Hapsembler: An Assembler for Highly Polymorphic Genomes. - Nilgun Donmez; Michael Brudno (RECOMB, 2011)

Concepture: A Regular Language Based Framework for Recognizing Gestures with Varying and Repetitive Patterns. - Nilgun Donmez; Karan Singh (SBIM@Expressive, 2012)

Polymorphism and Genome Assembly. - Nilgun Donmez (2012)

SCARPA: scaffolding reads with practical algorithms. - Nilgun Donmez; Michael Brudno (Bioinform., 2013)

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. - Phuong Dao; Ibrahim Numanagic; Yen-Yi Lin; Faraz Hach; Emre Karakoç; Nilgun Donmez; Colin C. Collins; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2014)

Clonality inference in multiple tumor samples using phylogeny. - Salem Malikic; Andrew W. McPherson; Nilgun Donmez; S. Cenk Sahinalp (Bioinform., 2015)

Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data. - Nilgun Donmez; Salem Malikic; Alexander W. Wyatt; Martin E. Gleave; Colin C. Collins; Süleyman Cenk Sahinalp (J. Comput. Biol., 2017)

The evolutionary history of 2,658 cancers. - Moritz Gerstung; Clemency Jolly; Ignaty Leshchiner; Stefan C. Dentro; Santiago Gonzalez; Thomas J. Mitchell; Yulia Rubanova; Pavana Anur; Kaixian Yu; Maxime Tarabichi; Amit G. Deshwar; Jeff Wintersinger; et al. (Nat., 2020)