MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. - Amira Djebbari; Svetlana Karamycheva; Eleanor Howe; John Quackenbush (Bioinform., 2005)

Seeded Bayesian Networks: Constructing genetic networks from microarray data. - Amira Djebbari; John Quackenbush (BMC Syst. Biol., 2008)

An ensemble machine learning approach to predict survival in breast cancer. - Amira Djebbari; Ziying Liu; Sieu Phan; Fazel Famili (Int. J. Comput. Biol. Drug Des., 2008)

Refining gene signatures: a Bayesian approach. - Amira Djebbari; Aurélie Labbe (BMC Bioinform., 2009)

AI Methods for Analyzing Microarray Data. - Amira Djebbari; Aedín C. Culhane; Alice Armstrong; John Quackenbush (Encyclopedia of Artificial Intelligence, 2009)

Next-generation, scalable network visualization and analysis. - Amira Djebbari; Igor Jurisica (CASCON, 2011)

NAViGaTOR: Large Scalable and Interactive Navigation and Analysis of Large Graphs. - Amira Djebbari; Muhammad Ali; David Otasek; Max Kotlyar; Kristen Fortney; Serene Wong; Anthony Hrvojic; Igor Jurisica (Internet Math., 2011)

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. - Benjamin Haibe-Kains; Catharina Olsen; Amira Djebbari; Gianluca Bontempi; Mick Correll; Christopher Bouton; John Quackenbush (Nucleic Acids Res., 2012)