Mario Stanke

Summary

Country: Germany

Publications

  1. ncbi request reprint Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003
  2. pmc AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Universitat Gottingen, Goldschmidtstrasse, 37077 Gottingen, Germany
    Genome Biol 7:S11.1-8. 2006
  3. pmc AUGUSTUS: ab initio prediction of alternative transcripts
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 34:W435-9. 2006
  4. pmc Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    Mario Stanke
    lnstitut für Mikrobiologie und Genetik, Universitat Gottingen, Gottingen, Germany
    BMC Bioinformatics 7:62. 2006
  5. pmc AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
    Mario Stanke
    Universitat Gottingen, Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 33:W465-7. 2005
  6. pmc AUGUSTUS: a web server for gene finding in eukaryotes
    Mario Stanke
    University of Gottingen, Institut fur Mikrobiologie und Genetik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 32:W309-12. 2004
  7. doi request reprint Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    Mario Stanke
    Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
    Bioinformatics 24:637-44. 2008
  8. pmc jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
    Ming Zhang
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 34:W463-5. 2006
  9. pmc jpHMM: improving the reliability of recombination prediction in HIV-1
    Anne Kathrin Schultz
    Institut fur Mikrobiologie und Genetik, Abteilung für Bioinformatik, Georg August Universitat Gottingen, Goldschmidtstr 1, 37077, Gottingen, Germany
    Nucleic Acids Res 37:W647-51. 2009
  10. pmc HIV classification using the coalescent theory
    Ingo Bulla
    Abteilung Bioinformatik, Institut fur Mikrobiologie und Genetik, Georg August Universitat Gottingen, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Bioinformatics 26:1409-15. 2010

Detail Information

Publications17

  1. ncbi request reprint Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003
    ..Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons...
  2. pmc AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Universitat Gottingen, Goldschmidtstrasse, 37077 Gottingen, Germany
    Genome Biol 7:S11.1-8. 2006
    ..AUGUSTUS was among the tools that were tested in this project...
  3. pmc AUGUSTUS: ab initio prediction of alternative transcripts
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 34:W435-9. 2006
    ..The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from http://augustus.gobics.de...
  4. pmc Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    Mario Stanke
    lnstitut für Mikrobiologie und Genetik, Universitat Gottingen, Gottingen, Germany
    BMC Bioinformatics 7:62. 2006
    ..Therefore extrinsic evidence is most valuable when it is balanced with sequence-intrinsic evidence...
  5. pmc AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
    Mario Stanke
    Universitat Gottingen, Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 33:W465-7. 2005
    ..The web interface and the downloadable stand-alone program are available free of charge at http://augustus.gobics.de/submission...
  6. pmc AUGUSTUS: a web server for gene finding in eukaryotes
    Mario Stanke
    University of Gottingen, Institut fur Mikrobiologie und Genetik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 32:W309-12. 2004
    ..The advantage of our program becomes apparent especially for larger input sequences containing more than one gene. The server is available at http://augustus.gobics.de...
  7. doi request reprint Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    Mario Stanke
    Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
    Bioinformatics 24:637-44. 2008
    ..For many eukaryotic genomes, expressed sequence tags (ESTs) are available as evidence for genes. Related genomes that have been sequenced, annotated, and aligned to the target genome provide evidence of existence and structure of genes...
  8. pmc jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
    Ming Zhang
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 34:W463-5. 2006
    ..jpHMM is available online at http://jphmm.gobics.de/...
  9. pmc jpHMM: improving the reliability of recombination prediction in HIV-1
    Anne Kathrin Schultz
    Institut fur Mikrobiologie und Genetik, Abteilung für Bioinformatik, Georg August Universitat Gottingen, Goldschmidtstr 1, 37077, Gottingen, Germany
    Nucleic Acids Res 37:W647-51. 2009
    ..Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/...
  10. pmc HIV classification using the coalescent theory
    Ingo Bulla
    Abteilung Bioinformatik, Institut fur Mikrobiologie und Genetik, Georg August Universitat Gottingen, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Bioinformatics 26:1409-15. 2010
    ....
  11. pmc Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
    Oliver Keller
    Universitat Gottingen, Institut fur Informatik, Lotzestr 16 18, 37083 Göttingen, Germany
    BMC Bioinformatics 9:278. 2008
    ..Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection, which is time consuming and requires considerable experience...
  12. pmc jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus
    Anne Kathrin Schultz
    Abteilung für Bioinformatik, Institut fur Mikrobiologie und Genetik, Georg August Universitat Gottingen, Goldschmidtstr 1, 37077 Gottingen, Germany
    Nucleic Acids Res 40:W193-8. 2012
    ..We apply the method to genomic sequences of HBV and visualize its output in a circular form. jpHMM is available online at http://jphmm.gobics.de for download and as a web server for HIV-1 and HBV sequences...
  13. doi request reprint A novel hybrid gene prediction method employing protein multiple sequence alignments
    Oliver Keller
    Institute of Computer Science, University of Gottingen, Goldschmidtstrasse 7, Greifswald, Germany
    Bioinformatics 27:757-63. 2011
    ..While the classification of proteins into families is a task heavily relying on correct gene predictions, it can at the same time provide a source of additional information for the prediction, complementary to those presently used...
  14. pmc Detection of viral sequence fragments of HIV-1 subfamilies yet unknown
    Thomas Unterthiner
    Institute of Microbiology and Genetics, University of Gottingen, Goldschmidtstr, 1, 37077 Gottingen, Germany
    BMC Bioinformatics 12:93. 2011
    ..In its current version, however, the BI does not provide predicted boundaries of unknown fragments...
  15. pmc A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
    Anne Kathrin Schultz
    Institute of Microbiology and Genetics, University of Gottingen, Goldschmidtstr, 1, 37077 Gottingen, Germany
    BMC Bioinformatics 7:265. 2006
    ..This approach is particularly useful for dealing with recombination events...
  16. pmc Draft genome of the filarial nematode parasite Brugia malayi
    Elodie Ghedin
    Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
    Science 317:1756-60. 2007
    ..malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design...
  17. pmc Genome sequence of Aedes aegypti, a major arbovirus vector
    Vishvanath Nene
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 316:1718-23. 2007
    ..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species...