الاوراق العلمية المحكمة التى قدمها د. الافندي والتى نشرت في عدد كبير من المجلات العلمية المحكمة العالمية اعتبار ا من العام 1990 م وحتى يومنا هذا
C. Journal Articles: * "'Discovering the South': Sudanese Dilemmas for Islam in Africa," 18pp., pp. 371-389, African Affairs, vol. 89 (1990), ISSN 0001-9909 * "The Long March from Lahore to Khartoum: Beyond the Muslim Reformation," 14pp., pp. 137 51, BRISMES Bulletin, vol. 17 (1990), ISSN 1353-0194. "Studying My Movement: Social Science without Cynicism,” 11pp., pp. 83 94 International Journal of Middle Eastern Studies, vol. 23 (1991), ISSN 0020-7438. * "The Eclipse of Reason: The Media in the Muslim World," 30pp., pp. 163-193, Journal of International Affairs, vol. 47, (Winter 1993), ISSN 0022-197x “Islam and the Future of Dissent after the ‘End of History,” 13pp., pp. 191-204, Futures, vol. 31 (1999), ISSN 0016-3287. “Reviving Controversy: Islamic Revivalism and Modern Human Rights,” 33pp., pp. 117-150, in Encounter, vol. 6 (2000), ISSN 1358-5770. “Al-Sudan ila Ayn?” (Whither Sudan?), 21pp., pp. 158-179, Al-Mstaqbal al-‘Arabi vol. 23, July 2000), ISSN, 1024-9834.. “Al-Muwatana fi’l-Fikr al-Islami” (Citizenship in Islamic Thought) Al-Mustaqbal Al-Arabi, vol. 23 (2001) ISSN 1024-9834. * “The Impasse in the IGAD Peace Process for Sudan: The Limits of Regional Cooperation,” 18pp., 581-599, African Affairs, vol. 100 (2001), ISSN 0001-9909. “Islam and Human Rights: The Lessons from Sudan,” 25pp., pp. 481-506, The Muslim World, vol. 91 (Fall, 2001), ISSN 0027-4909.
Forthcoming: “The People on the Edge: Religious Reform and the Burden of the Western Muslim Intellectual”, Harvard Middle Eastern and Islamic Review, Autumn, 2007, ISSN: 1074-5408. “Sudan’s Futures: One State or Many?” Contemporary Arab Affairs, 1 (1), 2008, ISSN: 1755-0912 “The Perils of Regionalism: Regional Integration as a Source of Instability in the Horn of Africa” Journal of Intervention and Statebuilding, ISSN: 1750-2977
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