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Associate Professor Alexie Papanicolaou

Doctor Alexie Papanicolaou

A/Professor 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 the Heliconius butterflies, Helicoverpa armigera the cotton bollworm moth, invasive Tephritid fruit flies and eucalyptus trees.

A/Professor 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.

Alexie joined the 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.

A/Professor 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.

Visit Alexie's Lab website at http://stressedfruitfly.com (opens in a new window).

Current activities

  1. 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)
  2. 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.
  3. 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.

Current grants

2014-2018: CSIRO Office of the Chief (OCE) 3 year post-doctoral fellowship on quantitative genetics in Bactrocera species for Dr Heng Lin Yeap. Co-supervising (with Dr John Oakeshott, CSIRO)

2014-2018: Horticulture Australia: Diet mediated RNAi in Bactrocera; 2,363,145 AUD direct costs (with Owain Edwards, CSIRO)

2012-2015: Working group on Curation of Evolutionary and Ecological Functional Genomics (opens in a new window) (EEFG) data; NESCent/National Science Foundation; ca 140,000 USD (principal investigator)

2012-2015: Dissecting adaptive potential using transcriptomics and geospatial data; CSIRO; ca 1,400,000 AUD direct costs (with Owain Edwards, CSIRO)

Five representative publications

Title: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Author(s): Haas BJ, Papanicolaou A, Yassour M, et al.
Source: Nature Protocols, vol.8, no.8, pp 1494-1512 Published: 2013
ISI Times Cited till Jan 2015: 90
DOI: 10.1038/nprot.2013.084

Title: Novel Aquatic Silk Genes from Simulium (Psilozia) vittatum (Zett) Diptera: Simuliidae
Author(s): Papanicolaou A, Woo A, Brei B, et al.
Source: Insect Biochemistry and Molecular Biology, vol.43, no.12, pp 1181-1188 Published: 2013
ISI Times Cited till Jan 2015: 1
DOI: 10.1016/j.ibmb.2013.09.008

Title: Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
Author(s): The Heliconius Genome Consortium
Source: Nature Volume: advance online publication
Published: 2012 ISI Times Cited till Jan 2015: 182
DOI: 10.1038/nature11041

Title: Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation
Author(s): Hines HM, Papa R, Ruiz M, et al.
Source: BMC genomics, vol.13, no.1, p 288 Published: 2012
ISI Times Cited till Jan 2015: 10
DOI: 10.1186/1471-2164-13-288

Title: RNA interference in Lepidoptera: An overview of successful and unsuccessful studies and implications for experimental design
Author(s): Terenius O, Papanicolaou A, Garbutt J S, et al.
Source: Journal of Insect Physiology, vol.57, no.2, pp 231-245 Published: 2011
ISI Times Cited till Jan 2015: 115
DOI: 10.1016/j.jinsphys.2010.11.006

Publications

Sahu N, Indic B, Wong-Bajracharya J, Merenyi Z, Ke HM, Ahrendt S, Monk TL, Kocsube S, Drula E, Lipzen A, Balint B, Henrissat B, Andreopoulos B, Martin FM, Harder CB, Rigling D, Ford KL, Foster GD, Pangilinan J, Papanicolaou A, Barry K, LaButti K, Viragh M, Koriabine M, Yan M, Riley R, Champramary S, Plett KL, Grigoriev IV, Tsai IJ, Slot J, Sipos G, Plett J, Nagy LG, (2023) 'Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria', Nature Microbiology, vol.8, pp 1668–1681

Anantanawat K, Papanicolaou A, Hill K, Xu W, (2022) 'Mediterranean fruit fly genes exhibit different expression patterns between heat and cold treatments', Bulletin of Entomological Research, vol.112, no.2 pp 236-242

El-Kamand S, Steiner M, Ramirez C, Halliday C, Chen SC-A, Papanicolaou A, Morton CO, (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, Article no.428

Guo R, Papanicolaou A, Fritz ML, (2022) 'Validation of reference-assisted assembly using existing and novel Heliothine genomes', Genomics, vol.114, no.5, Article no.110441

Paudel L, Kerr S, Prentis P, Tanurdzic M, Papanikolaou A, Plett J, Cazzonelli CI, (2022) 'Horticultural Innovation by Viral-Induced Gene Regulation of Carotenogenesis', Horticulture Research, vol.9, Article uhab008

Anantanawat K, Papanicolaou A, Hill K, 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

Bayega A, Djambazian H, Tsoumani KT, Gregoriou M-E, Sagri E, Drosopoulou E, Mavragani-Tsipidou P, Giorda K, Tsiamis G, Bourtzis K, Oikonomopoulos S, Dewar K, Church DM, Papanicolaou A, Mathiopoulos KD, 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, Article no.259

Brenya E, Chen Z-H, Tissue D, Papanicolaou A, Cazzonelli CI, (2020) 'Prior exposure of Arabidopsis seedlings to mechanical stress heightens jasmonic acid-mediated defense against necrotrophic pathogens', BMC Plant Biology, vol.20, no.1, Article no.548

Yeap HL, Lee SF, Robinson F, Mourant RG, Sved JA, Frommer M, Papanicolaou A, Edwards OR, Oakeshott JG, (2020) 'Separating two tightly linked species-defining phenotypes in Bactrocera with hybrid recombinant analysis', BMC Genetics, vol.21, Article no.132

Zhang H-J, Xu W, Chen Q-M, Sun L-N, Anderson A, Xia Q-Y, Papanicolaou A, (2020) 'A phylogenomics approach to characterizing sensory neuron membrane proteins (SNMPs) in Lepidoptera', Insect Biochemistry and Molecular Biology, vol.118, Article no.103313

Surm JM, Stewart ZK, Papanicolaou A, Pavasovic A, Prentis PJ, (2019) 'The draft genome of Actinia tenebrosa reveals insights into toxin evolution', Ecology and Evolution, vol.9, no.19, pp 11314-11328

Fritz ML, DeYonke AM, Papanicolaou A, Micinski S, Westbrook J, 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

Harm GFS, Papanicolaou A, Cuddy WS, Park RF, Moffitt MC, (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, Article no.e01442-17

Watson-Lazowski A, Papanicolaou A, Sharwood R, Ghannoum O, (2018) 'Investigating the NAD-ME biochemical pathway within C-4 grasses using transcript and amino acid variation in C-4 photosynthetic genes', Photosynthesis Research, vol.138, no.2, pp 233-248

Papanicolaou A, Schetelig MF, Arensburger P, Atkinson PW, Benoit JB, Bourtzis K, Castanera P, Cavanaugh JP, Chao H, Childers C, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs RA, Giers SD, Gomulski LM, Gonzalez-Guzman M, Guillem-Amat A, Han Y, Hatzigeorgiou AG, Hernandez-Crespo P, Hughes DST, Jones JW, Karagkouni D, Koskinioti P, Lee SL, Malacrida AR, Manni M, Mathiopoulos K, Meccariello A, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Oberhofer G, Ortego F, Paraskevopoulou MD, Poelchau M, Qu JX, Reczko M, Robertson HM, Rosendale AJ, Rosselot AE, Saccone G, Salvemini M, Savini G, Schreiner P, Scolari F, Siciliano P, Sim SB, Tsiamis G, Urena E, Vlachos IS, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM, (2017) '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 (vol 17, 192, 2016)', Genome Biology, vol.18, Article no.11

Pearce SL, Clarke DF, East PD, Elfekih S, Gordon KHJ, Jermiin LS, McGaughran A, Oakeshott JG, Papanikolaou A, Perera OP, Rane RV, Richards S, Tay WT, Walsh TK, Anderson A, Anderson CJ, Asgari S, Board PG, Bretschneider A, Campbell PM, Chertemps T, Christeller JT, Coppin CW, Downes SJ, Duan G, Farnsworth CA, Good RT, Han LB, Han YC, Hatje K, Horne I, Huang YP, Hughes DST, Jacquin-Joly E, James W, Jhangiani S, Kollmar M, Kuwar SS, Li S, Liu N-Y, Maibeche MT, Miller JR, Montagne N, Perry T, Qu J, Song SV, Sutton GG, Vogel H, Walenz BP, Xu W, Zhang H-J, Zou Z, Batterham P, Edwards OR, Feyereisen R, Gibbs RA, Heckel DG, McGrath A, Robin C, Scherer SE, Worley KC, Wu YD, (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, Article no.63

Van Belleghem SM, Rastas P, Papanicolaou A, Martin SH, Arias CF, Supple MA, Hanly JJ, Mallet J, Lewis JJ, Hines HM, Ruiz M, Salazar C, Linares M, Moreira GRP, Jiggins CD, Counterman BA, McMillan WO, Papa R, (2017) 'Complex modular architecture around a simple toolkit of wing pattern genes', Nature Ecology & Evolution, vol.1, no.3, Article no.UNSP 0052

Ertl NG, O'Connor WA, Papanicolaou A, Wiegand AN, Elizur A, (2016) 'Transcriptome analysis of the Sydney rock oyster, Saccostrea glomerata: Insights into molluscan immunity', PLoS One, vol.11, no.6, Article no.e0156649

Good RT, Varghese T, Golz JF, Russell DA, Papanicolaou A, Edwards O, Robin C, (2016) 'OfftargetFinder: A web tool for species-specific RNAi design', Bioinformatics, vol.32, no.8, pp 1232-1234

Kanost MR, Arrese EL, Cao XL, Chen YR, Chellapilla S, Goldsmith MR, Grosse-Wilde E, Heckel DG, Herndon N, Jiang HB, Papanicolaou A, Qu JX, Soulages JL, Vogel H, Walters J, Waterhouse RM, Ahn SJ, Almeida FC, An CJ, Aqrawi P, Bretschneider A, Bryant WB, Bucks S, Chao H, Chevignon G, Christen JM, Clarke DF, Dittmer NT, Ferguson LCF, Garavelou S, Gordon KHJ, Gunaratna RT, Han Y, Hauser F, He Y, Heidel-Fischer H, Hirsh A, Hu YX, Jiang HB, Kalra D, Klinner C, Konig C, Kovar C, Kroll AR, Kuwar SS, Lee SL, Lehman R, Li K, Li ZF, Liang HQ, Lovelace S, Lu ZQ, Mansfield JH, McCulloch KJ, Mathew T, Morton B, Muzny DM, Neunemann D, Ongeri F, Pauchet Y, Pu LL, Pyrousis I, Rao XJ, Redding A, Roesel C, Sanchez-Gracia A, Schaack S, Shukla A, Tetreau G, Wang Y, Xiong GH, Traut W, Walsh TK, Worley KC, Wu D, Wu WB, Wu YQ, Zhang XF, Zou Z, Zucker H, Briscoe AD, Burmester T, Clem RJ, Feyereisen R, Grimmelikhuijzen CJP, Hamodrakas SJ, Hansson BS, Huguet E, Jermiin LS, Lan Q, Lehman HK, Lorenzen M, Merzendorfer H, Michalopoulos I, Morton DB, Muthukrishnan S, Oakeshott JG, Palmer W, Park Y, Passarelli AL, Rozas J, Schwartz LM, Smith W, Southgate A, Vilcinskas A, Vogt R, Wang P, Werren J, Yu XQ, Zhou JJ, Brown SJ, Scherer SE, Richards S, Blissard GW, (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

Livernois A, Hardy K, Domaschenz R, Papanicolaou A, Georges A, Sarre SD, Rao S, Ezaz T, Deakin JE, (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

Papanicolaou A, (2016) 'The life cycle of a genome project: Perspectives and guidelines inspired by insect genome projects', F1000Research, vol.5, Article no.18

Papanicolaou A, Schetelig MF, Arensburger P, Atkinson PW, Benoit JB, Bourtzis K, Castanera P, Cavanaugh JP, Chao H, Childers C, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs RA, Giers SD, Gomulski LM, Gonzalez-Guzman M, Guillem-Amat A, Han Y, Hatzigeorgiou AG, Hernandez-Crespo P, Hughes DST, Jones JW, Karagkouni D, Koskinioti P, Lee SL, Malacrida AR, Manni M, Mathiopoulos K, Meccariello A, Murali SC, Murphy TD, Muzny DM, Oberhofer G, Ortego F, Paraskevopoulou MD, Poelchau M, Qu JX, Reczko M, Robertson HM, Rosendale AJ, Rosselot AE, Saccone G, Salvemini M, Savini G, Schreiner P, Scolari F, Siciliano P, Sim SB, Tsiamis G, Urena E, Vlachos IS, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM, (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, Article no.192

Xu W, Papanicolaou A, Zhang HJ, Anderson A, (2016) 'Expansion of a bitter taste receptor family in a polyphagous insect herbivore', Scientific Reports, vol.6, Article no.23666

Bain PA, Papanicolaou A, 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, Article no.e0142636

Jones CM, Papanicolaou A, Mironidis GK, Vontas J, Yang Y, Lim KS, Oakeshott JG, Bass C, Chapman JW, (2015) 'Genomewide transcriptional signatures of migratory flight activity in a globally invasive insect pest', Molecular Ecology, vol.24, no.19, pp 4901-4911

Leitch O, Papanicolaou A, Lennard C, Kirkbride KP, Anderson A, (2015) 'Chemosensory genes identified in the antennal transcriptome of the blowfly Calliphora stygia', BMC Genomics, vol.16, Article no.255

Eucalyptus Leaf