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khalimat.bsky.social
Khalimat Murtazalieva
@khalimat.bsky.social
70 followers 100 following 64 posts
PhD student interested in molecular arms race and protein biology @cam.ac.uk. MD, Russian National Research Medical University.
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khalimat.bsky.social
Khalimat Murtazalieva @khalimat.bsky.social · Jun 8
Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at ‪EMBL-EBI (@ebi.embl.org)‬
and the University of Cambridge (@cam.ac.uk‬)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
Elucidating the mechanisms of action and evolutionary history of phage anti-defence proteins
Phages and bacteria are locked in a molecular arms race, with phage anti-defence proteins (ADPs) enabling them to evade bacterial immune systems. To streamline access to information on ADPs, we develo...
www.biorxiv.org
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khalimat.bsky.social
Khalimat Murtazalieva @khalimat.bsky.social · 8h
Absolutely loved the paper! Such a beautiful mechanism!
Reposted by Khalimat Murtazalieva
benadler.bsky.social
Ben Adler @benadler.bsky.social · 7d
Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.

Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
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Reposted by Khalimat Murtazalieva
benmorehouse.bsky.social
Ben Morehouse @benmorehouse.bsky.social · 7d
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature
The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.
www.nature.com
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khalimat.bsky.social
Khalimat Murtazalieva @khalimat.bsky.social · 5d
Seeing this I am so convinced to do a postdoc in Switzerland!
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Reposted by Khalimat Murtazalieva
kranzuschlab.bsky.social
Kranzusch Lab @kranzuschlab.bsky.social · 9d
>18,000 new genomes of giant DNA viruses! An incredible trove of new genes and insights into evolution of host-virus interactions from @fmschu.bsky.social and @jgi.doe.gov

www.biorxiv.org/content/10.1...
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Reposted by Khalimat Murtazalieva
ulad-litvin.bsky.social
Ulad Litvin @ulad-litvin.bsky.social · 12d
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵

📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
doi.org
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Reposted by Khalimat Murtazalieva
ebi.embl.org
EMBL-EBI @ebi.embl.org · 12d
Antimicrobial resistance (AMR) causes over a million deaths each year, and is rising.

Scientists analysed 40,000 bacterial plasmids across 100 years and six continents, to reveal that a few plasmids evolved after antibiotic use to drive most multi-drug resistance.

www.ebi.ac.uk/about/news/r...
🧬💻
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Reposted by Khalimat Murtazalieva
mjendrusch.bsky.social
Michael Jendrusch @mjendrusch.bsky.social · 14d
With this, the last bit of my PhD at @embl.org is finally out!
We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models.
Paper: nature.com/articles/s42256-…
Code: github.com/mjendrusch/salad
Data: zenodo.org/records/14711580
1/🧵
embl.org
EMBL @embl.org · 14d
‘Salad’ – a new AI model from EMBL scientists – offers major improvements in synthetic protein design.

Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields.

www.nature.com/articles/s42...
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Reposted by Khalimat Murtazalieva
biorxiv-microbiol.bsky.social
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 14d
The co-localizing Zorya II, Druantia III, and ARMADA II defense systems on O-island 172 confer synergistic anti-phage defense in enterohemorrhagic Escherichia coli https://www.biorxiv.org/content/10.1101/2025.09.22.677730v1
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Reposted by Khalimat Murtazalieva
jeremyjbarr.bsky.social
Jeremy Barr @jeremyjbarr.bsky.social · 14d
Excited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology.

www.nature.com/articles/s41...
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections - Nature Microbiology
The Entelli-02 phage product containing five phages has frontline potential to address infections caused by the multidrug-resistant Enterobacter cloacae complex.
www.nature.com
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khalimat.bsky.social
Khalimat Murtazalieva @khalimat.bsky.social · 16d
Drafted the thesis 💃🎉, so hopefully 🤞 I’ll have time to clean the apartment and go to the gym 😅.
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Reposted by Khalimat Murtazalieva
dplazasaez.bsky.social
Daniel Plaza Sáez @dplazasaez.bsky.social · 19d
Great time at The New Microbiology @embo.org | FEBS course at Spetses! 🇬🇷

Truly thankful to attend and meet amazing researchers that shared their great stories and advice!

One of the best courses I have ever participated! 😄

Lots of new insights, connections, and inspiration! 🦠 🧬

Thanks @AMI 🙏
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Reposted by Khalimat Murtazalieva
mmarbout.bsky.social
Martial Marbouty @mmarbout.bsky.social · 19d
You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social

www.nature.com/articles/s41...
Phages with a broad host range are common across ecosystems - Nature Microbiology
Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.
www.nature.com
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Reposted by Khalimat Murtazalieva
natmethods.nature.com
Nature Methods @natmethods.nature.com · 20d
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio

www.nature.com/articles/s41...
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
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khalimat.bsky.social
Khalimat Murtazalieva @khalimat.bsky.social · 20d
Can't wait to read this! Exciting that filtering based on genome tropisms works so well!
kevinkaichuang.bsky.social
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 21d
Genome language models can generate new, high-fitness bacteriophages!

@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social

www.biorxiv.org/content/10.1...
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Reposted by Khalimat Murtazalieva
zaminiqbal.bsky.social
Zamin Iqbal @zaminiqbal.bsky.social · 21d
John is one of the best PhD supervisors you could hope for, recommended highly!!
bacpop.org
John Lees @bacpop.org · 21d
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...

We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
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Reposted by Khalimat Murtazalieva
emmseveri.bsky.social
Emmanuele Severi @emmseveri.bsky.social · 22d
academic.oup.com/nar/article/...

#phagesky #phage

OLDie but goodie
OLD amputates the anticodon arm of tRNAs during P2–Lambda interference
Abstract. ATPase-coupled Toprim (Topoisomerase-primase) nucleases, known as Overcoming Lysogenization Defect (OLD) proteins, are crucial for diverse antiph
academic.oup.com
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Reposted by Khalimat Murtazalieva
emmseveri.bsky.social
Emmanuele Severi @emmseveri.bsky.social · 22d
www.biorxiv.org/content/10.1...

#phagesky #phage
YprA family helicases provide the missing link between diverse prokaryotic immune systems
Bacteria and archaea possess an enormous variety of antivirus immune systems that often share homologous proteins and domains, some of which contribute to diverse defense strategies. YprA family helic...
www.biorxiv.org
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Reposted by Khalimat Murtazalieva
natmethods.nature.com
Nature Methods @natmethods.nature.com · 26d
Mutational effect transfer learning (METL) is a biophysics-based protein language model that excels in challenging protein engineering tasks.

www.nature.com/articles/s41...
Biophysics-based protein language models for protein engineering - Nature Methods
Mutational effect transfer learning (METL) is a protein language model framework that unites machine learning and biophysical modeling. Transformer-based neural networks are pretrained on biophysical ...
www.nature.com
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Reposted by Khalimat Murtazalieva
cam.ac.uk
University of Cambridge @cam.ac.uk · 27d
What if your sore joints could treat themselves? 🦴

Cambridge scientists have developed an ‘artificial cartilage’ that could transform treatment for #arthritis – and improve outcomes for millions of people.

Learn more about this 'squishy' material 👇
https://bit.ly/4mPMzkq
Close-up of a person holding their knee, with an inset diagram illustrating artificial cartilage technology. A text overlay beneath the image reads: "'Artificial cartilage' could improve arthritis treatment, say Cambridge researchers".
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Reposted by Khalimat Murtazalieva
jrpenades.bsky.social
José R Penadés @jrpenades.bsky.social · 29d
Our second paper with @tcostalab.bsky.social and GoogleDeepMind
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution
By solving a previously unsolved biological question, the AI co-scientist predicted a complex mechanism of gene transfer and generated hypotheses that opened new research directions, illustrating AI's...
www.cell.com
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Reposted by Khalimat Murtazalieva
drdorsalomon.bsky.social
Dor Salomon @drdorsalomon.bsky.social · Sep 8
🚨 Happy to share our new preprint in which we explore different layers of the phage-bacteria arms race.
The highlight: phage homing endonucleases attenuate bacterial defenses 🤯
A 🧵... (1/7)
#bacteriology #antiphage #T6SS
www.biorxiv.org/content/10.1...
Phage-encoded homing endonucleases attenuate bacterial immunity
The arms race between bacteria and bacteriophages (phages) gave rise to multiple layers of antagonistic mechanisms, many of which remain unexplored. Here, we investigated the anti-phage defense system...
www.biorxiv.org
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khalimat.bsky.social
Khalimat Murtazalieva @khalimat.bsky.social · Sep 8
Любопытно открыть статью с огромным числом цитат и обнаружить там такое...
Reposted by Khalimat Murtazalieva
emmseveri.bsky.social
Emmanuele Severi @emmseveri.bsky.social · Sep 8
www.biorxiv.org/content/10.1...

#phagesky #phage
Phage-encoded homing endonucleases attenuate bacterial immunity
The arms race between bacteria and bacteriophages (phages) gave rise to multiple layers of antagonistic mechanisms, many of which remain unexplored. Here, we investigated the anti-phage defense system...
www.biorxiv.org
4 8
Reposted by Khalimat Murtazalieva
zaminiqbal.bsky.social
Zamin Iqbal @zaminiqbal.bsky.social · Sep 7
For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...
Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling
Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...
www.biorxiv.org
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