Melike Dönertaş

maybe now i can finally learn german - just built a telegram bot that pings me every 30min with random prompts to make me speak, tracks my personal errors & resurfaces them until i get it right 3x, has conversation memory, 16k SRS cards & voice support. Hallo, Welt 🇩🇪 👋

It's a super nice snapshot of where the field stands and where we think it's heading. Thanks to the Nature Aging editors for bringing our perspectives together!

Almost everyone agreed we need better biomarkers and a shift toward prevention rather than treating diseases one by one. Several of us also emphasised the need for longitudinal cohorts and warned against overpromising.

Reading through everyone's responses, a few recurring themes emerge: epigenetic clocks and multi-omics have transformed how we measure aging. But translation from model organisms to humans remains hard, and effect sizes that look dramatic in mice often don't hold up in people.

Nature Aging @nataging.nature.com turns 5 and asked ~50 researchers to reflect on the field. I am honored to contribute alongside colleagues whose work has shaped how I think about #aging science.

Past, present and future perspectives on the science of aging
www.nature.com/articles/s43...

Our work led by wonderful Jing Lu and contributed by İsmail Güderer, Tayyaba Alvi, and Mark Olenik; funded by @carlzeissstiftung.bsky.social

Feedback is most welcome! 🙌

@leibnizfli.bsky.social

Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity Cross-sectional transcriptome analysis of mice, covering the whole lifespan, reveals that inter-tissue divergence during development is accompanied by a weaker but widespread convergence during ageing...

I was expecting our cell-identity loss / divergence-convergence story (elifesciences.org/articles/68048) to be related to cellular senescence. After seeing the entropy results from SA-β-gal+ cells, not so sure anymore... will explore more!!

With all the caveats like the original data being regeneration/injury-associated senescence, SA-β-gal+ being only one aspect, excited to see what we have discovered in the re-analysis of this paper. beyond "senescence is extremely complex and heterogeneous",

The classifier detects age-associated senescence increase in most cell types. Senescent cells show reduced transcriptional entropy consistent across most cell types, except MSCs, which showed higher entropy in senescence and were enriched in young ages.

ML features seem to trace senescence progression along pseudotime. IGF signaling emerges as a directional axis: senescent FAPs & myeloid cells → satellite cells. Taking predicted SA-β-gal+ status as senescence, we applied the classifier to Tabula Muris Senis limb tissue 👇

p16, p21, Tgfb1 barely distinguish SA-β-gal+ vs - cells at single-cell level (AUC ~0.5; coin flip territory). Even curated gene sets don't agree and show cell-type dependency. ML classifiers achieve superior performance in the held-out biological replicate.

Integrative transcriptomic identification of cellular senescence beyond marker limitations Cellular senescence lacks a universal marker and varies across cell types, tissues, and stressors, complicating identification. Using SPiDER SA-β-gal labeled single-cell RNA-seq from regenerating mous...

Super happy to share the first research paper from our group! 🎉

We asked if the transcriptome helps us predict SA-β-gal status using Moiseeva mouse senescence atlas data 🐭

Spoiler: single gene markers don't perform well, ML can make a difference 👇

doi.org/10.64898/202...

Happy to share that this is now out in Microbial Ecology 🥳 Huge thanks to the whole team, especially @sultanova.bsky.social 🙌

link.springer.com/article/10.1...

@leibnizfli.bsky.social @uniofeastanglia.bsky.social

Join EMBL's Interdisciplinary Postdoc Programme!
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.

In particular: AI&Theory, use mathem. models, physics principles and AI

www.embl.org/about/info/p...

Still, since the world seems to have kept turning without my replies, I’m adopting a slower, more intentional approach to email & communication from now on. There’s a lesson in everything, if we pay attention to it. 😅

I hereby declare email bankruptcy.
If you’ve written to me in the past months and haven’t heard back — it’s not you, it’s the inbox. I recently discovered that hundreds of messages had been flagged as spam and never reached me. 👇

(4/4) Late registration + poster submissions remain open until we hit capacity.

👉 Register: amc25.leibniz-fli.de/registration/
👉 Full program: amc25.leibniz-fli.de/speakers-pro...

#Microbiome #Aging #Ageing #SystemsBiology #Metagenomics #Neuroscience #AMC2025 #Jena

(3/4) 🤝 Networking & “Meet the Speaker” sessions
🔭 “Voyager” dome show at the Zeiss-Planetarium Jena
🍴 Conference dinner with integrated networking
🥇 Awards for best poster, talk, and “top connector”
💼 Sponsor interactions + sponsor bingo
👇

(2/4) 🗣️ Keynotes: Karine Clément, Niranjan Nagarajan (online), Gianni Panagiotou
🗣️ Invited talks: Eran Blacher, Reena Debray, Daniel Erny, Christoph Kaleta, Yvonne Nolan, Veronica Witte, Bahtiyar Yilmaz
🗣️ Fantastic selected talks from abstracts
📊 Interactive poster sessions

👇

#AMC2025 is almost here (Oct 28–29, Jena) and we’ve opened a few more seats! If you work on host-microbiome interactions, aging, or age-related diseases, bring a poster and join this amazing crowd!

amc25.leibniz-fli.de/registration/

✨ Highlights 👇 🧵 (1/4)

Come find us if you are interested in applications of computational biology and statistical methods on #aging and #microbiome research!

Looking forward! #ISMBECCB2025 (3/3)

I will then participate in the ISCBSC Symposium, joining a panel discussion on multi-omics, organised by the amazing student group of ISCB.

Tayyaba Alvi and Mark Olenik will be presenting their posters in the Microbiome and Machine Learning COSI tracks. #ISMBECCB2025 (2/3)

We are in Liverpool for the #ISMBECCB2025!

Tayyaba Alvi, Mark Olenik and I will be delivering a tutorial on Mendelian Randomization on the first day of the conference. (1/3)

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/...

👇🏽

📢 REMINDER ‼️ AMC - Abstract submission deadline: June 30, 2025

The Aging and Microbiome Conference 2025 #AMC2025 will take place from October 28-29, 2025 in #Jena. Join us for the latest developments and exciting discussions on #microbiome & #aging.

📅 amc25.leibniz-fli.de/registration/

📢 Update! The abstract submission deadline for the #AMC2025 Aging and Microbiome Conference has been extended to June 30, 2025!

🔗 amc25.leibniz-fli.de
📌 Jena, Germany
📆 Oct 28-29, 2025

I'm participating the ISMB/ECCB 2025 conference, join me! Register now

I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Who else is going? Register here and don't miss it! invt.io/1bxb8kd9bqu

📢 Update! The abstract submission deadline for the #AMC2025 Aging and Microbiome Conference has been extended to June 30, 2025!

🔗 amc25.leibniz-fli.de
📌 Jena, Germany
📆 Oct 28-29, 2025

A blood-based epigenetic clock for intrinsic capacity predicts mortality and is associated with clinical, immunological and lifestyle factors - Nature Aging Fuentealba and colleagues build and validate a DNA methylation clock of intrinsic capacity (IC) to bridge resource-intensive clinical assessments of IC with molecular readouts of aging, highlighting…

A blood-based epigenetic clock for intrinsic capacity predicts mortality and is associated with clinical, immunological and lifestyle factors - Nature Aging www.nature.com/articles/s43...

Abstract submission deadline in two days!!