The gene family-free median of three. - Daniel Doerr; Metin Balaban; Pedro Feijão; Cédric Chauve (Algorithms Mol. Biol., 2017)

Simulated Annealing Algorithm for Graph Coloring. - Alper Köse; Berke Aral Sonmez; Metin Balaban (CoRR, 2017)

APPLES: Fast Distance-Based Phylogenetic Placement. - Metin Balaban; Shahab Sarmashghi; Siavash Mirarab (RECOMB, 2019)

Phylogenetic double placement of mixed samples. - Metin Balaban; Siavash Mirarab (Bioinform., 2020)

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. - Shahab Sarmashghi; Metin Balaban; Eleonora Rachtman; Behrouz Touri; Siavash Mirarab; Vineet Bafna (PLoS Comput. Biol., 2021)

Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements. - Navid Bin Hasan; Avijit Biswas; Metin Balaban; Siavash Mirarab; Md. Shamsuzzoha Bayzid (RECOMB-CG, 2022)

Distance-aware Algorithms for Scalable Evolutionary and Ecological Analyses - Metin Balaban (2022)

Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. - Cong Ma 008; Metin Balaban; Jingxian Liu; Siqi Chen; Li Ding; Benjamin J. Raphael (RECOMB, 2024)