University of Göttingen  |  Faculty of Biology  |  Institute of Microbiology and Genetics  |  Dept. of Bioinformatics

jpHMM-HIV [References]

References

  1. A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, B. Korber, B. Morgenstern, M. Stanke. jpHMM: Improving the reliability of recombination prediction in HIV-1. Nucleic Acids Research, 37:W647-51. 2009
  2. A.-K. Schultz, M. Zhang, T. Leitner, B. Korber, B. Morgenstern, M. Stanke. jpHMM: Erkennung von Rekombinationen bei HIV. BIOforum 2/2008, 44-46.
  3. M. Zhang, A.-K. Schultz, C. Calef, C. Kuiken, T. Leitner, B. Korber, B. Morgenstern, M. Stanke. jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. Nucleic Acids Res., 34:W463-5. 2006.
    (Description of the jpHMM web server)
  4. A.-K. Schultz, M. Zhang, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke. A Jumping Profile Hidden Markov Model and Applications to Recombination Sites in HIV and HCV Genomes. BMC Bioinformatics 7:265. 2006.
    (Description of the jpHMM algorithm and the evaluation of the program)
  5. M. Zhang, A.-K. Schultz, B. Morgenstern, M. Stanke, B. Korber, T. Leitner. Greater HIV Genome Diversities Inferred From Re-subtyping of HIV Database Sequences. Proc. German Conference on Bioinformatics (Discovery Notes, Poster Abstracts), pp 5 - 7. 2005.
    (Abstract of the talk given by M. Zhang at the GCB 2005 in Hamburg)
  6. A.-K. Schultz. Ein springendes Profil-Hidden-Markov-Modell und Anwendungen auf Rekombinationen in viralen Genomen. Diplom thesis, Universität Göttingen, Germany, pdf (German). 2005.
    (Diplom thesis of A.-K. Schultz that describes the jpHMM algorithm in detail)
  7. Rainer Spang and Marc Rehmsmeier and Jens Stoye. A Novel Approach to Remote Homology Detection: Jumping Alignments. Journal of Computational Biology. p 747-760. 2002.
    (Description of the jumping alignment algorithm (JALI))