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pygenstrat: a Python package for EIGENSTRAT data processing
Koptekin D.
Bioinformatics advances · doi:10.1093/bioadv/vbag022 · PMC12895063
Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data
Koptekin D, Yapar E, Vural KB, Sağlıcan E, Altınışık NE, Malaspinas AS, Alkan C, Somel M.
Genome biology · doi:10.1186/s13059-024-03462-w · PMC11721506
Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise
Çokoğlu SS, Koptekin D, Fidan FR, Somel M.
Evolutionary applications · doi:10.1111/eva.13743 · PMC11217591
The time and place of origin of South Caucasian languages: insights into past human societies, ecosystems and human population genetics
Gavashelishvili A, Chukhua M, Sakhltkhutsishvili K, Koptekin D, Somel M.
Scientific reports · doi:10.1038/s41598-023-45500-w · PMC10689496
Investigating DNA methylation changes associated with food production using paleogenomes
Çokoğlu SS, Koptekin D, Fidan FR, Somel M.
Preprint (PPR753486) · doi:10.1101/2023.11.04.565610
A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition
Altınışık NE, Kazancı DD, Aydoğan A, Gemici HC, Erdal ÖD, Sarıaltun S, Vural KB, Koptekin D, Gürün K, Sağlıcan E, Fernandes D, Çakan G, Koruyucu MM, Lagerhol…
Science advances · doi:10.1126/sciadv.abo3609 · PMC9635823
MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes
Atağ G, Vural KB, Kaptan D, Özkan M, Koptekin D, Sağlıcan E, Doğramacı S, Köz M, Yılmaz A, Söylev A, Togan İ, Somel M, Özer F.
Open research Europe · doi:10.12688/openreseurope.14936.3 · PMC10565424
MTaxi : A comparative tool for taxon identification of ultra low coverage ancient genomes
Atağ G, Vural KB, Kaptan D, Özkan M, Koptekin D, Sağlıcan E, Doğramacı S, Köz M, Yılmaz A, Söylev A, Togan İ, Somel M, Özer F.
Preprint (PPR503109) · doi:10.1101/2022.06.06.491147
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data
Söylev A, Çokoglu SS, Koptekin D, Alkan C, Somel M.
PLoS computational biology · doi:10.1371/journal.pcbi.1010788 · PMC9873172
Human population dynamics and <i>Yersinia pestis</i> in ancient northeast Asia
Kılınç GM, Kashuba N, Koptekin D, Bergfeldt N, Dönertaş HM, Rodríguez-Varela R, Shergin D, Ivanov G, Kichigin D, Pestereva K, Volkov D, Mandryka P, Kharinski…
Science advances · doi:10.1126/sciadv.abc4587 · PMC7787494