Prof. Dr. Burkhard Morgenstern

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  • 2022 | Journal Article | 
    ​ ​Birth, Niklas, Thomas Dencker, and Burkhard Morgenstern. "Insertions and deletions as phylogenetic signal in an alignment-free context​." ​PLOS Computational Biology ​18, no. 8 (2022): ​e1010303​. ​https://doi.org/10.1371/journal.pcbi.1010303.
    ​Details  DOI 
  • 2021 | Journal Article | Research Paper | 
    ​ ​Harting, Rebekka, Jessica Starke, Harald Kusch, Stefanie Pöggeler, Isabel Maurus, Rabea Schlüter, Manuel Landesfeind et al. "A 20‐kb lineage‐specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum​." ​Molecular Plant Pathology (2021): . ​https://doi.org/10.1111/mpp.13071.
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​Leonard, Miriam, Anika Kühn, Rebekka Harting, Isabel Maurus, Alexandra Nagel, Jessica Starke, Harald Kusch et al. "Verticillium longisporum Elicits Media-Dependent Secretome Responses With Capacity to Distinguish Between Plant-Related Environments​." ​Frontiers in Microbiology ​11 (2020): . ​https://doi.org/10.3389/fmicb.2020.01876.
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​Röhling, Sophie, Alexander Linne, Jendrik Schellhorn, Morteza Hosseini, Thomas Dencker, and Burkhard Morgenstern. "The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances​." ​PLoS One ​15, no. 2 (2020): ​e0228070​. ​https://doi.org/10.1371/journal.pone.0228070.
    ​Details  DOI 
  • 2019 | Journal Article | 
    ​ ​Zielezinski, Andrzej, Hani Z. Girgis, Guillaume Bernard, Chris-Andre Leimeister, Kujin Tang, Thomas Dencker, Anna Katharina Lau et al. "Benchmarking of alignment-free sequence comparison methods​." ​Genome Biology ​20, no. 1 (2019): . ​https://doi.org/10.1186/s13059-019-1755-7.
    ​Details  DOI 
  • 2019 | Journal Article | 
    ​ ​Lau, Anna-Katharina, Svenja Dörrer, Chris-André Leimeister, Christoph Bleidorn, and Burkhard Morgenstern. "Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage​." ​BMC Bioinformatics ​20, no. Suppl 20 (2019): ​638​. ​https://doi.org/10.1186/s12859-019-3205-7.
    ​Details  DOI  PMID  PMC 
  • 2017 | Journal Article | 
    ​ ​Morgenstern, Burkhard, Svenja Schöbel, and Chris-André Leimeister. "Phylogeny reconstruction based on the length distribution of k-mismatch common substrings​." ​Algorithms for Molecular Biology ​12, no. 1 (2017): ​27​. ​https://doi.org/10.1186/s13015-017-0118-8.
    ​Details  DOI 
  • 2017 | Journal Article | 
    ​ ​Leimeister, Chris-Andre, Salma Sohrabi-Jahromi, and Burkhard Morgenstern. "Fast and accurate phylogeny reconstruction using filtered spaced-word matches​." ​Bioinformatics ​33, no. 7 (2017): ​971​-979​. ​https://doi.org/10.1093/bioinformatics/btw776.
    ​Details  DOI  PMID  PMC  WoS 
  • 2016 | Journal Article | 
    ​ ​Hahn, Lars, Chris-Andre Leimeister, Rachid Ounit, Stefano Lonardi, and Burkhard Morgenstern. "rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison​." ​PLoS Computational Biology ​12, no. 10 (2016): ​e1005107​. ​https://doi.org/10.1371/journal.pcbi.1005107.
    ​Details  DOI  PMID  PMC  WoS 
  • 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 | Research Paper | 
    ​ ​Schmitt-Engel, Christian, Dorothea Schultheis, Jonas Schwirz, Nadi Stroehlein, Nicole Troelenberg, Upalparna Majumdar, Van Anh Dao et al. "The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology​." ​Nature Communications ​6 (2015): ​7822​. ​https://doi.org/10.1038/ncomms8822.
    ​Details  DOI  PMID  PMC  WoS 
  • 2015 | Journal Article | 
    ​ ​Morgenstern, Burkhard, Bingyao Zhu, Sebastian Horwege, and Chris Andre Leimeister. "Estimating evolutionary distances between genomic sequences from spaced-word matches​." ​Algorithms for Molecular Biology ​10 (2015): ​x​. ​https://doi.org/10.1186/s13015-015-0032-x.
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Horwege, Sebastian, Sebastian Lindner, Marcus Boden, Klas Hatje, Martin Kollmar, Chris-Andre Leimeister, and Burkhard Morgenstern. "Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches​." ​Nucleic Acids Research ​42, no. W1 (2014): ​W7​-W11​. ​https://doi.org/10.1093/nar/gku398.
    ​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 | 
    ​ ​Leimeister, Chris-Andre, Marcus Boden, Sebastian Horwege, Sebastian Lindner, and Burkhard Morgenstern. "Fast alignment-free sequence comparison using spaced-word frequencies​." ​Bioinformatics ​30, no. 14 (2014): ​1991​-1999​. ​https://doi.org/10.1093/bioinformatics/btu177.
    ​Details  DOI  PMID  PMC  WoS 
  • 2013 | Journal Article | 
    ​ ​Al Ait, Layal, Zaher Yamak, and Burkhard Morgenstern. "DIALIGN at GOBICS-multiple sequence alignment using various sources of external information​." ​Nucleic Acids Research ​41, no. W1 (2013): ​W3​-W7​. ​https://doi.org/10.1093/nar/gkt283.
    ​Details  DOI  PMID  PMC  WoS 
  • 2012 | Journal Article | 
    ​ ​Schultz, Anne-Kathrin, Ingo Bulla, Mariama Abdou-Chekaraou, Emmanuel Gordien, Burkhard Morgenstern, Fabien Zoulim, Paul Deny, and Mario Stanke. "jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus​." ​Nucleic Acids Research ​40, no. W1 (2012): ​W193​-W198​. ​https://doi.org/10.1093/nar/gks414.
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article | 
    ​ ​Truong, Cong V. C., Linn F. Groeneveld, Burkhard Morgenstern, and Eildert Groeneveld. "MolabIS - An integrated information system for storing and managing molecular genetics data​." ​BMC Bioinformatics ​12 (2011): ​425​. ​https://doi.org/10.1186/1471-2105-12-425.
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article | 
    ​ ​Unterthiner, Thomas, Anne-Kathrin Schultz, Jan Bulla, Burkhard Morgenstern, Mario Stanke, and Ingo Bulla. "Detection of viral sequence fragments of HIV-1 subfamilies yet unknown​." ​BMC Bioinformatics ​12 (2011): ​93​. ​https://doi.org/10.1186/1471-2105-12-93.
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article | 
    ​ ​Zhang, Ming, Brian Foley, Anne-Kathrin Schultz, Jennifer P. Macke, Ingo Bulla, Mario Stanke, Burkhard Morgenstern, Bette Korber, and Thomas Leitner. "The role of recombination in the emergence of a complex and dynamic HIV epidemic​." ​Retrovirology ​7, no. 25 (2010): -15​. ​https://doi.org/10.1186/1742-4690-7-25.
    ​Details  DOI 
  • 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 
  • 2009 | Journal Article | 
    ​ ​Schreiber, Fabian, Kerstin Pick, Dirk Erpenbeck, Gert Woerheide, and Burkhard Morgenstern. "OrthoSelect: a protocol for selecting orthologous groups in phylogenomics​." ​BMC Bioinformatics ​10 (2009): ​219​. ​https://doi.org/10.1186/1471-2105-10-219.
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article | 
    ​ ​Subramanian, Amarendran R., Michael Kaufmann, and Burkhard Morgenstern. "DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment​." ​Algorithms for molecular biology ​3, no. 6 (2008): ​1​-11​. ​
    ​Details 
  • 2008 | Journal Article | 
    ​ ​Weiberg, Arne, Dirk Poehler, Burkhard Morgenstern, and Petr Karlovsky. "Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA​." ​BMC Genomics ​9 (2008): ​480​. ​https://doi.org/10.1186/1471-2164-9-480.
    ​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 | 
    ​ ​Wagner, Holger, Burkhard Morgenstern, and Andreas Dress. "Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family​." ​Algorithms for Molecular Biology ​3 (2008): ​15​. ​https://doi.org/10.1186/1748-7188-3-15.
    ​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 
  • 2007 | Journal Article | 
    ​ ​Chen, Xiao Hua, Alexandra Koumoutsi, Romy Scholz, Andreas Eisenreich, Kathrin Schneider, Isabelle Heinemeyer, Burkhard Morgenstern et al. "Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42​." ​Nature Biotechnology ​25, no. 9 (2007): ​1007​-1014​. ​https://doi.org/10.1038/nbt1325.
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Stanke, Mario, Ana Tzvetkova, and Burkhard Morgenstern. "AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome​." ​Genome Biology ​7 (2006): ​S11​. ​https://doi.org/10.1186/gb-2006-7-s1-s11.
    ​Details  DOI  WoS 
  • 2006 | Journal Article | 
    ​ ​Stanke, Mario, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, and Burkhard Morgenstern. "AUGUSTUS: ab initio prediction of alternative transcripts​." ​NUCLEIC ACIDS RESEARCH ​34 (2006): ​W435​-W439​. ​https://doi.org/10.1093/nar/gkl200.
    ​Details  DOI 
  • 2006 | Journal Article | 
    ​ ​Zhang, Ming, Anne-Kathrin Schultz, Charles Calef, Carla Kuiken, Thomas Leitner, Bette Korber, Burkhard Morgenstern, and Mario Stanke. "jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1​." ​NUCLEIC ACIDS RESEARCH ​34 (2006): ​W463​-W465​. ​https://doi.org/10.1093/nar/gkl255.
    ​Details  DOI 
  • 2006 | Journal Article | 
    ​ ​Schultz, Anne-Kathrin, M. Zhang, Thomas Leitner, Carla Kuiken, Bette Korber, Burkhard Morgenstern, and Mario Stanke. "A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes​." ​BMC Bioinformatics ​7 (2006): ​265​. ​https://doi.org/10.1186/1471-2105-7-265.
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Stanke, Mario, O. Schoffmann, Burkhard Morgenstern, and S. Waack. "Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources​." ​BMC Bioinformatics ​7 (2006): ​62​. ​https://doi.org/10.1186/1471-2105-7-62.
    ​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 | Letter Note | 
    ​ ​Morgenstern, Burkhard, and Peter F. Stadler. "New journal: Algorithms for molecular biology​." ​Algorithms for Molecular Biology ​1 (2006): ​1​. ​https://doi.org/10.1186/1748-7188-1-1.
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Morgenstern, Burkhard, Sonja J. Prohaska, Dirk Poehler, and Peter F. Stadler. "Multiple sequence alignment with user-defined anchor points​." ​Algorithms for Molecular Biology ​1 (2006): ​6​. ​https://doi.org/10.1186/1748-7188-1-6.
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article | 
    ​ ​Subramanian, A. R., J. Weyer-Menkhoff, M. Kaufmann, and Burkhard Morgenstern. "DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment​." ​BMC Bioinformatics ​6 (2005): ​66​. ​https://doi.org/10.1186/1471-2105-6-66.
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article | 
    ​ ​Pohler, D., N. Werner, R. Steinkamp, and Burkhard Morgenstern. "Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC​." ​Nucleic Acids Research ​33 (2005): ​W532​-W534​. ​https://doi.org/10.1093/nar/gki386.
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article | 
    ​ ​Stanke, Mario, and Burkhard Morgenstern. "AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints​." ​Nucleic Acids Research ​33 (2005): ​W465​-W467​. ​https://doi.org/10.1093/nar/gki458.
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Brudno, M., R. Steinkamp, and Burkhard Morgenstern. "The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences​." ​Nucleic Acids Research ​32 (2004): ​W41​-W44​. ​https://doi.org/10.1093/nar/gkh361.
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Morgenstern, Burkhard. "DIALIGN: multiple DNA and protein sequence alignment at BiBiServ​." ​Nucleic Acids Research ​32 (2004): ​W33​-W36​. ​https://doi.org/10.1093/nar/gkh373.
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Schmollinger, M., K. Nieselt, M. Kaufmann, and Burkhard Morgenstern. "DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors​." ​BMC Bioinformatics ​5 (2004): ​128​. ​https://doi.org/10.1186/1471-2105-5-128.
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Stanke, Mario, R. Steinkamp, S. Waack, and Burkhard Morgenstern. "AUGUSTUS: a web server for gene finding in eukaryotes​." ​Nucleic Acids Research ​32 (2004): ​W309​-W312​. ​https://doi.org/10.1093/nar/gkh379.
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Taher, L., O. Rinner, S. Garg, A. Sczyrba, and Burkhard Morgenstern. "AGenDA: gene prediction by cross-species sequence comparison​." ​Nucleic Acids Research ​32 (2004): ​W305​-W308​. ​https://doi.org/10.1093/nar/gkh386.
    ​Details  DOI  PMID  PMC  WoS 
  • 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.
    ​Details  DOI  PMID  PMC  WoS 
  • 2003 | Journal Article | 
    ​ ​Brudno, M., Mark A. Chapman, B. Gottgens, S. Batzoglou, and Burkhard Morgenstern. "Fast and sensitive multiple alignment of large genomic sequences​." ​BMC Bioinformatics ​4 (2003): ​66​. ​https://doi.org/10.1186/1471-2105-4-66.
    ​Details  DOI  PMID  PMC  WoS 
  • 2002 | Journal Article | 
    ​ ​Mewes, H. W., D. Frishman, U. Güldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Münsterkötter, S. Rudd, and B. Weil. "MIPS: a database for genomes and protein sequences.​." ​NUCLEIC ACIDS RESEARCH ​30, no. 1 (2002): ​31​-34​. ​
    ​Details 

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