Areas of expertise
- Molecular Evolution 060409
- Biological Mathematics 010202
- Medical Genetics (Excl. Cancer Genetics) 110311
- Anthropological Genetics 060401
- Genomics 060408
- Applied Statistics 010401
- Genome Structure And Regulation 060407
- Genetics 0604
- Biochemistry And Cell Biology 0601
- Other Biological Sciences 0699
- Epigenetics (Incl. Genome Methylation And Epigenomics) 060404
- Population, Ecological And Evolutionary Genetics 060411
- Bioinformatics 060102
- Bioinformatics Software 080301
- Software Engineering 080309
- Biostatistics 010402
Biography
Professor Gavin Huttley is a group leader in the Research School of Biology at the Australian National University. He obtained a B.Sc (Hons I) from Macquarie University in Sydney, a PhD in Molecular Population Genetics from the University of California, Riverside and undertook postdoctoral research in the Laboratory of Genomic Diversity, National Cancer Institute (USA). He is a recipient of the Howard Florey Young Investigator award. Professor Huttleys research is focussed on genome decryption — identifying regions of the genome which encode functions that influence susceptibility to disease — through analysis of genetic variation.
Available student projects
The Huttley lab offers a dynamic research environment enriched by collaborations with high profile, highly productive researchers at international institutions. Our research spans several traditional scientific disciplines that are now largely amalgamated under the label of Bioinformatics — comparative and population genomics, mathematical statistics and computer science. A major research product from the group is the open source Bioinformatics software package Cogent3. Students in my group need to have some facility with programming, either formally (in terms of course work) or an aptitude for it. Other valuable backgrounds include chemistry and physics.
Please see the lab web page for projects.
Publications
- Ying, H, Hayward, D, Klimovich, A et al. 2022, 'The role of DNA methylation in genome defense in Cnidaria and other invertebrates', Molecular Biology and Evolution, vol. 39, no. 2.
- Su, X, Jing, G, Sun, Z et al 2020, 'Multiple-Disease Detection and Classification Across Cohorts via Microbiome Search', mSystems, vol. 5, no. 2, pp. e001500-20.
- Zhu, Y, Ong, C & Huttley, G 2020, 'Machine Learning Techniques for Classifying the Mutagenic Origins of Point Mutations', Genetics (online), vol. 215, pp. 25-40.
- Simon, H & Huttley, G 2020, 'Quantifying influences on intragenomic mutation rate', G3: Genes, Genomes, Genetics, vol. 10, no. 8, pp. 2641-2652.
- Bolyen, E, Rideout, J, Dillon, M et al 2019, 'Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2', Nature Biotechnology, vol. 37, no. 8, pp. 848-857.
- McDonald, D, Kaehler, B, Gonzalez, A et al 2019, 'redbiom: a Rapid Sample Discovery and Feature Characterization System', mSystems, vol. 4, no. 4, pp. e00215-e00219.
- Kaehler, B, Bokulich, N, McDonald, D et al. 2019, 'Species abundance information improves sequence taxonomy classification accuracy', Nature Communications, vol. 10, no. 4643, pp. 1-10.
- Bokulich, N, Kaehler, B, Rideout, J et al 2018, 'Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin', Microbiome, vol. 6, no. 90, pp. 17pp.
- Sutherland, T, Sriskantha, A, Rapson, T et al 2018, 'Did aculeate silk evolve as an antifouling material?', PLOS ONE (Public Library of Science), vol. 13, no. 9, pp. 1-13pp.
- Ying, H, Cooke, I, Sprungala, S et al. 2018, 'Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages', Genome Biology, vol. 19, no. 175, pp. 1-24pp.
- Bokulich, N, Dillon, M, Bolyen, E et al. 2018, 'q2-sample-classifier: machine-learning tools for microbiome classification and regression', The Journal of Open Source Software, vol. 3, no. 30, pp. 1-4.
- Wong, M, Arcos-Burgos PhD, M, Liu, S et al. 2017, 'The PHF21B gene is associated with major depression and modulates the stress response', Molecular Psychiatry, vol. 22, no. 7, pp. 1015-1025.
- Kaehler, B, Yap, V & Huttley, G 2017, 'Standard codon substitution models overestimate purifying selection for nonstationary data', Genome Biology and Evolution, vol. 9, no. 1, pp. 134-149.
- Huttley, G, Neeman, T, Yap, V et al 2017, 'Statistical Methods for Identifying Sequence Motifs Affecting Point Mutations', Genetics (online), vol. 205, no. 2, pp. 843-856 pp.
- Padovan, A, Patel, H, Chuah, A et al 2015, 'Transcriptome Sequencing of Two Phenotypic Mosaic Eucalyptus Trees Reveals Large Scale Transcriptome Re-Modelling', PLOS ONE (Public Library of Science), vol. 10, no. 5, pp. e0123226-e0123226.
- Kaehler, B, Yap, V, Zhang, R et al. 2015, 'Genetic distance for a general non-stationary markov substitution process', Systematic Biology, vol. 64, no. 2, pp. 281-293.
- Johar, A, Mastronardi, C, Rojas-Villarraga, A et al. 2015, 'Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome', Journal of Translational Medicine, vol. 13, no. 173, pp. 173-173.
- Maitip, J, Trueman, H, Kaehler, B et al 2015, 'Folding behavior of four silks of giant honey bee reflects the evolutionary conservation of aculeate silk proteins', Insect Biochemistry and Molecular Biology, vol. 59, pp. 72-79.
- Perez-Bercoff, A, Papanicolaou, A, Ramsperger, M et al 2015, 'DRAFT GENOME OF AUSTRALIAN ENVIRONMENTAL STRAIN WM 09 24 OF THE OPPORTUNISTIC HUMAN PATHOGEN SCEDOSPORIUM AURANTIACUM', Genome Announcements, vol. 3, no. 1, pp. e01526-14.
- Kitahara, M, Lin, M, Foret, S et al 2014, 'The "Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly', PLOS ONE (Public Library of Science), vol. 9, no. 4, pp. -.
- Engelthaler, D, Hicks, N, Gillece, J et al 2014, 'Cryptococcus gattii in North American Pacific Northwest: Whole-Population Genome Analysis Provides Insights into Species Evolution and Dispersal', mBio, vol. 5, no. 4.
- Da Paz Filho, G, Boguszewski, M, Mastronardi, C et al. 2014, 'Whole Exome Sequencing of Extreme Morbid Obesity Patients: Translational Implications for Obesity and Related Disorders', GENES, vol. 5, no. 3, pp. 709-725.
- Ye, Y, Woolfit, M, Huttley, G et al 2013, 'Infection with a Virulent Strain of Wolbachia Disrupts Genome Wide-Patterns of Cytosine Methylation in the Mosquito Aedes aegypti', PLOS ONE (Public Library of Science), vol. 8, no. 6.
- Verbyla, K, Yap, V, Pahwa, A et al. 2013, 'The Embedding Problem for Markov Models of Nucleotide Substitution', PLOS ONE (Public Library of Science), vol. 8, no. 7.
- Casewell, N, Huttley, G & Wuster, W 2012, 'Dynamic evolution of venom proteins in squamate reptiles', Nature Communications, vol. 3, pp. 1066-1066.
- Huttley, G & Yap, V 2012, 'Robust estimation of natural selection using parametric codon models', in Gina M. Cannarozzi and Adrian Schneider (ed.), Codon Evolution Mechanisms and Models, Oxford University Press, UK, pp. 111-125.
- Bellani, M, Epps, J & Huttley, G 2012, 'A Comparison of Periodicity Profile Methods for Sequence Analysis', IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012), IEEE Engineering in Medicine and Biology Society, Washington DC USA, p. 4.
- Nekrasov, M, Amrichova, J, Parker, B et al., 'Histone H2A.Z inheritance during the cell cycle and its impact on promoter organization and dynamics', Nature Structural and Molecular Biology. 2012, vol. 19, no. 11, pp. 1076-1083.
- Soboleva TA, Nekrasov M, Pahwa A, Williams R, Huttley GA, Tremethick DJ. 'A unique H2A histone variant occupies the transcriptional start site of active genes', Nature Structural and Molecular Biology. 2012 Jan; 19(1): 25-30.
- Epps, J, Ying, H & Huttley, G 2011, 'Statistical methods for detecting periodic fragments in DNA sequence data', Biology Direct, vol. 6, no. 21, p. 16.
- Ying, H & Huttley, G 2011, 'Exploiting CpG Hypermutability to Identify Phenotypically Significant Variation Within Human Protein-Coding Genes', Genome Biology and Evolution, vol. 3, no. 1, pp. 938-949.
- Adcock, G, Easteal, S, Huttley, G et al 2001, 'Human origins and ancient human DNA [3]', Science, vol. 292, no. 5522, pp. 1655-1656.
- Smith, A, Box, N, Marks, L et al 2001, 'The human melanocortin-1 receptor locus: Analysis of transcription unit, locus polymorphism and haplotype evolution', Gene, vol. 281, no. 1-2, pp. 81-94.
- Huttley, G, Easteal, S, Southey, M et al 2000, 'Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees', Nature Genetics, vol. 25, no. 4, pp. 410-413.
- Sammut, R & Huttley, G 2011, 'Regional Context in the Alignment of Biological Sequence Pairs', Journal of Molecular Evolution, vol. 72, no. 2, pp. 147-159.
- Yap, V, Lindsay, H, Easteal, S et al 2010, 'Estimates of the effect of natural selection on protein-coding content', Molecular Biology and Evolution, vol. 27, no. 3, pp. 726-734.
- Ying, H, Epps, J, Williams, R et al 2010, 'Evidence that localized variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair', Molecular Biology and Evolution, vol. 27, no. 3, pp. 637-649.
- Caporaso, J, Kuczynski, J, Stombaugh, J et al 2010, 'QIIME allows analysis of high-throughput community sequencing data', Nature Methods: techniques for life scientists and chemists, vol. 7, no. 5, pp. 335-336.
- Simpson, N, Gatenby, P, Wilson, A, Malik, S, Fulcher, DA, Tangye, SG, Manku, H,Vyse, TJ, Roncador, G, Huttley, G, Goodnow, CC, Vinuesa, CG, Cook, MC, 2010, 'Expansion of Circulating T Cells Resembling Follicular Helper T Cells Is a Fixed Phenotype That Identifies a Subset of Severe Systemic Lupus Erythematosus', Arthritis & Rheumatism, vol. 62, no. 1, pp. 234-244.
- Huttley, G 2009, 'Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?', Australian Journal of Zoology, vol. 57, pp. 167-174.
- Caporaso, J, Smit, S, Easton, B et al. 2008, 'Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics', BMC Evolutionary Biology (now BMC Ecology and Evolution), vol. 8:327, pp. 1-25.
- Lindsay, H, Yap, V, Ying, H et al 2008, 'Pitfalls of the most commonly used models of context dependent substitution', Biology Direct, vol. 3, no. 52, pp. 1-17.
- Oscamou, M, McDonald, D, Yap, V et al 2008, 'Comparison of methods for estimating the Nucleotide Substitution Matrix', BMC Bioinformatics, vol. 9, pp. 1-18.
- Warren, W, Hillier, L, Graves, J et al. 2008, 'Genome analysis of the platypus reveals unique signatures of evolution', Nature, vol. 453, no. 7192, pp. 175-83.
- Schranz, H, Yap, V, Easteal, S et al 2008, 'Pathological rate matrices: from primates to pathogens', BMC Bioinformatics, vol. 9, no. 1, pp. 1-10.
- Faux, N, Huttley, G, Mahmood, K et al 2007, 'RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins', Genome Research, vol. 17, no. 7, pp. 1118-27.
- MacArthur, D, Seto, J, Raftery, J et al 2007, 'Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans', Nature Genetics, vol. 39, no. 10, pp. 1261-5.
- Mikkelsen, T, Wakefield, M, Aken, B et al. 2007, 'Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences', Nature, vol. 447, no. May 10, pp. 167-178.
- Huttley, G, Wakefield, M & Easteal, S 2007, 'Rates of genome evolution and branching order from whole genome analysis', Molecular Biology and Evolution, vol. 24, no. 8, pp. 1722-30.
- Knight, R, Maxwell, P, Birmingham, A et al 2007, 'PyCogent: a toolkit for making sense from sequence', Genome Biology, vol. 8, no. 8, pp. R171.
- Easton, B, Isaev, A, Huttley, G et al 2007, 'A probabilistic method to identify compensatory substitutions for pathogenic mutations', Asia-Pacific Bioinformatics Conference (APBC 2007), ed. David Sankoff, Lusheng Wang, Francis Chin, Imperial College Press, London, UK, pp. 195-204.
- Wakefield, M, Maxwell, P & Huttley, G 2005, 'Vestige: Maximum likelihood phylogenetic footprinting', BMC Bioinformatics, vol. 6, no. 130, pp. 1-9.
- Robinson, A, Huttley, G, Booth, H et al 2004, 'Modelling and bioinformatics studies of the human Kappa-class glutathione transferase predict a novel third glutathione transferase family with similarity to prokaryotic 2-hydroxychromene-2-carboxylate isomerases', Biochemical Journal, vol. 379, pp. 541-552.
- Butterfield, A, Vedagiri, V, Lang, E et al 2004, 'Pyevolve: a toolkit for statistical modelling of molecular evolution', BMC Bioinformatics, vol. 5, no. 1, pp. 1-12.
- Huttley, G 2004, 'Modeling the Impact of DNA Methylation on the Evolution of BRCA1 in Mammals', Molecular Biology and Evolution, vol. 21, no. 9, pp. 1760-1768.
- Wilson, S & Huttley, G 2002, 'Non-replicability of disease gene results: A modelling perspective', International Conference on Statistics, Combinatorics and Related Areas / International Conference of the Forum for the Interdisciplinary Mathematics 2001, ed. Gulati C, Lin Y-X, Mishra S, Rayner J, World Scientific Publishing Company, Singapore, pp. 374-382.
- Prichard, Z, Jorm, A, Prior, M et al. 2002, 'Association of polymorphisms of the estrogen receptor gene with anxiety-related traits in children and adolescents: A longitudinal study', American Journal of Medical Genetics, Part A, vol. 114, no. 2, pp. 169-176.
- Peacock, W, Dennis, E, Easteal, S et al 2001, 'Lake Mungo 3: A response to recent critiques', Archaeology in Oceania, vol. 36, pp. 163-174.
- Adcock, G, Dennis, E, Easteal, S et al 2001, 'Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 2, pp. 537-542.
- Cooper, A, Rambaut, A, Macaulay, V et al 2001, 'Human Origins and Ancient Human DNA', Science, vol. 292, no. 2001, pp. 1656-1656.
- Huttley, G, Jakobsen, I, Wilson, S et al. 2000, 'How important is DNA replication for mutagenesis?', Molecular Biology and Evolution, vol. 17, pp. 929 - 937.
- Huttley, G & Wilson, S 2000, 'Testing for concordant equilibria between population samples', Genetics (Print) ceased Dec 2009 - don't use, vol. 156, pp. 2127 - 2135.
- Huttley, G, Jakobsen, I & Easteal, S 2000, 'How important is DNA replication for mutagenesis?', Molecular Biology and Evolution, vol. 17, pp. 929-937.
- Huttley, G, Smith, M, Carrington, M et al 1999, 'A scan for linkage disequilibrium across the human genome', Genetics (Print) ceased Dec 2009 - don't use, vol. 152, no. 4, pp. 1711-1722.
Projects and Grants
Grants information is drawn from ARIES. To add or update Projects or Grants information please contact your College Research Office.
- cogent3 python APIs for IQ-TREE and GraphBin via a plug-in architecture (Primary Investigator)
- Beyond the genome: impact of microbial communities and epigenetic regulations for adaptation (Secondary Investigator)
- Robust bioinformatics for predicting bacterial pathogens from microbiome sequencing (Primary Investigator)
- Genetic variants and environmental factors in depression (Secondary Investigator)
- Functional and phenotypic effect of dopamine transporter gene variation (Secondary Investigator)
- Uncovering the genetic basis of fungal virulence (Primary Investigator)
- 40TB Network Attached Storage (See 22085) (Primary Investigator)
- Improving the accuracy of phylogenetic reconstruction by improving models of sequence divergence (Primary Investigator)
- Genetic pathology of Roquin in human autoimmune disease (Secondary Investigator)
- Exploiting Sexual Differences in Germline Biology to Resolve the Causes of Germline Mutation (Primary Investigator)
