Olson PD; Hughes J; Cotton JA, 2016, Next generation systematics,

Cotton JA; Olson PD, 2016, Introduction: studying diversity in an era of ubiquitous genomics,

Cotton J, 2013, The Australian School of International Relations

Cotton J, 2012, Australia and the United Nations

Cotton J, 2010, International relations for Australia : Michael Lindsay, Martin Wight, and the first department at the Australian National University, Working Paper 2010/2, Australian National University: Department of International Relations, Canberra,

2007, Trading on Alliance Security: Australia in World Affairs 2001-2005, Cotton J, (ed.), Oxford University Press, Melbourne

Cotton J, 2006, East Timor, Australia and Regional Order, paperback, Routledge, London & New York

Cotton J; Ungorer C; Harris S, 2006, The Road to a Nuclear North Korea: Regional Reactions, Global Impacts, Australian Interests, Strategic Insights 32, Australian Strategic Policy Institute, Canberra

Cotton J, 2004, East Timor, Australia and Regional Order: intervention and its aftermath in SE Asia, Routledge Curzon, London and NY,

2002, The National Interest in a Global Era: Australia in World Affairs 1996-2000, Cotton J, (ed.), Oxford University Press, Australia

Cotton J, 2002, Crossing Borders in the Asia Pacific, Original, Nova Science Publications, New York, USA

1999, East Timor and Australia: AIIA contributions to the policy debate, Cotton J, (ed.), Canberra ADSC/AIIA, Canberra

Cotton J; Neary I, 1989, The Korean War in History, Manchester University Press

Cotton J, 1989, Asian Frontier Nationalism Owen Lattimore and the American Policy Debate

Book Chapters

Cotton J, 2018, '‘Relations with Indonesia in the Whitlam Era: the Centrality of the East Timor issue’', in Ministers for Foreign Affairs 1972-83, edn. Australian Ministers for Foreign Affairs, Australian Institute of International Affairs, Canberra, pp. 115 - 143

Cotton JA, 2016, 'From sequence reads to evolutionary inferences', in , pp. 305 - 335,

Cotton J, 2016, 'Diplomacy in the 1990s: Issues for the Washington embassy.', in Lowe, D ; Bridge, C ; Lee D (ed.), Australia goes to Washington : 75 years of Australian representation in the United States, ANU EPress, Canberra, pp. 209 - 232

Cotton J, 2015, 'Ideology and the legitimation crisis in North Korea', in , pp. 86 - 101,

Cotton J, 2014, 'Barwick, Hasluck and the Management of Foreign Policy towards Northeast Asia: the Limits of Australian "Realism"', in Tyler (ed.), Ministers for Foreign Affairs 1960-72, Australian Institute of International Affairs, Canberra, pp. 151 - 180

Peterson KJ; Cotton JA; Gehling JG; Pisani D, 2009, 'The Ediacaran emergence of bilaterians: Congruence between the genetic and the geological fossil records', in ,

Cotton J, 2009, '‘Australia and Asian Institutional Networks: Bilateral Preferences, Multi-lateral Gains’', in Thomas N (ed.), Governance and Regionalism in Asia, Routledge, London, pp. 146 - 171,

Cotton J, 2009, 'Australia and the Asian Strategic Context: Balancing Relations with the Major Powers', in Sisodia NS; Krishnappa V (ed.), Global Power Shifts and Strategic Transition in Asia, edn. Original, Academic Foundation, New Delhi, pp. 151 - 179

Cassis G; Wall M; Schuh R, 2007, 'Insect Biodiversity and Industrializing the Taxonomic Process: The Plant Bug Case Study (Insecta: Heteroptera: Miridae)', in Hodkinson TR; Parnell JAN (ed.), Reconstructing the tree of life: taxonomy and systematics of species rich taxa, edn. Systematics Association Special Volume Series, CRC Press, Boca Raton, pp. 193 - 212,

Cotton J, 2007, 'The Crisis in East Timor: Understanding the Past, Imagining the Future', in The Crisis of the Timor-Leste State in Comparative Perspective, edn. Original, Charles Darwin University Press, Darwin, pp. 13 - 22

Cotton J, 2007, 'After the Flood: Foreign Policy and the Management of Intelligence', in Cotton J; Ravenhill J (ed.), Trading on Alliance Security: Australia in World Affairs 2001-2005, edn. First, Oxford University Press, Melbourne, pp. 329 - 351

Cotton J; Ravenhill J, 2007, 'Trading on Alliance Security: Foreign Policy in the post-11 September era', in Cotton J; Ravenhill J (ed.), Trading on Alliance Security: Australia in World Affairs 2001-2005, edn. First, Oxford University Press, Melbourne, pp. 3 - 19

Cotton J, 2006, 'The Domestic Sources of Regional Order in Michael Leifer`s Analysis of Southeast Asia', in Liow JC; Emmers R (ed.), Order and Security in Southeast Asia, Routledge Curzon, London & New York, pp. 212 - 227,

Cotton J, 2006, 'ASEAN and Regional Institutions in the Asia-Pacific: Ambitions Versus Performance', in Globalization and Regionalization: Views from the Pacific Rim, edn. Original, UTS and Universidad de Guadalajara, Mexico, pp. 73 - 111

Cotton J, 2006, 'Regionalization, Marketization and Political Change in the Pacific Rim', in East Timor/timor Leste: national, Regional and International Sources of Political Legitimacy, edn. First, UTS and Universidad de Guadalaljara, Mexico, pp. 147 - 177

Cotton J, 2003, 'The Rhetoric of Australia`s Regional Policy', in Asia-Pacific Security: Policy Challenges, ISEAS Publishers, Singapore, pp. 29 - 46

Cotton J, 2002, 'North Korea and the Axis of Evil', in Williams M; Suh C-S (ed.), The Inter-Korean relationship in the post September 11 environment, edn. Original, Korea-Australasia Research Centre (KAREC), Sydney, Australia, pp. 42 - 56

Cotton J, 2001, 'Sun Zi: Diplomacy and war', in The Strategists, edn. Original, Australian Defence Studies Centre, Canberra, pp. 15 - 26

Cotton J, 2000, 'The Asian crisis and the perils of enterprise association: explaining the different outcomes in Singapore, Taiwan and Korea', in Politics and Markets in the Wake of the Asian Crisis, edn. Original, Routledge Press, London & New York, pp. 151 - 168

Cotton J, 1998, 'The Rajin-Sonbong Free Trade Zone experiment: North Korea in pursuit of new international linkages', in North Korean foreign policy in the post-Cold War era, edn. Original, Oxford University Press, Hong Kong, pp. 212 - 233

Edited Books

Cotton J, (ed.), 2019, Australia and the World 1920-1930. Documents on Australian Foreign Policy, University of New South Wales Press, Sydney

Journal articles

Cotton J, 2020, ''We are nearer the East than the other states': Frederic Jones of Queensland, the first official from Australia in Shanghai', Queensland Review, vol. 27, pp. 39 - 59,

Cotton J, 2020, 'The Elusive Reginald Benjamin Levien: Victoria's commercial agent in Asia, fraudster, recidivist', Journal of the Royal Australian Historical Society, vol. 106, pp. 7 - 28

Cotton J, 2020, '‘We are nearer the East than the other states’: Frederic Jones of Queensland, the first official from Australia in Shanghai', Queensland Review, vol. 27, pp. 7 - 28,

Doyle SR; Cotton JA, 2019, 'Genome-wide Approaches to Investigate Anthelmintic Resistance', Trends in Parasitology, vol. 35, pp. 289 - 301,

Coghlan A; Tyagi R; Cotton JA; Holroyd N; Rosa BA; Tsai IJ; Laetsch DR; Beech RN; Day TA; Hallsworth-Pepin K; Ke HM; Kuo TH; Lee TJ; Martin J; Maizels RM; Mutowo P; Ozersky P; Parkinson J; Reid AJ; Rawlings ND; Ribeiro DM; Swapna LS; Stanley E; Taylor DW; Wheeler NJ; Zamanian M; Zhang X; Allan F; Allen JE; Asano K; Babayan SA; Bah G; Beasley H; Bennett HM; Bisset SA; Castillo E; Cook J; Cooper PJ; Cruz-Bustos T; Cuéllar C; Devaney E; Doyle SR; Eberhard ML; Emery A; Eom KS; Gilleard JS; Gordon D; Harcus Y; Harsha B; Hawdon JM; Hill DE; Hodgkinson J; Horák P; Howe KL; Huckvale T; Kalbe M; Kaur G; Kikuchi T; Koutsovoulos G; Kumar S; Leach AR; Lomax J; Makepeace B; Matthews JB; Muro A; O’Boyle NM; Olson PD; Osuna A; Partono F; Pfarr K; Rinaldi G; Foronda P; Rollinson D; Samblas MG; Sato H; Schnyder M; Scholz T; Shafie M; Tanya VN; Toledo R; Tracey A; Urban JF; Wang LC; Zarlenga D; Blaxter ML; Mitreva M; Berriman M, 2019, 'Comparative genomics of the major parasitic worms', Nature Genetics, vol. 51, pp. 163 - 174,

Cotton J, 2018, 'Sir Alfred Zimmern lectures Australia, 1938: a utopian on Munich?', Cambridge Review of International Affairs, vol. 31, pp. 494 - 515,

Thiele EA; Eberhard ML; Cotton JA; Durrant C; Berg J; Hamm K; Ruiz-Tiben E, 2018, 'Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations', PLoS Neglected Tropical Diseases, vol. 12, pp. e0006747,

Cuypers B; Berg M; Imamura H; Dumetz F; De Muylder G; Domagalska MA; Rijal S; Bhattarai NR; Maes I; Sanders M; Cotton JA; Meysman P; Laukens K; Dujardin JC, 2018, 'Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent', Infection, Genetics and Evolution, vol. 62, pp. 170 - 178,

Cotton JA; Berriman M; Dalén L; Barnes I, 2018, 'Eradication genomics—Lessons for parasite control', Science, vol. 361, pp. 130 - 131,

Gilchrist CA; Cotton JA; Burkey C; Arju T; Gilmartin A; Lin Y; Ahmed E; Steiner K; Alam M; Ahmed S; Robinson G; Zaman SU; Kabir M; Sanders M; Chalmers RM; Ahmed T; Ma JZ; Haque R; Faruque ASG; Berriman M; Petri WA, 2018, 'Genetic diversity of cryptosporidium hominis in a bangladeshi community as revealed by whole-genome sequencing', Journal of Infectious Diseases, vol. 218, pp. 259 - 264,

Coughlan S; Taylor AS; Feane E; Sanders M; Schonian G; Cotton JA; Downing T, 2018, 'Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus', Royal Society Open Science, vol. 5,

Sallé G; Laing R; Cotton JA; Maitland K; Martinelli A; Holroyd N; Tracey A; Berriman M; Smith WD; Newlands GFJ; Hanks E; Devaney E; Britton C, 2018, 'Transcriptomic profiling of nematode parasites surviving vaccine exposure', International Journal for Parasitology, vol. 48, pp. 395 - 402,

Böhme U; Otto TD; Cotton JA; Steinbiss S; Sanders M; Oyola SO; Nicot A; Gandon S; Patra KP; Herd C; Bushell E; Modrzynska KK; Billker O; Vinetz JM; Rivero A; Newbold CI; Berriman M, 2018, 'Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals', Genome Research, vol. 28, pp. 547 - 560,

Sargison ND; Redman E; Morrison AA; Bartley DJ; Jackson F; Naghra-van Gijzel H; Holroyd N; Berriman M; Cotton JA; Gilleard JS, 2018, 'A method for single pair mating in an obligate parasitic nematode', International Journal for Parasitology, vol. 48, pp. 159 - 165,

Doyle SR; Laing R; Bartley DJ; Britton C; Chaudhry U; Gilleard JS; Holroyd N; Mable BK; Maitland K; Morrison AA; Tait A; Tracey A; Berriman M; Devaney E; Cotton JA; Sargison ND, 2018, 'A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry', Genome Biology and Evolution, vol. 10, pp. 396 - 409,

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