1.Ali Masoudi-Nejad, Ali Salehzadeh, Shiva Akbari, Yazdan Asgari. Integration of Metabolic Knowledge for Genome-scale Metabolic Reconstruction. Invited chapter in book "Biological Knowledge Discovery Handbook: Preprocessing, Mining and Post processing of Biological Data ". ISBN: 978-1-1181-3273-9. John Wiley 2014.
2.Ali Masoudi-Nejad, Susumu Goto, Takashi Endo and Minoru Kanehisa. KEGG/EGENES resource for plant bioinformatics in post-sequence era. Invited chapter in book "Plant Bioinformatics”. Humana Press, USA 2007.
3.Bahman Yari, Daryanaz Dargahi, Nima Aghaeepour and Ali Masoudi-Nejad. Support Vector Clustering: From Local Constraint to Global Stability. Invited chapter in book " Foundations of Computational Intelligence Volume 6: Data Mining ". Springer 2009.
4.Saeed Omidi and Ali Masoudi-Nejad. Network Evolution: Theory and Mechanisms. Invited chapter in book "Computational Network Analysis". Springer 2009.