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Aydogan Lab

@aydoganlab.bsky.social
1.1K followers 365 following 74 posts

Columbia University & HHMI We study principles of biological time control with a focus on the emerging concept of autonomous clocks. See more at: aydoganlab.com

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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Aydogan Lab @aydoganlab.bsky.social · 28/09/2026
Looks like an amazing workshop!!
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 28/09/2026
Are you looking for a postdoc exploring the cell biology of development, defining how cells change shape and move? Do you want to develop a research program & teaching skills preparing you for a position at a college or small University? Our new NIH grant will support those goals 1/n Please share
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Al Jord Lab @aljordlab.bsky.social · 28/09/2026
♻️ Our new review explores how multiciliated cells repurpose the cell cycle for ciliogenesis ♻️ Congrats Gonzalo Ortiz Álvarez & @adelaljord.bsky.social, and many thanks to @aydoganlab.bsky.social ! Read the paper here : link.springer.com/chapter/10.1... @crg.eu @prbb.org @springernature.com
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Development @dev-journal.bsky.social · 27/09/2026
The curious case of the placental genome In this Review, Zoé Ducarne, @agathechaigne.bsky.social and @myanhtruong.bsky.social highlight the placenta, the only mammalian organ that harbors a cancer-like genome while remaining functional and healthy. doi.org/10.1242/dev....
Diagrams of a blastocyst and full-term placenta in human. More details in the paper.
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Aydogan Lab @aydoganlab.bsky.social · 11/09/2026
Just noticing this very cool work from @osman-lab.bsky.social! Highly important for our understanding of how the nucleus could gauge the needs of mitochondria (or vice versa) by coupling a critical nuclear-encoded mitochondrial enzyme to the translation of mitochondrially encoded mRNAs!
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Osman Lab @osman-lab.bsky.social · 29/08/2026
🧬 New preprint from our lab! After years of work, we're excited to share our story: the pyruvate dehydrogenase complex (PDHc) — best known for feeding the TCA cycle — has a second, non-catalytic role supporting mitochondrial DNA gene expression in yeast.
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Aydogan Lab @aydoganlab.bsky.social · 11/09/2026
Did you know that enhancers transcribe?? Wonder why? Check out this very exciting work out from our department colleague and friend @philippebatut.bsky.social!!!
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Teresa Rayon @trayon.bsky.social · 09/09/2026
Our article is on the COVER of this month’s issue of @cp-devcell.bsky.social! Congrats to all the authors for the hard work, especially Shota, Despina and @jamesbriscoe.bsky.social
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Al Jord Lab @aljordlab.bsky.social · 21/08/2026
Transcription stops. RNA splicing takes over 🧬 ✨ Our new preprint uncovers the post-transcriptional RNA splicing landscape powering mammalian oocyte development. Read it here 👇 www.biorxiv.org/content/10.6...
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bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 24/08/2026
Kinetic Control of Nuclear-encoded Mitochondrial mRNA Localization and Local Translation www.biorxiv.org/content/10.64898/20…
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Ákos T Kovács @evolvedbiofilm.bsky.social · 19/08/2026
A bacterial metabolite rewires fungal metabolism, triggering the hyphae-to-yeast transition @currentbiology.bsky.social by Manasa Bharathwaj @mbharathwaj.bsky.social et al from Ana Traven www.cell.com/current-biol...
cell.com
A bacterial metabolite rewires fungal metabolism, triggering the hyphae-to-yeast transition
The hyphae-to-yeast morphological transition promotes dissemination of the pathogen Candida albicans, but the mechanisms underlying this process are poorly defined. By identifying a bacterial metaboli...
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preLights @prelights.bsky.social · 19/08/2026
Cellularization as a mechanism to build cells. #CellBio #DevBio Supported by @girishkalephd.bsky.social, Anne Ruess highlights a #preprint of @margaridaaraujo.bsky.social et al. @hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social #preLight⬇️ prelights.biologists.com/highlights/m...
prelights.biologists.com
Microtubules sustain the fidelity of cellularization in a coenocytic relative of animals - preLights
Cellularization as a mechanism to build cells
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Aydogan Lab @aydoganlab.bsky.social · 15/08/2026
Many congrats Teresa!!! Can’t wait to read in full and think further!
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Teresa Rayon @trayon.bsky.social · 15/08/2026
Our work on the role of the proteasome in developmental tempo is out!!!! 🐭⌛️👤⏳ Six years after identifying an association between protein stability and developmental tempo, we now demonstrate a causal link between protein turnover and developmental tempo through proteasomal degradation
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Reichow Lab @reichowlab.bsky.social · 13/08/2026
Long-timescale simulations reveal multi-ion flux through wide pore gap junction channels -– and an unexpected transition involving loop–NT domain interactions that suggest a dynamic ensemble of micro-states define the “open” channel www.biorxiv.org/content/10.6...
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The Interactive Fly @interactivefly.bsky.social · 12/08/2026
Battistolli, M., Varponi, I., Romoli, O., Sandrelli, F. (2025). The circadian clock gene period regulates the composition and daily bacterial load of the gut microbiome in Drosophila melanogaster. Scientific reports, 15(1):1016 www.nature.com/articles/s41...
nature.com
The circadian clock gene period regulates the composition and daily bacterial load of the gut microbiome in Drosophila melanogaster - Scientific Reports
Scientific Reports - The circadian clock gene period regulates the composition and daily bacterial load of the gut microbiome in Drosophila melanogaster
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Matthew Taliaferro @jmtali.bsky.social · 12/08/2026
Excited to share our newest work! We asked whether RNA molecules need to be in a specific place in the cell to do their job. We found that a single RNA must reach the midbody, the structure that pinches two dividing cells apart, for cell division to finish efficiently. 🧵⬇️
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Jeremy Baskin @jeremybaskin.bsky.social · 06/08/2026
Thrilled to share our new work, co-developed w/Adrian Salic's lab: bioorthogonal probes for labeling PE, a multifunctional membrane lipid and source of important protein modifications. Congrats to Yuan-Ting Cho, Brittany White-Mathieu, Jade Xia, & Cindy Jao! onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
Bioorthogonal Tools for Ethanolamine Lipids and Protein Conjugates
An alkyne-tagged ethanolamine analog (AlkEA) enables bioorthogonal, metabolic labeling of endogenous phosphatidylethanolamine (PE) and its protein modifications. AlkEA is incorporated into PE via the...
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Abby Buchwalter @abbybuch.bsky.social · 06/08/2026
We are looking to hire a technician to join the team. This project focuses on the nuclear lamina, a cellular structure that protects and organizes the genome. Will build skills in genetic screening, genomics, and stem cell culture. Please share, please apply! aprecruit.ucsf.edu/JPF06185
aprecruit.ucsf.edu
Junior Specialist, Buchwalter Laboratory, Cardiovascular Research Institute
University of California, San Francisco is hiring. Apply now!
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Pawel Burkhardt @pawelburkhardt.bsky.social · 04/08/2026
Our Dispatch "Evolution: Ancient monoamines in a neuron-less animal" out in @currentbiology.bsky.social. Monoamine signaling and behavioral responses in placozoans suggest this system predates bilaterians. authors.elsevier.com/a/1nYJl3QW8S... @annaferraioli.bsky.social @msarscentre.bsky.social
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Aydogan Lab @aydoganlab.bsky.social · 04/08/2026
If you are attending the ASCB | EMBO 2026 Meeting this December, be sure to catch Andrew’s presentation of his exciting endeavor! GO, ANDREW!!!
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Aydogan Lab @aydoganlab.bsky.social · 04/08/2026
For now, check out Andrew’s latest contributions to our lab’s recent collaborative work with Paolo Rinaudo’s lab, which begins to reveal—and experimentally test—key aspects of this quality-control logic during mammalian preimplantation development. www.biorxiv.org/content/10.6...
biorxiv.org
Self-reinforcing ROS-aneuploidy feedback loop shapes preimplantation development
Aneuploidy and oxidative stress have each been implicated in impaired embryonic development, yet their relationship remains unclear. Here we discover a self-reinforcing ROS-aneuploidy feedback loop wi...
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Aydogan Lab @aydoganlab.bsky.social · 04/08/2026
Andrew then set out to uncover the broader molecular logic of embryonic quality control—an entirely new research direction in our lab and the ambitious centerpiece of his PhD thesis. Stay tuned for a preprint on this major work during the 2026–2027 academic year!
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Aydogan Lab @aydoganlab.bsky.social · 04/08/2026
He found that such autonomy of the cytoplasm is a critical feature of the developing embryo, as it enables the extrusion of mitotically stalled genomes from the epithelium—a cell biological feature of embryonic quality control conserved to mammal embryos as discovered by the Vermeesch lab recently:
cell.com
Origin and development of uniparental and polyploid blastomeres
Molecular biology; Omics
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Aydogan Lab @aydoganlab.bsky.social · 04/08/2026
Next, as a co-first author, Andrew helped discover that cytoplasmic divisions can operate autonomously from nuclei and CDK/Cyclins using Drosophila embryos. www.sciencedirect.com/science/arti...
sciencedirect.com
Cytoplasmic division cycles without the nucleus and mitotic CDK/cyclin complexes
Cytoplasmic divisions are thought to rely on nuclear divisions and mitotic signals. We demonstrate in Drosophila embryos that cytoplasm can divide rep…
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Aydogan Lab @aydoganlab.bsky.social · 04/08/2026
Andrew’s first major contribution to our lab was his thoughtful role in developing our perspective on autonomous clocks, which outlined their shared and generalizable features. elifesciences.org/articles/72104
elifesciences.org
Autonomous clocks that regulate organelle biogenesis, cytoskeletal organization, and intracellular dynamics
Latest advances in biological timing studies substantiate an emerging concept of autonomous clocks that are normally entrained by the cell cycle and/or the circadian clock to run in synchrony, but hav...
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Aydogan Lab @aydoganlab.bsky.social · 04/08/2026
🧵Heartfelt congratulations to our lab’s first PhD student—and soon-to-be graduate—Andrew Alamban on receiving the 2026 ASCB | EMBO Porter Prize for Research Excellence! 👇In celebration of his work, here is a brief thread highlighting Andrew’s accomplishments in the lab!
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Andy Truman PhD @trumanlab.bsky.social · 03/01/2026
We are looking for talented graduate students to join our group for Fall 2026 studying the role and regulation of Hsp70 PTMs! If you are interested please check out www.trumanlab.org
trumanlab.org
Cancer Research Laboratory | Trumanlab | UNC Charlotte | United States
The Trumanlab at UNC Charlotte incorporates protein biochemistry, molecular biology, proteomics, systems biology, bacterial and yeast genetics as well as cell culture technologies to identify novel an...
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Jeremy Baskin @jeremybaskin.bsky.social · 03/01/2026
To all lipid-curious cell biologists: check out this comprehensive overview of lipid-based methods by @gerryhammond.bsky.social and colleagues in @jcb.org — a school of Babel fish for #lipidtime: rupress.org/jcb/article/...
rupress.org
The cell biologist’s guide to detecting and modulating membrane phospholipids | Journal of Cell Biology | Rockefeller University Press
Worcester et al. describe a suite of molecular tools and approaches that can be used to probe and experimentally study lipids.
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Jeremy Baskin @jeremybaskin.bsky.social · 31/12/2025
Proximity labeling users: check out this study by @zhixingchen2.bsky.social and Peng Zou, which establishes how much contact-dependence vs. diffusion is responsible for biotinylation — tl;dr TurboID has a much smaller effective radius! www.nature.com/articles/s41... 1/2
nature.com
Spatial barcoding reveals reaction radii and contact-dependent mechanism of proximity labeling - Nature Chemical Biology
A DNA nanoruler platform enables precise measurement of the labeling radii of TurboID and APEX2, uncovering their contact-dependent mechanisms. These findings redefine the enzymology of proximity labe...
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Jeremy Reiter @reitergroup.bsky.social · 31/12/2025
Modern biology research is biased towards investigating genes that are widely conserved and present in humans. What about genes that ARE widely conserved but NOT present in humans? Can genes missing from humans tell us something about what makes our biology different from that of other animals? 1/8
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Aydogan Lab @aydoganlab.bsky.social · 31/12/2025
Interesting analysis, Jeremy! Do you see them being exclusively metabolism related genes, or do you find structural or otherwise housekeeping stuff? I feel that this is quite expected in metabolism since it's highly attuned to the feeding habits and extracellular milieu.
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Arjun Raj @arjunraj.bsky.social · 30/12/2025
Bad antibodies are such a huge problem. It’s not just the money wasted on buying them. It’s the amount of time spent trying to validate them.
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Máté Varga @mvargam.eurosky.social · 13/12/2025
I was today years old when I learned that there is a superb (freely available) documentary from 1961 on early zebrafish development by J.V. Durden. collection.nfb.ca/film/embryon... (1/2)
A still picture from the 1961 documentary on zebrafish development by J.V. Durden showing a 1 dpf zebrafish embryo.
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paveltomancak.bsky.social @paveltomancak.bsky.social · 13/12/2025
#Mastodon, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To #cite or not to cite shall no longer be the question 🙃, because the #preprint. Software is available in every #Fiji near you. www.biorxiv.org/content/10.6...
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Aydogan Lab @aydoganlab.bsky.social · 13/12/2025
I was just wondering about this the other day!! A timely print!
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Aydogan Lab @aydoganlab.bsky.social · 12/12/2025
Didn’t we already know that for along time?? See this classic McIntosh piece from 2001 (Figure 2C) www.pnas.org/doi/10.1073/...
pnas.org
Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography | PNAS
The positional relationships among all of the visible organelles in a densely packed region of cytoplasm from an insulin secreting, cultured mamm...
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Aydogan Lab @aydoganlab.bsky.social · 10/12/2025
The final night at #CellBio25! Ended the day with wonderful talks at the centrosomes in cell division session - the field is strong 💪 💪 Sponsored by @jcellsci.bsky.social & @nikonmicroanz.bsky.social! Thanks to the amazing organizers Tim Megraw, Renata Basto, @lablerit.bsky.social & Chad Pearson!
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Stirling Churchman @stirlingchurchman.bsky.social · 03/12/2025
Oxidative phosphorylation complexes contain subunits encoded by both the nuclear and mitochondrial genomes. How do cells coordinate the synthesis and assembly of these complexes at the inner membrane? We teamed up with Martin Ott (@mitolab.bsky.social) to address this in two recent papers.
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Mia Levine @levine-lab.bsky.social · 28/11/2025
How to keep in step when your (protein) partner speeds up… Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection. Congrats to whole team! www.science.org/doi/10.1126/...
science.org
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...
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Leslie B Vosshall PhD @leslievosshall.bsky.social · 22/11/2025
@hhmi.org Summer Undergraduate Research Experience - #CechFellows named in honor of Prof Tom Cech Deadline to apply: 12/22/2025 Spend 9 weeks in a paid, mentored biomedical research experience in an HHMI lab. See you next summer!!! www.hhmi.org/programs/cec...
hhmi.org
Summer Undergraduate Research Experience | HHMI
The Cech Fellows Program is a paid, nine-week summer research experience empowering the next generation of scientific leaders.
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John Wallingford @jbwallingford.bsky.social · 19/11/2025
SAVE THE DATE! Stoked to organize the 2026 Santa Cruz Developmental Biology Meeting with @rashmi-priya.bsky.social, @lowelab.bsky.social, and Shelbi Russell. Come learn about Biomedicine, Biomechanics, and the Biosphere, August 24-28, 2026. Registration dates, etc., coming soon! Please RT
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Aydogan Lab @aydoganlab.bsky.social · 10/11/2025
Dylan, such a stunning video! Do you know if a portion of these cardiomyocytes are binucleated like you'd see postnatally in heart formation?
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Andrew Deans @genomestability.bsky.social · 09/11/2025
🧬 List of 2026 DNA repair and genome stability conferences, now updated. Please let me know if there is anything missing! docs.google.com/spreadsheets...
docs.google.com
DNA REPAIR/GENOME STABILITY CONFERENCES
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Henne lab @hennelab.bsky.social · 06/11/2025
New paper in Science identifying adipogenin as a critical seipin regulator in LD biogenesis. So glad our lab could help a little in this monumental study. Congrats to all authors! www.science.org/doi/10.1126/...
science.org
Adipogenin promotes the development of lipid droplets by binding a dodecameric seipin complex
The microprotein adipogenin (Adig) is predominantly expressed in adipose tissues. Here, we found that Adig interacts with seipin to form a stable, rigid complex. We present the structure of the seipin...
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Teresa Lee @snickclunk.bsky.social · 31/10/2025
Happy Halloween! 🎃 Continuing my tradition of Nobel-prize-winning discoveries, this year's costume is Ubx!!! It honors Edward B. Lewis, Christiane Nüsslein-Volhard, & Eric Wieschaus's work on the genetics of development 🧬🪰 (Please clap for the accuracy of those wing veins on *both* pairs of wings.)
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Snezhka Oliferenko @alebenoit.bsky.social · 29/10/2025
Minimal CDK continues delivering 💥 www.biorxiv.org/content/10.1...
biorxiv.org
Regulation of cell proliferation by a novel feedback system on Cdk function
The proliferation of eukaryotic cells is regulated by a complex network of regulatory systems that promotes efficient cell cycle progression and ensures proper responses to the environment. Despite th...
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Aydogan Lab @aydoganlab.bsky.social · 30/10/2025
Still so much to learn!
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Aydogan Lab @aydoganlab.bsky.social · 30/10/2025
So exciting!!! I hope all goes well Monica!
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