Fortinbras Research provides the research community with web-based sequence tools, and its clients custom bioinformatics code and applications, with an emphasis on the genetic analysis of infectious organisms.

Mark A. Jensen, PhD
Senior Consultant and Principal
jensen -at-

LinkedIn profile
Ohloh profile for Mark A. Jensen

Selected Publications

  1. 2010. US Patent #7,655,774. Ancestral and COT viral sequences, proteins, and immunogenic compositions. Inventors: Mullins; James I., Rodrigo; Allen G., Learn; Gerald H., Li; Fusheng, Nickle; David C., Jensen; Mark A.. Assignee: University of Washington.
  2. 2010. Swenson, L. C, A. Moores, A. J. Low, A. Thielen, W. Dong, C. Woods, M. A. Jensen, B. Wynhoven, D. Chan, C. Glascock, and P. R. Harrigan. Improved detection of CXCR4-using HIV by V3 genotyping: application to plasma RNA, proviral DNA, and "deep" sequencing. Journal of AIDS, in press.
  3. 2009. Kandathil, A. J., R. Kannangai, O. C. Abraham, S. A. Pulimood, M. A. Jensen, and G. Sridharan. HIV-1 with predicted CXCR4 genotype identified in clade C from India. Molecular Diagnosis and Therapy, 13:19-24.
  4. 2009. Kandathil, A. J., R. Kannangai, O. C. Abraham, S. A. Pulimood, M. A. Jensen, and G. Sridharan. A comparison of interpretation by three different HIV-1 genotypic drug resistance algorithms using sequences from non-clade B HIV-1 strains. AIDS Research and Human Retroviruses, 25:315-318
  5. 2008. van 't Wout, A. B. and M. A. Jensen. HIV-1 tropism and its detection - impact on infection, transmission and treatment. European Infectious Disease 2:60-64.
  6. 2008. Jensen, M. A. Predicting disease outcomes in the clinic. Nature Biotechnology, 26:611-612.
  7. 2007. Low, A. J., W. Dong, D. Chan, T. Sing, R. Swanstrom, M. Jensen, S. Pillai, B. Good, and P. R. Harrigan. Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates. AIDS, 21:F17-24
  8. 2007. Rolland, M., M. A. Jensen, D. C. Nickle, J. Yan, G. H. Learn, L. Heath, D. Weiner, J. I. Mullins. Reconstruction and function of Ancestral Center-Of-Tree (COT) HIV-I Proteins. Journal of Virology 81:8507-8514.
  9. 2007. Gottlieb, G. S., D. C. Nickle, M. A. Jensen, K. G. Wong, R. A. Kaslow, J. C. Shepherd, J. B. Margolick, J. I. Mullins. HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case report. Clinical Infectious Diseases 45:501-509.
  10. 2007. Nickle, D. C., M. Rolland, M. A. Jensen, S. L. Kosokovsy-Pond, W. Deng, M. Seligman, D. Heckerman, J. I. Mullins, N. Jojic. Coping with viral diversity in HIV vaccine design. PLoS Computational Biology 3:e75.
  11. 2007. Nickle, D.C., L. Heath, M. A. Jensen, P. B. Gilbert, J. I. Mullins, S. L. Kosakovsky-Pond. HIV-Specific Probabilistic Models of Protein Evolution. PLoS ONE 2:e503.
  12. 2007. Ross H.A., D. C. Nickle, Y. Liu, L. Heath, M. A. Jensen, A. G. Rodrigo, J. I. Mullins. Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes. Evolutionary Bioinformatics Online 2:53-76.
  13. 2006. Jensen, M. A., S. M. Faruque, J. J. Mekalanos, and B. R. Levin. The role of bacteriophage in the control of cholera epidemics. PNAS 103:171-192.
  14. 2006. Jensen, M. A., M. Coetzer, A. B. van 't Wout, L. Morris, and J. I. Mullins. A reliable phenotype predictor for HIV-1 subtype C based on envelope V3 sequences. Journal of Virology 80:4698-4704.
  15. 2006. Mullins, J. I. and M. A. Jensen. Evolutionary dynamics of HIV-1 and the control of AIDS. Current Topics in Microbiology and Immunology 299:171-192.
  16. 2005. Troyer, R.M., K.R. Collins, A. Abraha, E. Fraundorf, D.M. Moore, R.W. Krizan, Z. Toossi, R.L. Colebunders, M.A. Jensen, J.I. Mullins, G. Vanham, and E. J. Arts. Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progression. Journal of Virology, 79:9006-9018.
  17. 2004. Gottlieb, G. S., D. C. Nickle, M. A. Jensen, K. G. Wong, J. Grobler, F. Li, S.-L. Liu, C. Rademeyer, G. H. Learn, S. S. A. Karim, C. Williamson, L. Corey, J. B. Margolick, and J. I. Mullins. Dual HIV-1 infection associated with rapid disease progression. The Lancet 363:619-622.
  18. 2004. Shriner, D., R. Shankarappa, M. A. Jensen, D. C. Nickle, J. E. Mittler, J. B. Margolick, and J. I. Mullins. Influence of random genetic drift on HIV-1 env evolution during chronic infection. Genetics 166:1155-1164.
  19. 2004. Liu, Y., D. C. Nickle, D. Shriner, M. A. Jensen, G. H. Learn, Jr., J. E. Mittler, and J. I. Mullins. Molecular clock-like evolution of human immunodeficiency virus type 1. Virology 329:101-108.
  20. 2003. Jensen, M. A., F.-S. Li, A. B. van 't Wout, D. C. Nickle, D. Shriner, H.-X. He, S. McLaughlin, R. Shankarappa, J. B. Margolick, and J. I. Mullins. Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of HIV-1 env V3 loop sequences. Journal of Virology 77:13376-13388.
  21. 2003. Jensen, M. A. and A. B. van 't Wout. Predicting HIV-1 coreceptor usage using sequence analysis. AIDS Reviews 5:104-112.
  22. 2003. Nickle, D. C., M. A. Jensen, G. S. Gottlieb, D. Shriner, G. H. Learn, A. G. Rodrigo and J. I. Mullins. Consensus and ancestral state HIV vaccines. Science 299:1515-1517.
  23. 2003. Z. L. Brumme, W. W. Y. Dong, B. Yip, B. Wynhoven, N. G. Hoffman, R. Swanstrom, M. A. Jensen, J. I. Mullins, R. S. Hogg, J. S. G. Montaner and P. R. Harrigan. Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. AIDS 18:F1-F9.
  24. 2003. Shriner, D., D. C. Nickle, M. A. Jensen, and J. I. Mullins. The potential impact of recombination on sitewise approaches for detecting positive natural selection. Genetical Research 81:115-121.
  25. 2003. Nickle, D. C., M. A. Jensen, D. Shriner, S. J. Brodie, L. M. Frenkel, J. E. Mittler, and J. I. Mullins. Evolutionary indicators of HIV-1 reservoirs and compartments. Journal of Virology 77:5540-5546.
  26. 2003. Dybul, M., M. Daucher, M. A. Jensen, C. W. Hallahan, T.-W. Chun, M. Belson, B. Hidalgo, D. C. Nickle, C. Yoder, J. A. Metcalf, R. T. Davey, L. Ehler, D. Kress-Rock, E. Nies-Kraske, S. Liu, J. I. Mullins and A. S. Fauci. Genetic characterization of rebounding plasma HIV-1 during multiple interruptions of highly active antiretroviral therapy. Journal of Virology 77:3229-3237.

FR icon 09 Feb 2010