Background

Associate Professor Alyssa Barry is Head of the Translational Genomics Working Group. She also holds a co-appointment as Associate Professor of Systems Epidemiology of Infection with Deakin University’s Institute for Physical and Mental Health and Clinical Translation (IMPACT), where some of her team is based.

Alyssa was previously a Laboratory Head in the Population Health and Immunity Division at the Walter and Eliza Hall Institute and the Department of Medical Biology, University of Melbourne from 2011-19. She has also held positions at the Burnet Institute (2006-11), New York University School of Medicine (USA, 2004-6) and University of Oxford (UK, 2000-2004). Alyssa was a recipient of two prestigious NHMRC Postdoctoral Fellowships, was a veski Innovation Fellow, and received the Georgina Sweet Award for Women in Quantitative Biosciences in 2017.

She has been CI on six NHMRC Project Grants (four as CIA) and is a Technical Director of a DFAT IndoPacific Centre for Health Security grant supporting the development of molecular surveillance capacity in Papua New Guinea. She leads genomics research in two NIH-funded International Centres for Excellence in Malaria Research (ICEMR) programs in Asia-Pacific and West Africa. She is also a member of the Australian Centre of Research Excellence in Malaria Elimination (ACREME), the Asia Pacific Malaria Elimination Network (APMEN) and the Malaria Genomic Epidemiology Network (MalariaGEN).

Research in the lab seeks to understand the complex dynamic that exists between host, pathogen and environment that contributes to patterns of exposure, infection and disease. The research explores systems biology on a population level using well-characterised epidemiological studies and has a strong translational focus. Current projects include (i) malaria parasite genomic surveillance to understand transmission dynamics and antimalarial drug resistance and how they change in response to interventions; (ii) characterising malaria vaccine candidate diversity and how this contributes to immune escape; (iii) understanding how immunity develops to diverse malaria parasites, and (iv) identifying host and parasite factors contributing to asymptomatic malaria.

The group is using cutting edge technologies to characterise malaria parasites and their hosts, combining this information with epidemiological data and advanced analytical approaches (bioinformatics, population genetics and biostatistics) to answer key questions in malaria biology and epidemiology. Our work is informing strategies for malaria control and elimination including stratification of control efforts, diagnostics, drugs and vaccines.

We work closely with a large network of local and international collaborators including field researchers and malaria control programs. We frequently host trainees for advanced molecular training. In addition to our malaria work, we have contributed to research on other infectious diseases such as yaws and melioidosis, and recently have embarked on new projects focusing on the Buruli ulcer epidemic in Victoria and COVID-19. Alyssa’s Deakin/Burnet co-appointment aims to build further collaboration in genomics, infectious diseases and microbiome research across the two organisations.

Appointments

• 2017-19 Associate Professor, Department of Medical Biology, University of Melbourne
• 2011-17 Senior Research Fellow, Department of Medical Biology, University of Melbourne
• 2006-2011 Adjunct Senior Lecturer, Monash University

Positions

• 2015-9 Group Leader, Population Health and Immunity Division, Walter and Eliza Hall Institute
• 2011-5 Group Leader, Infection and Immunity Division, Walter and Eliza Hall Institute
• 2009-11 Co-Laboratory Head, Centre for Population Health, Burnet Institute
• 2006-9 Senior Research Fellow, Centre for Population Health, Burnet Institute
• 2004-6 Instructor, New York University School of Medicine, New York, USA
• 2001-4 Senior Postdoctoral Fellow, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
• 2000-1 Postdoctoral Fellow, Wellcome Trust Centre for Epidemiology of Infectious Diseases, University of Oxford, Oxford, UK
• 1999-2000 Postdoctoral Research Officer, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Qualifications

• PhD UoM 2000
• BSc(Hons) UTas 1996

Awards

• 2017 Georgina Sweet Award for Women in Quantitative Biosciences
• 2008 veski Innovation Fellow
• 2008 NHMRC Howard Florey Centenary Fellow
• 2000 NHMRC/Royal Society(UK) Howard Florey Postdoctoral Fellow

Publications (44)

2020 (2)

• The epidemiology of Plasmodium falciparum and Plasmodium vivax in East Sepik Province, Papua New Guinea, pre- and post-implementation of national malaria control efforts.
  Kattenberg JH, Gumal DL, Ome-Kaius M, Kiniboro B, Philip M, Jally S, Kasian B, Sambale N, Siba PM, Karl S, Barry AE, Felger I, Kazura JW, Mueller I, Robinson LJ
  Malar J. 2020 Jun; 19(1):198
• A Natural Peptide Antigen within the Plasmodium Ribosomal Protein RPL6 Confers Liver TRM Cell-Mediated Immunity against Malaria in Mice.
  Valencia-Hernandez AM, Ng WY, Ghazanfari N, Ghilas S, de Menezes MN, Holz LE, Huang C, English K, Naung M, Tan PS, Tullett KM, Steiner TM, Enders MH, Beattie L, Chua YC, Jones CM, Cozijnsen A, Mollard V, Cai Y, Bowen DG, Purcell AW, La Gruta NL, Villadangos JA, de Koning-Ward T, Barry AE, Barchet W, Cockburn IA, McFadden GI, Gras S, Lahoud MH, Bertolino P, Schittenhelm RB, Caminschi I, Heath WR, Fernandez-Ruiz D
  Cell Host Microbe. 2020 May; Epub ahead of print

2019 (1)

• Protective Immunity against Severe Malaria in Children Is Associated with a Limited Repertoire of Antibodies to Conserved PfEMP1 Variants.
  Sofonias K Tessema, Rie Nakajima, Algis Jasinskas, Stephanie L Monk, Lea Lekieffre, Enmoore Lin, Benson Kiniboro, Carla Proietti, Peter Siba, Philip L Felgner, Denise L Doolan, Ivo Mueller, Alyssa E Barry
  Cell Host Microbe. 2019 Nov; 26(5):579-590.e5

2018 (5)

• Antibodies to Intercellular Adhesion Molecule 1-Binding Plasmodium falciparum Erythrocyte Membrane Protein 1-DBLbeta Are Biomarkers of Protective Immunity to Malaria in a Cohort of Young Children from Papua New Guinea.
  Sofonias K Tessema, Digjaya Utama, Olga Chesnokov, Anthony N Hodder, Clara S Lin, G L Abby Harrison, Jakob S Jespersen, Bent Petersen, Livingstone Tavul, Peter Siba, Dominic Kwiatkowski, Thomas Lavstsen, Diana S Hansen, Andrew V Oleinikov, Ivo Mueller, Alyssa E Barry
  Infect Immun. 2018 Aug; 86(8)
• Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens.
  Lyndal Henden, Stuart Lee, Ivo Mueller, Alyssa Barry, Melanie Bahlo
  PLoS Genet. 2018 May; 14(5):e1007279
• Re-emergence of yaws after single mass azithromycin treatment followed by targeted treatment: a longitudinal study.
  Oriol Mitja, Charmie Godornes, Wendy Houinei, August Kapa, Raymond Paru, Haina Abel, Camila Gonzalez-Beiras, Sibauk V Bieb, James Wangi, Alyssa E Barry, Sergi Sanz, Quique Bassat, Sheila A Lukehart
  Lancet. 2018 Apr; 391(10130):1599-1607
• Nationwide genetic surveillance of Plasmodium vivax in Papua New Guinea reveals heterogeneous transmission dynamics and routes of migration amongst subdivided populations.
  Abebe A Fola, Elma Nate, G L Abby Harrison, Celine Barnadas, Manuel W Hetzel, Jonah Iga, Peter Siba, Ivo Mueller, Alyssa E Barry
  Infect Genet Evol. 2018 Mar; 58:83-95
• Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific.
  Andreea Waltmann, Cristian Koepfli, Natacha Tessier, Stephan Karl, Abebe Fola, Andrew W Darcy, Lyndes Wini, G L Abby Harrison, Celine Barnadas, Charlie Jennison, Harin Karunajeewa, Sarah Boyd, Maxine Whittaker, James Kazura, Melanie Bahlo, Ivo Mueller, Alyssa E Barry
  PLoS Negl Trop Dis. 2018 Jan; 12(1):e0006146

2017 (4)

• Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea.
  Charmie Godornes, Lorenzo Giacani, Alyssa E Barry, Oriol Mitja, Sheila A Lukehart
  PLoS Negl Trop Dis. 2017 Dec; 11(12):e0006113
• Sustained malaria control over an eight-year period in Papua New Guinea: the challenge of low-density asymptomatic infections.
  Koepfli C, Ome-Kaius M, Jally S, Malau E, Maripal S, Ginny J, Timinao L, Kattenberg JH, Obadia T, White M, Rarau P, Senn N, Barry AE, Kazura JW, Mueller I, Robinson LJ
  J Infect Dis. 2017 Sep; 2016(11):1434-1443
• Higher Complexity of Infection and Genetic Diversity of Plasmodium vivax Than Plasmodium falciparum Across All Malaria Transmission Zones of Papua New Guinea.
  Abebe A Fola, G L Abby Harrison, Mita Hapsari Hazairin, Celine Barnadas, Manuel W Hetzel, Jonah Iga, Peter M Siba, Ivo Mueller, Alyssa E Barry
  Am J Trop Med Hyg. 2017 Mar; 96(3):630-641
• Dissecting malaria biology and epidemiology using population genetics and genomics.
  Sarah Auburn, Alyssa E Barry
  Int J Parasitol. 2017 Feb; 47(2-3):77-85

2016 (3)

• Spatial Effects on the Multiplicity of Plasmodium falciparum Infections.
  Stephan Karl, Michael T White, George J Milne, David Gurarie, Simon I Hay, Alyssa E Barry, Ingrid Felger, Ivo Mueller
  PLoS One. 2016 Oct; 11(10):e0164054
• Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax.
  Daniel N Hupalo, Zunping Luo, Alexandre Melnikov, Patrick L Sutton, Peter Rogov, Ananias Escalante, Andres F Vallejo, Socrates Herrera, Myriam Arevalo-Herrera, Qi Fan, Ying Wang, Liwang Cui, Carmen M Lucas, Salomon Durand, Juan F Sanchez, G Christian Baldeviano, Andres G Lescano, Moses Laman, Celine Barnadas, Alyssa Barry, Ivo Mueller, James W Kazura, Alex Eapen, Deena Kanagaraj, Neena Valecha, Marcelo U Ferreira, Wanlapa Roobsoong, Wang Nguitragool, Jetsumon Sattabonkot, Dionicia Gamboa, Margaret Kosek, Joseph M Vinetz, Lilia Gonzalez-Ceron, Bruce W Birren, Daniel E Neafsey, Jane M Carlton
  Nat Genet. 2016 Aug; 48(8):953-958
• Structurally conserved erythrocyte-binding domain in Plasmodium provides a versatile scaffold for alternate receptor engagement.
  Jakub Gruszczyk, Nicholas T Y Lim, Alicia Arnott, Wen-Qiang He, Wang Nguitragool, Wanlapa Roobsoong, Yee-Foong Mok, James M Murphy, Katherine R Smith, Stuart Lee, Melanie Bahlo, Ivo Mueller, Alyssa E Barry, Wai-Hong Tham
  Proc Natl Acad Sci U S A. 2016 Jan; 113(2):E191-E200

2015 (7)

• Designing malaria vaccines to circumvent antigen variability.
  Ouattara A, Barry AE, Dutta S, Remarque EJ, Beeson JG, Plowe CV
  Vaccine. 2015 Oct; 33(52):7506-7512
• Malaria Molecular Epidemiology: Lessons from the International Centers of Excellence for Malaria Research Network.
  Ananias A Escalante, Marcelo U Ferreira, Joseph M Vinetz, Sarah K Volkman, Liwang Cui, Dionicia Gamboa, Donald J Krogstad, Alyssa E Barry, Jane M Carlton, Anna Maria van Eijk, Khageswar Pradhan, Ivo Mueller, Bryan Greenhouse, M Andreina Pacheco, Andres F Vallejo, Socrates Herrera, Ingrid Felger
  Am J Trop Med Hyg. 2015 Sep; 93(3 Suppl):79-86
• Blood-Stage Parasitaemia and Age Determine Plasmodium falciparum and P. vivax Gametocytaemia in Papua New Guinea.
  Cristian Koepfli, Leanne J Robinson, Patricia Rarau, Mary Salib, Naomi Sambale, Rahel Wampfler, Inoni Betuela, Wang Nuitragool, Alyssa E Barry, Peter Siba, Ingrid Felger, Ivo Mueller
  PLoS One. 2015 May; 10(5):e0126747
• Uncovering the transmission dynamics of Plasmodium vivax using population genetics.
  Alyssa E Barry, Andreea Waltmann, Cristian Koepfli, Celine Barnadas, Ivo Mueller
  Pathog Glob Health. 2015 May; 109(3):142-152
• High Rates of Asymptomatic, Sub-microscopic Plasmodium vivax Infection and Disappearing Plasmodium falciparum Malaria in an Area of Low Transmission in Solomon Islands.
  Andreea Waltmann, Andrew W Darcy, Ivor Harris, Cristian Koepfli, John Lodo, Ventis Vahi, David Piziki, G Dennis Shanks, Alyssa E Barry, Maxine Whittaker, James W Kazura, Ivo Mueller
  PLoS Negl Trop Dis. 2015 May; 9(5):e0003758
• Plasmodium vivax Populations Are More Genetically Diverse and Less Structured than Sympatric Plasmodium falciparum Populations.
  Jennison C, Arnott A, Tessier N, Tavul L, Koepfli C, Felger I, Siba PM, Reeder JC, Bahlo M, Mueller I, Barry AE
  PLoS Negl Trop Dis. 2015 Apr; 9(4):e0003634
• Phylogeography of var gene repertoires reveals fine-scale geospatial clustering of Plasmodium falciparum populations in a highly endemic area.
  Tessema SK, Monk SL, Schultz MB, Tavul L, Reeder JC, Siba PM, Mueller I, Barry AE
  Mol Ecol. 2015 Jan; 24(2):484-497

2014 (3)

• Limited antigenic diversity of Plasmodium falciparum apical membrane antigen 1 supports the development of effective multi-allele vaccines.
  Terheggen U, Drew DR, Hodder AN, Cross NJ, Mugyenyi CK, Barry AE, Anders RF, Dutta S, Osier F, Elliott SR, Senn N, Stanisic DI, Marsh K, Siba PM, Mueller I, Richards JS, Beeson JG
  BMC Med. 2014 Oct; 12(1):183
• Strategies for designing and monitoring malaria vaccines targeting diverse antigens.
  Alyssa E Barry, Alicia Arnott
  Front Immunol. 2014 Jul; 5:359
• Genetic diversity of VAR2CSA ID1-DBL2Xb in worldwide Plasmodium falciparum populations: impact on vaccine design for placental malaria.
  Bita Bordbar, Nicaise Tuikue Ndam, Emmanuelle Renard, Sayeh Jafari-Guemouri, Livingstone Tavul, Charlie Jennison, Sedami Gnidehou, Rachida Tahar, Dionicia Gamboa, Jorge Bendezu, Didier Menard, Alyssa E Barry, Philippe Deloron, Audrey Sabbagh
  Infect Genet Evol. 2014 Jul; 25:81-92

2013 (5)

• Escaping the immune system: How the malaria parasite makes vaccine development a challenge.
  Danielle I Stanisic, Alyssa E Barry, Michael F Good
  Trends Parasitol. 2013 Dec; 29(12):612-622
• Global Population Structure of the Genes Encoding the Malaria Vaccine Candidate, Plasmodium vivax Apical Membrane Antigen 1 (PvAMA1).
  Arnott A, Mueller I, Ramsland PA, Siba PM, Reeder JC, Barry AE
  PLoS Negl Trop Dis. 2013 Oct; 7(10):e2506
• A Large Plasmodium vivax Reservoir and Little Population Structure in the South Pacific.
  Cristian Koepfli, Lincoln Timinao, Tiago Antao, Alyssa E Barry, Peter Siba, Ivo Mueller, Ingrid Felger
  PLoS One. 2013 Jun; 8(6):e66041
• High genetic diversity of Plasmodium vivax on the north coast of Papua New Guinea.
  Arnott A, Barnadas C, Senn N, Siba P, Mueller I, Reeder JC, Barry AE
  Am J Trop Med Hyg. 2013 May; 89(1):188-194
• High levels of genetic diversity of Plasmodium falciparum populations in Papua New Guinea despite variable infection prevalence.
  Barry AE, Schultz L, Senn N, Nale J, Kiniboro B, Siba PM, Mueller I, Reeder JC
  Am J Trop Med Hyg. 2013 Feb; 88(4):718-725

2012 (2)

• The Plasmodium falciparum erythrocyte invasion ligand Pfrh4 as a target of functional and protective human antibodies against malaria.
  Reiling L, Richards JS, Fowkes FJ, Wilson DW, Chokejindachai W, Barry AE, Tham WH, Stubbs J, Langer C, Donelson J, Michon P, Tavul L, Crabb BS, Siba PM, Cowman AF, Mueller I, Beeson JG
  PLoS One. 2012 Sep; 7(9):e45253
• Understanding the population genetics of Plasmodium vivax is essential for malaria control and elimination.
  Arnott A, Barry AE, Reeder JC
  Malar J. 2012 Jan; 11:14

2011 (3)

• The stability and complexity of antibody responses to the major surface antigen of Plasmodium falciparum are associated with age in a malaria endemic area.
  Barry AE, Trieu A, Fowkes FJ, Pablo J, Kalantari-Dehaghi M, Jasinskas A, Tan X, Kayala MA, Tavul L, Siba PM, Day KP, Baldi P, Felgner PL, Doolan DL
  Mol Cell Proteomics. 2011 Aug; 10(11):M111.008326
• Population genetic analysis of the Plasmodium falciparum 6-cys protein Pf38 in Papua New Guinea reveals domain-specific balancing selection.
  Reeder JC, Wapling J, Mueller I, Siba PM, Barry AE
  Malar J. 2011 May; 10:126
• A molecular epidemiological study of var gene diversity to characterize the reservoir of Plasmodium falciparum in humans in Africa.
  Chen DS, Barry AE, Leliwa-Sytek A, Smith TA, Peterson I, Brown SM, Migot-Nabias F, Deloron P, Kortok MM, Marsh K, Daily JP, Ndiaye D, Sarr O, Mboup S, Day KP
  PLoS One. 2011 Feb; 6(2):e16629

2010 (2)

• Multilocus haplotypes reveal variable levels of diversity and population structure of Plasmodium falciparum in Papua New Guinea, a region of intense perennial transmission.
  Schultz L, Wapling J, Mueller I, Ntsuke PO, Senn N, Nale J, Kiniboro B, Buckee CO, Tavul L, Siba PM, Reeder JC, Barry AE
  Malar J. 2010 Nov; 9:336
• Evidence that the erythrocyte invasion ligand PfRh2 is a target of protective immunity against Plasmodium falciparum malaria.
  Reiling L, Richards JS, Fowkes FJ, Barry AE, Triglia T, Chokejindachai W, Michon P, Tavul L, Siba PM, Cowman AF, Mueller I, Beeson JG
  J Immunol. 2010 Nov; 185(10):6157-6167

2009 (1)

• Contrasting population structures of the genes encoding ten leading vaccine-candidate antigens of the human malaria parasite, Plasmodium falciparum.
  Barry AE, Schultz L, Buckee CO, Reeder JC
  PLoS One. 2009 Dec; 4(12):e8497

2007 (2)

• Population genomics of the immune evasion (var) genes of Plasmodium falciparum.
  Alyssa E Barry, Aleksandra Leliwa-Sytek, Livingston Tavul, Heather Imrie, Florence Migot-Nabias, Stuart M Brown, Gilean A V McVean, Karen P Day
  PLoS Pathog. 2007 Mar; 3(3):e34
• Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum.
  Sarah K Volkman, Elena Lozovsky, Alyssa E Barry, Trevor Bedford, Lara Bethke, Alissa Myrick, Karen P Day, Daniel L Hartl, Dyann F Wirth, Stanley A Sawyer
  Gene. 2007 Jan; 387(1-2):1-6

2006 (1)

• Variable SNP density in aspartyl-protease genes of the malaria parasite Plasmodium falciparum.
  Alyssa E Barry, Aleksandra Leliwa-Sytek, Kitty Man, Jacob M Kasper, Daniel L Hartl, Karen P Day
  Gene. 2006 Jul; 376(2):163-173

2003 (1)

• DNA sequence artifacts and the estimation of time to the most recent common ancestor (TMRCA) of Plasmodium falciparum.
  Alyssa E Barry, Aleksandra Leliwa, Mehee Choi, Kaare M Nielsen, Daniel L Hartl, Karen P Day
  Mol Biochem Parasitol. 2003 Aug; 130(2):143-147

2002 (1)

• The paradoxical population genetics of Plasmodium falciparum.
  Daniel L Hartl, Sarah K Volkman, Kaare M Nielsen, Alyssa E Barry, Karen P Day, Dyann F Wirth, Elizabeth A Winzeler
  Trends Parasitol. 2002 Jun; 18(6):266-272

2001 (1)

• Recent origin of Plasmodium falciparum from a single progenitor.
  S K Volkman, A E Barry, E J Lyons, K M Nielsen, S M Thomas, M Choi, S S Thakore, K P Day, D F Wirth, D L Hartl
  Science. 2001 Jul; 293(5529):482-484