Associate Professor Alexie Papanicolaou

Associate Professor Alexie Papanicolaou

Associate Professor in Bioinformatics,
Hawkesbury Institute for the Environment


Dr Alexie Papanicolaou blends the frontiers of molecular biology and computer science to secure Australia's agricultural and natural ecosystems in the face of a changing climate. 

He is a genome bioinformatician working on ecological and economically important species, such as theHeliconius butterflies, Helicoverpa armigera the cotton bollworm moth, invasive Tephritid fruit flies and eucalyptus trees.

Dr Alexie Papanicolaou's main interest is developing bioinformatics capability to address evolutionary questions such as how organisms adapt to a changing or novel environment and therefore works on the crux of biosecurity, climate adaptation and evolutionary biology.

Dr Papanicolaou joined the Hawkesbury Institute in 2015 after previous positions in the CSIRO, the University of Exeter conducting his PhD research at the Max Planck Institute for Chemical Ecology. 

He currently splits his time between addressing evolutionary genomics questions, conduct genomic and geospatial data analysis and engineer new bioinformatic software. He has worked on a number of international genome consortia, is the leader of the i5k working group on Manual Curation and a coauthor of the Trinity RNA-Seq, the Just Annotate My Genome and others.

Dr Papanicolaou's research is currently focused on using gene expression experiments to dissect the molecular basis of adaptive traits using a number of organisms as models. 

Further, he is passionate about post-graduate education especially on the topic of computer science and bioinformatics, community curation of data and is also interested in exploring new concepts and methods that can integrate genomics with spatial ecology.

His lab webpage is at

This information has been contributed by Associate Professor Papanicolaou.


  • PhD Friedrich Schiller University Jena
  • MSC University of Edinburgh
  • BSc University of Edinburgh


  • Bioinformatics
  • Biosecurity
  • Genomics

Organisational Unit (School / Division)

  • Hawkesbury Institute for the Environment


Phone: (02) 4570 1385
Mobile: 0468581247
Location: L3.G.07

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Previous Teaching Areas

  • 301118 Genomic Data Science, 2017
  • 301118 Genomic Data Science, 2018
  • 301118 Genomic Data Science, 2019
  • 301118 Genomic Data Science, 2020
  • 800220 Researcher Development 2: Proposing and Justifying Research, 2020


Journal Articles

  • Sahu, N., Indic, B., Wong-Bajracharya, J., Merenyi, Z., Ke, H., Ahrendt, S., Monk, T., Kocsube, S., Drula, E., Lipzen, A., Balint, B., Henrissat, B., Andreopoulos, B., Martin, F., Bugge, H., Rigling, D., Ford, K., Foster, G., Pangilinan, J., Papanicolaou, A., Barry, K., LaButti, K., Viragh, M., Koriabine, M., Yan, M., Riley, R., Champramary, S., Plett, K., Grigoriev, I., Tsai, I., Slot, J., Sipos, G., Plett, J., Plett, J. and Nagy, L. (2023), 'Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria', Nature Microbiology, vol 8, no 9 , pp 1668 - 1681.
  • Sharpe, S., Morrow, J., Cook, J., Papanicolaou, A. and Riegler, M. (2023), '[In Press] Transmission mode predicts coinfection patterns of insect-specific viruses in field populations of the Queensland fruit fly', Molecular Ecology, .
  • Paudel, L., Kerr, S., Prentis, P., Tanurd?ic, M., Papanicolaou, A., Plett, J. and Cazzonelli, C. (2022), 'Horticultural innovation by viral-induced gene regulation of carotenogenesis', Horticulture Research, vol 9 .
  • El-Kamand, S., Steiner, M., Ramirez, C., Halliday, C., Chen, S., Papanicolaou, A. and Morton, C. (2022), 'Assessing differences between clinical isolates of Aspergillus fumigatus from cases of proven invasive aspergillosis and colonizing isolates with respect to phenotype (virulence in Tenebrio molitor larvae) and genotype', Pathogens, vol 11, no 4 .
  • Guo, R., Papanicolaou, A. and Fritz, M. (2022), 'Validation of reference-assisted assembly using existing and novel Heliothine genomes', Genomics, vol 114, no 5 .
  • Nguyen, T., Mendez, V., Ward, C., Crisp, P., Papanicolaou, A., Choo, A., Taylor, P. and Baxter, S. (2021), 'Disruption of duplicated yellow genes in Bactrocera tryoni modifies pigmentation colouration and impacts behaviour', Journal of Pest Science, vol 94, no 3 , pp 917 - 932.
  • Watson-Lazowski, A., Papanicolaou, A., Koller, F. and Ghannoum, O. (2020), 'The transcriptomic responses of C4 grasses to subambient CO2 and low light are largely species specific and only refined by photosynthetic subtype', Plant Journal, vol 101, no 5 , pp 1170 - 1184.
  • Zhang, H., Xu, W., Chen, Q., Sun, L., Anderson, A., Xia, Q. and Papanicolaou, A. (2020), 'A phylogenomics approach to characterizing sensory neuron membrane proteins (SNMPs) in Lepidoptera', Insect Biochemistry and Molecular Biology, vol 118 .
  • Bayega, A., Djambazian, H., Tsoumani, K., Gregoriou, M., Sagri, E., Drosopoulou, E., Mavragani-Tsipidou, P., Giorda, K., Tsiamis, G., Bourtzis, K., Oikonomopoulos, S., Dewar, K., Church, D., Papanicolaou, A., Mathiopoulos, K. and Ragoussis, J. (2020), 'De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly', BMC Genomics, vol 21, no 1 .
  • Xu, W., Zhang, H., Liao, Y. and Papanicolaou, A. (2020), 'Characterization of sensory neuron membrane proteins (SNMPs) in cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae)', Insect Science, vol 28, no 3 , pp 769 - 779.
  • Brenya, E., Chen, Z., Tissue, D., Papanicolaou, A. and Cazzonelli, C. (2020), 'Prior exposure of Arabidopsis seedlings to mechanical stress heightens jasmonic acid-mediated defense against necrotrophic pathogens', BMC Plant Biology, vol 20, no 1 .
  • Yeap, H., Lee, S., Robinson, F., Mourant, R., Sved, J., Frommer, M., Papanicolaou, A., Edwards, O. and Oakeshott, J. (2020), 'Separating two tightly linked species-defining phenotypes in Bactrocera with hybrid recombinant analysis', BMC Genetics, vol 21, no Suppl. 2 .
  • Anantanawat, K., Papanicolaou, A., Hill, K. and Xu, W. (2020), 'Molecular response of the Mediterranean fruit fly (Diptera: Tephritidae) to heat', Journal of Economic Entomology, vol 113, no 5 , pp 2495 - 2504.
  • Surm, J., Stewart, Z., Papanicolaou, A., Pavasovic, A. and Prentis, P. (2019), 'The draft genome of Actinia tenebrosa reveals insights into toxin evolution', Ecology and Evolution, vol 9, no 19 , pp 11314 - 11328.
  • El-Kamand, S., Papanicolaou, A. and Morton, C. (2019), 'The use of whole genome and next-generation sequencing in the diagnosis of invasive fungal disease', Current Fungal Infection Reports, vol 13, no 4 , pp 284 - 291.
  • Harm, G., Papanicolaou, A., Cuddy, W., Park, R. and Moffitt, M. (2018), 'Draft genome sequence of the fungus Lecanicillium psalliotae strain HWLR35, isolated from a wheat leaf infected with leaf rust (caused by Puccinia triticina)', Genome Announcements, vol 6, no 2 .
  • Fritz, M., DeYonke, A., Papanicolaou, A., Micinski, S., Westbrook, J. and Gould, F. (2018), 'Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices', Molecular Ecology, vol 27, no 1 , pp 167 - 181.
  • Watson-Lazowski, A., Papanicolaou, A., Sharwood, R. and Ghannoum, O. (2018), 'Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes', Photosynthesis Research, vol 138, no 2 , pp 233 - 248.
  • Van Belleghem, S., Rastas, P., Papanicolaou, A., Martin, S., Arias, C., Supple, M., Hanly, J., Mallet, J., Lewis, J., Hines, H., Ruiz, M., Salazar, C., Linares, M., Moreira, G., Jiggins, C., Counterman, B., McMillan, W. and Papa, R. (2017), 'Complex modular architecture around a simple toolkit of wing pattern genes', Nature Ecology and Evolution, vol 1 .
  • Pearce, S., Clarke, D., East, P., Elfekih, S., Gordon, K., Jermiin, L., McGaughran, A., Oakeshott, J., Papanikolaou, A., Perera, O., Rane, R., Richards, S., Tay, W., Walsh, T., Anderson, A., Anderson, C., Asgari, S., Board, P., Bretschneider, A., Campbell, P., Chertemps, T., Christeller, J., Coppin, C., Downes, S., Duan, G., Farnsworth, C., Good, R., Han, L., Han, Y., Hatje, K., Horne, I., Huang, Y., Hughes, D., Jacquin-Joly, E., James, W., Jhangiani, S., Kollmar, M., Kuwar, S., Li, S., Liu, N., Maibeche, M., Miller, J., Montagne, N., Perry, T., Qu, J., Song, S., Sutton, G., Vogel, H., Walenz, B., Xu, W., Zhang, H., Zou, Z., Batterham, P., Edwards, O., Feyereisen, R., Gibbs, R., Heckel, D., McGrath, A., Robin, C., Scherer, S., Worley, K. and Wu, Y. (2017), 'Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species', BMC Biology, vol 15, no 1 .
  • Xu, W., Papanicolaou, A., Zhang, H. and Anderson, A. (2016), 'Expansion of a bitter taste receptor family in a polyphagous insect herbivore', Scientific Reports, vol 6 .
  • Papanicolaou, A. (2016), 'The life cycle of a genome project : perspectives and guidelines inspired by insect genome projects.', F1000Research, vol 5 .
  • Good, R., Varghese, T., Golz, J., Russell, D., Papanicolaou, A., Edwards, O. and Robin, C. (2016), 'OfftargetFinder : a web tool for species-specific RNAi design', Bioinformatics, vol 32, no 8 , pp 1232 - 1234.
  • Livernois, A., Hardy, K., Domaschenz, R., Papanicolaou, A., Georges, A., Sarre, S., Rao, S., Ezaz, T. and Deakin, J. (2016), 'Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data', Immunogenetics, vol 68, no 9 , pp 719 - 731.
  • Ertl, N., O'Connor, W., Papanicolaou, A., Wiegand, A. and Elizur, A. (2016), 'Transcriptome analysis of the Sydney rock oyster, Saccostrea glomerata : insights into molluscan immunity', PLoS One, vol 11, no 6 .
  • Kanost, M., Arrese, E., Cao, X., Chen, Y., Chellapilla, S., Goldsmith, M., Grosse-Wilde, E., Heckel, D., Papanicolaou, A. and et al, .. (2016), 'Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta', Insect Biochemistry and Molecular Biology, vol 76 , pp 118 - 147.
  • Papanicolaou, A., Schetelig, M., Arensburger, P., Atkinson, P., Benoit, J., Bourtzis, K., Castanera, P., Cavanaugh, J., Chao, H. and et al, .. (2016), 'The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species', Genome Biology, vol 17, no 192 .
  • Leitch, O., Papanicolaou, A., Lennard, C., Kirkbride, K. and Anderson, A. (2015), 'Chemosensory genes identified in the antennal transcriptome of the blowfly Calliphora stygia', BMC Genomics, vol 16, no 1 .
  • Jones, C., Papanicolaou, A., Mironidis, G., Vontas, J., Yang, Y., Lim, K., Oakeshott, J., Bass, C. and Chapman, J. (2015), 'Genomewide transcriptional signatures of migratory flight activity in a globally invasive insect pest', Molecular Ecology, vol 24, no 19 , pp 4901 - 4911.
  • Xu, W., Papanicolaou, A., Liu, N., Dong, S. and Anderson, A. (2015), 'Chemosensory receptor genes in the Oriental tobacco budworm Helicoverpa assulta', Insect Molecular Biology, vol 24, no 2 , pp 253 - 263.
  • Bain, P., Papanicolaou, A. and Kumar, A. (2015), 'Identification of putative nuclear receptors and steroidogenic enzymes in Murray-Darling rainbowfish (Melanotaenia fluviatilis) using RNA-Seq and de novo transcriptome assembly', PLoS One, vol 10, no 11 , pp 0142636 - 0142636.
  • Perez-Bercoff, A., Papanicolaou, A., Ramsperger, M., Kaur, J., Patel, H., Harun, A., Duan, S., Elbourne, L., Bouchara, J., Paulsen, I., Nevalainen, H., Meyer, W. and Huttley, G. (2015), 'Draft genome of Australian environmental strain WM 09.24 of the opportunistic human pathogen Scedosporium aurantiacum', Genome Announcements, vol 3, no 1 .
  • Liu, N., Xu, W., Papanicolaou, A., Dong, S. and Anderson, A. (2014), 'Identification and characterization of three chemosensory receptor families in the cotton bollworm Helicoverpa armigera', BMC Genomics, vol 15, no 1 .
  • Greenfield, P., Duesing, K., Papanicolaou, A. and Bauer1, D. (2014), 'Blue : correcting sequencing errors using consensus and context', Bioinformatics, vol 30, no 19 , pp 2723 - 2732.
  • Timmermans, M., Baxter, S., Clark, R., Heckel, D., Vogel, H., Collins, S., Papanicolaou, A., Fukova, I., Joron, M., Thompson, M., Jiggins, C., ffrench-Constant, R. and Vogler, A. (2014), 'Comparative genomics of the mimicry switch in Papilio dardanus', Proceedings of the Royal Society B: Biological Sciences, vol 281, no 1787 .
  • Haas, B., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P., Bowden, J., Couger, M., Eccles, D., Li, B. and et al, .. (2013), 'De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis', Nature Protocols, vol 8, no 8 , pp 1494 - 1512.
  • Papanicolaou, A., Woo, A., Brei, B., Ma, D., Masedunskas, A., Gray, E., Xiao, G., Cho, S. and Brockhouse, C. (2013), 'Novel aquatic silk genes from Simulium (Psilozia) vittatum (Zett) Diptera : Simuliidae', Insect Biochemistry and Molecular Biology, vol 43, no 12 , pp 1181 - 1188.
  • Evans, J., Brown, S., Hackett, K., Robinson, G., Richards, S., Lawson, D., Elsik, C., Coddington, J., Edwards, O., Papanicolaou, A. and et al, .. (2013), 'The i5K Initiative : advancing arthropod genomics for knowledge, human health, agriculture, and the environment', Journal of Heredity, vol 104, no 5 , pp 595 - 600.
  • Hines, H., Papa, R., Ruiz, M., Papanicolaou, A., Wang, C., Nijhout, H., McMillan, W. and Reed, R. (2012), 'Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation', BMC Genomics, vol 13, no 1 .
  • Papanicolaou, A. and Heliconius Genome Consortium, .. (2012), 'Butterfly genome reveals promiscuous exchange of mimicry adaptations among species', Nature, vol 487, no 7405 , pp 94 - 98.
  • Edwards, O. and Papanicolaou, A. (2012), 'A roadmap for whitefly genomics research : lessons from previous insect genome projects', Journal of Integrative Agriculture, vol 11, no 2 , pp 269 - 280.
  • Terenius, O., Papanicolaou, A., Garbutt, J., Eleftherianos, I., Huvenne, H., Kanginakudru, S., Albrechtsen, M., An, C., Aymeric, J. and et al, .. (2011), 'RNA interference in Lepidoptera : an overview of successful and unsuccessful studies and implications for experimental design', Journal of Insect Physiology, vol 57, no 2 , pp 231 - 245.
  • Ferguson, L., Lee, S., Chamberlain, N., Nadeau, N., Joron, M., Baxter, S., Wilkinson, P., Papanicolaou, A., Kumar, S., Kee, T., Clark, R., Davidson, C., Glithero, R., Beasley, H., Vogel, H., ffrench-Constant, R. and Jiggins, C. (2010), 'Characterization of a hotspot for mimicry : assembly of a butterfly wing transcriptome to genomic sequence at the HmYb/Sb locus', Molecular Ecology, vol 19, no Suppl. 1 , pp 240 - 254.
  • Papanicolaou, A. and Heckel, D. (2010), 'The GMOD Drupal bioinformatic server framework', Bioinformatics, vol 26, no 24 , pp 3119 - 3124.
  • Papanicolaou, A., Stierli, R., ffrench-Constant, R. and Heckel, D. (2009), 'Next generation transcriptomes for next generation genomes using est2assembly', BMC Bioinformatics, vol 10 .
  • Beldade, P., McMillan, W. and Papanicolaou, A. (2008), 'Butterfly genomics eclosing', Heredity, vol 100, no 2 , pp 150 - 157.
  • Papanicolaou, A., Gebauer-Jung, S., Blaxter, M., McMillan, W. and Jiggins, C. (2008), 'ButterflyBase : a platform for lepidopteran genomics', Nucleic Acids Research, vol 36, no suppl. 1 , pp 582 - 587.
  • Pringle, E., Baxter, S., Webster, C., Papanicolaou, A., Lee, S. and Jiggins, C. (2007), 'Synteny and chromosome evolution in the Lepidoptera : evidence from mapping in Heliconius melpomene', Genetics, vol 177, no 1 , pp 417 - 426.
  • Joron, M., Jiggins, C., Papanicolaou, A. and McMillan, W. (2006), 'Heliconius wing patterns : an evo-devo model for understanding phenotypic diversity', Heredity, vol 97, no 3 , pp 157 - 167.
  • Papanicolaou, A., Joron, M., McMillan, W., Blaxter, M. and Jiggins, C. (2005), 'Genomic tools and cDNA derived markers for butterflies', Molecular Ecology, vol 14, no 9 , pp 2883 - 2897.
  • With a number of collaborators across the world, we are creating genomic model species using Next-Gen sequencing, novel bioinformatics software, thorough annotation and manual curation
    • a. for agriculture: Helicoverpa cotton bollworm moths (Lepidoptera:Noctuidae) and Mediterranean & Queensland fruit flies (Diptera:Tephritidae)
    • b. for basic evolutionary biology: Heliconius South American postman butterflies (Lepidoptera:Nymphalidae)
    • c. for biomedicine in Africa: Simulium sp. black flies (Diptera:Simuliidae)
  • With Dr Heng Lin Yeap, Dr John Oakeshott (CSIRO) and others we are dissecting the molecular basis (QTL mapping) of a number of potentially adaptive traits in Tephritid fruit flies and try to build this species group to become a powerful model for evolutionary biology.
  • With Dr Charles Brockhouse (USA), John Colbourne, Rory Post (UK) and others we are trying to understand how Simulium black flies determine their sex and trying to develop a marker for reproductive ability. These insects are a target for elimination by the World Health Organization as they transmit river blindness, a most debilitating disease, in some of the poorest parts of Africa.

This information has been contributed by Associate Professor Papanicolaou.

Previous Projects

Title: Molecular basis of response to (sub)lethal stresses [via Murdoch Uni]
  • PB CRC Ltd
Western Researchers: Alexie Papanicolaou
Years: 2016-05-12 - 2018-03-31
ID: P00022803
Title: Industrial Transformation Training Centre for Fruit Fly Biosecurity Innovation [via Macquarie Uni]
  • Australian Research Council (ACRG)
Western Researchers: Markus Riegler, James Cook and Alexie Papanicolaou
Years: 2016-06-27 - 2022-06-26
ID: P00022804
Title: Sexual conflict and the evolution of nuptial gifts
  • Australian Research Council (ACRG)
Western Researchers: John Hunt and Alexie Papanicolaou
Years: 2018-01-01 - 2022-12-31
ID: P00023953
Title: Smithsonian butterfly genome (USD 10K) Phase 1 and 2
  • Smithsonian Tropical Research Institute (USA)
Western Researchers: Alexie Papanicolaou
Years: 2015-08-17 - 2016-11-23
ID: P00024314
Title: Assess citrus varieties for link to pathogen resistance
  • Superior Production Company Pty Ltd
Western Researchers: Alexie Papanicolaou
Years: 2023-12-11 - 2024-02-29
ID: P00029021
Title: National Tree Genomics Program - Genotype Prediction Toolbox [via QUT]
  • Horticulture Innovation Australia (non ACRG)
Western Researchers: Chris Cazzonelli, Jonathan Plett and Alexie Papanicolaou
Years: 2018-03-01 - 2023-12-01
ID: P00025295


Title: Lab webpage
Description: Learn more about work, read blog posts and screencasts of our software.

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