FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. - Stefan A. Koestler; Begum Alaybeyoglu; Christian X. Weichenberger; Arzu Celik (F1000Research, 2015)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

Assessment of Drug-Induced Toxicity Biomarkers in the Brain Microphysiological System (MPS) Using Targeted and Untargeted Molecular Profiling. - Sara G. Mina; Begum Alaybeyoglu; William L. Murphy; James A. Thomson; Cynthia L. Stokes; Murat Cirit (Frontiers Big Data, 2019)