- Shattariyah Silsilah in Aceh, Java, and Mindanao (akan terbit di Tokyo Unviersity of Foreign Studies).
- The Library of an Islamic Scholar of Mindanao: The Shaykh Muhammad Said Collection at the Al-Imam As-Sadiq (AS) Library, Marawi City, Philippines: An Annotated Catalogue with Essays (akan terbit di Sophia University, Tokyo, co-writer bersama KAWASHIMA Midori).
- Filologi Indonesia: Teori dan Metode, Jakarta: Prenadamedia Group, 2015.
- Ithaf al-Dhaki: Tafsir Wahdatul Wujud bagi Muslim Nusantara, Jakarta: Mizan, bekerja sama dengan EFEO, Yayasan Rumah Kitab, dan ISIF, 2012.
- Filologi dan Islam Indonesia, Jakarta: Kementerian Agama RI Badan Litbang dan Diklat, Puslitbang Lektur Keagamaan, 2010.
- A Provisional Catalogue of Southeast Asian Kitabs in the Sophia University Collection, Tokyo: NIHU Program, 2010 (one of editors).
- Katalog Naskah Dayah Tanoh Abee, Aceh Besar (Aceh Manuscripts: Dayah Tanoh Abee Collection), published by Komunitas Bambu, Jakarta, in collaboration with TUFS, Manassa, PPIM UIN Jakarta, PKPM Aceh, and Dayah Tanoh Abee), 2010.
- Tarekat Syattariyah di Minangkabau: Teks dan Konteks (Shattariyyah Order in Minangkabau: Text and Context), Jakarta: Prenada, EFEO, PPIM, KITLV, and Total Indonesie, 2008.
- Katalog Naskah Ali Hasjmy (Catalogue of Aceh Manuscripts: Ali Hasjmy's Collection), with Munawar Holil, Tokyo: C-DATS Tokyo University of Foreign Studies, PPIM UIN Jakarta, and Manassa, 2007).
- Tentang Perempuan Islam: Wacana dan Gerakan (On Muslim Women: Discourse and Movement), co-editor with Jajat Burhanudin, Jakarta: Penerbit PT Gramedia Pustaka Utama, 2004.
- Khazanah Naskah: Panduan Koleksi Naskah Indonesia se-Dunia (Manuscript Treasures: World Guide to the Indonesian Manuscript Collection), co-writer with Henri Chambert-Loir, Jakarta: EFEO & Yayasan Obor Indonesia, 1999.
- Menyoal Wahdatul Wujud: Kasus Abdurrauf Singkel di Aceh Abad ke-17 (Debating Wahdatul Wujud: A Case Study of Abdurrauf Singkel in Aceh in the 17th Century), Bandung: Mizan & EFEO Jakarta, 1999.
- Jawa Barat: Koleksi Naskah Lima Lembaga (West Java: Manuscript Collections in Five Institutions), Jakarta: EFEO & Yayasan Obor Indonesia, 1999 (as editor; Catalogue of manuscripts compiled by Edi S Ekadjati and Undang A Darsa).
B) Articles or Part of Books
- “New Textual Evidence for Intellectual and Religious Connections between the Ottomans and Aceh” in A.C.S. Peacock & Annabel Teh Gallop [eds.], From Anatolia to Aceh: Ottomans, Turks and Southeast Asia, Oxford: Oxford University Press, 2015.
- "Kitabs from Cairo: An Overview of the New Collection of Southeast Asian Kitabs at Sophia University", Comparative Study of Southeast Asian Kitabs, Tokyo: NIHU Program, 2012.
- "The Roots of the Writing Tradition of Hadith Works in Nusantara : Hidayat al-habib by Nur al-Din al-Raniri", Studia Islamika, Vol. 19, No. 1, 2012.
- "Sulalat al-Salatin Karya Tun Seri Lanang: Kebesaran Karya Sastra Melayu yang Melampaui Zamannya", Jurnal Jumantara, Vol. 3 No. 1, 2012.
- "Sejarah Pengkafiran dan Marginalisasi Paham Keagamaan di Melayu dan Jawa: Sebuah Telaah Sumber", Jurnal Analisis, Vol.XI, No. 2, 2011.
- "Islamic Manuscript of Southern Philippines : A Research Note with Description of Three Manuscripts", The Journal of Sophia Asian Studies No.29, 2011.
- "Karakteristik Naskah Islam Indonesia: Contoh dari Zawiyah Tanoh Abee, Aceh Besar", Jurnal Manassa Vol. 1 No. 1, 2011.
- “Ithaf al-dhaki by Ibrahim al-Kurani: A Commentary of Wahdat al-wujud for Jawi Audiences”. Articel in Archipel 81 (Paris, France), April 2011, pp. 177-198.
- "Perkembangan Mutakhir Digitalisasi dan Katalogisasi Naskah Nusantara di Indonesia", in Aprinus Salam, Henri Chambert-Loir, M. Haji Salleh (eds.), Jejak Sastra & Budaya, prosiding seminar internasional persembahan untuk 70 tahun Prof. Dr. Siti Chamamah Soeratno, Yogyakarta: Penerbit Elmatera, bekerja sama dengan Jurusan Sastra Indonesia FIB UGM, dan Program S-2 Ilmu Sastra FIB UGM, p. 419-437.
- "Jawharat al-Ma'arif", in Henri Chambert-Loir, Massir Q. Abdullah, S. Suryadi, Oman Fathurahman, H. Siti Maryam Salahuddin, Iman dan Diplomasi: Serpihan Sejarah Kerajaan Bima. Jakarta: KPG, 2010.
- "Penulis dan Penerjemah Ulama Palembang: Menghubungkan Dua Dunia", in Henri Chambert-Loir (ed.), Sadur: Sejarah Terjemahan di Indonesia dan Malaysia, Jakarta: Kepustakaan Populer Gramedia (KPG) and EFEO, 2009: 1045-1056.
- "Further Research on Ithaf al-Dhaki Manuscripts by Ibrahim al-Kurani", in Stefanie Brinkmann & Beate Wiesmueller (eds.), From Codicology to Technology: Islamic Manuscripts and their Place in Scholarship, Berlin: Frank & Timme, 2009: 47-58.
- "Jamaat al-Jawiyyin dan Pembentukan Tradisi Intelektual Islam di Dunia Melayu-Nusantara" ("The Jawi Community and the Development of the Intellectual Islamic Tradition in the Malay World"), Jurnal Afkar, Cairo, September 2007.
- "Menelusuri Warisan Budaya Melayu di Negeri Kincir Angin", Media Indonesia, 18 August 2007, p. 17.
- "Urban Sufism: Perubahan dan Kesinambungan Ajaran Tasawwuf", in Gerakan & Pemikiran Islam Indonesia Kontemporer, by Rizal Sukma and Clara Joewono (eds.), Jakarta: CSIS & PPIM UIN Jakarta, 2007.
- "Pembaharuan dan Rekonsiliasi dalam Tradisi Intelektual Islam di Dunia Melayu-Indonesia", Book Review Article of "The Origins of Islamic Reformism in Southeast Asia: Networks of Malay-Indonesian and Middle Eastren 'Ulama' in the Seventeenth and Eighteenth Centuries" by Azyumardi Azra, Studia Islamika, Vol. 11 No. 2, 2004.
- “Reinforcing Neo-Sufism in the Malay Indonesian World: Shattariyyah Order in West Sumatra”, Studia Islamika, Vol. 10 No. 3, 2003.
- “Jaringan Ulama” (“The Networking of Ulamas”), in Ensiklopedi Tematis Dunia Islam (Thematic Encyclopedia of Islamic World Volume 5), co-writer with Azyumardi Azra.
- “Filologi dan Penelitian Teks-teks Keagamaan” (“Philology and the Study of Religious Texts”), Al-Turas, Volume 9, no. 2, 2003.
- “Usûl al-Madhâhib al-Sûfiyyah al-Muhaddathah (Neo-Sufisme) bi Indûnîsiyyâ: Mulâhazât ‘alâ Kitâb Ithâf al-Zakî li al-Shaikh Ibrâhîm al-Kûrânî” (Neo-Sufism in Indonesia: A Preliminary Study on Kitab Ithâf al-Zakî by al-Shaikh Ibrâhîm al-Kûrânî, in Studia Islamika, vol. 9 no. 1, 2002, pp. 139-158.
- “Pria-Wanita sebagai Korespondensi Kosmis: Perempuan dalam Literatur Tasawwuf” (“Male-Female as Cosmic Correspondence: Women in Tasawwuf Perspective”) (co-writer with Kautsar Azhari Noer) in Ali Munhanif (ed.) Perempuan dalam Literatur Islam Klasik, Jakarta: PT Gramedia Pustaka Utama, 2002, pp. 209-258.
- “Tradisi Intelektual Islam Melayu-Indonesia: Adaptasi dan Pembaharuan” (The Islamic Intellectual Tradition in the Malay-Indonesia World: Adaptation and Reformism), dalam Studia Islamika, Vol. 8. no. 3, 2001, pp. 207-222.
- “Transformasi Sistem Pendidikan Islam: Pergulatan Identitas Muslim Melayu Patani” (The Tranformation of Islamic Education System: A Struggle of Identity of Malay Muslim in Patani), in Studia Islamika, Vol. 8. no. 1, 2001, pp. 181-203.
- “Demokrasi dalam Tradisi Politik Islam Melayu: Mencari Hitam dalam Gelap” (“Democracy in the Tradition of Malay Islamic Politics), in Jawa Pos, November 18, 2001.
- “Abdurrauf Singkel: Ulama Santun dari Serambi Mekkah” (“Abdurrauf Singkel: A Wise Ulama from Mecca Veranda”) in J. B. Kristanto (ed.) Seribu Tahun Nusantara, Jakarta: PT Kompas Media Nusantara, 2000, pp. 457-469.
- “Dunia di Balik Tulisan Jawi: Akulturasi Budaya Melayu dan Islam” (The World behind Jawi Script: Aculturation between Malay and Islam”), in Al-Turas, no. 11, 2000.
- “Penelitian Naskah-naskah Arab: Mengejar Ketinggalan” (Studying on Arabic Manuscripts: A Race) in Al-Turas, no. 08, 1999.
- “Respon Abdurrauf Singkel Terhadap Kontroversi Doktrin Wujudiyah: Kasus di Aceh Abad 17” (al-Sinkili’s Response on Controversy of the Wujudiyyah Doctrine in Aceh in the 17th Century), in Mimbar Budaya, 15, 1999.
C) Published and Unpublished Contribution of Academic Conferences
- "Further Research on Ithaf al-Dhaki: A Philological and Codicological Perspective", paper presented at the Deutscher Orientalistentag in Freiburg, Germany, 26 September 2007.
- "The Cultural Emergency Relief Action:The Rebuilding Manuscript Library in Dayah Tanoh Abee, Aceh", paper presented at the International Conference on "Culture as A Basic Need", organized by CER Prince Claus Fund in Den Haag, September 26, 2006.
- "The Aceh Manuscripts and the Sanad of the Moslem Intellectuals:From Haramayn to Bilād Jāwah", paper presented at the International Workshop in Tokyo University of Foreign Studies, October 02, 2005.
- “Jawi Script as Identity Marker: An Indonesian Experience”, paper presented at the International Workshop on “Script as Identity Marker in Southeast Asia”, hold by KITLV, LIPI, and IIAS; Jakarta, 29 Nop-1 Dec 2004.
- “Naskah Banten dan Tradisi Intelektual Islam Indonesia” (“Banten Manuscripts and the Indonesian Islamic Intellectual Tradition”), paper presented at a conference on History and Civilization of Banten, hold by State Islamic Institute (STAIN) of Serang, 2 July, 2004.
- “Penulis dan Penerjemah Ulama Palembang: Menghubungkan Dua Dunia” (“The Prolific Translator Ulemas from Palembang”), paper presented at the Seminar on “History of Translation in Indonesia and Malaysia”, Project of Association Archipel, Paris 1-5 April 2002.
- “Penelitian naskah dan Rekonstruksi Islam Lokal” (Manuscripts and Reconstruction of Local Islam), paper presented at the International Symposium V MANASSA, Padang, West Sumatra, 28-31 July 2001.
- “Melacak Pola Pemikiran Tasawuf di Indonesia Melalui Naskah Nusantara: Studi Kasus Kitab Tanbîh al-Mâshî” (Tracing the Typology of Tasawuf Thought in Indonesia through Archipelago’s Manuscripts: A Case Study on Tanbih al-Mashi”), paper presented at the International Symposium II MANASSA, UI Depok, 28 November 1998.
The Following Above-mentioned papers have evolved from my Doctoral thesis:
B) 5