Xiaojing Gao
@synbiogaolab.bsky.social
Pinned
Xiaojing Gao
@synbiogaolab.bsky.social
· Sep 19
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.
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).
November 13, 2025 at 5:18 AM
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).
Reposted by Xiaojing Gao
Whether you think limiting student visas to 4 years is a good or bad thing, please comment. Be heard.
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...
www.federalregister.gov/documents/20...
Establishing a Fixed Time Period of Admission and an Extension of Stay Procedure for Nonimmigrant Academic Students, Exchange Visitors, and Representatives of Foreign Information Media
Unlike most nonimmigrant classifications, which are admitted for a fixed time period, aliens in the F (academic student), J (exchange visitor), and most I (representatives of foreign information media...
www.federalregister.gov
September 27, 2025 at 2:35 PM
Whether you think limiting student visas to 4 years is a good or bad thing, please comment. Be heard.
Reposted by Xiaojing Gao
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
Postdoctoral Research Associate - Developmental Neurobiology
A postdoctoral research associate position is available in the laboratory of Dr. Lindsay Schwarz in the Department of Developmental Neurobiology at St. Jude Children’s Research Hospital. The Schwarz l...
tinyurl.com
September 24, 2025 at 3:41 PM
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.
September 24, 2025 at 4:32 PM
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.
September 19, 2025 at 3:21 AM
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.
Reposted by Xiaojing Gao
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
July 18, 2025 at 2:40 PM
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
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...
www.biorxiv.org
July 17, 2025 at 5:08 PM
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...
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.
June 3, 2025 at 5:26 PM
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.
Reposted by Xiaojing Gao
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 ...
www.biorxiv.org
May 31, 2025 at 2:32 PM
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...
Reposted by Xiaojing Gao
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)
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)
April 21, 2025 at 7:21 PM
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)
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.
April 3, 2025 at 9:05 PM
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.
March 28, 2025 at 4:44 PM
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.
Reposted by Xiaojing Gao
If you have time in your life to read only one of @jeremymberg.bsky.social’s bluetorials, please read this one
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.
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.
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
March 9, 2025 at 8:08 AM
If you have time in your life to read only one of @jeremymberg.bsky.social’s bluetorials, please read this one
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
March 1, 2025 at 4:09 AM
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...
Reposted by Xiaojing Gao
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
sciencehomecoming.com
Science Homecoming
sciencehomecoming.com
February 18, 2025 at 5:12 PM
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
sciencehomecoming.com
Reposted by Xiaojing Gao
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.
February 8, 2025 at 9:21 PM
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.
Reposted by Xiaojing Gao
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
My format is generally:
NIH is important for the nation, both in terms of health knowledge and economics/competitiveness
1/n
What should one say in these emails/calls?
January 23, 2025 at 2:57 PM
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
My format is generally:
NIH is important for the nation, both in terms of health knowledge and economics/competitiveness
1/n
Reposted by Xiaojing Gao
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
January 18, 2025 at 1:07 AM
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/...
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
January 15, 2025 at 7:25 PM
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
Reposted by Xiaojing Gao
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 (...
www.biorxiv.org
January 14, 2025 at 1:32 AM
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...
Reposted by Xiaojing Gao
Super excited to finally share PANCS-Binders: our group's decade-long quest to accelerate protein binder discovery.
TLDR: PANCS-binders is fast (2 days), cheap (pennies), has extremely high fidelity (low false positive and negatives), and high-throughput.
1/n
TLDR: PANCS-binders is fast (2 days), cheap (pennies), has extremely high fidelity (low false positive and negatives), and high-throughput.
1/n
While everyone esle has been concentrating on generative binder design, this group has demonstrated screening libraries in vivo! www.biorxiv.org/content/10.1...
#biosky
#biosky
High-throughput protein binder discovery by rapid in vivo selection
Proteins that selectively bind to a target of interest are foundational components of research pipelines, diagnostics, and therapeutics. Current immunization-based, display-based, and computational ap...
www.biorxiv.org
January 7, 2025 at 8:50 PM
Super excited to finally share PANCS-Binders: our group's decade-long quest to accelerate protein binder discovery.
TLDR: PANCS-binders is fast (2 days), cheap (pennies), has extremely high fidelity (low false positive and negatives), and high-throughput.
1/n
TLDR: PANCS-binders is fast (2 days), cheap (pennies), has extremely high fidelity (low false positive and negatives), and high-throughput.
1/n
Reposted by Xiaojing Gao
I'm happy to see this paper I handled finally out! -- Directed evolution in mammalian cells using an orthogonal alphaviral RNA replication system with antiviral-induced mutagenesis #ChemBio #synbio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Orthogonal RNA replication enables directed evolution and Darwinian adaptation in mammalian cells - Nature Chemical Biology
An orthogonal alphaviral RNA replication system with chemically inducible control of RNA mutagenesis enables RNA-based directed evolution in mammalian cells.
www.nature.com
January 6, 2025 at 10:12 PM
I'm happy to see this paper I handled finally out! -- Directed evolution in mammalian cells using an orthogonal alphaviral RNA replication system with antiviral-induced mutagenesis #ChemBio #synbio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Xiaojing Gao
Thank you to @urochester.bsky.social for writing this nice piece about our new PNAS article, which explains how we engineered bacteria to encapsulate themselves in glass, allowing them to focus light like microlenses! @pnas.org
www.rochester.edu/newscenter/w...
www.rochester.edu/newscenter/w...
Can sea sponge biology transform imaging technology?
University of Rochester researchers draw inspiration from nature to create tiny, powerful microlenses for advanced image sensors.
www.rochester.edu
December 17, 2024 at 4:25 PM
Thank you to @urochester.bsky.social for writing this nice piece about our new PNAS article, which explains how we engineered bacteria to encapsulate themselves in glass, allowing them to focus light like microlenses! @pnas.org
www.rochester.edu/newscenter/w...
www.rochester.edu/newscenter/w...
Reposted by Xiaojing Gao
qPCR can measure expression of virtually any gene... in homogenized tissues. Here, we show an "in-vivo qPCR" equivalent, where we measure a sequence-specific transcript with synthetic serum markers and enzyme-based signal amplification.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 12, 2024 at 4:51 PM
qPCR can measure expression of virtually any gene... in homogenized tissues. Here, we show an "in-vivo qPCR" equivalent, where we measure a sequence-specific transcript with synthetic serum markers and enzyme-based signal amplification.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Xiaojing Gao
1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk
December 17, 2024 at 12:56 AM
1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk