Doctor Alexie Papanicolaou

Doctor Alexie Papanicolaou

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 the Heliconius 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 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.

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

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

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