Jain_Akanksha_
Asa. Prof. Of Neural MorphoGenomics @DMLS, Uni Zurich. •4D tissue morphogenesis •Human organoids •Developmental biology •Evolution of tissue mechanics. Previous @ETH @mpicbg @DBS-TIFR
akankshajain2022.github.io/AkankshaJain.github.io/
- Reposted by Jain_Akanksha_Checkout this updated preprint-a tour de force and truly globe-spanning collaboration with an exceptional group of scientists.
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- Reposted by Jain_Akanksha_Open-source atlas of fruit fly development DynamicAtlas is a high-res framework for morphological studies 📹 M. F. Lefebvre, V. Jain-Sharma, N. Claussen & N. P. Mitchell et al @streichan.bsky.social lab University of California Santa Barbara in @natmethods.nature.com ➡️ bpod.org.uk/archive/2026...
- 📣Registration deadline approaching !📣 Check out @embo.org @biologists.bsky.social workshop "biophysical & molecular mechanisms of animal homeostasis & repair" 6-10th April, with a fantastic lineup of speakers! meetings.embo.org/event/26-hom.... Register/Abstract submission by 10th January.
- Reposted by Jain_Akanksha_Excited to share Alison's @alisonkickuth.bsky.social paper from the lab out in @nature.com this week! We uncovered how a mechanical ratchet mechanism drives cytokinesis in early #zebrafish embryos. Read more in this thread 🧵 and at www.nature.com/articles/s41... 🤩 @poldresden.bsky.social @mpi-cbg.de
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- Reposted by Jain_Akanksha_1 To predict the behaviour of a primate, would you rather base your guess on a closely related species or one with a similar brain shape? We looked at brains & behaviours of 70 species, you’ll be surprised! 🧵Thread on our new preprint with @r3rt0.bsky.social , doi.org/10.1101/2025...
- I am extremely happy to see this work online! Long discussions about which, when and how much of morphogens or combinations result in what neural cell type/brain patterning culminated in this wonderful story, powered by multiplexed single-cell RNAseq. Follow the thread for a concise intro 🎊📣
- Reposted by Jain_Akanksha_Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets biorxiv.org/content/10.64898/20…
- Reposted by Jain_Akanksha_We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji. It ships many new features, detailed below, but that are articulated around the following:
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- 🧠 Join us @uzh-ch.bsky.social ! We are a new lab looking for PhDs, Postdocs & Master’s students interested in studying how human neural systems emerge & go awry using brain organoids, light-sheet imaging & genomics. 🚀 Deadline for LSZGS 1st Nov! www.lifescience-graduateschool.uzh.ch/en.html.
- Reposted by Jain_Akanksha_If you’re applying to your dream lab for an internship/PhD/postdoc, always send a second email 1-2 weeks after the first one if you don’t hear back. I promise we will be grateful rather than annoyed. My email inbox is a disaster and I’m quite junior - and very few of us have secretarial support
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- Reposted by Jain_Akanksha_Ever wondered how robust cellular identity is to external perturbations? Here we disrupt cellular environmnent in vivo and in vitro, and find cell population specific sensitivities. Environment sculpts development yes, but not all cells are made of the same wood. www.science.org/doi/10.1126/...
- Reposted by Jain_Akanksha_This is absolutely a must read. We are in deep trouble and I am even less optimistic than the authors.
- AI can now generate fake microscopy images that are nearly impossible to detect. A serious threat to scientific integrity—and we’re not prepared for it. Commentary in @natnano.nature.com #nanotechnology
- Reposted by Jain_Akanksha_Another #preprint: "Elasticity and plasticity of epithelial gap closure", from the #PhD work of Maryam Setoudeh: arxiv.org/abs/2509.05110 This one required a lot of (I think) beautiful #mechanics! @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social
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Super excited that our group will be supported by an ERC Starting Grant! In project "InfoFate" we will study how cells use information in dynamical, neighborhood & mechanical signals to make decisions. We'll have PhD and Postdoc positions available, please get in touch if interested!- Why do some cells become neurons and others muscle? Physicist Prof. David Brückner @davidbrueckner.bsky.social @biozentrum.unibas.ch @unibas.ch receives a prestigious #ERCStartingGrant to uncover how cells make life-shaping decisions. @erc.europa.eu www.biozentrum.unibas.ch/news/detail/...
- Reposted by Jain_Akanksha_We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
- Reposted by Jain_Akanksha_Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...
- Thrilled to share 🎉 I’m starting my lab at University of Zurich, DMLS as Assistant Professor (tenure track) from Jan 2026! The Neural MorphoGenomics & Developmental Dynamics Lab will be exploring how genes + morphogenesis shape brain development with organoids, imaging & spatial genomics 🧠🔬🧬
- I am grateful to my mentors @paveltomancak.bsky.social, Barbara Treutlein, Anastasios Pavlopoulos, Gray Camp and Krishanu Ray, colleagues, and collaborators for their invaluable support, and I look forward to starting this new chapter at the University of Zurich.
- Reposted by Jain_Akanksha_Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
- We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up... #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)
- Reposted by Jain_Akanksha_We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up... #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)
- Reposted by Jain_Akanksha_🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...
- Reposted by Jain_Akanksha_Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism. www.nature.com/articles/s41...
- Reposted by Jain_Akanksha_Honored to receive the @isrbio.bsky.social Rising Star Award for our work in regeneration biology! Grateful to the committee and our colleagues for the recognition. A huge motivation for the lab. Excited to give the award talk in Madison next week and connect with everyone! 😎🥳🍾 shorturl.at/LnkSt
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- Nostalgia and Deja vu! Listening to @maweigert.bsky.social back at the incredible @mpi-cbg.de for @embo.org #LISH2025. Here after six years, the gray auditorium reminds of my thoughts when I sat here for my PhD selection interviews that included him!
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- Reposted by Jain_Akanksha_🤩 Very excited to share our new work! We have derived euploid and aneuploid trophoblast organoids and extra-embryonic mesoderm cell lines from early human embryos. In doing so, we have characterised the tissue requirements for their specification. If you want to know more, continue reading….
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- Reposted by Jain_Akanksha_Very happy that the first article from my postdoc work in the Tomancak lab is now published @PNAS! www.pnas.org/doi/10.1073/.... We studied the self-organization of actin in aggregates made from Hydra cells. Thread below (1/9)
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- Reposted by Jain_Akanksha_My postdoc work at Treutlein lab and @graycamplab.bsky.social with @jasperjanssens.bsky.social is out in @science.org ! We screen for neuron subtypes using pro-neural TFs + morphogen combinations + scRNA-seq and profiled over 700,000 cells in 480 conditions. www.science.org/doi/10.1126/...
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- Reposted by Jain_Akanksha_Do you like developing new AI vision methods for microscopy image analysis? You love theory & implementation? 1 week left to apply for a fully funded PhD position in our lab in Dresden 🇩🇪! Topics: object detection/tracking, multimodal models & more. DM/email for details! #PhD #AcademicJobs #GPUsgoBrr
- Reposted by Jain_Akanksha_Sign up to attend our next Development presents... webinar on early #embryogenesis, featuring talks from @lakshmib02.bsky.social, @dias-andre.bsky.social and @nikhil-mishra.bsky.social 📅Wed 9 July 15:00BST (UTC+1) Register here: us02web.zoom.us/webinar/regi... #DevBio @dev-journal.bsky.social
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- Very happy to share it’s online! If you read the preprint, updates include tracking cells and tissue flow, Histo4i timecourse (69 Abs) comparing spatial patterning emergence and a new WLS KO ipsc line establishing mechanosensing via YAP-WLS/WNT caudalizes organoids www.nature.com/articles/s41...
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- Reposted by Jain_Akanksha_Join the challenge, get the data, contribute your solution!!! 🎉
- The 2nd AI4Life Challenge is live! Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail. 📦 Paired noisy/clean datasets 📈 Ground-truth evaluation 🧠 DL focus Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
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- Reposted by Jain_Akanksha_We just released and uploaded a new version of *Mastodon*, the large-scale tracking and track-editing framework for large, multi-view images. Mastodon is available via Fiji, via a dedicated update site. mastodon.readthedocs.io/en/latest/do... Below is a thread that survey some of the novelties ⏬️
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- Reposted by Jain_Akanksha_Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social www.nature.com/articles/s41... rdcu.be/epIB7
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- You cannot beat us in style, especially when it comes to FOOD and the local Basel favorite hangouts. Yes we booked and an entire giant restaurant and the tournament was very competitive!
- Reposted by Jain_Akanksha_⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.
