Sid Venkatesh
@flash-point.bsky.social
Assistant Professor at ISB and UW Microbiology in Seattle, WA | Lover of collaboration, generosity and trust in science | Opinions are my own | https://venkatesh.isbscience.org/
Reposted by Sid Venkatesh
📣 Join us for the 2025 @isbscience.org Virtual Microbiome Symposium, focused on "Gut Microbial Metabolites and Their Impact on Host Systems".
co-director - @flash-point.bsky.social 🦠💥
It's free, & we have an amazing line-up of speakers!
Dec. 12th. Please share!
isbscience.org/2025-isb-vir...
co-director - @flash-point.bsky.social 🦠💥
It's free, & we have an amazing line-up of speakers!
Dec. 12th. Please share!
isbscience.org/2025-isb-vir...
2025 ISB Virtual Microbiome Symposium - Institute for Systems Biology (ISB)
Symposium Schedule All presentation times are shown in Pacific Daylight Time (GMT -07:00 / UTC -07:00) Time Talk / Session 9:00 Welcoming remarks by Sid Venkatesh Session One: Neural Effects
isbscience.org
November 13, 2025 at 7:13 AM
📣 Join us for the 2025 @isbscience.org Virtual Microbiome Symposium, focused on "Gut Microbial Metabolites and Their Impact on Host Systems".
co-director - @flash-point.bsky.social 🦠💥
It's free, & we have an amazing line-up of speakers!
Dec. 12th. Please share!
isbscience.org/2025-isb-vir...
co-director - @flash-point.bsky.social 🦠💥
It's free, & we have an amazing line-up of speakers!
Dec. 12th. Please share!
isbscience.org/2025-isb-vir...
Reposted by Sid Venkatesh
Reposted by Sid Venkatesh
Dr. Meghan Koch from @fredhutch.org has discovered a biological mechanism sprung in the first week of life that trains a mouse pup’s #ImmuneSystem to tolerate harmless gut bugs and new foods.
⚗️ Abstract: https://bit.ly/4nt6qGh
📰 Press release: https://bit.ly/46N7vBY
⚗️ Abstract: https://bit.ly/4nt6qGh
📰 Press release: https://bit.ly/46N7vBY
October 1, 2025 at 8:15 PM
Dr. Meghan Koch from @fredhutch.org has discovered a biological mechanism sprung in the first week of life that trains a mouse pup’s #ImmuneSystem to tolerate harmless gut bugs and new foods.
⚗️ Abstract: https://bit.ly/4nt6qGh
📰 Press release: https://bit.ly/46N7vBY
⚗️ Abstract: https://bit.ly/4nt6qGh
📰 Press release: https://bit.ly/46N7vBY
Reposted by Sid Venkatesh
Rubbing shoulders with a @nobelprize.bsky.social laureate! 🤩What a week!
Couldn’t have happened to a nicer person: isbscience.org/news/press-r...
@isbscience.org @naehasubramanian.bsky.social @flash-point.bsky.social @annabiosys.bsky.social
Couldn’t have happened to a nicer person: isbscience.org/news/press-r...
@isbscience.org @naehasubramanian.bsky.social @flash-point.bsky.social @annabiosys.bsky.social
October 8, 2025 at 12:19 AM
Rubbing shoulders with a @nobelprize.bsky.social laureate! 🤩What a week!
Couldn’t have happened to a nicer person: isbscience.org/news/press-r...
@isbscience.org @naehasubramanian.bsky.social @flash-point.bsky.social @annabiosys.bsky.social
Couldn’t have happened to a nicer person: isbscience.org/news/press-r...
@isbscience.org @naehasubramanian.bsky.social @flash-point.bsky.social @annabiosys.bsky.social
Reposted by Sid Venkatesh
This morning, @isbscience.org's Dr. Mary Brunkow was awarded the 2025 Nobel Prize in Physiology or Medicine! Dr. Brunkow shares the award with Fred Ramsdell and Shimon Sakaguchi. Read the press release here: www.nobelprize.org/.../medicine....
What a tremendous honor! Congratulations!
What a tremendous honor! Congratulations!
October 6, 2025 at 4:19 PM
This morning, @isbscience.org's Dr. Mary Brunkow was awarded the 2025 Nobel Prize in Physiology or Medicine! Dr. Brunkow shares the award with Fred Ramsdell and Shimon Sakaguchi. Read the press release here: www.nobelprize.org/.../medicine....
What a tremendous honor! Congratulations!
What a tremendous honor! Congratulations!
Reposted by Sid Venkatesh
The 2025 #NobelPrize in Physiology or Medicine has been awarded to Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi “for their discoveries concerning peripheral immune tolerance.”
October 6, 2025 at 9:51 AM
The 2025 #NobelPrize in Physiology or Medicine has been awarded to Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi “for their discoveries concerning peripheral immune tolerance.”
Many congratulations, Mary Brunkow! Couldn’t be happier for you and @isbscience.org ! ♥️
www.nobelprize.org
www.nobelprize.org
The official website of the Nobel Prize - NobelPrize.org
The Nobel Prize rewards science, humanism and peace efforts. This is one of the central concepts in the will of Alfred Nobel, and it also permeates the outreach activities that have been developed for...
www.nobelprize.org
October 6, 2025 at 11:46 AM
Many congratulations, Mary Brunkow! Couldn’t be happier for you and @isbscience.org ! ♥️
www.nobelprize.org
www.nobelprize.org
Reposted by Sid Venkatesh
It was an honor to highlight this fantastic work by Cheng and Venkatesh et al of the Gordon lab. Many thanks to them, and to Francis Chandra for doing all the heavy lifting on this Spotlight! @cp-cellchembiol.bsky.social
Great highlight by Chandra and @pipethero.bsky.social on recently published work by my colleague @flash-point.bsky.social (from his postdoc work) on endocannabanoids produced by specific members of the gut microbiota that likely impact host satiety/appetite. @isbscience.org
doi.org/10.1016/j.ch...
doi.org/10.1016/j.ch...
Redirecting
doi.org
January 4, 2025 at 9:40 AM
It was an honor to highlight this fantastic work by Cheng and Venkatesh et al of the Gordon lab. Many thanks to them, and to Francis Chandra for doing all the heavy lifting on this Spotlight! @cp-cellchembiol.bsky.social
Reposted by Sid Venkatesh
Happy to kick off 2025 with this new review on gut microbiota-neuroepithelial signaling by the very talented Taka Ohara!
January 4, 2025 at 9:50 AM
Happy to kick off 2025 with this new review on gut microbiota-neuroepithelial signaling by the very talented Taka Ohara!
Reposted by Sid Venkatesh
Great highlight by Chandra and @pipethero.bsky.social on recently published work by my colleague @flash-point.bsky.social (from his postdoc work) on endocannabanoids produced by specific members of the gut microbiota that likely impact host satiety/appetite. @isbscience.org
doi.org/10.1016/j.ch...
doi.org/10.1016/j.ch...
Redirecting
doi.org
January 3, 2025 at 5:44 PM
Great highlight by Chandra and @pipethero.bsky.social on recently published work by my colleague @flash-point.bsky.social (from his postdoc work) on endocannabanoids produced by specific members of the gut microbiota that likely impact host satiety/appetite. @isbscience.org
doi.org/10.1016/j.ch...
doi.org/10.1016/j.ch...
Reposted by Sid Venkatesh
Happy to see this paper, led by former grad student Cassie Chartier, out in its final form at Protein Science! We characterized the interaction between PTP1B and the ubiquitous signaling adaptor Grb2 and identified new PTP1B interactors along the way!
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
Allosteric regulation of the tyrosine phosphatase PTP1B by a protein–protein interaction
The rapid identification of protein–protein interactions has been significantly enabled by mass spectrometry (MS) proteomics-based methods, including affinity purification-MS, crosslinking-MS, and pr...
onlinelibrary.wiley.com
December 26, 2024 at 3:49 PM
Happy to see this paper, led by former grad student Cassie Chartier, out in its final form at Protein Science! We characterized the interaction between PTP1B and the ubiquitous signaling adaptor Grb2 and identified new PTP1B interactors along the way!
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
Reposted by Sid Venkatesh
Excited to share a new preprint from our lab, joint with the Bussemaker group, where we combined peptide display and selection with biophysically interpretable machine learning to build affinity models for SH2-phosphopeptide recognition.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression
Short linear peptide motifs play important roles in cell signaling. They can act as modification sites for enzymes and as recognition sites for peptide binding domains. SH2 domains bind specifically t...
www.biorxiv.org
December 24, 2024 at 6:00 PM
Excited to share a new preprint from our lab, joint with the Bussemaker group, where we combined peptide display and selection with biophysically interpretable machine learning to build affinity models for SH2-phosphopeptide recognition.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sid Venkatesh
Fantastic work! Congrats @nandangokhale.bsky.social, @ramlabuw.bsky.social and team.
Our work on cellular RNA interactions with MAVS that promote antiviral signaling is finally live. So grateful to our indispensable collaborators as well as reviewers who helped to strengthen our work. #RNA #innateimmunity #virology
@ramlabuw.bsky.social
www.science.org/doi/10.1126/...
@ramlabuw.bsky.social
www.science.org/doi/10.1126/...
Cellular RNA interacts with MAVS to promote antiviral signaling
Antiviral signaling downstream of RIG-I–like receptors (RLRs) proceeds through a multi-protein complex organized around the adaptor protein mitochondrial antiviral signaling protein (MAVS). Protein co...
www.science.org
December 20, 2024 at 5:02 PM
Fantastic work! Congrats @nandangokhale.bsky.social, @ramlabuw.bsky.social and team.
Finally caught up with some beautiful work from Alex Meeske in Nature! His lab has identified proteins in Listeria that either substitute for Cas in Cascade complexes (anti-type I-B CRISPR immunity) or degrade crRNA (anti-type VI-A CRISPR immunity). Inspiring stuff!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Diverse viral cas genes antagonize CRISPR immunity - Nature
We demonstrate that phages have co-opted cas genes from CRISPR defence systems, which subsequently evolved anti-defence functions.
www.nature.com
December 17, 2024 at 10:22 PM
Finally caught up with some beautiful work from Alex Meeske in Nature! His lab has identified proteins in Listeria that either substitute for Cas in Cascade complexes (anti-type I-B CRISPR immunity) or degrade crRNA (anti-type VI-A CRISPR immunity). Inspiring stuff!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Warm congratulations to my @isbscience.org colleagues @gibbological.bsky.social, Andrew Magis, and team for winning a 2024 Amazon Web Services IMAGINE grant for developing "My Digital Gut", an online platform for personalized, predictive, and preventive healthcare!
isbscience.org/news/2024/12...
isbscience.org/news/2024/12...
ISB Named Winner of 2024-2025 Amazon Web Services IMAGINE Grant for Nonprofits
ISB was selected as a winner of the 2024 Amazon Web Services (AWS) IMAGINE Grant, which will support continued development of My Digital Gut.
isbscience.org
December 12, 2024 at 5:08 PM
Warm congratulations to my @isbscience.org colleagues @gibbological.bsky.social, Andrew Magis, and team for winning a 2024 Amazon Web Services IMAGINE grant for developing "My Digital Gut", an online platform for personalized, predictive, and preventive healthcare!
isbscience.org/news/2024/12...
isbscience.org/news/2024/12...
Reposted by Sid Venkatesh
Bactericidal antibiotics release bacterial DNA that activates TLR9, while static antibiotics do not. This can profoundly impact treatment outcome. Should clinicians consider this when choosing antibiotics to prescribe?
Amazing work by Julia Gross and collaboration with Iain Fraser!
rdcu.be/d1Phk
Amazing work by Julia Gross and collaboration with Iain Fraser!
rdcu.be/d1Phk
Bactericidal antibiotic treatment induces damaging inflammation via TLR9 sensing of bacterial DNA
Nature Communications - The immunologic differences induced by bactericidal versus bacteriostatic antibiotics remain unclear. Gross et al. show that, in contrast to static antibiotics, cidal...
rdcu.be
December 2, 2024 at 2:17 PM
Bactericidal antibiotics release bacterial DNA that activates TLR9, while static antibiotics do not. This can profoundly impact treatment outcome. Should clinicians consider this when choosing antibiotics to prescribe?
Amazing work by Julia Gross and collaboration with Iain Fraser!
rdcu.be/d1Phk
Amazing work by Julia Gross and collaboration with Iain Fraser!
rdcu.be/d1Phk
Reposted by Sid Venkatesh
ISB Associate Professor Dr. Wei Wei has developed a promising new companion diagnostic tool called MetaboCore to help physicians quickly select the most effective systemic therapy for each cancer patient. Learn more: isbscience.org/news/2024/11...
ISB-Developed MetaboCore Offers Precision Cancer Care Faster Than Ever
ISB's MetaboCore is a diagnostic tool that can help physicians quickly select the most effective systemic therapy for each cancer patient.
isbscience.org
December 2, 2024 at 3:13 PM
ISB Associate Professor Dr. Wei Wei has developed a promising new companion diagnostic tool called MetaboCore to help physicians quickly select the most effective systemic therapy for each cancer patient. Learn more: isbscience.org/news/2024/11...
Reposted by Sid Venkatesh
This job has so many ups and downs, but one constant that I’m always thankful for is this creative, hard-working, supportive group (they support me, too!!). I’m also thankful for all the awesome ideas and cool data they generate, which keep us all motivated and stimulated and make this so much fun!
November 28, 2024 at 1:41 PM
This job has so many ups and downs, but one constant that I’m always thankful for is this creative, hard-working, supportive group (they support me, too!!). I’m also thankful for all the awesome ideas and cool data they generate, which keep us all motivated and stimulated and make this so much fun!
Innovative and inspiring biochemistry from Joe Luna @virologistjoe.bsky.social and colleagues that combines CLIP with proximity labeling to reveal RNA:RBP interactions at subcellular resolution! Congratulations for your first paper as a corresponding author ♥️
rnajournal.cshlp.org/content/30/7...
rnajournal.cshlp.org/content/30/7...
Mapping RNA–protein interactions with subcellular resolution using colocalization CLIP
A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
rnajournal.cshlp.org
November 27, 2024 at 6:53 PM
Innovative and inspiring biochemistry from Joe Luna @virologistjoe.bsky.social and colleagues that combines CLIP with proximity labeling to reveal RNA:RBP interactions at subcellular resolution! Congratulations for your first paper as a corresponding author ♥️
rnajournal.cshlp.org/content/30/7...
rnajournal.cshlp.org/content/30/7...
Reposted by Sid Venkatesh
First post on a lovely story from the lab that shows that Faecalibacterium prausnitzii can package its own genome in bite-size segments in phage-like capsids
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 26, 2024 at 5:14 PM
First post on a lovely story from the lab that shows that Faecalibacterium prausnitzii can package its own genome in bite-size segments in phage-like capsids
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sid Venkatesh
Delighted to share work by Kristie Yu, Celine Son, & co showing that selective fructan metabolism by the gut microbiome can contribute to host associative learning of dietary preference, even when it comes to choosing between diets with the same perceptual salience (and macronutrient composition!)
Complex carbohydrate utilization by gut bacteria modulates host food preference https://www.biorxiv.org/content/10.1101/2024.02.13.580152v1
Complex carbohydrate utilization by gut bacteria modulates host food preference https://www.biorxiv.org/content/10.1101/2024.02.13.580152v1
The gut microbiota interacts directly with dietary nutrients and has the ability to modify host feed
www.biorxiv.org
February 16, 2024 at 2:10 PM
Delighted to share work by Kristie Yu, Celine Son, & co showing that selective fructan metabolism by the gut microbiome can contribute to host associative learning of dietary preference, even when it comes to choosing between diets with the same perceptual salience (and macronutrient composition!)
Reposted by Sid Venkatesh
Some really beautiful biochemistry here. Seeing one dalton shifts to pinpoint how an enzyme from a nutrition-therapy-linked microbe works must be gratifying. Basic biochemistry lighting the way on an important problem. Congrats to my buddy Sid (@flash-point.bsky.social) and team on this one!
Last month, my co-first author, Dr. Jiye Cheng and I reported the identification of a gut microbial enzyme that impacts satiety-related signaling pathways in undernourished children treated with a microbiota-directed complementary food.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
A human gut Faecalibacterium prausnitzii fatty acid amide hydrolase
Undernutrition in Bangladeshi children is associated with disruption of postnatal gut microbiota assembly; compared with standard therapy, a microbiota-directed complementary food (MDCF) substantially...
www.science.org
November 25, 2024 at 8:32 PM
Some really beautiful biochemistry here. Seeing one dalton shifts to pinpoint how an enzyme from a nutrition-therapy-linked microbe works must be gratifying. Basic biochemistry lighting the way on an important problem. Congrats to my buddy Sid (@flash-point.bsky.social) and team on this one!
Co-varying coffee-derived metabolites are associated with L. asaccharolyticus! A cool paper by multiple luminaries in the field that set the stage for causal roles.
Accompanied by a commanding News & Views piece by Nate McNulty@npmcnulty.bsky.social and colleagues.
www.nature.com/articles/s41...
Accompanied by a commanding News & Views piece by Nate McNulty@npmcnulty.bsky.social and colleagues.
www.nature.com/articles/s41...
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts - Nature Microbiology
Coffee consumption is associated with the presence and abundance of a specific member of the human gut microbiome, Lawsonibacter asaccharolyticus, and changes to the plasma metabolome.
www.nature.com
November 26, 2024 at 2:44 PM
Co-varying coffee-derived metabolites are associated with L. asaccharolyticus! A cool paper by multiple luminaries in the field that set the stage for causal roles.
Accompanied by a commanding News & Views piece by Nate McNulty@npmcnulty.bsky.social and colleagues.
www.nature.com/articles/s41...
Accompanied by a commanding News & Views piece by Nate McNulty@npmcnulty.bsky.social and colleagues.
www.nature.com/articles/s41...
Mulling over a preprint from @nshahlab.bsky.social and colleagues on deep mutational scanning to yield insights into activity and regulation of the tyrosine phosphatase SHP2, as well as uncharacterized clinical variants. Beautiful work! ❤️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Deep mutational scanning of a multi-domain signaling protein reveals mechanisms of regulation and pathogenicity
Multi-domain signaling enzymes are often regulated through extensive inter-domain interactions, and disruption of inter-domain interfaces by mutations can lead to aberrant signaling and diseases. For ...
www.biorxiv.org
November 25, 2024 at 7:07 PM
Mulling over a preprint from @nshahlab.bsky.social and colleagues on deep mutational scanning to yield insights into activity and regulation of the tyrosine phosphatase SHP2, as well as uncharacterized clinical variants. Beautiful work! ❤️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...