Discovery of Biomarkers for Hexachlorobenzene Toxicity Using Population Based Methods on Gene Expression Data. - Cem Meydan; Alper Küçükural; Deniz Yörükoglu; Osman Ugur Sezerman (PRIB, 2008)

An entropy based heuristic model for predicting functional sub-type divisions of protein families. - Deniz Yörükoglu; Yasin Bakis; Osman Ugur Sezerman (GECCO (Companion), 2009)

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. - Fereydoun Hormozdiari; Iman Hajirasouliha; Phuong Dao; Faraz Hach; Deniz Yörükoglu; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2010)

Dissect: detection and characterization of novel structural alterations in transcribed sequences. - Deniz Yörükoglu; Faraz Hach; Lucas Swanson; Colin C. Collins; Inanç Birol; Süleyman Cenk Sahinalp (Bioinform., 2012)

Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. - Yun William Yu; Deniz Yörükoglu; Bonnie Berger (RECOMB, 2014)

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. - Emily Berger; Deniz Yörükoglu; Jian Peng 001; Bonnie Berger (PLoS Comput. Biol., 2014)

HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. - Emily Berger; Deniz Yörükoglu; Bonnie Berger (RECOMB, 2015)

Topological Signatures for Population Admixture. - Laxmi Parida; Filippo Utro; Deniz Yörükoglu; Anna Paola Carrieri; David Kuhn; Saugata Basu (RECOMB, 2015)

Fast genotyping of known SNPs through approximate k-mer matching. - Ariya Shajii; Deniz Yörükoglu; Yun William Yu; Bonnie Berger (Bioinform., 2016)

Scalable methods for storage, processing and analysis of sequencing datasets. - Deniz Yörükoglu (2017)