Mehmet Somel

Seven Millennia of Human Exploitation drove genomic Changes in Iberian Sheep

This study analyzes ancient Iberian sheep genomes to show how human activities shaped their genetic diversity over 7,000 years, including maritime introduction, Steppe ancestry influx, and Roman-era expansion.

DeepKin: Predicting relatedness from low-coverage genomes and paleogenomes with convolutional neural networks

DeepKin predicts relatedness from low-coverage genomes and paleogenomes using CNNs, achieving accuracy >90% with 10K shared SNPs and outperforming READv2.

The mini yet mighty stapes: a comparison of ancient DNA yields among ossicles and the petrous bone

This study compares ancient DNA yields among ossicles and the petrous bone, finding the stapes has higher endogenous DNA preservation than the petrous bone.

Female lineages and changing kinship patterns in Neolithic Catalhöyük

The paper analyzes genetic data from Neolithic Catalhöyük to show changes in kinship patterns and persistent female roles over time.

Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean

This study uses 30 new palaeogenomes to show that Neolithic expansion into Western Anatolia involved both indigenous assimilation and eastern population influx, with cultural diversity decoupled from genetic differences.

Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome data

This paper compares methods to reduce reference bias and postmortem damage in ancient genome data, finding that graph alignment and bamRefine improve accuracy and genotyped loci.

An age-specific burial practice reflected in ancient DNA preservation in Neolithic Catalhöyük

The paper identifies age-specific burial practices at Neolithic Catalhöyük by analyzing ancient DNA preservation differences between subadults and adults.

Ancient DNA analyses of two Early Chalcolithic Individuals from the West Mound

The paper analyzes ancient DNA from two Early Chalcolithic individuals from the West Mound, finding no close genetic kinship and no eastern gene flow signature.

An explanation for the sister repulsion phenomenon in Patterson's f-statistics

The paper explains the sister repulsion phenomenon in Patterson's f-statistics by proposing a demographic model involving gene flow from an external source.

The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus)

The paper presents paleogenomes of three Anatolian equids from the 1st millennium BCE, identifying them as the extinct European wild ass, E. hydruntinus, and revealing genetic relationships and diversity loss.

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations

This study benchmarks four kinship estimation tools for ancient genomes using simulated pedigrees and finds varying accuracy depending on the tool and SNP count.

READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics

READv2 improves ancient DNA relatedness analysis by being faster, more accurate, and easier to use than previous methods.

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

CONGA genotypes copy number variants in ancient genomes and low-coverage data, showing coherent deletion frequencies and purifying selection across 50 ancient human genomes.

Somatic copy number variant load in neurons of healthy controls and Alzheimer's disease patients

The paper examines somatic copy number variant (CNV) frequencies in neurons from Alzheimer's disease patients and healthy controls using low-coverage single-cell whole-genome sequencing, finding slightly higher CNV frequencies in AD patients but no statistically significant differences.

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

This study analyzes ancient genomes from Upper Mesopotamia during the Neolithic Transition, revealing genetic diversity, immigration, and cultural practices such as head-shaping.

MTaxi : A comparative tool for taxon identification of ultra low coverage ancient genomes

MTaxi classifies closely related species from low coverage ancient DNA data using mitochondrial DNA substitutions, achieving 100% accuracy on tested samples.

Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity

The paper analyzes gene expression in multiple tissues across development and ageing in mice, finding that tissues converge in expression patterns with age, associated with loss of tissue identity.

Human inbreeding has decreased in time through the Holocene

This study shows inbreeding frequency decreased over time in ancient Eurasian populations, linked to population growth from agricultural practices.

Gene expression heterogeneity during brain development and aging: temporal changes and functional consequences

This study shows that gene expression heterogeneity increases with aging in the human brain and is linked to lifespan regulation and neuronal functions.

Convergent evolution of primate testis transcriptomes reflects mating strategy

The paper analyzes testis transcriptomes across primates to show convergent evolution linked to mating strategies, finding both tissue composition shifts and cell-autonomous changes.