: https://doi.org/10.1105/tpc.111.084095 
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article
    ​ ​Mixture models for analysis of the taxonomic composition of metagenomes​
    Meinicke, P. ; Asshauer, K. P. & Lingner, T.​ (2011) 
    Bioinformatics, 27(12) pp. 1618​-1624​.​ DOI: https://doi.org/10.1093/bioinformatics/btr266 
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article
    ​ ​Treephyler: fast taxonomic profiling of metagenomes​
    Schreiber, F.; Gumrich, P.; Daniel, R.   & Meinicke, P. ​ (2010) 
    Bioinformatics, 26(7) pp. 960​-961​.​ DOI: https://doi.org/10.1093/bioinformatics/btq070 
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article
    ​ ​The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development​
    Nahlik, K.; Dumkow, M.; Bayram, O.; Helmstaedt, K.; Busch, S.; Valerius, O.   & Gerke, J. et al.​ (2010) 
    Molecular Microbiology, 78(4) pp. 964​-979​.​ DOI: https://doi.org/10.1111/j.1365-2958.2010.07384.x 
    ​Details  DOI  PMID  PMC 
  • 2010 | Journal Article | 
    ​ ​DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS​
    Subramanian, A. R.; Hiran, S.; Steinkamp, R.; Meinicke, P. ; Corel, E. & Morgenstern, B. ​ (2010) 
    Nucleic Acids Research, 38 pp. W19​-W22​.​ DOI: https://doi.org/10.1093/nar/gkq442 
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article | 
    ​ ​Predicting phenotypic traits of prokaryotes from protein domain frequencies​
    Lingner, T.; Muehlhausen, S. ; Gabaldon, T.; Notredame, C. & Meinicke, P. ​ (2010) 
    BMC Bioinformatics, 11 art. 481​.​ DOI: https://doi.org/10.1186/1471-2105-11-481 
    ​Details  DOI  PMID  PMC  WoS 
  • 2009 | Conference Abstract
    ​ ​Identification of metabolic changes after wounding in Arabidopsis thaliana by an unbiased UPLC-MS approach​
    Goebel, C.; Feussner, K.; Kaever, A.; Meinicke, P. ; Morgenstern, B.   & Feussner, I.​ (2009)
    Chemistry and Physics of Lipids, 160 ​50th International Conference on Bioscience of Lipids​, Regenburg, GERMANY.
    Clare​: Elsevier Ireland Ltd. DOI: https://doi.org/10.1016/j.chemphyslip.2009.06.024 
    ​Details  DOI  WoS 
  • 2009 | Journal Article | 
    ​ ​Orphelia: predicting genes in metagenomic sequencing reads​
    Hoff, K. J.; Lingner, T.; Meinicke, P.   & Tech, M. ​ (2009) 
    Nucleic Acids Research, 37 pp. W101​-W105​.​ DOI: https://doi.org/10.1093/nar/gkp327 
    ​Details  DOI  PMID  PMC  WoS 
  • 2009 | Journal Article | 
    ​ ​MarVis: a tool for clustering and visualization of metabolic biomarkers​
    Kaever, A.; Lingner, T.; Feussner, K.; Goebel, C.; Feussner, I. & Meinicke, P. ​ (2009) 
    BMC Bioinformatics, 10 art. 92​.​ DOI: https://doi.org/10.1186/1471-2105-10-92 
    ​Details  DOI  PMID  PMC  WoS 
  • 2009 | Review | 
    ​ ​UFO: a web server for ultra-fast functional profiling of whole genome protein sequences​
    Meinicke, P. ​ (2009)
    BMC Genomics, 10​.​
    Biomed Central Ltd. DOI: https://doi.org/10.1186/1471-2164-10-409 
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps​
    Meinicke, P. ; Lingner, T.; Kaever, A.; Feussner, K.; Goebel, C.; Feussner, I. & Karlovsky, P.  et al.​ (2008) 
    Algorithms for Molecular Biology, 3 art. 9​.​ DOI: https://doi.org/10.1186/1748-7188-3-9 
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Gene prediction in metagenomic fragments: A large scale machine learning approach​
    Hoff, K. J.; Tech, M. ; Lingner, T.; Daniel, R.; Morgenstern, B.   & Meinicke, P. ​ (2008) 
    BMC Bioinformatics, 9 art. 217​.​ DOI: https://doi.org/10.1186/1471-2105-9-217 
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Word correlation matrices for protein sequence analysis and remote homology detection​
    Lingner, T. & Meinicke, P. ​ (2008) 
    BMC Bioinformatics, 9 art. 259​.​ DOI: https://doi.org/10.1186/1471-2105-9-259 
    ​Details  DOI  PMID  PMC  WoS 
  • 2007 | Journal Article
    ​ ​Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detection​
    Igel, C.; Glasmachers, T.; Mersch, B.; Pfeifer, N. & Meinicke, P. ​ (2007) 
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(2) pp. 216​-226​.​ DOI: https://doi.org/10.1109/tcbb.2007.070208 
    ​Details  DOI  PMID  PMC  WoS 
  • 2007 | Journal Article
    ​ ​Evolutionary optimization of sequence kernels for detection of bacterial gene starts​
    Mersch, B.; Glasmachers, T.; Meinicke, P.   & Igel, C.​ (2007) 
    International Journal of Neural Systems, 17(5) pp. 369​-381​.​ DOI: https://doi.org/10.1142/S0129065707001214 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Conference Paper
    ​ ​Evolutionary optimization of sequence kernels for detection of bacterial gene starts​
    Mersch, B.; Glasmachers, T.; Meinicke, P.   & Igel, C.​ (2006)
    In:Kollias, Stefanos​ (Ed.), ​Artificial neural networks - ICANN 2006 pp. 827​-836. (Vol. 2). ​16th International Conference on Artificial Neural Networks (ICANN 2006)​, Athens.
    Berlin, Heidelberg​: Springer. DOI: https://doi.org/10.1007/11840930_86 
    ​Details  DOI  WoS 
  • 2006 | Journal Article | 
    ​ ​Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models​
    Waack, S.; Keller, O.; Asper, R.; Brodag, T.; Damm, C. ; Fricke, W. F. & Surovcik, K. et al.​ (2006) 
    BMC Bioinformatics, 7 art. 142​.​ DOI: https://doi.org/10.1186/1471-2105-7-142 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​An unsupervised classification scheme for improving predictions of prokaryotic TIS​
    Tech, M.   & Meinicke, P. ​ (2006) 
    BMC Bioinformatics, 7 art. 121​.​ DOI: https://doi.org/10.1186/1471-2105-7-121 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​P-value based visualization of codon usage data​
    Meinicke, P. ; Brodag, T.; Fricke, W. F. & Waack, S.​ (2006) 
    Algorithms for Molecular Biology, 1 art. 10​.​ DOI: https://doi.org/10.1186/1748-7188-1-10 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article
    ​ ​Remote homology detection based on oligomer distances​
    Lingner, T. & Meinicke, P. ​ (2006) 
    Bioinformatics, 22(18) pp. 2224​-2231​.​ DOI: https://doi.org/10.1093/bioinformatics/btl376 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites​
    Tech, M. ; Morgenstern, B.   & Meinicke, P. ​ (2006) 
    Nucleic Acids Research, 34 pp. W588​-W590​.​ DOI: https://doi.org/10.1093/nar/gkl313 
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article
    ​ ​TICO: a tool for improving predictions of prokaryotic translation initiation sites​
    Tech, M. ; Pfeifer, N.; Morgenstern, B.   & Meinicke, P. ​ (2005) 
    Bioinformatics, 21(17) pp. 3568​-3569​.​ DOI: https://doi.org/10.1093/bioinformatics/bti563 
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article
    ​ ​Principal surfaces from unsupervised kernel regression​
    Meinicke, P. ; Klanke, S.; Memisevic, R. & Ritter, H.​ (2005) 
    IEEE Transactions on Pattern Analysis and Machine Intelligence, 27(9) pp. 1379​-1391​.​ DOI: https://doi.org/10.1109/TPAMI.2005.183 
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites​
    Meinicke, P. ; Tech, M. ; Morgenstern, B.   & Merkl, R.​ (2004) 
    BMC Bioinformatics, 5 art. 169​.​ DOI: https://doi.org/10.1186/1471-2105-5-169 
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article
    ​ ​BCI competition 2003 - Data set IIb: Support vector machines for the P300 speller paradigm​
    Kaper, M.; Meinicke, P. ; Grossekathoefer, U.; Lingner, T. & Ritter, H.​ (2004) 
    IEEE Transactions on Biomedical Engineering, 51(6) pp. 1073​-1076​.​ DOI: https://doi.org/10.1109/TBME.2004.826698 
    ​Details  DOI  PMID  PMC  WoS 
  • 2001 | Journal Article
    ​ ​Resolution-Based Complexity Control for Gaussian Mixture Models​
    Meinicke, P.   & Ritter, H.​ (2001) 
    Neural Computation, 13(2) pp. 453​-475​.​ DOI: https://doi.org/10.1162/089976601300014600 
    ​Details  DOI 

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