Heading to mSBW? Check out our work brought to you by Connor (Poster 47, genetically encoded urinary reporter to noninvasively monitor live molecular events), JS (Poster 46, efficient biophysical design of orthogonal DNA duplex libraries), and Meng (talk, ablating cancer using RADAR).

Please RT: We're hiring! Computational postdoc for foundation model and sequence-structure-function studies of intrinsic disordered proteins through a consortium and unique large datasets. Ideal candidates have led ML/AI projects in protein design/analysis.

Efficient generation of epitope-targeted antibodies with Germinal - @brianhie.bsky.social @synbiogaolab.bsky.social @stanford.edu @arcinstitute.org www.nature.com/articles/s41...

Efficient generation of epitope-targeted antibodies with Germinal - Nature Biotechnology

Germinal achieves epitope-targeted, de novo complementarity-determining region design with high experimental success rates.

nature.com

Don't feel bad about missing the mSBW abstract deadline. We have extended it! We also keep the registration fee affordable ($150 for students) so that mammalian synbio-curious trainees can check it out, especially if you are in the Atlanta area. Meeting link below:

A neat amplification system to improve the limited sensitivity/dynamic range of RADAR pubs.acs.org/doi/10.1021/...

Establishing an RNA Sensor with High Sensitivity and Dynamic Range Utilizing a Signal Amplifier Platform

Precise control of gene expression in a cell-state-specific manner is essential for effective therapeutic interventions in complex and dynamic disease microenvironments. Traditional targeting strategi...

pubs.acs.org

We just updated our Germinal preprint for de novo antibody-like binder design! Featuring additional scFv designs, extensive experimental validation of epitope specificity and polyreactivity, and CryoEM structure courtesy of Jim Zhang and Bing Rao from Feng Liang's lab.

Xiaojing Gao@synbiogaolab.bsky.social · 12mo ago

Having often dealt with the frustration of binder-limited projects, we sought a more accessible source for nanobodies than yeast display or llama. Here we introduce Germinal, computationally designing antibody-like binders with such a hit rate that only tens need to be screened for each target.

SEED 2026 Abstract due in 3 days! We've got an excellent line up of keynotes & invited speakers. Join us to present your work & hear the latest SynBio breakthroughs. A major theme this year is AI+Bio! 🧬🔬🤖💻🦠 synbioconference.org/2026

Excited to share our latest preprint on work led by postdoc Robert Lusi (@rflusi.bsky.social)! Introducing ALTER (AGO-Led Targeted Editing of RNA) for non-downregulatory RNA manipulation by repurposing hAGO2, non-immunogenic and capitalizing on evolution. www.biorxiv.org/content/10.6...

So you think your mammalian plasmids have nothing to fear from cloning and propagation in E.coli? Quantitative profiling of millions of nucleotides by Tom Copeman will prove you wrong! Supervised with the amazing @proftomellis.bsky.social and AZ, now on BioRxiv: doi.org/10.64898/202...

Quantitative profiling of millions of nucleotides reveals sequence-encoded interactions that govern plasmid propagation

Plasmids are central to modern biotechnology, especially therapeutic development, yet their propagation in Escherichia coli remains difficult to predict. Although expression-induced burden is well und...

doi.org

New in ACS SynBio: led by Dennis Bolshakov, we used the awesome power of yeast to define how expression levels, noise, and sequence program the dynamics of synthetic protein waves, allowing us to genetically encode new cellular timescales stable over generations! pubs.acs.org/doi/full/10....

Have you ever wondered what it would've been like to live in a different kind of society? After a record number of rejections, I'm self-archiving my first attempt at... flash fiction, featuring "Hemingway-esque economy" and "Ishiguro's measured revelation" (if you ask Claude).

Whether you think limiting student visas to 4 years is a good or bad thing, please comment. Be heard.

Dr. Kat Napaaqtuk❄️@napaaqtuk.bsky.social · 12mo ago

Comment period ends on Monday for a proposed rule change that would terminate student visas after 4 years. It also puts limits on exchange visitors and reps of foreign media, and shortens the length of time at the end of the visa from 60 days to 30 days. www.federalregister.gov/documents/20...

With 2 postdocs moving on to faculty positions🥳, we're looking to hire someone new. If you're interested in norepinephrine and neural circuits, please apply! tinyurl.com/42bfe24k

Having often dealt with the frustration of binder-limited projects, we sought a more accessible source for nanobodies than yeast display or llama. Here we introduce Germinal, computationally designing antibody-like binders with such a hit rate that only tens need to be screened for each target.

We previously built programmable RNA sensors based on editing by housekeeping ADAR enzymes. But they can't sense arbitrary sequences due to design constraints (analogous to PAM for CRISPR). With our new "modulADAR", we overcome that constraint by leveraging ADAR's modularity.

Excited to share our latest: we engineered the reactivity of a bacterial E1-like enzyme for ATP-driven modification of C termini. Our tool mimics the logic of peptide bond formation in biology for precision modification of proteins in vitro. 🧪https://rdcu.be/ewN7C

Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein and peptide C termini

Nature Chemistry - In living systems, ATP provides an energetic driving force for protein synthesis and modification. Now, an engineered enzymatic tool has been developed for high-yield, ATP-driven...

rdcu.be

Have you always wanted to take a protein from its native context and make it work elsewhere? Our novel sampler computationally “cytosolize” a secreted enzyme while maintaining its structure, generalizable to other multi-objective guided generation tasks www.biorxiv.org/content/10.1...

ProVADA: Generation of Subcellular Protein Variants via Ensemble-Guided Test-Time Steering

Engineering protein variants to function in exogenous environments remains a significant challenge due to the complexity of sequence and fitness landscapes. Experimental strategies often require exten...

biorxiv.org

The machine-guided humanization paper is out after peer review! doi.org/10.1016/j.ce... Key contributions from current and previous international students on visas, representing 5+ countries.

Xiaojing Gao@synbiogaolab.bsky.social · 2y ago

So we beat on. Gene/cell therapies would benefit many patients, but often use proteins that could be recognized as non-self by our immune system and cause problems. We combine algorithms to build proteins that are therapeutically relevant and can masquerade as our own parts doi.org/10.1101/2025...

Our latest work developing AND-gate probes for imaging caspase-1 mediated inflammation is out. Very productive collaboration with Merck & Co. in South San Francisco. #chembio. www.biorxiv.org/content/10.1...

A caspase-1-cathepsin AND-gate probe for selective imaging of inflammasome activation

Caspase-1 is a key mediator of the inflammasome pathway, which is associated with several inflammatory disorders including obesity, diabetes mellitus (DM), cardiovascular diseases (CVDs), cancers and ...

biorxiv.org

Hello Community! Are you a postdoc/grad student preparing to launch a faculty search? Do you have a track record of excellence in research, leadership, mentorship & community engagement? Apply to the 2025 Next Generation Faculty Symposium: www.berkeleystanfordnextgensymposium.com! Pls repost! (1/3)

Grateful for the recognition and for my team's dedication. When I wrote it in Oct, I didn't anticipate that the title would feel defiant. The original draft even had a now quaint reference to "the comparative comfort of the ivory tower", which was wisely removed.

LIDAR is out! rdcu.be/efugD We are one baby step closer to making it useful for therapeutics. NIH high-risk high-reward program provides key support.

Post-transcriptional modular synthetic receptors

Nature Chemical Biology - Zhang, Mille-Fragoso and colleagues developed a synthetic receptor platform named LIDAR (Ligand-Induced Dimerization-Activating RNA editing), which enables...

rdcu.be

Xiaojing Gao@synbiogaolab.bsky.social · 2y ago

Hi bskyers (is that the right word?)! Though we don't have a lot of new contents to contribute yet, we did just update our preprint on the modular post-transcriptional "LIDAR" receptors doi.org/10.1101/2024....

If you have time in your life to read only one of @jeremymberg.bsky.social’s bluetorials, please read this one

Jeremy Berg@jeremymberg.bsky.social · 2y ago

Bluetorial: Women, courage, and leadership What follows will include some generalizations based on population averages of what I have experienced over the course of my career. There are, of course, exceptions in every group who are substantially more to one extreme or the other.

So we beat on. Gene/cell therapies would benefit many patients, but often use proteins that could be recognized as non-self by our immune system and cause problems. We combine algorithms to build proteins that are therapeutically relevant and can masquerade as our own parts doi.org/10.1101/2025...

Machine-Guided Dual-Objective Protein Engineering for Deimmunization and Therapeutic Functions

Cell and gene therapies often rely on the expression of exogenous proteins derived from nonhuman organisms. An emerging consensus is to reduce the potential immunogenicity of such therapies by instead...

doi.org

Join us! Science Homecoming helps scientists reconnect with communities by writing about the importance of science funding in their hometown newspapers. We’ve mapped every small newspaper in the U.S. and provide resources to get you started. Help science get back home 🧪🔬🧬 🏠 sciencehomecoming.com

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

Your biggest power is as a constituent who cares about the issue and may be directly or indirectly affected by them My format is generally: NIH is important for the nation, both in terms of health knowledge and economics/competitiveness 1/n

Kayden Stockwell@kaydenstockwell.bsky.social · 2y ago

What should one say in these emails/calls?

Excited to share this beast of a review on the potential of protein-based degraders from trainees who are all not on the Sky! Herein we cover choice of binders, selection strategies, E3 ligases, and DELIVERY! pubs.acs.org/doi/10.1021/...

Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics

The nascent field of targeted protein degradation (TPD) could revolutionize biomedicine due to the ability of degrader molecules to selectively modulate disease-relevant proteins. A key limitation to ...

pubs.acs.org

Proteases might serve as versatile control knobs for gene and cell therapies, but there looms the risk of immunogenicity as we and others have been using viral proteases. We now report a control system based on a an engineered human protease and its clinically approved inhibitor. rdcu.be/d6kVt

Orthogonalized human protease control of secreted signals

Nature Chemical Biology - Engineering of a human-derived protease controlled exogenously by its FDA-approved inhibitor enables control over cytokine activity in cell-based therapies with reduced...

rdcu.be

If you’re feeling too boxed in focusing on one protein, take a journey across the evolutionary tree of life. It’s full of cool surprises. A spider ortholog of my favorite protein sequence, the chromodomain, shares a feature with an enhanced version we engineered. www.biorxiv.org/content/10.1...

An engineered chromatin protein with enhanced preferential binding of H3K27me3 over H3K9me3

The human genome is organized within the nucleus as chromatin, which is largely comprised of histone proteins that assemble on DNA into nucleosome complexes. Histone post-translational modifications (...

biorxiv.org