Ongoing projects:

Archaeogenomic analysis of the Near East
Studying population changes, social structures and human adaptation in the Near East. For more info, see
Includes collaborations Anders Gotherstrom (Stokholm), Mattias Jakobsson (Uppsala), Bayram Yuksel (TUBITAK IGBAM), Marin Pilloud (UNR). We work together with Tepecik-Ciftlik (Erhan Bicakci, Ali Metin Buyukkarakaya), Catalhoyuk (Chris Knusel, Clark Larsen, Scott Haddow, Ian Hodder), Boncuklu (Douglas Baird), and Cemialo (Asli Ozdogan Yasemin Yilmaz) excavation teams.

Primate evolution in the light of transcriptomics
Analyzing comparative genome, transcriptome and histone modification data, we study the developmental and regulatory bases of phenotypic divergence among primates.
Collaborations with Philipp Khaitovich, Haiyang Hu, Rori Rohlfs, Xiling Liu, Ding Ding Han.

Molecular and evolutionary mechanisms underlying transcriptome change during aging
We are using transcriptome data to test evolutionary hypotheses on aging.

Genome evolution and adaptative mechanisms of the Van pearl mullet
The pearl mullet (“inci kefali”) is an excellent example of adaptation to highly alkaline (pH9.8) water. We plan to study its genome evolution, regulation of transcriptome changes while acclimatization to alkaline water, and population genetics.
Collaboration with Can Alkan, Mustafa Sari, Bayram Yuksel (TUBITAK IGBAM).

Human genome evolution and population genetics.
Analysis of mutational biases and signatures of adaptive change using comparative genomics and population genomics data.
Collaborations with Rasmus Nielsen, Peter Ralph, Matt Dean, Emilia Huerta Sanchez.

Neandertal contribution in Anatolia
Studying the relative contribution of Neandertal DNA in the Near/Middle East.
Collaborations with Omer Gokcumen.

Past work and collaborations (since 2010):

Regulatory basis of human neoteny
We studied human neoteny at the brain transcriptome level. We found extended synaptogenesis in the human prefrontal cortex and its regulation through microRNA and transcription factors. The Khaitovich group is continuing to study trans regulators of these human-specific changes.
Work done at the Philipp Khaitovich lab.

Relaxation of evolutionary constraints in humans
Using comparative and population genetics data, we studied processes that have become less essential during human evolution.
Work done at the Rasmus Nielsen lab.

Population genetics in Turkey
Analysis of whole genome sequencing data from individuals across Turkey – Turkiye Genom Projesi.
Collaboration with Cemalettin Bekpen, Can Alkan, Omer Gokcumen, Nesrin Ozoren.

Aging vs chronic stress
Similarities between transcriptome changes during normal aging and under chronic stress.
Collaboration with Jenny Tung & Noah Snyder-Mackler.

The impact of chronic stress on the aging brain
This is a follow-up on our work on sexual heterochrony in prefrontal cortex aging, where we found indication that female cortex might be aging faster than males at the transcriptome level, and that this might be explained by chronic stress exposure.
Collaboration with Eva Dogru, Ayca Ergul.

Effects of caloric restriction in primate brain aging
This follows our work showing that human longevity, relative to chimpanzee, cannot be explained by transcriptome changes that mimic caloric restriction. Collaboration with Fabienne Aujard, Julia Marchal, Philipp Khaitovich, Tulin Yanik.

Cancer genomics and evolution
Understanding the dynamics of multifocal tumor development and mutation accumulation in bladder cancer.
Collaboration with Nathan Lack, Can Alkan.


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