Associate Professor Minh Bui
Areas of expertise
- Phylogeny And Comparative Analysis 060309
- Molecular Evolution 060409
- Bioinformatics Software 080301
- Distributed Computing 0805
Research interests
My research focuses on efficient bioinformatics methods, statistical models, algorithms and high performance computing techniques for phylogenetic inference from ultra-large genomic data.
More details on my lab website: https://anu-phylogenomics.github.io/
Biography
I obtained B.Sc. in Computer Science from Vietnam National University in 2001; M.Sc. in Applied Computer Sience from University of Freiburg (Germany) in 2005; Ph.D. in Bioinformatics from University of Vienna (Austria) in 2009. I had several postdoc positions in Vienna at Max F. Perutz Laboratories, Gregor Mendel Institute and University of Vienna. From 2018 I am a Research Fellow at the Research School of Biology, Australian National University Canberra. In 2019 I joint the Research School of Computer science (ANU) as a Lecturer.
I was recently named the Field Leader in Evolutionary Biology by The Australian.
Researcher's projects
Research Theme 1: Bioinformatics method and software for evolutionary biology
I have developed three widely used bioinformatics methods for the phylogenetic community: a fast and accurate model selection approach (ModelFinder), an effective tree reconstruction method (IQ-TREE) and a novel ultrafast bootstrap approach (UFBoot). These methods represent three key steps in every phylogenetic analysis.
A significant outcome from this research theme is the widely used IQ-TREE phylogenetic software (www.iqtree.org), which I have continuously developed since 2011. IQ-TREE has received a lot of user enthusiasms and integrated in many phylogenetic pipelines. Currently, I am leading an international team from Austria, Australia and Vietnam to jointly develop IQ-TREE.
Research Theme 2: Statistical models for phylogenomics
Driven by the rapid growth of large phylogenomic datasets coupled with increasing impact of model violation, I jointly developed many new statistical models for phylogenomics including partition models, polymorphism-aware models, distribution free models, mixture models and site-specific models. These advanced models have been implemented in IQ-TREE, representing the first time availability in a prominent maximum likelihood framework.
Research Theme 3: Phylogenetic applications
Applications play an important role in my search, not only to show the usefulness of bioinformatics methods but also to identify potential limitations of existing models. Hence, I have collaborated with many biologists to analyse empirical datasets ranging from virus to bacteria and eukaryotes. Such collaborations include: the origin of photosynthetic enzymes, deep insect phylogeny using transcriptomic data, origin of helizoan protists, Algae and Cryptista using phylogenomic data, HIV full-genome phylogeny.
Research Theme 4: Efficient algorithms for biodiversity optimisation
During my PhD study I introduced efficient algorithms for many biodiversity conservation questions such as: Which species/areas should we prioritise for conservation, such that the phylogenetic diversity conserved is maximised? How to measure biodiversity when evolution is not treelike? The algorithms that I developed range from greedy algorithm to dynamic programming and integer linear programming. Especially the last technique generally works for extended conservation problems under budget constraint or prey-predator interactions.
Available student projects
I have several open projects for Graduate, Honours and PhD students. For details see my research themes above. Please send me a motivation letter, why you think you would be suitable, and I am happy discuss further.
Current student projects
I am co-supervising Suha Naser-Khdour (with A/Prof. Rob Lanfear) to study the impact of model violations in phylogenetics.
Publications
- Mo, Y, Lanfear, R, Hahn, M et al. 2023, 'Updated site concordance factors minimize effects of homoplasy and taxon sampling', Bioinformatics, vol. 39, no. 1, pp. 2pp.
- Naser, S, Bui, M & Lanfear, R 2022, 'Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals', Systematic Biology, vol. 71, no. 4, pp. 959-972.
- Dang, C, Bui, M, McShea, H et al. 2022, 'nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models', Systematic Biology, vol. 71, no. 5, pp. 1110-1123.
- Hodcroft, E, de Maio, N, Lanfear, R et al. 2021, 'Want to track pandemic variants faster? Fix the bioinformatics bottleneck', Nature, vol. 591, pp. 30-33.
- Bui, M, Dang, C, Vinh, L et al. 2021, 'QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution', Systematic Biology, vol. 70, no. 5, pp. 1046-1060.
- Spence, M, Mortimer, M, Buckle, A et al. 2021, 'A Comprehensive Phylogenetic Analysis of the Serpin Superfamily', Molecular Biology and Evolution, vol. 38, no. 7, pp. 2915-2929.
- Crotty, S, Bui, M, Bean, N et al. 2020, 'GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments', Systematic Biology, vol. 69, no. 2, pp. 249-264.
- Bui, M, Schmidt, H, Chernomor, O et al 2020, 'IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era', Molecular Biology and Evolution, vol. 37, no. 5, pp. 1530-1534.
- Bui, M, Hahn, M & Lanfear, R 2020, 'New Methods to Calculate Concordance Factors for Phylogenomic Datasets', Molecular Biology and Evolution, vol. 37, no. 9, pp. 2727-2733.
- Dombrowski, N, Williams, T, Sun, J et al. 2020, 'Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution', Nature Communications, vol. 11, no. 1, pp. 16pp.
- Parajuli, P, Bui, M & Verma, N 2020, 'Newly Emerged Serotype 1c of Shigella flexneri: Multiple Origins and Changing Drug Resistance Landscape', GENES, vol. 11, no. 1042, pp. 1-14.
- Vanderpool, D, Bui, M, Lanfear, R et al. 2020, 'Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression', PLoS Biology, vol. 18, no. 12, pp. 27pp.
- Schrempf, D, Bui, M, von Haeseler, A et al 2019, 'Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity', Molecular Biology and Evolution, vol. 36, no. 6, pp. 1294-1301.
- Schenk, S, Bannister, S, Sedlazeck, F et al 2019, 'Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase', eLife, vol. 8, no. e41556, pp. 1-39.
- Naser, S, Bui, M, Zhang, W et al. 2019, 'The Prevalence and Impact of Model Violations in Phylogenetic Analysis', Genome Biology and Evolution, vol. 11, no. 12, pp. 3341-3352.
- Alves, R, Bui, M, Urich, T et al. 2018, 'Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes', Nature Communications, vol. 9, no. 1517, pp. 1-17pp.
- Hoang, D, Chernomor, O, von Haeseler, A et al 2018, 'UFBoot2: Improving the Ultrafast Bootstrap Approximation', Molecular Biology and Evolution, vol. 35, no. 2, pp. 518-522pp.
- Wang, H, Bui, M, Susko, E et al. 2018, 'Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation', Systematic Biology, vol. 67, no. 2, pp. 216-235pp.
- Hoang, D, Vinh, L, Flouri, T et al. 2018, 'MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation', BMC Evolutionary Biology (now BMC Ecology and Evolution), vol. 18, no. 11, pp. 1-11pp.
- Nguyen, L, von Haeseler, A & Bui, M 2017, 'Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model', Systematic Biology, vol. 67, no. 3, pp. 552-558pp.
- Kalyaanamoorthy, S, Bui, M, Wong, K et al. 2017, 'ModelFinder: fast model selection for accurate phylogenetic estimates', Nature Methods: techniques for life scientists and chemists, vol. 14, no. 6, pp. 587-589pp.
- Ratmann, O, Wymant, C, Colijn, C et al 2017, 'HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences', AIDS Research and Human Retroviruses, vol. 33, no. 11, pp. 1083-1098pp.
- Schrempf, D, Bui, M, De Maio, N et al 2016, 'Reversible polymorphism-aware phylogenetic models and their application to tree inference', Journal of Theoretical Biology, vol. 407, pp. 362-370pp.
- Chernomor, O, von Haeseler, A & Bui, M 2016, 'Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices', Systematic Biology, vol. 65, no. 6, pp. 997-1008pp.
- Trifinopoulos, J, Nguyen, L, von Haeseler, A et al 2016, 'W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis', Nucleic Acids Research, vol. 44, pp. 232-235pp.
- Burki, F, Kaplan, M, Tikhonenkov, D et al 2016, 'Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista', Proceedings of the Royal Society of London Series B: Biological Sciences, vol. 283, no. 20152802, pp. 1-10pp.
- Flouri, T, Izquierdo-Carrasco, F, Darriba, D et al. 2015, 'The Phylogenetic Likelihood Library', Systematic Biology, vol. 64, no. 2, pp. 356-362pp.
- Chernomor, O, Bui, M, Forest, F et al. 2015, 'Split diversity in constrained conservation prioritization using integer linear programming', Methods in Ecology and Evolution, vol. 6, no. 1, pp. 83-91pp.
- Chernomor, O, Bui, M & von Haeseler, A 2015, 'Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference', Journal of Computational Biology, vol. 22, no. 12, pp. 1129-1142pp.
- Hai, D, Thanh, N, Trang, P et al 2015, 'Whole genome analysis of a Vietnamese trio', Journal of Biosciences (India), vol. 40, no. 1, pp. 113-124pp.
- Pollak, D, Bui, M, Cicvaric, A et al 2014, 'A novel fibroblast growth factor receptor family member promotes neuronal outgrowth and synaptic plasticity in aplysia', Amino Acids, vol. 46, pp. 2477-2488pp.
- Kaschner, M, Loeschcke, A, Krause, J et al 2014, 'Discovery of the first light�dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria', Molecular Microbiology, vol. 93, no. 5, pp. 1066-1078pp.
- Nguyen, L, Schmidt, H, von Haeseler, A et al 2014, 'IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies', Molecular Biology and Evolution, vol. 32, no. 1, pp. 268-274pp.
- Bui, M, Nguyen, M & von Haeseler, A 2013, 'Ultrafast approximation for phylogenetic bootstrap', Molecular Biology and Evolution, vol. 30, no. 5, pp. 1188-1195.
- Dell'Ampio, E, Meusemann, K, Szucsich, N et al 2013, 'Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects', Molecular Biology and Evolution, vol. 31, no. 1, pp. 239-249.
- Hofmann, J, Frenzel, K, Bui, M et al 2010, 'Quantitative detection and typing of hepatitis D virus in human serum by real-time polymerase chain reaction and melting curve analysis', Diagnostic Microbiology and Infectious Disease, vol. 67, pp. 172-179.
- Krauss, U, Bui, M, Losi, A et al. 2009, 'Distribution and Phylogeny of Light-Oxygen-Voltage-Blue-Light-Signaling Proteins in the Three Kingdoms of Life', Journal of Bacteriology, vol. 191, no. 23, pp. 7234-7242.
- Bui, M, Klaere, S & von Haeseler, A 2009, 'Taxon Selection under Split Diversity', Systematic Biology, vol. 58, no. 6, pp. 586-594.
- Bui, M, Pardi, F, Klaere, S et al 2008, 'Budgeted Phylogenetic Diversity on Circular Split Systems', IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 22-29.
- Bui, M, Klaere, S & von Haeseler, A 2006, 'Phylogenetic Diversity within Seconds', Systematic Biology, vol. 55, no. 5, pp. 769-773.
- Bui, M, Vinh, L, von Haeseler, A et al 2005, 'pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies', Bioinformatics, vol. 21, no. 19, pp. 3794-3796.
Projects and Grants
Grants information is drawn from ARIES. To add or update Projects or Grants information please contact your College Research Office.
- Real-time genomic epidemiology with IQ-TREE (Primary Investigator)
- Efficient phylogenetic methods that manage the curse of genomic complexity (Secondary Investigator)
- New phylogenomic models and methods to resolve the prokaryotic to eukaryotic transition (Secondary Investigator)
- IQ-TREE for ultra-large genomic data (Primary Investigator)
