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, vol. 18, no. 8, ​2022, p. e1010303​, ​doi: 10.1371/journal.pcbi.1010303. 
    ​Details  DOI 
  • 2021 | Journal Article | Research Paper | 
    ​ ​Harting, Rebekka, et al. "A 20‐kb lineage‐specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum​." ​Molecular Plant Pathology, ​2021, , ​doi: 10.1111/mpp.13071. 
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​Leonard, Miriam, et al. "Verticillium longisporum Elicits Media-Dependent Secretome Responses With Capacity to Distinguish Between Plant-Related Environments​." ​Frontiers in Microbiology, vol. 11, ​2020, , ​doi: 10.3389/fmicb.2020.01876. 
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​Röhling, Sophie, et al. "The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances​." ​PLoS One, vol. 15, no. 2, ​2020, p. e0228070​, ​doi: 10.1371/journal.pone.0228070. 
    ​Details  DOI 
  • 2019 | Journal Article | 
    ​ ​Zielezinski, Andrzej, et al. "Benchmarking of alignment-free sequence comparison methods​." ​Genome Biology, vol. 20, no. 1, ​2019, , ​doi: 10.1186/s13059-019-1755-7. 
    ​Details  DOI 
  • 2019 | Journal Article | 
    ​ ​Lau, Anna-Katharina, et al. "Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage​." ​BMC Bioinformatics, vol. 20, no. Suppl 20, ​2019, , ​doi: 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, vol. 12, no. 1, ​2017, , ​doi: 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, vol. 33, no. 7, ​2017, pp. 971​-979​, ​doi: 10.1093/bioinformatics/btw776. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2016 | Journal Article | 
    ​ ​Hahn, Lars, et al. "rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison​." ​PLoS Computational Biology, vol. 12, no. 10, ​2016, , ​doi: 10.1371/journal.pcbi.1005107. 
    ​Details  DOI  PMID  PMC  WoS 
  • 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 | Research Paper | 
    ​ ​Schmitt-Engel, Christian, et al. "The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology​." ​Nature Communications, vol. 6, ​2015, , ​doi: 10.1038/ncomms8822. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2015 | Journal Article | 
    ​ ​Morgenstern, Burkhard, et al. "Estimating evolutionary distances between genomic sequences from spaced-word matches​." ​Algorithms for Molecular Biology, vol. 10, ​2015, , ​doi: 10.1186/s13015-015-0032-x. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2014 | Journal Article | 
    ​ ​Horwege, Sebastian, et al. "Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches​." ​Nucleic Acids Research, vol. 42, no. W1, ​2014, pp. W7​-W11​, ​doi: 10.1093/nar/gku398. 
    ​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 | 
    ​ ​Leimeister, Chris-Andre, et al. "Fast alignment-free sequence comparison using spaced-word frequencies​." ​Bioinformatics, vol. 30, no. 14, ​2014, pp. 1991​-1999​, ​doi: 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, vol. 41, no. W1, ​2013, pp. W3​-W7​, ​doi: 10.1093/nar/gkt283. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2012 | Journal Article | 
    ​ ​Schultz, Anne-Kathrin, et al. "jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus​." ​Nucleic Acids Research, vol. 40, no. W1, ​2012, pp. W193​-W198​, ​doi: 10.1093/nar/gks414. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article | 
    ​ ​Truong, Cong V. C., et al. "MolabIS - An integrated information system for storing and managing molecular genetics data​." ​BMC Bioinformatics, vol. 12, ​2011, , ​doi: 10.1186/1471-2105-12-425. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2011 | Journal Article | 
    ​ ​Unterthiner, Thomas, et al. "Detection of viral sequence fragments of HIV-1 subfamilies yet unknown​." ​BMC Bioinformatics, vol. 12, ​2011, , ​doi: 10.1186/1471-2105-12-93. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article | 
    ​ ​Zhang, Ming, et al. "The role of recombination in the emergence of a complex and dynamic HIV epidemic​." ​Retrovirology, vol. 7, no. 25, ​2010, -15​, ​doi: 10.1186/1742-4690-7-25. 
    ​Details  DOI 
  • 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 
  • 2009 | Journal Article | 
    ​ ​Schreiber, Fabian, et al. "OrthoSelect: a protocol for selecting orthologous groups in phylogenomics​." ​BMC Bioinformatics, vol. 10, ​2009, , ​doi: 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, vol. 3, no. 6, ​2008, pp. 1​-11​. ​
    ​Details 
  • 2008 | Journal Article | 
    ​ ​Weiberg, Arne, et al. "Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA​." ​BMC Genomics, vol. 9, ​2008, , ​doi: 10.1186/1471-2164-9-480. 
    ​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 | 
    ​ ​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, vol. 3, ​2008, , ​doi: 10.1186/1748-7188-3-15. 
    ​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 
  • 2007 | Journal Article | 
    ​ ​Chen, Xiao Hua, et al. "Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42​." ​Nature Biotechnology, vol. 25, no. 9, ​2007, pp. 1007​-1014​, ​doi: 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, vol. 7, ​2006, , ​doi: 10.1186/gb-2006-7-s1-s11. 
    ​Details  DOI  WoS 
  • 2006 | Journal Article | 
    ​ ​Stanke, Mario, et al. "AUGUSTUS: ab initio prediction of alternative transcripts​." ​NUCLEIC ACIDS RESEARCH, vol. 34, ​2006, pp. W435​-W439​, ​doi: 10.1093/nar/gkl200. 
    ​Details  DOI 
  • 2006 | Journal Article | 
    ​ ​Zhang, Ming, et al. "jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1​." ​NUCLEIC ACIDS RESEARCH, vol. 34, ​2006, pp. W463​-W465​, ​doi: 10.1093/nar/gkl255. 
    ​Details  DOI 
  • 2006 | Journal Article | 
    ​ ​Schultz, Anne-Kathrin, et al. "A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes​." ​BMC Bioinformatics, vol. 7, ​2006, , ​doi: 10.1186/1471-2105-7-265. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Stanke, Mario, et al. "Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources​." ​BMC Bioinformatics, vol. 7, ​2006, , ​doi: 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, vol. 34, ​2006, pp. W588​-W590​, ​doi: 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, vol. 1, ​2006, , ​doi: 10.1186/1748-7188-1-1. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2006 | Journal Article | 
    ​ ​Morgenstern, Burkhard, et al. "Multiple sequence alignment with user-defined anchor points​." ​Algorithms for Molecular Biology, vol. 1, ​2006, , ​doi: 10.1186/1748-7188-1-6. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article | 
    ​ ​Subramanian, A. R., et al. "DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment​." ​BMC Bioinformatics, vol. 6, ​2005, , ​doi: 10.1186/1471-2105-6-66. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2005 | Journal Article | 
    ​ ​Pohler, D., et al. "Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC​." ​Nucleic Acids Research, vol. 33, ​2005, pp. W532​-W534​, ​doi: 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, vol. 33, ​2005, pp. W465​-W467​, ​doi: 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, vol. 32, ​2004, pp. W41​-W44​, ​doi: 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, vol. 32, ​2004, pp. W33​-W36​, ​doi: 10.1093/nar/gkh373. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Schmollinger, M., et al. "DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors​." ​BMC Bioinformatics, vol. 5, ​2004, , ​doi: 10.1186/1471-2105-5-128. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Stanke, Mario, et al. "AUGUSTUS: a web server for gene finding in eukaryotes​." ​Nucleic Acids Research, vol. 32, ​2004, pp. W309​-W312​, ​doi: 10.1093/nar/gkh379. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2004 | Journal Article | 
    ​ ​Taher, L., et al. "AGenDA: gene prediction by cross-species sequence comparison​." ​Nucleic Acids Research, vol. 32, ​2004, pp. W305​-W308​, ​doi: 10.1093/nar/gkh386. 
    ​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 
  • 2003 | Journal Article | 
    ​ ​Brudno, M., et al. "Fast and sensitive multiple alignment of large genomic sequences​." ​BMC Bioinformatics, vol. 4, ​2003, , ​doi: 10.1186/1471-2105-4-66. 
    ​Details  DOI  PMID  PMC  WoS 
  • 2002 | Journal Article | 
    ​ ​Mewes, H. W., et al. "MIPS: a database for genomes and protein sequences.​." ​NUCLEIC ACIDS RESEARCH, vol. 30, no. 1, ​2002, pp. 31​-34​. ​
    ​Details 

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