david bersten

A Molecular Biologist and Biochemist. Transcription factors, genomics, synthetic biology and the molecular basis of disease.

[david bersten @davidbersten]

Finally out in ⁦⁦@NatureComms⁩ thanks to all the contributors. Special thanks to Tim and Ali as well as the labs that have supported me and this work over years (none on social media). ⁦@RobsInstitute⁩ https://t.co/c6d7T01hJS

[david bersten @davidbersten]

@anshulkundaje @MoKhalilLab It’s worth considering that zero length x-links and spatial constraints will have roles in biases of ChiP-seq and also cut&run(tag). Estimates of TF molecules/cell are often much less than ChiP-seq peaks soooo perhaps the ground truth isn’t so solid…

[Maarten Boudry @mboudry]

Amazing graph. One the best visualizations of human progress.

[Ning Zhao @NingInScience]

We have developed a cysteine-free, highly thermostable tagging system, UTag, that enables single-mRNA translation tracking in live cells. You may wonder how different tagging systems affect translation kinetics—we addressed this by performing a systematic comparison.

[Raktim Mitra @Raktim7879]

Generative design of sequence specific DNA binding proteins.

Most fun paper I have ever written, with @enishasehgal and @YPolitansk15183 and the team, on a project which is a testament to the power of RFdiffusion3.
https://t.co/iYmdXRDBhQ

[Kenneth Loi @kenjmloi]

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR.

We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets.

Thread + link below.

[david bersten @davidbersten]

@anandcpatelmdms @FelixHorns @natrevbioeng This is somewhat addressed in their initial publication in cell (protection from Rnases) and discussed in this commentary (I.e. circRNA and saRNA). In addition transient is often what is preferred (i.e. editors etc). Additional modalities and approaches would be useful though

[david bersten @davidbersten]

@GallowayLabMIT @ProfTomEllis Would be good!

[American Institute of Chemical Engineers (AIChE) @ChEnected]

🌐 🧬SEED 2026: Bigger, Broader, Better. Join the largest program in synthetic biology and make your mark. Submit your abstract and register now https://t.co/yE8G34aWh1 #SEED2026 #SyntheticBiology #SynBio #BiotechInnovation #Biomanufacturing #GenomeEngineering

[david bersten @davidbersten]

Are AI DNA foundational models the new homeopathy?

[Steven Salzberg 💙💛 @StevenSalzberg1]

In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: https://t.co/83cv4HqVMB

[david bersten @davidbersten]

I enjoyed this too much

[Thomas Vierbuchen @TommyVierbuchen]

AP-1 TFs control everything, example #312:

https://t.co/9rS4fwlNTC

https://t.co/GrbMGrXYyV

[Sergey Ovchinnikov @sokrypton]

@mkoeris Actually... 250K structures was overkill. Technically, one structure with a good alpha/beta mix should've been enough. AlphaFold didn't solve the protein folding problem, it solved the low-resolution to high-resolution problem. (1/2)

[Jacob Boysen @jboysen0]

Behold peasants, 10k synthetic enhancers with no wetlab verification

[Bashor Lab @BashorLab]

We are pleased to share a paper from our lab out in this week’s issue of @Nature, where we show that HT + ML can dramatically speed up the synbio DBTL cycles, profiling gene circuit design spaces at unprecedented scale: https://t.co/7FwDVN4259 (1/16)

[Businessweek @BW]

A new robotic lab that makes human embryos using AI is now responsible for 19 babies. Is it better at IVF than humans are? https://t.co/3QsLVKARjX

[Daniel McDougal @DanielMcDougal_]

Excited to share that the most recent paper from my PhD is now online in @NatureComms! We made new inroads to further our understanding of how the estrogen receptor is regulated and mechanistic conservation across vertebrates. https://t.co/2iNaPtMAyR

[david bersten @davidbersten]

@DanielMcDougal_ @NatureComms Well done Dan!!

[david bersten @davidbersten]

Beautiful as you could only expect from Mikko’s lab….. but we are also clearly only scratching the surface re-assaying the most well characterised pathways. The juice will really come from broader more scalable iterations. Not a critique BTW, love the paper!!

[Mikko Taipale @mike_tilapia]

Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8

[Mikko Taipale @mike_tilapia]

Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8

[Martin Pacesa @MartinPacesa]

The GUI for processing BindCraft inputs is fantastic, something I always wished BindCraft would have!

[Kyle Tretina, Ph.D. @AllThingsApx]

Boltz-2 is available as an accelerated, downloadable NVIDIA NIM microservice!