Anatolian Shepherd

New paper: Independent amylase gene duplications

Stefan (Ruhl) and I recently published a comprehensive survey of the amylase gene copy number and salivary enzyme activity among mammalian species eLife. Petar (Pajic) was the driving force for the sample collection and analysis. Briefly, we found that 1. Amylase copy number evolves extremely fast leading to independent (I daresay convergent) bursts among mammals … Continue reading New paper: Independent amylase gene duplications

Anatolian Shepherd

New paper: Structural variants are awesome – And they affect detoxification genes

Our lab has been excited by genomic structural variation because we believe that they underlie a considerable and underappreciated part of the phenotypic variation in primates. It is just that they are challenging to study and come up with straightforward evolutionary stories. Most of the time, what we find is much more complicated than we … Continue reading New paper: Structural variants are awesome – And they affect detoxification genes

Anatolian Shepherd

New paper: Of light, duplications and UV protection

We have helped Cemali Bekpen and the Max Planck Evolutionary Biology Group of Dr. Tautz in resolving a very complicated and variable gene duplication. Even though, some of the trends remain fuzzy, it is now clear that gene duplications of SPATA31 diversified in humans and remain variable. What is more, some of their function has to do … Continue reading New paper: Of light, duplications and UV protection

Anatolian Shepherd

New Paper in PNAS: Primate genome architecture influences structural variation mechanisms and functional consequences

Our efforts to resequence and analyze primate genomes with a focus on genomic structural variation has now been published. Here is the link for the paper and here is the link for the curated datasets. The study, I think, is a major step forward to understand evolution of primate genomes. Now that several papers from Eichler … Continue reading New Paper in PNAS: Primate genome architecture influences structural variation mechanisms and functional consequences

Anatolian Shepherd

New Paper in Journal of Virology: Vif proteins from diverse primate lentiviral lineages use a same binding site in APOBEC3G

This paper describing a nice evolutionary story about interaction between HIV and the host immune system, is mostly the effort of our collaborators in Mount Sinai. You can find the abstract below and here is the link to the article.  APOBEC3G (A3G) is a cytidine deaminase that restricts HIV-1 and other lentiviruses. Most of these … Continue reading New Paper in Journal of Virology: Vif proteins from diverse primate lentiviral lineages use a same binding site in APOBEC3G

Anatolian Shepherd

Bilim kazanında günün kepçesi oldum

Bilim kazanı için İlker ve Aysu ile uzunca bir muhabbet ettik. Tatlı dillerinden ayrılıp da eve dönmem gece yarısı 1'i buldu. Ama galiba ayırdığımız 5 saate değdi. İnsanı insan yapan nedir diye sorduk - Dinlemek için basın buraya. Bu arada iyice yaşlandığımı tasdikleyecek ama, FatBoy Slim'in şu klibini hatırlamadım değil... 🙂 https://www.youtube.com/watch?v=ub747pprmJ8  

Anatolian Shepherd

Paper in PNAS – Regulatory element copy number differences shape primate expression profiles

I am the co-first author of a recent paper with Rebecca (Iskow), discussing the impact of copy number differences between primate species to expression regulation. I do think that copy number differences of regulatory genes (e.g., transcription factors) and other regulatory regions (non-coding RNAs, enhancer, etc.) may be key to understand phenotypic variation among primates. … Continue reading Paper in PNAS – Regulatory element copy number differences shape primate expression profiles