Sidra Khan
@sidrakhan.bsky.social
All about bacterial immunity and why it's cool.
Postdoc at University of Virginia
Postdoc at University of Virginia
Reposted by Sidra Khan
Identifying #antiphage defense systems can be challenging. This study by @duerkoplab.bsky.social describes a #bioinformatic pipeline that uses a small serine recombinase as a genetic marker to identify novel antiphage defense systems across diverse bacterial phyla.
🧪 #AcademicSky
plos.io/4i4ZrUu
🧪 #AcademicSky
plos.io/4i4ZrUu
September 3, 2026 at 12:05 PM
Identifying #antiphage defense systems can be challenging. This study by @duerkoplab.bsky.social describes a #bioinformatic pipeline that uses a small serine recombinase as a genetic marker to identify novel antiphage defense systems across diverse bacterial phyla.
🧪 #AcademicSky
plos.io/4i4ZrUu
🧪 #AcademicSky
plos.io/4i4ZrUu
Reposted by Sidra Khan
Wen Zhou previously led research in our group on evolution of the DNA-binding sites that control human cGAS activation. Beautiful work from his own lab at SUSTech University now extends similar insights to evolution of TREX1 regulation:
www.cell.com/immunity/abs...
www.cell.com/immunity/abs...
April 27, 2026 at 8:22 PM
Wen Zhou previously led research in our group on evolution of the DNA-binding sites that control human cGAS activation. Beautiful work from his own lab at SUSTech University now extends similar insights to evolution of TREX1 regulation:
www.cell.com/immunity/abs...
www.cell.com/immunity/abs...
Reposted by Sidra Khan
Want to find #prophage in your #bacteria genomes? We built PhiSpy a long time ago, and now we've created a new web page for it: linsalrob.github.io/PhiSpyWeb/
Best of all, the data never leaves your computer!
#phage #phagesky
Best of all, the data never leaves your computer!
#phage #phagesky
PhiSpyWeb – Browser-based Prophage Prediction
Browser-based prophage prediction using PhiSpy, Pyodide, and WebAssembly
linsalrob.github.io
May 6, 2026 at 12:26 AM
Want to find #prophage in your #bacteria genomes? We built PhiSpy a long time ago, and now we've created a new web page for it: linsalrob.github.io/PhiSpyWeb/
Best of all, the data never leaves your computer!
#phage #phagesky
Best of all, the data never leaves your computer!
#phage #phagesky
Reposted by Sidra Khan
🔥Preprint fresh off the press🔥
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
www.biorxiv.org
April 4, 2026 at 1:23 AM
🔥Preprint fresh off the press🔥
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
Reposted by Sidra Khan
A defense system that protects against RNA viruses by sensing a conserved RNA structure in the viral genome - cool!
Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
March 21, 2026 at 8:22 PM
A defense system that protects against RNA viruses by sensing a conserved RNA structure in the viral genome - cool!
Reposted by Sidra Khan
Reposted by Sidra Khan
How diverse is bacterial immunity ?
We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...
Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...
Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
www.science.org
April 2, 2026 at 6:44 PM
How diverse is bacterial immunity ?
We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...
Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...
Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
Reposted by Sidra Khan
How do you kill a MRSA superbug armed with 15 different anti-phage defense systems? You make a smarter phage. Check out our latest preprint on overcoming bacterial immunity using defense-guided engineering to build durable therapeutic phage cocktails! Led by Sarah Voss. doi.org/10.64898/202...
March 27, 2026 at 6:08 PM
How do you kill a MRSA superbug armed with 15 different anti-phage defense systems? You make a smarter phage. Check out our latest preprint on overcoming bacterial immunity using defense-guided engineering to build durable therapeutic phage cocktails! Led by Sarah Voss. doi.org/10.64898/202...
Reposted by Sidra Khan
Happy to share the final version of my postdoc work on bacterial CBASS immunity with @aaronwhiteley.bsky.social published in @cp-cellhostmicrobe.bsky.social
www.cell.com/cell-host-mi...
www.cell.com/cell-host-mi...
Bacterial 2′,3′-cGAMP activates a SAVED effector to form membrane-disrupting filaments and restrict phage replication
Tak et al. discover that bacteria use 2′,3′-cGAMP, the same signaling molecule employed
by mammalian cGAS-STING, for phage defense. In response to phage, 2′,3′-cGAMP activates
filament formation of Ca...
www.cell.com
March 27, 2026 at 4:32 PM
Happy to share the final version of my postdoc work on bacterial CBASS immunity with @aaronwhiteley.bsky.social published in @cp-cellhostmicrobe.bsky.social
www.cell.com/cell-host-mi...
www.cell.com/cell-host-mi...
Reposted by Sidra Khan
Host innate immune response profiling reveals hidden viral infections across diverse animal species https://www.biorxiv.org/content/10.64898/2026.03.16.711951v1
March 17, 2026 at 3:26 AM
Host innate immune response profiling reveals hidden viral infections across diverse animal species https://www.biorxiv.org/content/10.64898/2026.03.16.711951v1
Can't believe I actually managed to get my name as a social media handle, sans the random numbers or letters
November 13, 2024 at 8:05 PM
Can't believe I actually managed to get my name as a social media handle, sans the random numbers or letters
I’m really enjoying the vibe on Bluesky right now. I joined Twitter super late (like a year ago) and always felt like I was playing catch-up. Here, it feels like everyone’s figuring things out together, and it’s exciting! You know what I mean?😅
November 13, 2024 at 12:41 PM
I’m really enjoying the vibe on Bluesky right now. I joined Twitter super late (like a year ago) and always felt like I was playing catch-up. Here, it feels like everyone’s figuring things out together, and it’s exciting! You know what I mean?😅
Sharing this preprint here again🚨📢
The study shows that a clinical mutation in the uvrA DNA repair gene gives Mycobacterium tuberculosis a survival edge inside the host!🦠🔬This finding could open doors to understanding Mtb resistance and persistence. Check it out!🔗
www.biorxiv.org/content/10.1...
The study shows that a clinical mutation in the uvrA DNA repair gene gives Mycobacterium tuberculosis a survival edge inside the host!🦠🔬This finding could open doors to understanding Mtb resistance and persistence. Check it out!🔗
www.biorxiv.org/content/10.1...
A clinical mutation in uvrA, a DNA repair gene, confers survival advantage to Mycobacterium tuberculosis in the host
DNA repair pathways play an essential role in maintaining the genomic integrity of bacteria, and a perturbation in their biological activity helps bacteria survive under duress. In drug-resistant clin...
www.biorxiv.org
November 12, 2024 at 3:04 PM
Sharing this preprint here again🚨📢
The study shows that a clinical mutation in the uvrA DNA repair gene gives Mycobacterium tuberculosis a survival edge inside the host!🦠🔬This finding could open doors to understanding Mtb resistance and persistence. Check it out!🔗
www.biorxiv.org/content/10.1...
The study shows that a clinical mutation in the uvrA DNA repair gene gives Mycobacterium tuberculosis a survival edge inside the host!🦠🔬This finding could open doors to understanding Mtb resistance and persistence. Check it out!🔗
www.biorxiv.org/content/10.1...
Gotta say, I miss the bookmark button from Twitter. Guess I'm just over here bookmarking things in my brain now... wish me luck.
November 12, 2024 at 12:18 PM
Gotta say, I miss the bookmark button from Twitter. Guess I'm just over here bookmarking things in my brain now... wish me luck.
Nothing like a bit of academic peer pressure to push you to a new platform👋
Academic Twitter said, "The cool scientists are over here now!"
Academic Twitter said, "The cool scientists are over here now!"
November 11, 2024 at 5:30 PM
Nothing like a bit of academic peer pressure to push you to a new platform👋
Academic Twitter said, "The cool scientists are over here now!"
Academic Twitter said, "The cool scientists are over here now!"