Zikang (Dennis) Huang
@dennishuang.bsky.social
PhD student at Bugaj Lab UPenn | synbio | protein engineering | optogenetics | thermogenetics | systems bio | love weird dynamics, information flow, networks | BcLOV4 renovator | looking for postdoc positions
Pinned
How can an individual protein show adaptation? The light- and temp-sensitive BcLOV4 gives a pulse of translocation during a step input of light. Answer in our preprint: *intra-molecular* feed-forward regulation. bit.ly/3Rg9veD
A @bugajlab.bsky.social collab with @nmrkaygee.bsky.social 🧵
A @bugajlab.bsky.social collab with @nmrkaygee.bsky.social 🧵
Reposted by Zikang (Dennis) Huang
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/...
pubs.acs.org/doi/10.1021/...
February 2, 2026 at 12:21 PM
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/...
pubs.acs.org/doi/10.1021/...
Our new paper just out!
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
January 31, 2026 at 1:53 PM
Our new paper just out!
pubs.acs.org/doi/10.1021/...
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...
www.nature.com/articles/s41...
Scalable and multiplexed recorders of gene regulation dynamics across weeks - Nature
Nature - Scalable and multiplexed recorders of gene regulation dynamics across weeks
www.nature.com
January 31, 2026 at 2:03 AM
Wild that curling it up is the way to go for prolonging the recording period of protein tapes
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Zikang (Dennis) Huang
🧬🔬@science.org A genetically encoded device for #transcriptome storage in mammalian cells | Science www.science.org/doi/10.1126/... @broadinstitute.org
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...
www.science.org
January 15, 2026 at 8:31 PM
🧬🔬@science.org A genetically encoded device for #transcriptome storage in mammalian cells | Science www.science.org/doi/10.1126/... @broadinstitute.org
Reposted by Zikang (Dennis) Huang
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...
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...
January 14, 2026 at 11:32 AM
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...
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...
Reposted by Zikang (Dennis) Huang
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.
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.
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...
www.science.org
January 8, 2026 at 7:08 PM
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.
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.
Reposted by Zikang (Dennis) Huang
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
Apply by Feb 4, 2026
www.santafe.edu/csss
December 30, 2025 at 5:02 PM
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
Apply by Feb 4, 2026
www.santafe.edu/csss
Contextual computation by competitive protein dimerization networks www.cell.com/cell/fulltex...
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...
www.cell.com
December 30, 2025 at 11:25 PM
Contextual computation by competitive protein dimerization networks www.cell.com/cell/fulltex...
lol real love
December 25, 2025 at 6:11 PM
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.
🚨Preprint 2/2: Several studies implicate condensates in RTK fusion onco-signaling. So we were surprised to find that condensates are entirely dispensable😮(!). A study from proteins to mice, by dynamic duo @davidgonzmar.bsky.social and @trmumford.bsky.social.
www.biorxiv.org/content/10.6...
👇
www.biorxiv.org/content/10.6...
👇
December 17, 2025 at 5:40 PM
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.
🚨New preprint(1/2)! We show that RTK fusion oncoproteins broadly suppress EGFR signaling. How? Sequestration of adapters as the shared principle.
Led by superb PhD student Carol Gao.
www.biorxiv.org/content/10.1...
Implications for drug tolerance/resistance, and includes one big surprise🫧.👇
Led by superb PhD student Carol Gao.
www.biorxiv.org/content/10.1...
Implications for drug tolerance/resistance, and includes one big surprise🫧.👇
December 16, 2025 at 1:39 PM
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.
Reposted by Zikang (Dennis) Huang
Predicting and Controlling Collective Fate in Multicellular Systems https://www.biorxiv.org/content/10.64898/2025.12.11.693804v1
December 15, 2025 at 2:02 PM
Predicting and Controlling Collective Fate in Multicellular Systems https://www.biorxiv.org/content/10.64898/2025.12.11.693804v1
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...
Also fun to think about how this whole proteome coordination has evolved
www.nature.com/articles/s41...
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...
www.nature.com
December 9, 2025 at 4:49 AM
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...
Also fun to think about how this whole proteome coordination has evolved
www.nature.com/articles/s41...
Reposted by Zikang (Dennis) Huang
#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!
December 8, 2025 at 12:12 PM
#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!
Stop by to see our posters at #CellBio2025, including plenty of unpublished new directions!
December 8, 2025 at 6:11 AM
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!
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!
December 7, 2025 at 4:35 PM
#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!
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!
Reposted by Zikang (Dennis) Huang
#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
Note that this session does *not* appear in the app for some reason
December 7, 2025 at 3:34 PM
#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
Note that this session does *not* appear in the app for some reason
In vivo proteomics
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
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...
www.cell.com
December 2, 2025 at 6:53 PM
In vivo proteomics
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
One receptor per neuron problem in ants 😯
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
December 2, 2025 at 6:44 PM
One receptor per neuron problem in ants 😯
www.nature.com/articles/s41...
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!
A great demo of how intra-genome conflict can result in rapid evolution of “essential” genes
Congrats!
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/...
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/...
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...
www.science.org
December 1, 2025 at 6:31 PM
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!
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!
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 21, 2025 at 1:17 AM
Super clever design and beautiful counterintuitive intracellular plasmid evolution! Congrats!
See y’all there!
November 7, 2025 at 9:33 PM
See y’all there!
😲
Japanese botanist Kenji Suetsugu studies plants that steal carbon and nutrients from soil fungi. https://scim.ag/3IRHOrW
These ‘ghost flowers’ thrive without photosynthesis. One scientist is learning how
Japanese botanist Kenji Suetsugu studies plants that steal carbon and nutrients from soil fungi
www.science.org
October 14, 2025 at 12:26 AM
😲
Reposted by Zikang (Dennis) Huang
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 🧪
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 🧪
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.
www.nature.com
October 12, 2025 at 9:39 AM
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 🧪
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 🧪
Reposted by Zikang (Dennis) Huang
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...
www.cam.ac.uk/research/new...
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.
www.cam.ac.uk
October 7, 2025 at 4:02 PM
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...
www.cam.ac.uk/research/new...