Deniz Aksel

Engineering for & of biology
Previously: @CellinoBio | @Harvard Biophysics PhD | @MITdeptofBE
in vitro development, synbio, science automation, band shirts

[Deniz Aksel @duckcell3]

The killifish axis formation paper is now out in @ScienceMagazine ! It was such a fun project to work on, and I thank @Ohnolog and @schierlab for their mentorship and for letting me be a part of it - check it out!

[Phil Abitua 🧬 @Ohnolog]

I am pleased to share our paper on axis formation in annual killifish, published in @sciencemagazine! See the thread below for a summary of the story. https://t.co/dIMAqYINRw

[Deniz Aksel @duckcell3]

Check out this new paper from @rumya_r engineering nucleases to be less immunogenic! Awesome interdisciplinary work, going from in vitro, to in silico, to in vivo 🧫💻🐁

[Rumya @rumya_r]

1/ Thrilled to share an advancement in gene therapy from my PhD in @NatureComms! We've developed a new approach to reduce immune responses while maintaining efficiency—paving the way for safer, more effective therapies. Big thanks to @zhangf & @mircoscopy! https://t.co/eXZkpgiMXq

[The Nobel Prize @NobelPrize]

This year’s #NobelPrize laureate in physics John Hopfield created an associative memory that can store and reconstruct images and other types of patterns in data.

The Hopfield network can store patterns and has a method for recreating them. When the network is given an incomplete or slightly distorted pattern, the method can find the stored pattern that is most similar.

Read more about the research that led to this year’s physics prize: https://t.co/QuIdxRvuEP

[Eli Weinstein @EliWeinstein6]

I’m thrilled to announce: at @jura_bio we’ve constructed a new kind of generative protein model, which allows us to manufacture its generated designs in the real world at petascale.
Paper: https://t.co/qgxfNPP30K
Blog: https://t.co/An1USoCNoz

[Hiro Eto @HiromuneEto]

Happy to have this finally on BioRxiv! Oscillations matter! 😎 Also check out the cool techniques #singlecelltracking #microfluidics

[Eric Kernfeld @ekernf01]

After precisely 4 years of grad school, I'm excited to share that the FIRST PEER REVIEWED PAPER FROM MY PHD HAS LANDED!
https://t.co/Zbv2A623Cz

Indulge me in some back-story. 🧵

[Anshul Kundaje @anshulkundaje]

Deep learning is not fundamentally antagonistic to understanding mechanism, even though that is the general perception based on most common high profile use cases. 1/

[Deniz Aksel @duckcell3]

Great paper with intuitive metrics for characterizing self-organization! Interested to see how real developmental trajectories (from pre-patterned to not) map to their landscapes

[David Brückner @d_brueckner]

📢Our paper on self-organized information in development is now out in @PNASNews!

See below for a 🧵 on the preprint and check it out here👉https://t.co/wObm1q0NEt

[jared toettcher @toettch]

This being a collaboration with the @DJCohenEtAl lab, we just had to see how tissues would respond to local EGFR stimuli at macroscopic scales. Here is a 6 mm diameter tissue with a 1 mm light pattern. Cell rearrangements propagate hundreds of microns from the light boundary!

[National Academy of Sciences @theNASciences]

Congratulations Alexander Schier of @biozentrum, newly inducted #NASmember! #NAS161 #biology

[Nathan Lord @LordLab_Pitt]

We’re very excited to share the first preprint from my lab along with @h4rrymcnamara, @BillZJia, @AdamEzraCohen, and Alex Schier. We describe a set of methods for exerting spatial control over Nodal signaling in zebrafish development.

https://t.co/4Opufofwop

[Marta Shahbazi @Marta_Shahbazi]

Extremely happy to share the first manuscript of the lab! 🥳🥳🥳In this paper, we have looked at the coupling between delamination and differentiation at gastrulation. If you are interested in pluripotency, gastrulation, and mouse embryos keep reading! https://t.co/PIe2KmoiNn

[Deniz Aksel @duckcell3]

@the_tessallator Congrats Tessa (also on graduating)! Excited to check it out 😊

[StarkLab @stark_lab]

We are very excited to present a major breakthrough achievement – the de novo design of synthetic enhancers for selected tissues in fruit fly embryos in vivo using deep- and transfer learning, @deAlmeida_BPet al published today in @Nature https://t.co/TIlPrBKYaK. Thread 👇(1/N)

[Gurdon Institute @GurdonInstitute]

Many happy returns to our Sir John Gurdon on his 90th birthday 🎉

[Hongquan Li @hongquan_li]

Excited to share our latest work in microscope development from Prakash Lab, with @deepak_me90, @lietk12, @pranavvyas94, Nibha Akireddy, @ChewMChai and @PrakashLab: https://t.co/9Op79WzfPT. (1/n)

[Deniz Aksel @duckcell3]

@h4rrymcnamara This is so cool Harry! And beautiful pics and videos as always - congrats!

[Deniz Aksel @duckcell3]

Awesome work from @h4rrymcnamara capturing snapshots of signaling in living cells to get to the bottom of the symmetry breaking mystery of gastruloids under uniform conditions!

[Harry McNamara @h4rrymcnamara]

hello world! new results (with @toettch): https://t.co/EhwbUzPuOS

Stem cells can self-organize morphogenesis in vitro w/o spatial patterning cues. But how? We programmed cells to record their signaling histories to map symmetry breaking during gastruloid morphogenesis (1/n)

[Deniz Aksel @duckcell3]

Exciting news! @CellinoBio's #ARPAHDash idea for scalable personalized #celltherapies made it to Round 1 voting at the @ARPA_H challenge. Please #vote for "Your Cells, Your Cure" by Willie Reaves in the Scalable Solutions category at https://t.co/FLcPooFbX7. Voting ends tmrw! 🗳️

[Cellino @CellinoBio]

🗳️ Only 1 day left in Round 1 voting for scalable manufacturing of #iPSCs in the @ARPA_H #ARPAHDash challenge! Please #vote for “Your Cells, Your Cure” by Willie Reaves under Scalable Solutions to help us transform the future of #medicine for all at https://t.co/plfe6IfUvC.

[Michael F. Chiang, MD @NEIDirector]

I'm excited to announce Kapil Bharti's selection as Scientific Director for the @NatEyeInstitute.

Kapil is a superb basic/translational scientist - he'll lead >20 labs, 6 core facilities, & 300 staff in our Intramural Research Program. https://t.co/18dqdEKSC8

@KapilkBharti123