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Zoé Pochon

@zoepochon.bsky.social
836 followers 522 following 10 posts

PhD student in scientific archeology at #CPGSthlm. Ancient pathogens discovery, authentication and genetics. Coauthor of #aMeta pipeline. Studied in 🇨🇭🇺🇲🇸🇪

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Reposted by Zoé Pochon
SPAAM @spaam-community.bsky.social · 21/09/2026
A #methods paper for #MetagenomicsMonday! 🦠🧬💻 This new primer and #protocol provides practical guidance for assembling and validating #ancient #microbial #genomes. It introduces dedicated #aDNA support in #nf-core/mag. journals.plos.org/ploscompbiol... #SPAAM #Metagenomics #Bioinformatics
journals.plos.org
De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag
Author summary Advancements in genomic sequencing analyses are increasingly allowing researchers to reconstruct the genomes of microbial ‘dark matter’—those microbial species that are difficult to…
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Meriam Guellil PhD @meriamguellil.bsky.social · 15/09/2026
I am opening a PhD position at the University of Vienna to work with me on ancient pathogen aDNA 🦠🧬 Please help spread the word to any relevant candidates or contact me if you are interested! Join us here in Vienna!
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marcelkeller.bsky.social @marcelkeller.bsky.social · 11/09/2026
Our paper on the second plague pandemic is now finally published: www.pnas.org/doi/10.1073/... We present 11 new Y. pestis genomes from around Europe and introduce a new approach to refine the dating of ancient genomes that helped us to contextualize 75 plague genomes of the Second Pandemic.
Schematic workflow showing the Phylogenetically Informed Radiocarbon Modeling
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Kevin Daly @gingerhowley.bsky.social · 07/09/2026
I'm hiring a postdoc as part of my ERC project - the deadline is tomorrow noon GMT, apologies for the little notice If you have interest but can't make the deadline, please DM/email me immediately and i can try extend the deadline a few days
universityvacancies.com
University & College Vacancies
Connecting talent with opportunity in higher education
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Kevin Daly @gingerhowley.bsky.social · 02/09/2026
Our paper on ancient sheeppox virus genomes, including many found from parchment samples, is now published af Science Advances. Congrats to all our co-authors and particularly first author Louis. #aDNA share.google/JqVOTB2lvxcO...
share.google
Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes
Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded sinc...
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Amanda V. Meuser @amanda-meuser.bsky.social · 15/08/2026
I attended two conferences this summer, the first ever #ICP2026 in Stockholm 🇸🇪 and #SMBE2026 in Copenhagen! 🇩🇰 Both were an amazing opportunity to meet other researchers and professionals in my field and share my doctoral research! 🧬🌟
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Alex Hübner @alexhbnr.bsky.social · 13/08/2026
🚨 Paper alert: if you are working on #metagenomics, particularly from #ancientDNA, and want to get into de novo #assembly, check out our latest work: 📄 De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag (journals.plos.org/ploscompbiol...) (1/4)
journals.plos.org
De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag
Author summary Advancements in genomic sequencing analyses are increasingly allowing researchers to reconstruct the genomes of microbial ‘dark matter’—those microbial species that are difficult to iso...
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Reposted by Zoé Pochon
J. Camilo Chacón-Duque @jcchacond.bsky.social · 05/08/2026
🧵 New preprint: Have you ever tried to perform molecular clock dating of ancient mitogenomes using BEAST? Have you struggled using manual tools to create your input files, run your analyses and extract your results? We hope our pipeline provides a solution to this: www.biorxiv.org/content/10.6...
biorxiv.org
MitoDate: a Nextflow pipeline for molecular clock dating and phylogenetic inference using ancient mitogenomes
Summary Ancient DNA studies are increasingly targeting samples that are beyond the limit of radiocarbon dating (>50 thousand years old) and are often difficult or impossible to date using other geochr...
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Torsten Günther @trstngnthr.bsky.social · 31/07/2026
One week left to apply!
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Centre for Palaeogenetics @cpgsthlm.bsky.social · 02/07/2026
Our #CPGSthlm delegation had great presentations and posters at #SMBE2026! 👏👏👏 ♥️🧬🦣🫎🦠🦋🐝🐀💀🦬🧪
CPG researchers at SMBE2026
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Anne Stone @acstone.bsky.social · 02/07/2026
Thanks to my terrific students and colleagues who nominated me for the #SMBE2026 lifetime achievement award. You make science fun!
Miriam Bravo, Maria Nieves-Colon, Genevieve Houseman, me, Tanvi Honap and Joanna Malukiewicz Award picture with SMBE president Juliette de Meaux
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Torsten Günther @trstngnthr.bsky.social · 30/06/2026
Don't miss the lab's posters at #SMBE2026 today: Marianne Dehasque @maridehasque.bsky.social will present a pangenome graph pipeline for ancient DNA 🧬 (Arkaden 7, 297) Germán Hernández Alonso @germanha.bsky.social will present about the history of Central Asian sheep 🐑 (Arkaden 8, 267)
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Adria LeBoeuf @adriatica.bsky.social · 28/06/2026
Wise words about the ethics of being a scientist these days from @meauxjuliette.bsky.social #SMBE2026: “Don’t serve the system, serve the community.” Also, it is ok (and healthy!) to feel like an imposter; rather, finding others smarter is a blessing!
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schlebuschgroup.bsky.social @schlebuschgroup.bsky.social · 29/06/2026
The Schlebusch Group had a great time at #ICP2026 in Stockholm! Several group members attended, and Maja Vukovikj presented her poster, Ancient Pathogen Genomics in Africa. Great work, Maja! 👏 #AncientDNA #Palaeogenomics
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NBIS @nbis.se · 29/06/2026
NBIS is at #SMBE2026 🧬 Come talk to us and have a look at our poster in the Arlequin room!
Verena and André posing by our NBIS poster.
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Centre for Palaeogenetics @cpgsthlm.bsky.social · 29/06/2026
After #ICP2026, #CPGsthlm has officially landed in Copenhagen for #SMBE2026! 🇩🇰🧬 We are bringing a delegation from Stockholm to share our latest research. Here is a breakdown of every CPG presentation happening this week 🧵👇 Don't miss out!
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Centre for Palaeogenetics @cpgsthlm.bsky.social · 29/06/2026
@zoepochon.bsky.social will present her talk "Parvovirus B19 from early modern warships suggests genotype 2 continuity in Europe, bridging a millennium-long gap" tomorrow at 15:50 in the session "L06 From Ancient Pathogen Genomics to Palaeoepidemiology".
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Lucy van Dorp @lucyvandorp.bsky.social · 29/06/2026
@ugiatucl.bsky.social microbial genomics are at #SMBE2026! S14 - Marina Escalera-Zamudio - mapping fitness landscape of SARS-CoV-2 🧬 S13 - me/Pooja Swali - tracing 2 centuries of evolution in BFDV 🦜 Open 10a - Cedric Tan - Ranavirus evolution across hosts 🐸
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ICP2026 Stockholm @palaeogenomics.bsky.social · 26/06/2026
#ICP2026 Stockholm is over, but ICP will return... in 2028! #ICP2028 will be hosted by Trinity College Dublin 🎉☘️🇮🇪
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Marco Capodiferro @marcocapo.bsky.social · 26/06/2026
We're still absorbing tons of inspiring notes from #ICP2026, and already planning the next one. #ICP2028 is coming to Dublin 🍀 and we can't wait to welcome the ancient DNA 🧬 community in Ireland. We'll do our best to build on the outstanding work of the Stockholm committee. More info coming soon!
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Markella Moraitou @markella-morait.bsky.social · 21/06/2026
My main PhD paper is out on bioRxiv! 🎉 The microbiomes of wild animals, besides the gut, remain unexplored. To help remedy this, we used museum-preserved dental calculus to characterise the oral microbiome of 34 diverse mammal species. 💀🦠🦷 Read here: www.biorxiv.org/content/10.6...
Phylum-level composition of the oral microbiome across 34 mammal species, representing 8 taxonomic orders, 4 dietary categories, and including 3 marine species.
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Centre for Palaeogenetics @cpgsthlm.bsky.social · 22/05/2026
#CPGStlhm 's PhD candidate @officialernst.bsky.social is currently defending his thesis on using metagenomics sedimentary DNA to reconstruct past ecosystems 🧬🏞️ in Sweden with Laura Epp as opponent. Good luck, Ernst!
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SPAAM @spaam-community.bsky.social · 18/05/2026
Ancient DNA reveals a wandering #bear. 🐻🧬 A 9,600-year-old genome from Swedish lake #sediments shows a southern brown bear migrating north during #post-glacial recolonization. www.pnas.org/doi/10.1073/... #MetagenomicsMonday #SPAAM #aDNA #sedaDNA #biodiversity
pnas.org
Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia | PNAS
After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two direc...
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Zoé Pochon @zoepochon.bsky.social · 08/05/2026
Very promising pipeline for eucaryotic discovery in sedaDNA! 🐻 🫐 🌿 🧬
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ICP2026 Stockholm @palaeogenomics.bsky.social · 02/05/2026
Only ONE WEEK left to register for #ICP2026sthlm 👀 Deadline: 8th May Join us for an amazing week full of talks and networking on all things ancient DNA! Check the FULL conference program 👉 icp2026.palaeogenomics.org/wp-content/u... Register here 👉 icp2026.palaeogenomics.org/registration/
Panoramic view of Stockholm
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Felix M Key @keyfm.bsky.social · 30/04/2026
Can we reconstruct ancient pathogen genomes from animal remains? Can paleopathology help prioritize promising specimens? Our new paper demonstrates this by screening more than 300 specimens from across Eurasia over the past 6,000 years. www.nature.com/articles/s41...
nature.com
Probing the zooarchaeological record across time and space for ancient pathogen DNA - Nature Communications
Authors investigate ancient DNA from animal remains and identify multiple signatures of ancient zoonotic pathogens. They find ancient pathogen genomics from archaeological animal remains may inform zo...
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Youssef Tawfik @yotawfik.bsky.social · 30/04/2026
I’m happy to share the latest paper by our group in Mainz titled: “Demography and life histories across the Roman frontier in Germany 400–700 CE” that was just published in Nature. I’m proud to have been part of this amazing group effort! www.nature.com/articles/s41...
nature.com
Demography and life histories across the Roman frontier in Germany 400–700 ce - Nature
Analysis of 258 ancient genomes from southern Germany reveals a major demographic shift during the late fifth century, yet family structures persisted from Late Roman times, demonstrating cultural con...
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Nikolay Oskolkov @oskolkov.bsky.social · 22/04/2026
I have an open postdoc position in my group. If you're excited about developing machine learning methods for multi-omics data analysis in metabolic diseases, I’d love to hear from you. Please apply here euraxess.ec.europa.eu/jobs/430305
euraxess.ec.europa.eu
PostDoc of Metabolic Research Group
Latvian Institute of Organic Synthesis (LIOS) - the leading drug discovery centre in the Baltic countries is offering One permanent position of PostDoc of Metabolic Research Group.
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Centre for Palaeogenetics @cpgsthlm.bsky.social · 22/04/2026
New paper alert 🚨 A study led by #CPGSthlm researchers found DNA from a bear in 9.6k year old lake sediments. This potentially rewrites the history of brown bears in Scandinavia! 🧬🐻🐾🏔️🧊 Check @officialernst.bsky.social thread 👉 bsky.app/profile/offi... OA article 👉 www.pnas.org/doi/10.1073/...
pnas.org
Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia | PNAS
After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two direc...
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Centre for Palaeogenetics @cpgsthlm.bsky.social · 21/04/2026
We present DNAharvester 🎉🦴🚜🧬 A pipeline to process highly degraded ancient DNA data that integrates metagenomic filtering, competitive mapping, multiple alignment strategies, reference bias evaluation and much more. GitHub: github.com/NBISweden/DN... Preprint: www.biorxiv.org/content/10.6...
DNAharvester's workflow.
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Mikkel Winther Pedersen @mikkelwp.bsky.social · 21/04/2026
Interested in ancient environmental DNA, metagenomics, and bioinformatics? Sign up for our PhD course in Ancient Environmental Genomics at the University of Copenhagen, 20 to 25 Sept 2026. 5 ECTS Sign-up deadline: 1 Aug 2026 Read more and sign up: phdcourses.ku.dk/DetailKursus...
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Patrícia Pečnerová @patriciachrzan.bsky.social · 16/04/2026
Can you believe that until now there were more genomes sequenced for the woolly mammoth than for living African elephants? Today, we bring you the first genomic, continent-scale analyses of 232 high-quality genomes of both species, the savanna and forest elephant. www.nature.com/articles/s41...
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Ernst Johnson @officialernst.bsky.social · 14/04/2026
Very excited to share our study of an ancient environmental genome extracted from lake sediment! It originates from a brown bear that lived around 9,600 years ago close to the last ice-sheet remains in northern Sweden, and has an unexpected mitochondrial haplogroup. 1/7 www.pnas.org/doi/10.1073/...
pnas.org
Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia | PNAS
After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two direc...
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J. Camilo Chacón-Duque @jcchacond.bsky.social · 14/04/2026
Check this thread about our latest paper, written by one of the lead authors, @officialernst.bsky.social. It was such an exciting project!
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ICP2026 Stockholm @palaeogenomics.bsky.social · 07/04/2026
Meet our keynote speakers 💁‍♂️ KATERINA GUSCHANSKI (@kguschan.bsky.social) Katerina is expert in using genomics of museum collections to explore primate evolution, conservation genetics, and the historical impact of environmental change. Conference info & registration 👉 icp2026.palaeogenomics.org
Katja sampling a gorilla skull.ICP2026 flyer
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Love Dalén @lovedalen.bsky.social · 01/04/2026
How did catastrophic black death and myxomatosis outbreaks on an isolated island affect the genomes of humans & rabbits, respectively? And how did the microbes evolve in response to this? PhD position @cpgsthlm.bsky.social with Anders Götherström and me as supervisors! su.varbi.com/en/what:job/...
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ICP2026 Stockholm @palaeogenomics.bsky.social · 31/03/2026
We are looking forward to welcoming you to Stockholm in only 83 days 😍 Our conference will be packed with exciting oral presentations 💁‍♂️, poster sessions 🧾, coffee breaks ☕, and pre-conference workshops 👷‍♀️ Take a look at the preliminary program ⬇️⬇️⬇️
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CesarFortesLima @cesarforteslima.bsky.social · 30/03/2026
"The Cemetery at the Edge of the Islamic World" www.youtube.com/watch?v=OX1u... Evolutionary Insights by Anthropology net Podcast
youtube.com
The Cemetery at the Edge of the Islamic World
YouTube video by Kambiz Kamrani
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Centre for Palaeogenetics @cpgsthlm.bsky.social · 27/03/2026
New paper alert 🚨 Researchers at #CPGStlhm have analyzed ancient genomes from an Islamic cemetery in Ibiza (950–1150 CE) 🏖️ They found a highly diverse community with ancestry from Europe and North Africa! The paper was published in @natcomms.nature.com OA link www.nature.com/articles/s41...
Map of the Mediterranean during the Middle Ages, showing the Islamic areas of influence and Ibiza.Ricardo, lead author of the article, processing one of the samples in the lab.
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Centre for Palaeogenetics @cpgsthlm.bsky.social · 27/03/2026
By investigating the presence of pathogens in the remains, the authors detected one individual carrying Mycobacterium leprae 🦠 (the bacteria responsible for leprosy), providing insight into the health of medieval Ibiza societies.
Maximum-likelihood (ML) phylogeny of Mycobacterium leprae.Microscopy image of Mycobacterium leprae.
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ICP2026 Stockholm @palaeogenomics.bsky.social · 19/03/2026
Meet our keynote speakers 💁‍♂️ LUCY VAN DORP (@ugiatucl.bsky.social) Lucy is a leading expert in ancient microbe research, using ancient DNA to reconstruct the origins, evolution, and spread of major human pathogens throughout history. Conference info & registration 👉 icp2026.palaeogenomics.org
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Javier del Campo @fonamental.bsky.social · 10/03/2026
The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems www.sciencedirect.com/science/arti... #microbiome
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Stockholm University @stockholm-uni.bsky.social · 05/03/2026
An undisturbed seventeenth-century shipwreck is a time capsule offering a chance to encounter people of the past mid-step. For maritime archaeologist Niklas Eriksson the underwater world is an archaeological treasure trove rich in stories of everyday life from centuries ago www.su.se/english/news...
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Carina Schlebusch @cschlebu.bsky.social · 02/03/2026
We have a new preprint! - "Ancient Pathogen Genomics in Africa – Current Evidence and Future Directions" A review of current evidence, challenges, and opportunities for studying past epidemics and host–pathogen evolution using ancient DNA from African contexts. www.preprints.org/manuscript/2...
preprints.org
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Aida Andres @aidaandres.bsky.social · 02/03/2026
Job alert: open position for a Professor or Associate Professor of Computational Genomics in Health and Disease at University College London. Based in the Department of Genetics, Evolution and Environment of UCL, and UGI, and funded by the UCL Health Strategy. www.ucl.ac.uk/work-at-ucl/... 🧪
ucl.ac.uk
UCL – University College London
UCL is consistently ranked as one of the top ten universities in the world (QS World University Rankings 2010-2022) and is No.2 in the UK for research power (Research Excellence Framework 2021).
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Biancamaria Bonucci @bbonucci.bsky.social · 26/02/2026
Really happy to share our new preprint on the co-occurrance of Y.pestis and Erysipelothrix spp. during prehistory. 🔥🔥🔥 In the study, we find the earliest evidence to date of Y.pestis in Southern Europe and 60 new Erysipelothrix genomes spanning 20k years 🦠🐄🚶‍♂️⌛ www.biorxiv.org/content/10.6...
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Aris Katzourakis @ariskatzourakis.bsky.social · 15/02/2026
This is really not a headline I expected to have to read in 2026. www.theguardian.com/society/2026...
theguardian.com
Fast-spreading measles outbreak takes hold among under-10s in north London
UK Health Security Agency urges parents in Enfield to get their children vaccinated as Easter holiday travels approach
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SPAAM @spaam-community.bsky.social · 13/02/2026
🚨 Save the Date! We’re thrilled to announce #SPAAM8 – a gathering of experts in ancient metagenomics research! 🌎 📅 When: June 22nd 2026 📍Where: Stockholm, Sweden 🇸🇪 (and online) Stay tuned for updates and registration details!
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Lucas Anchieri @anchieri.bsky.social · 03/02/2026
Interested in using aDNA time-series datasets to estimate selection? Our study "Assessing Ancient DNA Sampling Strategies for Natural Selection Inference in Humans Using Allele Frequency Time Series Data" is now out in GBE! doi.org/10.1093/gbe/... @genomebiolevol.bsky.social @cegamorim.bsky.social
doi.org
Assessing Ancient DNA Sampling Strategies for Natural Selection Inference in Humans Using Allele Frequency Time Series Data
Abstract. The increased availability of genomic data from ancient humans allows estimating the strength of natural selection at a given locus using time se
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CompEvo & HumanG Labs @compevohumang.bsky.social · 28/01/2026
Great news from our research group! 🎉 We congratulate Mustafa Özkan, Kıvılcım Başak Vural, Ezgi Altınışık, and Duygu Deniz Kazancı, who have received significant support for their projects in recent months! 👏 Details below 👇 #Hacettepe #METU #AncientDNA #aDNA #TUBITAK
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