Islam and Nation: Separatist Rebellion in Aceh, Indonesia, Standford: Stanford University Press, 2009.
Opposing Suharto: Compromise, resistance and regime change in Indonesia, Standford: Stanford University Press, 2005.
Local Power and Politics in Indonesia: Democratisation and decentralisation (edited with Greg Fealy), Singapore: Institute of Southeast Asian Studies, 2003.
The Last Days of President Suharto (edited with Gerry van Klinken and Herb Feith),Clayton: Monash Asia Institute. 1999 (also published in translation in Indonesia by the Yogyakarta-based publisher, LKIS).
The Helsinki Peace Agreement: A more promising basis for peace in Aceh?, Washington: East West Center, Policy Paper series 2005.
The Peace Process in Aceh: Why it failed (co-authored with Harold Crouch), Washington: East West Center Policy Paper series, East West Center, 2003.
Student Dissent in Indonesia in the 1980s, Working Paper Number 79, Monash: Monash University, Centre of Southeast Asian Studies, 1993.
'The Construction of Grievance: Natural Resources and Identity in a Separatist Conflict', Journal of Conflict Resolution. Vol. 51, No. 6, 2007, pp. 950-972.
'From Islamism to Nationalism in Aceh, Indonesia', Nations and Nationalism Vol. 13, No. 2, 2007, pp. 245-263.
'Elections and the normalization of politics in Indonesia',South East Asia Research, Vol. 13, No. 2 (July 2005), pp. 117-156.
'Indonesia after the tsunami', Current History, Vol. 104, No. 680 (March 2005), pp. 105-109.
'Sovereignty, the successor state and universal human rights: history and the international structuring of Acehnese nationalism', Indonesia, No. 73 (April 2002), pp. 1-24.
'Modernity, history and ethnicity: Indonesian and Acehnese nationalism in conflict', Review of Indonesian and Malaysian Affairs, Vol 36, No. 1 (2002), pp. 3-33. Reprinted in 2003, Damien Kingsbury and Harry Aveling (eds) Autonomy and Disintegration in Indonesia, London: RoutledgeCurzon, pp. 128-47.
'The breakup of Indonesia? Nationalisms after decolonisation and the limits of the nation-state in post-cold war Southeast Asia' (co-authored with Mark T. Berger), Third World Quarterly: Journal of Emerging Areas, Vol. 22, No. 6 (2001), pp. 1003-24.
'Democratisation, the working class and the Indonesian crisis', Review of Indonesian and Malaysian Affairs, Vol. 33, No. 2 (1999), pp. 1-32.
'Students and the military: Regime friction and civilian dissent in the late Suharto period', Indonesia, No. 59 (April 1995) pp. 45-64.
'Country Report - Indonesia', Countries at the Crossroads 2006, Rowman and Littlefield/Freedom House, 2006.
'Violence and identity formation in Aceh under Indonesian rule', in Anthony Reid (ed), Verandah of Violence: The historical background of the Aceh problem, Singapore: Singapore University Press, 2006.
'Politics: Indonesia's year of elections and the end of the political transition', in Budy P. Resosudarmo (ed.), The Politics and Economics of Indonesia's Natural Resources, Singapore: ISEAS, 2005, (Indonesia Update series), pp. 13-30.
2004, 'Indonesia: Civil society and Democratic Breakthrough' in Muthiah Alagappa (ed.) Civil Society and Political Change in Asia. Expanding and Contracting Democratic Space. Stanford: Stanford University Press, pp. 61-96.
2003, (co-authored with Greg Fealy), 'Introduction: Democratisation and decentralisation', in Aspinall and Fealy (eds), Local Power and Politics in Indonesia: Democratisation and decentralisation, Singapore: Institute for Southeast Asian Affairs.
2002, 'The downfall of President Abdurrahman Wahid: A return to authoritarianism?' in Kathryn Robinson and Sharon Bessel (eds) Women in Indonesia: Gender, Equity and Development. Singapore: Institute of Southeast Asian Studies, pp. 28-40.
1999, 'The 1999 general election in Aceh' in Susan Blackburn (ed.) Pemilu: Tthe 1999 Indonesian election, Clayton: Monash Asia Institute, Annual Indonesia Lecture Series No. 22, pp. 29-42.
1999, 'The Indonesian student uprising of 1998', in Arief Budiman, Barbara Hatley and Damien Kingsbury (eds) Reformasi: Crisis and change in Indonesia, Clayton: Monash Asia Institute, pp. 212-238.
1998, 'Opposition and elite conflict in the fall of Soeharto', in Geoff Forrester and R.J. May (eds) The Fall of Soeharto, Bathurst: Crawford House Publishing, and Regime Change and Regime Maintenance in Asia and the Pacific Project, Australian National University, pp. 130-53.
1996, 'The broadening base of political opposition in Indonesia', in Garry Rodan (ed.) Political Oppositions in Industrialising Asia, London and New York: Routledge, pp. 215-40.
2005, 'The historical and political background to the Aceh conflict', in Kamarulzaman Askandar and Ang Ming Chee (eds) Building Peace in Aceh: Problems, strategies and lessons from Sri Lanka and Northern Ireland. Bangkok: Forum Asia, pp. 31-42.
2004, 'Indonesia' in Bogdan Szajkowski (ed), Revolutionary and Dissident Movements, London: John Harper Publishing, pp. 183-90. ISBN 0-9543811-2-2.
2001, "The Conflict in Aceh: Towards Impasse?", Strategic Update 2001: Presentation Summaries, Canberra: Australian Defence Studies Centre, Australian Defence Force Academy, p. 49-50.
1998, 'East Timorese Independence Movement (1975-)', in Jack A. Goldstone (ed.) The Encyclopedia of Political Revolutions, Congressional Quarterly Inc., Washington, pp. 146-7.
2006, 'Selective outrage and unacknowledged fantasies: Re-thinking Papua, Indonesia and Australia", Austral Policy Forum.
2006, 'Focus on Papua a symptom of narrow vision', Sydney Morning Herald, 27 April.
2005, 'Peace at last?', Inside Indonesia, No. 84 (Oct-Dec), p. 33.
2005, 'In the dock: Celebrity status for Australian detainee', Inside Indonesia, No. 83 (July-Sept), p. 33.
2005, 'A triumph for the Government', Asian Analysis (website), October edition.
2005, 'Tsunami relief and resurgent nationalism', Asian Analysis (website), April edition.
2005, 'After the tsunami: Journal of an Aceh volunteer', Inside Indonesia, No. 82 (April-June), pp. 28-30.
2005, 'Hardliners on both sides threaten Aceh settlement,' Sydney Morning Herald, February 23.
2005, 'Paranoia and politics in the disaster zone', Sydney Morning Herald, February 3.
2005, 'Aceh's lost legacy: Searching for Isa Sulaiman', Australian Author, April, pp. 8-14.
2004, 'New president will face same old problems,' Sydney Morning Herald. 20 September.
2004, 'The victims are ordinary, the carnage isn't', Sydney Morning Herald, 10 September, p. 2.
2004, 'The state of democracy', ABC Radio Australia 'Go Asia Pacific' web page, 6 September.
2004, 'Indonesia's elections: Is the cheer justified?', Inside Indonesia, No. 80, October-December, p. 33.
2004, 'A war that failed', Inside Indonesia, No. 79, July-September, p. 33.
2004, 'Rotten politicians', Inside Indonesia, No. 78, April-June, p. 33.
2003, 'Anti-insurgency logic in Aceh', Inside Indonesia, No. 76, October-December, pp. 23-24.
2003, 'Message for Aceh: The military's back', Sydney Morning Herald. May 23, p. 15.
2003, 'After the war, a lingering legacy of hate," Sydney Morning Herald, April 5-6, p. 34. (Part reprinted in The Age, April-5-6, 2003).
2003, "Indonesia: A Political crisis without end', Asean Focus Group, Asian Analysis (website) (March) http://www.aseanfocus.com/asiananalysis.
2003, 'A hybrid order', Inside Indonesia, No. 74, April-June, pp. 12-14.
2002, 'Still a long way to go in the search for peace in Aceh', The Canberra Times, December 11.
2002, Security and Political Implications of the Bali Bombings, AusAID Briefing Paper, November 13 (11 pages).
2002, 'Misused power could promote Islamic fringe', The Canberra Times, October 24.
2002, 'Aceh: the battle over history', ABC Radio National Perspective commentary program, August 21, 2002.
2002, 'Indonesia: Syariah Law comes to Aceh', Asean Focus Group, Asian Analysis (website) (August).
2002, 'The conflict in Aceh: Prospects for resolution after September 11', Australian Member Committee Of The Council For Security Cooperation In The Asia Pacific Committee Newsletter, No. 13, p. 19-20.
2002, 'Indonesia: Paradigm shift', What's Next, Jan/Feb edition (publication of Centre for International Strategic Analysis, CISA), p. 9.
2002, 'Cold comfort in hot pursuit',The Australian, February 8, p. 11 (Opinion Page).
2001, Indonesia: Political and Security Outlook, 18 page paper written as part of a consultancy for AusAID.
2001, 'Megawati treading a delicate path', The Canberra Times, October 15, p. 9 (Opinion page).
2001, 'Mother of the Nation', Inside Indonesia, No. 68, Oct-Dec, p. 23-24 (cover story).
2001, 'Indonesia: A return to authoritarianism?', Asean Focus Group, Asian Analysis (website) (August).
2000, 'Aceh's Hidden War', Asean Focus Group, Asian Analysis (website) (November).
2000, 'Whither Aceh?',Inside Indonesia, No. 62 (April-June), pp. 6-7.
1999, 'The Elections in Aceh,' Perspectives from the Periphery (Australian Council for Overseas Aid report on the 1999 Indonesian elections).
1999 (with Iain Wilson) 'Indonesia on the Net: Resources on two troubled regions - Aceh and Irian Jaya', Inside Indonesia, No. 60 (Oct - Dec).
1999, 'New challenge to our North', The Sydney Morning Herald, July 22 (Opinion page).
1998, 'What chance democracy?', The Weekend Australian (Focus Section), May 23-24. (reprinted in Aspinall, van Klinken and Feith (eds), The Last Days of President Suharto, 1999).
1998, 'Same frame, different picture', The Daily Telegraph, May 22 (reprinted in Aspinall, van Klinken and Feith (eds), The Last Days of President Suharto, 1999).
1997, 'What price victory? The 1997 elections', Inside Indonesia, July-September p. 2-4.
1996, 'What happened before the riots?', Inside Indonesia, No. 48, pp. 4-8.
1996, 'Jakarta rolls out communist bogey to control dissent', The Australian, August 13, p. 6.
1993, 'Practicing what you preach,' Inside Indonesia, No. 36, pp. 7-9 (under pseudonym of Edmund Thompson).
1993, 'Rock and riots', Inside Indonesia, No. 35, p. 4-6 (under pseudonym of Edmund Thompson).
2006, Jacques Bertrand, Nationalism and Ethnic Conflict in Indonesia, Cambridge: Cambridge University Press, 2004, Pacific Affairs, Vol. 79, no. 1, pp. 151-2.
2005, Anthony Reid, An Indonesian Frontier: Acehnese and Other Histories of Sumatra. Singapore: Singapore University Press. Inside Indonesia, No. 85, (Jan-March), p. 31.
2003, Cees van Dijk, 'A Country in Despair', Leiden: KITLV Press, Asian Studies Review.
2002, Review essay of Robert W. Hefner, Civil Islam. Muslims and Democratization in Indonesia, Princeton: Princeton University Press, 2000, Review of Indonesian and Malaysian Affairs, Vol. 35, No. 2, p. 99-106.
1998, Philip J. Eldridge, Non-Governmental Organizations and Democratic Participation in Indonesia, Oxford: Oxford University Press, 1995 in The Australian Journal of International Affairs, Vol. 52, No. 2 (July), pp. 13-4.
1998, Anders Uhlin, Indonesia and the 'Third Wave of Democratization', Richmond: Curzon, 1997 in Review of Indonesian and Malaysian Affairs, Vol. 32, No. 1 (June).
1996, David Bourchier and John Legge (eds), Democracy in Indonesia: 1950s and 1960s, Clayton: Monash, 1994; John Bresnan, Managing Indonesia: The Modern Political Economy, New York:, Columbia University Press, 1993; Adam Schwarz, A Nation in Waiting: Indonesia in the 1990s, St. Leonards:, Allen & Unwin, 1994 in The Australian Journal of International Affairs, Vol. 50, No. 3 (November), pp. 326-8.