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

Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data. - Ibrahim Numanagic; Salem Malikic; Victoria M. Pratt; Todd C. Skaar; David A. Flockhart; Süleyman 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)

Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. - Salem Malikic; Katharina Jahn 001; Jack Kuipers; Süleyman Cenk Sahinalp; Niko Beerenwinkel (RECOMB, 2018)

A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression. - Nikolai Karpov; Salem Malikic; Md. Khaledur Rahman; Süleyman Cenk Sahinalp (WABI, 2018)

A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression. - Nikolai Karpov; Salem Malikic; Md. Khaledur Rahman; Süleyman Cenk Sahinalp (Algorithms Mol. Biol., 2019)

Collaborative intra-tumor heterogeneity detection. - Sahand Khakabimamaghani; Salem Malikic; Jeffrey Tang; Dujian Ding; Ryan D. Morin; Leonid Chindelevitch; Martin Ester (Bioinform., 2019)

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. - Erfan Sadeqi Azer; Farid Rashidi Mehrabadi; Salem Malikic; Xuan Cindy Li; Osnat Bartok; Kevin Litchfield; Ronen Levy; Yardena Samuels; Alejandro A. Schäffer; E. Michael Gertz; Chi-Ping Day; Eva Pérez-Guijarro; et al. (Bioinform., 2020)

Identification of conserved evolutionary trajectories in tumors. - Ermin Hodzic; Raunak Shrestha; Salem Malikic; Colin C. Collins; Kevin Litchfield; Samra Turajlic; Süleyman Cenk Sahinalp (Bioinform., 2020)

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)

Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices. - Salem Malikic; Farid Rashidi Mehrabadi; Erfan Sadeqi Azer; Mohammad Haghir Ebrahim-Abadi; Süleyman Cenk Sahinalp (J. Comput. Biol., 2021)

Vision for Bosnia and Herzegovina in Artificial Intelligence Age: Global Trends, Potential Opportunities, Selected Use-cases and Realistic Goals. - Zlatan Ajanovic; Emina Alickovic; Aida Brankovic; Sead Delalic; Eldar Kurtic; Salem Malikic; Adnan Mehonic; Hamza Merzic; Kenan Sehic; Bahrudin Trbalic (CoRR, 2022)

Fast intratumor heterogeneity inference from single-cell sequencing data. - Can Kizilkale; Farid Rashidi Mehrabadi; Erfan Sadeqi Azer; Eva Pérez-Guijarro; Kerrie Marie; Maxwell P. Lee; Chi-Ping Day; Glenn Merlino; Funda Ergün; Aydin Buluç; Süleyman Cenk Sahinalp; Salem Malikic (Nat. Comput. Sci., 2022)

Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History. - Chih Hao Wu; Suraj Joshi; Welles Robinson; Paul F. Robbins; Russell Schwartz; Süleyman Cenk Sahinalp; Salem Malikic (RECOMB, 2024)

A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data. - Farid Rashidi Mehrabadi; Erfan Sadeqi Azer; John D. Bridgers; Eva Pérez-Guijarro; Kerrie Marie; Howard H. Yang; Charli Gruen; Chih Hao Wu; Welles Robinson; Huaitian Liu; Can Kizilkale; Michael C. Kelly; et al. (RECOMB, 2025)

Improved Algorithms for Bi-Partition Function Computation. - John D. Bridgers; Jan Hoinka; S. Cenk Sahinalp; Salem Malikic; Teresa M. Przytycka; Funda Ergün (WABI, 2025)