Zikang (Dennis) Huang

Structural ontogeny of protein-protein interactions: www.science.org/doi/10.1126/...

Fundamental work on how PPIs (co)evolve, combining directed evolution and machine learning to reveal the role of chance and contingency.

@GRC photoreceptor and signal transduction now! Please come and check my poster #22 on single proteins that’s adaptive to light stimulation!

Now in print at ACS Synbio! Introducing Aviatar: a concept for inducible translocation to any cell compartment using only a 1-component probe
pubs.acs.org/doi/10.1021/...

Thank you Joel!

Our new paper just out!
pubs.acs.org/doi/10.1021/...

Wild that curling it up is the way to go for prolonging the recording period of protein tapes
www.nature.com/articles/s41...

A genetically encoded device for transcriptome storage in mammalian cells Understanding how cells make decisions over time requires the ability to link past molecular states to future phenotypic outcomes. We present TimeVault, a genetically encoded system that records and s...

🧬🔬@science.org A genetically encoded device for #transcriptome storage in mammalian cells | Science www.science.org/doi/10.1126/... @broadinstitute.org

1/3 Jellyfish and anemones also sleep, despite not having a brain

Not only do they sleep, but their behavior is affected if they lack sleep; they become clumsier and need to catch up on lost sleep. Interestingly, they sleep 8 hours a day, just like us.

(paper) www.nature.com/articles/s41...

Computational design of conformation-biasing mutations to alter protein functions Conformational biasing (CB) is a rapid and streamlined computational method that uses contrastive scoring by inverse folding models to predict protein variants biased toward desired conformational sta...

Can we design mutations that bias proteins towards desired conformational states?

Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.

Now accepting applications for SFI’s 2026 CSSS program, a 3-week experience for graduate students, postdoctoral fellows, and professionals to explore foundational theory, engage in collaborative projects, and connect with a global research community.

Apply by Feb 4, 2026
www.santafe.edu/csss

Contextual computation by competitive protein dimerization networks Competitive dimerization networks, in which protein monomers dimerize in various combinations, can perform diverse biochemical computations and can adapt those computations for different cell contexts...

Contextual computation by competitive protein dimerization networks www.cell.com/cell/fulltex...

lol real love

Another surprising result from our lab showing that condensation is dispensable in RTK fusion oncogenic signaling. Please be sure to look at non-condensing cells in your plate:) Very smart exp. design and analysis to convincingly show sth *isn’t* important.

Latest from our group investigating how oncogenic RTK fusions both activate and suppress mitogenic signaling. Also beautifully demonstrated that condensates are dispensable for both roles together with another preprint coming out soon.

Predicting and Controlling Collective Fate in Multicellular Systems https://www.biorxiv.org/content/10.64898/2025.12.11.693804v1

Cell-autonomous innate immunity by proteasome-derived defence peptides - Nature Proteasomal degradation of cellular proteins generate defence peptides constitutively and in response to bacterial infection. Such peptides might provide a source of natural antibiotics that...

One of the most interesting discoveries of the year - the immune function of degraded proteins
Also fun to think about how this whole proteome coordination has evolved

www.nature.com/articles/s41...

#Cellbio2025 come see the latest from the lab, including on opto/thermogenetics, condensates, RTK fusions, stress granules, biosensors of clustering. Talks and posters today and tomorrow!

Our neighbor @hugheslabpenn.bsky.social grows cool opto-kidneys, check them out!

#cellbio2025 please stop by my talk (Mon 4:35 evolution) and poster (Mon 12:45 #B479 optogenetics) tmr!
Title: Intraprotein domain competition dictates pulsatile response of photoreceptors shaped by temperature and evolution.
BcLOV4 as a model.
I’m also looking for postdoc opportunities!

#CellBio2025 come check out the workshop on applying optogenetic tools in cell biology! Today (Sunday) at 5:30p in Rm 121.

Note that this session does *not* appear in the app for some reason

In vivo proteomic labeling reveals diverse proteomes for therapeutic targets Wang et al. establish an in vivo proteomic labeling (IVPL) system combining the Btn-Ph-3F substrate with APEX2-EGFPf/f Cre crosses to map cell-type-specific proteomes in intact organs and trace patien...

In vivo proteomics
www.cell.com/molecular-ce...

Transcriptional interferences ensure one olfactory receptor per ant neuron - Nature Ants evolved a transcriptional-interference-based mechanism to express a single odorant receptor from an array of Or genes with functionally similar promoters.

One receptor per neuron problem in ants 😯
www.nature.com/articles/s41...

Super cool work from @levine-lab.bsky.social !
A great demo of how intra-genome conflict can result in rapid evolution of “essential” genes
Congrats!

Super clever design and beautiful counterintuitive intracellular plasmid evolution! Congrats!

See y’all there!

😲

Boolean logic-gated protein presentation through autonomously compiled molecular topology - Nature Chemical Biology Programming stimulus responsiveness into living systems enables advanced biocomputation. Here, the authors autonomously compile proteins with defined topology that can be site-specifically tethered to and conditionally released from biomaterials and cells following user-specified Boolean logic.

Latest issue of curated #engineeredlivingmaterials feed:
biomed.news/bims-enlima/... #ELMs
via @biomednews.bsky.social

includes research on: boolean logic-gated protein presentation (h/t @coledeforest.bsky.social), bacterial grown living materials (h/t @proftomellis.bsky.social) & more 🧪

Nobel Laureate Professor Sir John Gurdon dies aged 92 It is with great sadness that the University shares the news of the death of Professor Sir John Gurdon, founder of the Gurdon Institute.

So sad to hear the news - John truly was an inspiration to so many, and one of a kind.

www.cam.ac.uk/research/new...

Generative design of synthetic gene circuits for functional and evolutionary properties https://www.biorxiv.org/content/10.1101/2025.09.26.678595v1

Predicting protein-protein interactions in the human proteome Protein-protein interactions (PPI) are essential for biological function. Coevolutionary analysis and deep learning (DL) based protein structure prediction have enabled comprehensive PPI identificatio...

www.science.org/doi/10.1126/...