Gökberk Alagöz

A South American lungfish against a black background, with text: This odd fish has 30 times as much DNA as humans—a new record for animals.

A species of lungfish found in South America has claimed the title of the animal with the biggest genome sequenced so far.

Learn more on #WorldAnimalDay: https://scim.ag/46OMl6v

Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information Abstract. Reference sequences are essential for reproducible genetic analyses but are often chosen without regard to evolutionary relevance within the anal

Köksal et al. introduce the Y-chromosomal ancestral-like reference sequence to improve the detection of evolutionarily informative variants on the Y chromosome, and introduce the tool polaryzer to annotate variants in Y chromosome data

🔗 doi.org/10.1093/molbev/msaf222

#evobio #molbio

Jane Goodall, the first primatologist and champion of chimpanzees, we will miss you and the tireless work you have begun, to protect critically endangered chimpanzees and their habitat into the future.

New @maxplanck.de study: We looked for left-right differences of gene expression and cell-type abundances in the brains of MICE 🐭using Xenium @10xgenomics.bsky.social. Possible clues to how functional brain asymmetry is supported !! www.biorxiv.org/content/10.1... Short thread below ⬇️

Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates Specialized cell types and links to psychiatric disorders are revealed by genetic mapping of primate amygdala neurons.

A spatially resolved transcriptomic atlas of the primate amygdala (human, macaque, and baboon) now out in Science Advances (www.science.org/doi/10.1126/...). The amygdala contains 32 types of neurons with many neuron types specific to particular subdivisions.

Lots of updates from the preprint!

Really proud of huge collaborative efforts from several teams in Translational Neuroscience Division @lieberinstitute.bsky.social w/ labs of @stephaniehicks.bsky.social and @alexisbattle.bsky.social to provide this resource on cell types and spatial organization in nucleus accumbens of human 🧠

MBE | A General Principle of Neuronal Evolution Reveals a Human-Accelerated Neuron Type Potentially Underlying the High Prevalence of Autism in Humans

@astarr2.bsky.social & Fraser used single-cell RNAseq to determine if abundant cell-types have more conserved gene expression patterns in primates; their findings also argue for a link between the evolution of human cognition and autism.

🔗 doi.org/10.1093/molbev/msaf189

#evobio #molbio #autism

A common cross-species atlas of cortical gray matter https://www.biorxiv.org/content/10.1101/2025.09.08.675002v1

Human-specific features of the cerebellum and ZP2-regulated synapse development Understanding the unique features of the human brain compared to non-human primates has long intrigued humankind. The cerebellum refines motor coordination and cognitive functions, contributing to the...

Great new preprint by @suelkeekim.bsky.social N. Sestan and collaborators, probing Human-specific features of the cerebellum by highlighting shared and divergent features across primates — key difference lies in synapse development 🧪🧠🧬
www.biorxiv.org/content/10.1...

Excited for the upcoming TIBBE online talks &discussions with the amazing @matosches.bsky.social & @pkatz.bsky.social around
How can we define homologous cell types across vertebrates and invertebrates?
Next Wednesday, September 10, 2pm UTC, 4pm Paris 🧠🦎🐣🐭🌊 Join us www.crowdcast.io/c/evolution-...

Complex genetic variation in nearly complete human genomes - Nature Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

Telomere-to-telomere DNA sequencing is set to transform the field of human genetics in coming years. For a flavour of what's coming, see this exciting work on nearly complete genomes of 65 individuals from diverse populations, out today in @nature.com by @glennislogsdon.bsky.social & colleagues. 👇🧬🧪

People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?"

(For the record, no one has ever asked me this, but it is a really good question!)

I think we know where they are.

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

dx.plos.org/10.1371/jour...

Decoding DNA sequence-driven evolution of the human brain epigenome at cellular resolution - Nature Communications How genetic changes prior to the human-chimpanzee split contributed to human brain evolution remains unknown. Here, the authors address this by identifying open-chromatin regions divergent in various ...

Revealing ancestral evolutionary patterns of the human brain at cell-type resolution, through comparative genomic analysis of open-chromatin regions across apes, old world monkeys & new world monkeys. New integrative paper from @konopkalab.bsky.social in @natcomms.nature.com. 🧠🧬🧪

A mouse brain stereotaxic topographic atlas with isotropic 1-μm resolution - Nature A stereotaxic atlas of the whole mouse brain, based on a Nissl-stained cytoarchitecture dataset with isotropic 1-μm resolution, achieved through continuous micro-optical sectioning tomography, promises to be a versatile brainsmatics tool for studying the whole brain at single-cell level.

Nature research paper: A mouse brain stereotaxic topographic atlas with isotropic 1-μm resolution

https://go.nature.com/4knEz8q

🧬In Neolithic Çatalhöyük, family was built on social relations rather than blood ties.
Genetic analysis shows that over time, co-residents were no longer genetic relatives. Female subadults were buried with 5x more grave goods.
🔍A surprising story of Neolithic social life.

A new theme issue in #PhilTransB looks at how and why animal minds have evolved to be so different from one another, framing animal #cognition as a diverse set of solutions to life’s many challenges buff.ly/csMZa3R

Out-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the Aegean West Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. In this work, we describe the changing genetic and cultural landscapes of early Hol...

Happy to share our new study from my PhD on the spread of farming across Anatolia and into the Aegean and then into Europe. @compevohumang.bsky.social

www.science.org/doi/10.1126/...

👇🏽

Addressing missing context in regulatory variation across primate evolution In primates, loci associated with adaptive trait variation often fall in noncoding regions. Understanding the mechanisms linking these regulatory vari…

Check out our new review about addressing missing context in regulatory variation across primate evolution 🧬🐒 www.sciencedirect.com/science/arti...

Methods and applications for single-cell and spatial multi-omics Nature Reviews Genetics - In this Review, the authors discuss the latest advances in profiling multiple molecular modalities from single cells, including genomic, transcriptomic, epigenomic and...

Methods and applications for single-cell and spatial multi-omics go.nature.com/3GkzmzZ #Review by Katy Vandereyken, Alejandro Sifrim, @bernthie.bsky.social & Thierry Voet
Free to read here: rdcu.be/c6JjL

Our Primate Past Our Primate Past is a video interview series featuring leading experts in primatology, paleoanthropology, evolutionary biology, and conservation. Through accessible, time-stamped interviews, world-ren...

🎥 Just launched: Our Primate Past — a new YouTube channel featuring interviews with leading experts in primatology and biological anthropology. The first 3 interviews are uploaded, with new videos to be added every few days. Subscribe to stay updated!

I’ve been studying gene regulation in primates for over 20 years, and using RNA-seq since 2008 to compare expression across species. We thought we were being careful. We used curated orthologous exons to minimize alignment bias and focused on biologically meaningful comparisons.

We were wrong.

We are delighted to share our new preprint “The evolution of gene regulatory programs controlling gonadal development in primates” www.biorxiv.org/content/10.1...

This is the first ever confirmed skull of a Denisovan Finally, we can put a face on a Denisovan.

'Scientists discovered a new kind of human with its pinkie bone. Now we have a skull' www.nationalgeographic.com/history/arti...

Major expansion in the human niche preceded out of Africa dispersal - Nature Analysis of species distribution models in a pan-African database comprising chronometrically dated archaeological sites over the past 120,000 years shows major expansion in the human niche from 70 ka...

1/5 Why do all non-Africans descended from a group that left Africa 50k ago? In @nature.com we model 120k years of human niche dynamics. From 70ka, a big expansion of the human niche in Africa likely equipped later OOA dispersals with a unique ecological flexibilty.
www.nature.com/articles/s41...

Great internship opportunities in our department if you are interested in neurodevelopment and brain organoids! 👇

M.Sc. internship: Using Human Induced Pluripotent Stem Cells and Neural Models to Explore the Genetics of Human Speech and Language www.mpi.nl/career-educa...

New posting for a Research Assistant in our division. Ideal position for recent graduate looking for experience in molecular neurobiology and microscopy. Team-oriented environment working across projects generating spatial transcriptomics data in human 🧠 tissue and human-derived neuronal cell models

#SpotSweeper is now published!

Check our journal club session summary of the pre-print version by @lahuuki.bsky.social

The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data!

youtu.be/f72XcXmtkfw?...

👇👇🧠🧬My new lab is hiring an imaging-genetics Postdoc, exploring how genetic factors (e.g., genomics, transcriptomics) and environmental factors (e.g., early life stress) influence brain development, psychopathology, and neurodevelopmental disorders (e.g., autism). I am happy to take any questions.