gobics.de [ Ming Zhang ]

Teachings Given During PhD Study:

• Feb 2006. Hands-On Computer Workshop on HIV Sequence, Immunology and Vaccine Databases- sequence analysis session. 13th International Conference on Retroviruses and Opportunistic Infections. Denver, CO, USA.
• Winter Semester 2004/2005, and Winter Semester 2005/2006: Molecular Biology Methods Course
  • Biological databases section
  • Phylogenetic analysis section
• Winter Semester 2003/2004: Molecular Biology Methods Course
  • Biological Databases section

Papers Published During PhD Study:

1. G. Didier, L. Debomy, M. Pupin, M. Zhang, A. Grossmann, C. Devauchelle, I. Laprevotte
   Comparing sequences without using alignments: Application to HIV/SIV subtyping.
   BMC Bioinformatics.8(1):1. 2007.
2. J. Xie, M. Zhang, T. Zhou, X. Hua, L. Tang, W. Wu.
   Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.
   Nucleic Acids Research. 35:D183-D187. 2007.
3. M. Li, JF.Salazar-Gonzalez, CA.Derdeyn, L.Morris, C.Williamson, JE.Robinson, JM.Decker, Y.Li, MG.Salazar, VR.Polonis, K.Mlisana, S.Karim, K.Hong, KM.Greene, M.Bilska, J.Zhou, S.Allen, E.Chomba, J.Mulenga, C.Vwalika, F.Gao, M.Zhang, B.Korber, E.Hunter, BH.Hahn, DC.Montefiori.
   Genetic and neutralization properties of acute and early subtype C human immunodeficiency virus type 1 molecular env clones from heterosexually acquired infections in Southern Africa.
   Journal of Virology. 80(23):11776-90. 2006.
4. JJ. Esposito, S. Sammons, A. Frace, J. Osborne, M. Olsen-Rasmussen, M. Zhang, D. Govil, I. Damon, R. Kline, M. Laker, Y. Li, G. Smith, H. Meyer, J. LeDuc, R. Wohlhueter.
   Genome sequence diversity and clues to the evolution of variola virus.
   Science. 313(5788):807-812. 2006.
5. M. Zhang, A. 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 Research. 34:W463-5. 2006.
6. 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.
7. C. Calef, C. Kuiken, J. Szinger, B. Gaschen, W. Abfalterer, M. Zhang, N. Tao, R. Funkhouser, K. Yusim, M. Flynn, A. Dalwani, B. Foley, W. Bruno, T. Leitner, B. Korber.
   Gateway to tools of the HIV and HCV databases.
   In HIV Molecular Immunology. p33-56. 2005. Korber et al, editors. Publisher: Los Alamos Natl Lab, Theoretical Biology and Biophysics, Los Alamos, New Mexico. LA-UR 06-0036.
8. M. Zhang, K. Wilbe, N. Wolfe, B. Gaschen, J. Carr, T. Leitner.
   HIV-1 CRF13-cpx revisited: identification of a new sequence from Cameroon and signal for sub-subtype J2.
   AIDS Research and Human Retroviruses. 21(11):955-960. 2005.
9. M. Zhang, B. Gaschen, W. Blay, B. Foley, N. Haigwood, C. Kuiken, B. Korber.
   Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV Envelopes, and Influenza Hemagglutinin.
   Glycobiology. 14(12):1229-1246. 2004.

Technical Talks Presented During PhD Study:

• Dec 2006. CHAVI sequence analysis working group meeting. NM, USA.
• Apr 2006. 13th International HIV Dynamics and Evolution Meeting. MA, USA.
• Nov 2005. Algorithmics group, Max Planck Institute for Molecular Genetics. Berlin, Germany.
• Oct 2005. German Conference on Bioinformatics 2005. Hamburg, Germany.
• Dec 2004. Laboratoire Genome et Informatique (CNRS). Evry, France.
• Aug 2004. The AIDS Vaccine 2004 International Conference. Lausanne, Switzerland.

Web-based Sequence Analysis Tools Developed During PhD Study:

• N-linked glycosylation sites tracking tool
• HIV-specific BLAST tool
• Entropy tool
• JpHMM for HIV subtyping
  (joint project between Prof. Burkhard Morgenstern's group and the Los Alamos Sequence Database group)

Biological Databases Worked on During PhD Study:

• Los Alamos HIV sequence database
• Los Alamos HCV sequence database
• Sno/scaRNA database
• Algae database