1994 The origins and early history of the Mahāratnakūṭa tradition of Mahāyāna Buddhism, with a s tudy of the Ratnarāśisūtra and related materials . – Unpublished PhD thesis, University of Michigan.
2006 Review of: Helmut Eimer and David Germano (eds), The many canons of Tibetan Buddhism: PIATS 2000: Tibetan studies: proceedings of the ninth seminar of the International Association for Tibetan Studies, Leiden 2000, Leiden 2002 (Brill’s Tibetan Studies Library 2,10). JAOS 125,2: 341-342.
2007 “Garlanding as sexual invitation: Indian Buddhist evidence.” IIJ 50: 5-10.
– “Good and evil in Indian Buddhism: the five sins of immediate retribution.” JIP 35,3: 253-286.
– “Bauddhavacana: notes on Buddhist vocabulary.” Sōka Daigaku Kokusai Bukkyōgaku Kōtō Kenkyūjo Nenpō 創価大学国際仏教学高等研究所年報 / Annual Report of The International Research Institute for Advanced Buddhology at Soka University 10: 171-179.
– “Bodhisattva” and “Mahāyāna Buddhism.” Encyclopaedia Britannica, published online. Stable URLs: http://www.search.eb.com/eb/print?articleId=50114&fullArticle=true&tocId=9050114 http://www.search.eb.com/eb/print?articleId=80362&fullArticle=true&tocId=9080362.
2008 Riven by lust: incest and schism in Indian Buddhist legend and historiography, Honolulu. – Reissued Delhi, 2009.
– Managing monks: administrators and administrative roles in Indian Buddhist monasticism, New York. – Also published in Oxford Scholarship Online, 2011: DOI: 10.1093/acprof:oso/9780195326840.001.0001
– Lies, slander and the study of Buddhism, Leiden. – Inaugural lecture delivered 1 April, 2008, at Leiden University.
– “The story of Dharmaruci: in the Divyāvadāna and Kṣemendra’s Bodhisattvāvadānakalpalatā.” IIJ 51: 137-185.
– “Maternity homes and abandoned children in Buddhist India.” JAOS 127,3: 297-314.
– “Putative Persian perversities: Buddhist condemnations of Zoroastrian close-kin marriage in context.” BSOAS 71,3: 433-464.
– “The Indian Buddhist Mahādeva in Tibetan sources.” Indo Tetsugaku Bukkyōgaku Kenkyū インド哲学仏教学研究 / Studies in Indian Philosophy and Buddhism 15: 27-55.
– “Forbidden women: a peculiar Buddhist reference.” In: Peter Zieme (ed.), Aspects of research into Central Asian Buddhism: in memorium Kōgi Kudara, Turnhout (Silk Road Studies 16), pp. 371-378.
– “Incestuous ancestries: on the family origins of Gautama Siddhārtha, interpretations of Genesis 20.12, and the status of scripture in Buddhism.” History of Religions 47,4: 253-281.
– “The Jifayue sheku tuoluoni jing—translation, non-translation, both or neither?” JIABS 30,1-2 [2010]: 369-420.
– “In memoriam Erik Zürcher (13 Sept. 1928 – 7 Feb. 2008).” JIABS 30,1-2 [2010]: 3-22.
– “*Parikarṣati reconsidered.” Sōka Daigaku Kokusai Bukkyōgaku Kōtō Kenkyūjo Nenpō 創価大学国際仏教学高等研究所年報 / Annual Report of The International Research Institute for Advanced Buddhology at Soka University 11: 61-69.
– “Kyōsei and Yogācāra Buddhism: a look at Vasubandhu’s Viṁśikā.” Kyōsei Shisō Kenkyū Nempō 共生思想研究年報 2008: 35-39.
– Review of: Yasuhiro Sueki, Bibliographical sources for Buddhist studies: from the viewpoint of Buddhist philology, 2nd edition revised and enlarged, Tokyo 2008. IIJ 51: 195-203.
2009 “A small problem of tense and person: Dhammapada 306 and its parallels.” JPTS 30: 161-176.
– “Remarks on the Kāśyapaparivarta commentary.” In: Martin Straube, Roland Steiner, Jayandra Soni, Michael Hahn und Mitsuyo Demoto (eds), Pāsādikadānaṃ: Festschrift für Bhikkhu Pāsādika (Indica et Tibetica 52), Marburg, pp. 381-397.
– Review of: Catherine Ludvik, Sarasvatī: riverine Goddess of knowledge: from the manu­script-carrying Vīṇā-player to the weapon-wielding defender of the Dharma (Brill’s Indological Library 27), Leiden-Boston, Mass. 2007; and of: Recontextualizing the praises of a Goddess: from the Harivaṁśa to Yijing’s Chinese translation of the Sutra of Golden Light (Italian School of East Asian Studies Occasional Papers 10), Kyoto 2006. AS/EA 63,4: 991-996.
2010 “Test sailing the ship of the teachings: hesitant notes on Kāśyapaparivarta §153-154.” In: Eli Franco and Monika Zin (eds), From Turfan to Ajanta: Festschrift for Dieter Schlingloff on the occasion of his eighteeth birthday, Lumbini, vol. 2, pp. 897-924.
– “Bouddhisme.” In: Oliver Pétré-Grenouilleau (ed.), Dictionnaire des esclavages, Paris: Larousse, pp. 123-125.
– “Imag(in)ing the Buddhist brain: editorial introduction.” With Lorenza S. Colzato. Zygon: Journal of Religion and Science 45/3: 591-595. [Largely written by Silk.]
– Review of: Stephen C. Berkwitz, Juliane Schober, Claudia Brown (eds), Buddhist manuscript cultures: knowledge, ritual, and art (Routledge Critical Studies in Buddhism 52), London 2009. IIJ 53: 285-296.
– Review of: Anton Schiefner, Hartmut Walravens (Hrsg.), Übersetzungen aus dem tibetischen Kanjur: Beiträge zur Buddhismus¬kunde und zur zentralasiatischen Märchenforschung (Sinologica Coloniensia 25), Wiesbaden 2007. IIJ 53,1: 65-70.
2011 Review of: Stephen C. Berkwitz, South Asian Buddhism: a survey, London 2009. IIJ 54: 275-285.
2012 “Kern and the study of Indian Buddhism: with a speculative note on the Ceylonese Dhammarucikas.” JPTS 31: 125-154.
– “A missed opportunity.” History of Religions 51,3: 262-272. – Review article on K. Buffetrille and D. S. Lopez, Introduction to the History of Indian Buddhism, by E. Burnouf (University of Chicago Press, 2010)
– Review of: Jin-il Chung, A survey of the Sanskrit fragments corresponding to the Chinese Saṁyuktāgama [Zōagonkyō sōtō bonbun danpen ichiran] (雜阿含經相當梵文斷片一覽). Tōkyō: Sankibō Busshorin 山喜房佛書林, 2008. IIJ 55: 92-96.
2013 “Review article: Buddhist sūtras in Sanskrit from the Potala.” IIJ 56,1: 61-87.
– “The proof is in the pudding: what is involved in editing and translating a Mahayana sutra?” IIJ 56,2: 157-178.
– Review of: Anālayo, The genesis of the Bodhisattva ideal, Hamburg: Hamburg University Press, 2010. IIJ 56,2: 193-199.
– & E. Zürcher E. (eds), Buddhism in China: collected papers of Erik Zürcher, Leiden: Brill.
– & P.C. Bisschop, “Editorial.” IIJ 56,1: 1-2.
2014 “Taking the Vimalakīrtinirdeśa seriously.” Sōka Daigaku Kokusai Bukkyōgaku Kōtō Kenkyūjo Nenpō 創価大学国際仏教学高等研究所年報/ Annual Report of the International Research Institute for Advanced Buddhology at Soka University 17: 157-188. pdf
– “Keeping up with the Joneses: from William Jones to John James Jones.” Sōka Daigaku Kokusai Bukkyōgaku Kōtō Kenkyūjo Nenpō 創価大学国際仏教学高等研究所年報/Annual Report of the International Research Institute for Advanced Buddhology at Soka University 17: 427-441. pdf
2015 Buddhist Cosmic Unity: an edition, translation and study of the “Anūnatvāpūrṇatvanirdeśaparivarta”, Hamburg: Hamburg University Press (Hamburg Buddhist Studies 4).
– “Out of the East: Tibetan scripture translations from Chinese.” Journal of Tibetology 9: 29-36.
– Ed. of Brill’s Encyclopedia of Buddhism, volume I: Literature and languages (Handbook of Oriental Studies, Section Two, India nr. 29/1).
– “Canonicity.” In: Brill’s Encyclopedia of Buddhism, volume I: Literature and languages (Handbook of Oriental Studies, Section Two, India nr. 29/1), pp. 5-37.
– Review of: Johannes Bronkhorst, Buddhism in the shadow of Brahmanism, Leiden: Brill, 2011. IIJ 58,2: 163-169.
2016 Materials toward the study of Vasubandhu’s Viṁśikā (I): Sanskrit and Tibetan Critical editions of the verses and autocommentary; an English translation and annotations. Cambridge MA: Department of South Asian Studies, Harvard University (Harvard Oriental Series 81).- Open access edition 2018
– “Peering through a funhouse mirror: trying to read Indic texts through Tibetan and Chinese translations.” In: Dorji Wangchuk (ed.), Cross-cultural transmission of Buddhist texts: theories and practices of translation, Hamburg, pp. 287-311. pdf
– “Guan Wuliangshoufo jing de goucheng: Ji xushi jiegou de ruogan Fojiao yu qinajiao pingxingben” 《觀無量壽佛經》的構成: 其敘事結構的若干佛教與耆那教平行本. Singaporean Journal of Buddhist Studies 3: 111-199. pdf
– “A Tibetan grammatical construction: verb + na go.” Revue d’Etudes Tibétaines 35: 309-344. pdf
2018 Open Access Edition of: Materials toward the study of Vasubandhu’s Viṁśikā (I): Sanskrit and Tibetan critical editions of the verses and autocommentary; an English translation and annotations. Cambridge MA: Department of South Asian Studies, Harvard University, 2016 (Harvard Oriental Series 81).
2019 & P.D. Szántó, “Trans-sectual identity: materials for the study of the Praśnottararatnamālikā, a Hindu/Jaina/Buddhist catechism (I).” IIJ 62,2: 103-161.
– “Chinese sūtras in Tibetan translation: a preliminary survey.” Annual Report of The International Research Institute for Advanced Buddhology at Soka University 22: 227-246.
– “In praise of his mighty name: A Tibetan poem on Amitābha from Dunhuang.” In: Georgios T. Halkias, Richard K. Payne (eds), Pure Lands in Asian texts and contexts: an anthology, Honolulu: University of Hawaii Press, pp. 496-539.
– “Mahādeva.” In: Brill’s Encyclopedia of Buddhism, volume II: Lives, no. 2: Brill. 298-301.
–& Richard Bowering, Richard McBride II & Miyaji Akira (2019), “Maitreya.” In: Silk J.A. (Ed.) Brill’s Encyclopedia of Buddhism, volume II: Lives, no. 2: Brill. 302-324.
–Review of: Richard Salomon, The Buddhist literature of ancient Gandhāra: an introduction with selected translation, Somerville, Mass.: Wisdom Publications, 2018. IIJ 62,3: 269-279.
–Review of: Jürgen Hanneder, To edit or not to edit: on textual criticism of Sanskrit works. A series of lectures delivered at the Ecole Pratique des Hautes Etudes Paris, March 2015, and the Department of Pali, Savitribai Phule Pune University, Pune, October and November 2015, Pune: Aditya Prakashan, 2017 (Pune Indological Series 1). IIJ 62,3: 280-291.
2020“Obituary [of Akira Yuyama].” IIJ 63,1: 1-2
– Review of: Oskar von Hinüber, Kleine Schriften III, ed. by Harry Falk, Haiyan Hu-von Hinüber and Walter Slaje, Wiesbaden: Harrassowitz Verlag, 2019 (Veröffentlichungen der Helmuth von Glasenapp-Stiftung 49). IIJ 63,1: 76-77.
–Review of: Gergely Hidas, A Buddhist Ritual Manual on Agriculture: Vajratuṇḍasamayakalparāja—Critical Edition and Translation, Berlin/Boston: Walter de Gruyter GmbH, [2019] (Beyond Boundaries: Religion, Region, Language and the State 3). IIJ 63,1: 78–93.
– Review of: Birgit Kellner, Buddhism and the dynamics of transculturality: new approaches, Berlin: Walter de Gruyter, 2019 (Religion and Society 64). IIJ 63,1: 94–101.
–“Indian Buddhist attitudes toward outcastes: rhetoric around caṇḍālas.” IIJ 63,2: 128-187.
–“A resurgent interest in ‘Hindu Fiction’: on and around the Kathāsaritsāgara, with special attention to Buddhism.” IIJ 63,3: 263-306.
–& Paul W. Kroll (eds), “At the shores of the sky” : Asian studies for Albert Hoffstädt. Leiden: Brill (Sinica Leidensia 151). Open Access: https://brill.com/view/title/57671. DOI: https://doi.org/10.1163/9789004438200
–& Paul W. Kroll. “Albert Hoffstädt: a tribute.” In: Paul W. Kroll and Jonathan A. Silk (eds.), “At the shores of the sky” : Asian studies for Albert Hoffstädt. Leiden: Brill (Sinica Leidensia 151), pp. 1-3.
–“A trust rooted in ignorance: why Ānanda’s lack of understanding makes him a reliable witness to the Buddha’s teachings.” In: Paul W. Kroll and Jonathan A. Silk (eds.), “At the shores of the sky” : Asian studies for Albert Hoffstädt. Leiden: Brill (Sinica Leidensia 151), pp. 23-37.
–“A trust rooted in ignorance: why Ānanda’s lack of understanding makes him a reliable witness to the Buddha’s teachings.” In: Paul W. Kroll, J.A. Silk (eds), At the shores of the sky”: Asian studies for Albert Hoffstädt. Sinica Leidensia no. 151 Leiden: Brill, pp. 23-37.
– “A Dunhuang Tibetan aspirational prayer for rebirth in Amitābha’s Pure Land.” Sōka Daigaku Kokusai Bukkyōgaku Kōtō Kenkyūjo Nenpō 23: 65-87.
– “Tekisuto sokei no nai kōtei: Bukkyō kyōten to yudayakyō rabi bunken kenkyū ni okeru honbun hihan, soshite ‘Hirakareta bunkengaku’ dejitaru hyūmanitīzu puroje­kuto” テキスト祖型のない校訂: 佛敎經典とユダヤ敎ラビ文獻硏究における本文批評、 そして「開かれた文獻學」デジタルヒューマニティーズ プロジェクト [Editing with­out an Ur-text: Buddhist Sūtras, Rabbinic Text Criticism, and the Open Philology Digital Humanities Project]. Translated by Notake Miyako 野武美彌子. , Tōyō no Shisō to Shūkyō 東洋の思想と宗敎 37: 22-58.
–Review article “Origins of the Mahāyāna” of Paul Harrison (ed.), Setting out in the Great Way: essays on early Mahāyāna Buddhism, Sheffield: Equinox, 2018. IIJ 63,4: 371-394.
2021“A brief introduction to recent Chinese studies on Sanskrit and Khotanese (chiefly Buddhist) literature.” IIJ 64,1: 51-64.
–“The Heart Sūtra as Dhāraṇī.” Acta Asiatica 121: 99-125.
–Review of: G. Hidas, Powers of protection: the Buddhist tradition of spells in the Dhāraṇīsaṁgraha collections, Berlin-Boston: De Gruyter (Beyond Boundaries), Indo-Iranian Journal 64(4): 377-386.
– Review of: O. Von Hinüber, The Saṃghāṭasūtra: a popular devotional buddhist Sanskrit text: editio maior. Annual report of the International Research Institute for Advanced Buddhology at Soka University for the academic year 2020, Indo-Iranian Journal 64(4): 392-402.
– Ed. for publication with Michael Radich: Stefano Zacchetti, The Da zhidu lun 大智度論 (*Mahāprajñāpāramitopadeśa) and the History of the Larger Prajñāpāramitā: Patterns of Textual Variation in Mahāyāna Sūtra Literature.  Hamburg Buddhist Studies 14 (Hamburg: projekt verlag).
2022& Kuijp L. van der (eds), From Khyung lung to Lhasa, A Festschrift for Dan Martin. Revue d’Etudes Tibétaines no. 64: University of Cambridge.
–“A Dunhuang Tibetan poem praising Amitābha and its rebirth among the Gter ma.” In: J. Silk and L. van der Kuijp (eds), From Khyung lung to Lhasa, A Festschrift for Dan Martin. Revue d’Etudes Tibétaines 64: 516-613.
– “The History of the *Kāsyapaparivarta ́ in Chinese Translations and Its Connection with the Mahāratnakūtạ (Da Baoji jing 大寶積經) Collection.” Journal of the American Oriental Society 142.3: 671–697. https://doi.org/10.7817/jaos.142.3.2022.ar028.
–“Thinking About the Study of Buddhist Texts: Ideas from Jerusalem, in More Ways Than One.” Journal of Indian Philosophy 50.4: 753–769. https://link.springer.com/article/10.1007/ s10781-022-09515-3. https://doi.org/10.1007/s10781-022-09515-3
–& Stefano Zacchetti† (eds), Chinese Buddhism and the Scholarship of Erik Zürcher. Leiden: Brill (Sinica Leidensia 157).
– “Serious play: recent scholarship on the Lalitavistara.” Indo-Iranian Journal 65(3): 267–301.
– Review of: M. Zin & D. Schlingloff, Saṁsāracakra: the wheel of rebirth in the Indian tradition, Indo-Iranian Journal 65(2): 171-180.
2023Ed.Brill’s Encyclopedia of Buddhism. Volume IV.2: History: Part Two: Central and East Asia. Handbook of Oriental Studies. Section Two, India, 29-4/2 (Leiden: Brill).
2024“Remarks on a Recent Study of the Śrīmālādevīsiṁhanādanirdeśasūtra.” Indo-Iranian Journal 67(1): 53–80. doi:10.1163/15728536-06701004.