Lin Zexu: Imperial China in a Globalizing World, New York, Oxford University Press, forthcoming 
"The Lhasa Uprisings of 1959 and 2008: Muslims in a Buddhist Land," In Islamic Ecumene: Comparing Global Muslim Societies, ed. Eric Tagliacozzo and David S. Powers. Ithaca, N.Y.: Cornell University Press, forthcoming .
The Panthay Rebellion: Islam, Ethnicity, the Dali Sultanate in Southwestern China, 1856-73 , London: Verso, 2023.
Sources in Chinese History: Diverse Perspectives from 1644 to the Present (Co-authored with Yurong Y. Atwill), New York, NY: Routledge, 2021. [SECOND EDITION - with new documents, new translations and new visual sources]
Islamic Shangri-la: Inter-Asian Relations and Lhasa's Muslim Communities, 1600-1960, University of California Press, 2018.
Religious Studies Review by Amy Holmes-Tagchungdarpa
Pacific Affairs Review by David Stroup
LSE Review of Books by Palden Gyal
"Lhasa's Departed Past," #AsiaNow, Association of Asian Studies (October 8, 2018)
“Boundaries of Belonging: Sino-Indian Relations and the 1960 Tibetan Muslim Incident,” Journal of Asian Studies 75(3) August 2016.
"A Tibetan By Any Other Name: The Case of Muslim Tibetans and Ambiguous Ethno-religious Identities” Cahiers d’Extrême Asie 23 2014: 31-61.
"十九世纪滇藏关系解释范式的反思" (Ruminations on the Interpretive Framework of 19th Century Tibet-Yunnan Relations),” 民族学刊 (Journal of Ethnology )1-2 (2010): 19-24.
Sources in Chinese History: Diverse Perspectives from 1644 to the Present (Co-authored with Yurong Y. Atwill), Upper Saddle River, NJ: Prentice Hall, 2009.
"Holy Culture Wars: Patterns of Ethno-Religious Violence in 19th and 20th Century China," in Belief and Bloodshed: Religion and Violence Across Time and Traditions. Ed. James Wellman, Rowman & Littlefield, 2007
The Chinese Sultanate: Islam, Ethnicity and the Panthay Rebellion in Southwestern China, 1856-1873, Stanford University Press, 2006.
H-War Review by Eva Goldschmidt
Journal of Chinese Studies by Laura Newby
American Historical Review by Zvi Ben-Dor Benite
"Blinkered Visions: Islamic Identity, Hui Ethnicity, and the Panthay Rebellion in Southwest China, 1856-1874," Journal of Asian Studies 62(4), 2003.
"Trading Places: Resistance, Ethnicity and Governance in 19th Century Yunnan," in Robert J. Antony and Jane K. Leonard, eds., Dragons, Tigers, and Dogs Qing Crisis Management and the Boundaries of State Power in Late Imperial China (Ithaca: Cornell East Asia Series, 2002): 245-273.
"Larger Than Life: French Imperialism in Southwest China, 1886-1904" in Shixue Luncong (Studies in History), no.7, Dec., 1999.
"Islam in the World of Yunnan: Muslim Yunnanese Identity in 19th Century Yunnan," Journal of Muslim Minority Affairs, 17(1) 1997, 9-30.