Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.4
A-1030 Wien, Austria
Phone: ++43 +1 / 4277 - 74326
Email: minh.bui(AT)
Google Scholar
Last update: Sep 12, 2017

Research interests

  • Bioinformatics
  • Phylogenetics
  • Evolution
  • Phylogenomics
  • Biodiversity and Conservation
  • Algorithms
  • High Performance Computing
  • Software Engineering


Software development is my hobby with C++ as favorite language. The following scientific software is all GNU-GPL licensed. IQ-TREE is my main interest right now, which has reached about 90,000 lines of codes.

Occasionally I also programmed in Java for fun. A five-in-a-row game engine, which reached a very competitive level vs. Human, is available for Android:


  • Jan 2006 - Jan 2009: Ph.D. in Bioinformatics, University of Vienna, Austria Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories Thesis: Computational Methods in Biodiversity Conservation Advisor: Prof. Dr. Arndt von Haeseler

  • Oct 2002 - Oct 2005: M.Sc. in Applied Computer Science, University of Freiburg, Germany Thesis: Parallel reconstruction of large maximum likelihood phylogenies Advisor: Prof. Dr. Susanne Albers

  • Sep 1997 - Jun 2001: B.Sc. in Computer Science, Vietnam National University, Hanoi, Vietnam Thesis: Solutions to Vietnamese in Linux Advisor: Assoc. Prof. Dr. Ha Quang Thuy

  • Sep 1994 - Jun 1997: High School for the Talents in Informatics, Hanoi University of Science, Vietnam.


  • Since Feb 2009: Postdoctoral researcher, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Austria.
  • Jan 2006 - Jan 2009: Research assistant, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Austria.
  • Aug 2005 - Oct 2005: Guest student, John von Neumann Institute for Computing, Research Center Juelich, Helmholtz Association, Germany.
  • May 2003 - Feb 2004: Student research assistant, Computer networks and telematics group (Prof.Dr. Stefan Leue), University of Freiburg, Germany.
  • Sep 2001 - Sep 2002: Teaching Assistant, Faculty of Technology, Vietnam National University, Hanoi, Vietnam.


  • 2013-2015: Fast methods for sequence analysis problems with large data sets, National Foundation for Science and Technology Development (NAFOSTED), Vietnam
  • 2010-2014: Computational and mathematical approaches for statistical sequence alignment and phylogenetic inference on emerging parallel architectures, within D-A-CH framework between Deutsche Forschungsgemeinschaft (DFG) and Fonds zur Foerderung der wissenschaftlichen Forschung (FWF), Austria.
  • 2010-2014: Initiativkolleg Computational Science: Algorithms for graph optimization and their applications in life and nano sciences, University of Vienna, Austria.


  • 2003-2005: Master study scholarship, Konrad-Adenauer-Stiftung (KAS), Germany.
  • 2004: 4th prize, Microsoft Germany Imagine Cup for the project Mobile Learning, Germany together with Duc Phuong Nguyen.
  • 2001: 2nd prize, Vietnam Fund for Supporting Technological Creations (VIFOTEC) for project “Solutions to Vietnamese in Linux”, Vietnam.
  • 2000: 3rd prize in the competition of Chinese chess computer players, Vietnam.
  • 2000: Youth Innovation Medal by Vietnam Youth Union, Vietnam.
  • 1998: Special prize, National Informatics Olympiad for Universities, Vietnam.
  • 1997: 1st prize in National Informatics Contest for High Schools, Vietnam.
  • 1994: 3rd prize in National Mathematics Contest for Secondary Schools, Vietnam.
  • 1994: 1st prize for Problem Solving Contest of Magazine for Mathematics and Youth, Vietnam.



  1. S.M. Crottye, B.Q. Minhe, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, and A. von Haeseler (submitted) GHOST: Recovering historical signal from heterotachously-evolved sequence alignments. Syst. Biol. e equal contribution. Preprint
  2. 2018

  3. R. Alves, B.Q. Minh, T. Urich, A. von Haeseler, and C. Schleper (2018) Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat. Commun., 9, 1517. (DOI: 10.1038/s41467-018-03861-1, PMID: 29666365, PMCID: PMC5904100)
  4. D.T. Hoange, O. Chernomore, A. von Haeseler, B.Q. Minhc, and L.S. Vinhc (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35, 518-522. (free reprint, DOI: 10.1093/molbev/msx281, PMID: 29077904, software)
    e contributed equally, c corresponding authors.
  5. D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeselerc, and B.Q. Minhc (2018) MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol., 18, 11. (DOI: 10.1186/s12862-018-1131-3, PMID: 29390973, software)
    c corresponding authors.
  6. L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2018) Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model. Syst. Biol., 67, 552-558. (DOI: 10.1093/sysbio/syx092, PMID: 29186593, software)
  7. H.C. Wange, B.Q. Minhe, S. Susko, and A.J. Roger (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol., 67, 216-235. (DOI: 10.1093/sysbio/syx068, PMID: 28950365, software)
    e contributed equally
  8. 2017

  9. S. Kalyaanamoorthye, B.Q. Minhe, T.K.F. Wonge, A. von Haeseler, and L.S. Jermiin (2017) ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates. Nat. Methods, 14, 587-589. (DOI: 10.1038/nmeth.4285, PMID: 28481363) PMCID: PMC5453245) software) press release by MFPL
    e contributed equally
  10. O. Ratmann, C. Wymant, C. Colijn, S. Danaviah, M. Essex, S.D.W. Frost, A. Gall, S. Gaiseitsiwe, M. Grabowski, R. Gray, S. Guindon, A. von Haeseler, P. Kaleebu, M. Kendall, A. Kozlov, J. Manasa, B.Q. Minh, S. Moyo, V. Novitsky, R. Nsubuga, S. Pillay, T.C. Quinn, D. Serwadda, D. Ssemwanga, A. Stamatakis, J. Trifinopoulos, M. Wawer, A. Leigh Brown, T. de Oliveira, P. Kellam, D. Pillay, and C. Fraser (2017) HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. AIDS Res. Hum. Retrovir., 33, 1083-1098. (DOI: 10.1089/AID.2017.0061, PMID: 28540766)
  11. 2016

  12. F. Burki, M. Kaplan, D.V. Tikhonekov, V. Zlatogursky, B.Q. Minh, L.V. Radaykina, A. Smirnov, A.P. Mylnikov, and P.J. Keeling (2016) Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta, and Cryptista. Proc. R. Soc. B, 283, 20152802. (free reprint, DOI: 10.1098/rspb.2015.2802, PMID: 26817772)
  13. O. Chernomor, A. von Haeseler, and B.Q. Minh (2016) Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Syst. Biol., 65, 997-1008. (free reprint, DOI: 10.1093/sysbio/syw037, PMID: 27121966, software)
  14. O. Chernomor, S. Klaere, A. von Haeseler, and B.Q. Minh (2016) Split diversity: measuring and optimizing biodiversity using phylogenetic split networks. In R. Pellens and P. Grandcolas (eds.) Biodiversity Conservation and Phylogenetic Systematics (Series: Topics in Biodiversity and Conservation, Vol. 14), 173-195, Springer, Heidelberg/New York. (DOI: 10.1007/978-3-319-22461-9_9, book-DOI: 10.1007/978-3-319-22461-9_9, eISBN: 978-3-319-22461-9, ISBN: 978-3-319-22460-2)
  15. D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, and B.Q. Minh (2016) A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation. Proceedings of the 8th International Conference on Knowledge and Systems Engeneering - KSE-2016 (Hanoi, Vietnam), 1-6, IEEE Computer Society, Piscataway, NJ, USA. (DOI: 10.1109/KSE.2016.7758020)
  16. D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, and C. Kosiol (2016) Reversible polymorphism-aware phylogenetic models and their application to tree inference. J. Theor. Biol., 407, 362-370. (DOI: 10.1016/j.jtbi.2016.07.042, PMID: 27480613, software, preprint-DOI:10.1101/048496)
  17. J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res., 44, W232-W235. (free reprint, DOI: 10.1093/nar/gkw256, PMID: 27084950, W-IQ-TREE webserver)
  18. 2015

  19. O. Chernomor, B.Q. Minhc, F. Forest, S. Klaere, T. Ingram, M. Henzinger, and A. von Haeseler (2015) Split Diversity in Constrained Conservation Prioritization using Integer Linear Programming. Methods Ecol. Evol., 6, 83-91. (DOI: 10.1111/2041-210X.12299), c corresponding author
  20. O. Chernomor, B.Q. Minh, and A. von Haeseler (2015) Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference. J. Comput. Biol., 22, 1129-1142. (DOI: 10.1089/cmb.2015.0146, PMID: 26448206)
  21. T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L.-T. Nguyen, B.Q. Minh, A. von Haeseler, and A. Stamatakis (2015) The phylogenetic Likelihood Library. Syst. Biol., 64, 356-362. (DOI: 10.1093/sysbio/syu084, PMID: 25358969, software)
  22. D.T. Hai, N.D. Thanh, P.T.M. Trang, L.S. Quang, P.T.T. Hang, D.C. Cuong, H.K. Phuc, N.H. Duc, D.D. Dong, B.Q. Minh, P.B. Son, and L.S. Vinh (2015) Whole genome analysis of a Vietnamese trio. J. Biosci., 40, 113-124. (DOI: 10.1007/s12038-015-9501-0, PMID: 25740146)
  23. D.T. Nguyen, T.M.T. Pham, T.H. Dang, H.A.T. Nguyen, S.Q. Le, B.Q. Minh, Q.M. Dao, B.S Pham, and L.S. Vinh (2015) Building population-specific reference genomes: A case study of Vietnamese reference genome. Proceedings of the 7th International Conference on Knowledge and Systems Engeneering - KSE-2015 (Ho Chi Minh City, Vietnam), 97-102, IEEE Computer Society, Los Alamitos, CA, USA. (DOI: 10.1109/KSE.2015.49)
  24. L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32, 268-274. (free reprint, DOI: 10.1093/molbev/msu300, PMID: 25371430, PMCID: PMC4271533, software)
  25. 2014

  26. E. Dell'Ampioe, K. Meusemanne, N.U. Szucsiche, R.S. Peterse, B. Meyer, J. Borner, M. Petersen, A.J. Aberer, A. Stamatakis, M.G. Walzl, B.Q. Minh, A. von Haeseler, I. Ebersberger, G. Pass, and B. Misof (2014) Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects. Mol. Biol. Evol., 31, 239-249. (DOI: 10.1093/molbev/mst196, PMID: 24140757)
    e contributed equally
  27. M. Kaschner, A. Loeschcke, J. Krause, B.Q. Minh, A. Heck, S. Endres, V. Svensson, A. Wirtz, A. von Haeseler K.-E. Jaeger, T. Drepper, and U. Krauss (2014) Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria. Mol. Microbiol., 93, 1066-1078. (DOI: 10.1111/mmi.12719, PMID: 25039543)
  28. D.D. Pollak, B.Q. Minh, A. Cicvaric, and F.J. Monje (2014) A novel Fibroblast Growth Factor Receptor family member promotes neuronal outgrowth and synaptic plasticity in Aplysia. Amino Acids, 2477-2488. (DOI: 10.1007/s00726-014-1803-2, PMID: 25059541)
  29. 2013

  30. B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultra-Fast Approximation for Phylogenetic Bootstrap. Mol. Biol. Evol., 30, 1188-1195. (free reprint, DOI: 10.1093/molbev/mst024, PMID: 23418397, software)
  31. 2010

  32. H.Q. Dinh, B.Q. Minh, H.X. Huan and A. von Haeseler (2010) ACOPHY: A simple and general ant colony optimization approach for phylogenetic tree reconstruction. LNCS, 6234 (Proceedings of the 7th Intl. Conf. on Swarm Intelligence, ANTS 2010), 360-367. (DOI: 10.1007/978-3-642-15461-4_32)
  33. J. Hofmann, K. Frenzel, B.Q. Minh, A. von Haeseler, A. Edelmann, R.S. Ross, D.H. Krueger, H. Meisel (2010) Quantitative detection and typing of Hepatitis D virus in human serum by real-time PCR and melting curve analysis. Diagn. Microbiol. Infect. Dis., 67, 172-179. (DOI: 10.1016/j.diagmicrobio.2010.02.003, PMID: 20466196)
  34. B.Q. Minh, S. Klaere, and A. von Haeseler (2010) SDA*: A Simple and Unifying Solution to Recent Bioinformatic Chaallenges for Conservation Genetics. Proceedings of the 2nd International Conference on Knowledge and Systems Engeneering - KSE-2010 (Hanoi, Vietnam), 33-37, IEEE Computer Society, Los Alamitos, CA, USA. (DOI: 10.1109/KSE.2010.24, ISBN: 978-0-7695-4213-3)
  35. 2009

  36. U. Krausse, B.Q. Minhe, A. Losi, W. Gaertner, T. Eggert, A. von Haeselerc, and K.E. Jaeger (2009) Distribution and phylogeny of light-oxygen-voltage-blue-light-signaling proteins in the three kingdoms of life. J. Bacteriol., 191, 7234-7242. (DOI: 10.1128/JB.00923-09, PMID: 19783626)
    e contributed equally, c corresponding author
  37. B.Q. Minh, S. Klaere, and A. von Haeseler (2009) Taxon Selection under Split Diversity. Syst. Biol., 57, 586-594. (DOI: 10.1093/sysbio/syp058)
  38. B.Q. Minh, F. Pardi, S. Klaere, and A. von Haeseler (2009) Budgeted Phylogenetic Diversity on Circular Split Systems. IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 22-29. (DOI: 10.1109/TCBB.2008.54, PMID: 19179696)
  39. 2006

  40. B.Q. Minh, S. Klaere, and A. von Haeseler (2006) Phylogenetic Diversity within Seconds. Syst. Biol., 55, 769-773. (DOI: 10.1080/10635150600981604)
  41. B.Q. Minh, L.S. Vinh, H.A. Schmidt, and A. von Haeseler (2006) Large Maximum Likelihood Trees. Proceedings of the NIC Symposium 2006. 357-365, Forschungszentrum Jülich, Germany. (free reprint, ISBN 3-00-017351-X)
  42. 2005

  43. B.Q. Minh, L.S. Vinh, A. von Haeseler, and H.A. Schmidt (2005) pIQPNNI -- Parallel Reconstruction of Large Maximum Likelihood Phylogenies. Bioinformatics, 21:3794-3796. (free reprint, DOI: 10.1093/bioinformatics/bti594, PMID: 16046495)