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Khalimat Murtazalieva

@khalimat.bsky.social
109 followers 147 following 79 posts

MD, PhD

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Reposted by Khalimat Murtazalieva
Carl Zimmer @carlzimmer.com · 27/09/2026
Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc
nyti.ms
Did Anthropic’s A.I. Really Make a Scientific Discovery on Its Own? (Gift Article)
An expert at the University of Copenhagen said his team had been sharing its research with the company’s A.I. model, Claude, and that its new finding matched their work.
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Alexander Harms @aharms485.bsky.social · 25/09/2026
The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4
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Anthropic @anthropic.extwitter.link · 23/09/2026
Claude has discovered a previously unknown enzyme system hidden in the DNA of bacteriophages. Beside the enzyme’s gene sits a long array of repeating DNA—a structure that looks somewhat similar to CRISPR. We don’t yet understand what this system does, but only a handful of known systems share it...
anthropic.com
Claude discovers a novel enzyme system with CRISPR-like repeats
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 23/09/2026
A genome language model reveals the interactions hidden in non-coding DNA, pointing to new putative RNAs and repetitive elements in bacterial genomes. @garykbrixi.bsky.social @maxewilkinson.bsky.social @mfgrp.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.6...
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Malcolm White @mfwhite2.bsky.social · 16/09/2026
Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...
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Reposted by Khalimat Murtazalieva
Jason Nomburg @jnoms.bsky.social · 10/09/2026
This application closes on Sept 15! If you're interested in a computational postdoc position in my lab, please apply here! Lots of fun science :)
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Khalimat Murtazalieva @khalimat.bsky.social · 08/09/2026
👀👀👀
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Reposted by Khalimat Murtazalieva
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 08/09/2026
A fast method for building phylogenetic trees with millions of sequences and then a model that leverages the tree structure to predict viral protein evolution! @seyonec.bsky.social @claudiadriscoll.bsky.social @garykbrixi.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.6...
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Reposted by Khalimat Murtazalieva
Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
We find that nuclear Pol II drops several-fold in abundance with age. This is a somatic phenomenon–the germline seems to maintain Pol II just fine. Somatic declines in Pol II begin at the start of adulthood, a time when individuals still look young and vigorous. 11/22
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Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22
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Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 19/08/2026
😱! www.nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
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ContempraInn 🌹 @contemprainn.bsky.social · 12/08/2026
Solar Eclipse August 12th 2026, Valencia Spain 🇪🇦
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Jay @jayinbold.bsky.social · 12/08/2026
I didn’t think I’d ever see a solar eclipse with 100% totality, but that was absolutely unreal
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Nature Biotechnology @natbiotech.nature.com · 14/07/2026
The July issue is live nature.com/nbt/volumes/... On the cover, @ycongzhang.bsky.social @efranzosa.bsky.social @hutlab.bsky.social introduce FUGAsseM, a method that uses microbial community data to infer the functions of previously uncharacterized gene products go.nature.com/435C4lp rdcu.be/ftNUV
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Nature Biotechnology @natbiotech.nature.com · 23/07/2026
AI model using AlphaFold3-predicted contact probabilities maps and reduces genome editor off-targets, enabling highly precise DNA base editing with improved specificity. #NBThighlight www.nature.com/articles/s41...
nature.com
Precise DNA base editing using AlphaFold3-based contact modelling - Nature
ContactSeek is an AlphaFold3-driven model that can improve the precision of genome-editing tools.
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Reposted by Khalimat Murtazalieva
Kotaro Chihara @kochihara.bsky.social · 19/07/2026
New preprint on bioRxiv! 🧬 “Structural mechanism of the type IX Retron-Kva2 anti-phage defense system” Led by the Nishimasu lab (Univ. Tokyo) — happy to have been part of the team! 🔗 doi.org/10.64898/202...
doi.org
Structural mechanism of the type IX Retron-Kva2 anti-phage defense system
Retrons are prokaryotic genetic elements that protect bacterial cells from invading phages. The type IX retron comprises a non-coding RNA, a reverse transcriptase (RT), and dual effectors: a putative ...
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 16/07/2026
1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...
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yuxuan-xi.bsky.social @yuxuan-xi.bsky.social · 11/07/2026
Our new preprint is out! Using AI-guided design (RFdiffusion + ProteinMPNN), we engineered a plant immune receptor to recognise non-cognate pathogen effectors. Huge thanks to our amazing co-authors for making this possible! doi.org/10.64898/202...
doi.org
Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors.
The rapid evolution of plant pathogens poses a persistent threat to global agricultural sustainability, often outpacing the discovery and deployment of natural disease resistance genes. While bioengin...
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artemisaev.bsky.social @artemisaev.bsky.social · 10/07/2026
Thrilled to share! We present the structure of a prototypical P2 OLD and reveal that its tRNAse activity is triggered by ssDNA hairpins in phage origins or unresolved termini in RecBCD-deficient cells. Great team effort with Wang, Bikard & Nudler labs. www.biorxiv.org/content/10.6...
biorxiv.org
OLD sentinel: an abortive tRNase surveys phage replication and DNA defects in RecBCD-compromised cells
OLD, an abortive immunity protein from prophage P2, consists of an ABC ATPase sensor and a TO-PRIM nuclease effector - a core architecture shared by a large protein family, including components of ant...
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Jue Wang @juewang.bsky.social · 10/07/2026
The protein design team at Deepmind is hiring! We are looking for someone to run design campaigns and contribute to model improvement. Should have expertise in design applications and using wetlab data feedback to improve methods. Please RT! DM with Qs. www.google.com/about/career...
google.com
Research Scientist, Protein Design, DeepMind
As an organization, Google maintains a portfolio of research projects driven by fundamental research, new product innovation, product contribution and infrastructure goals, while providing individuals...
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artemisaev.bsky.social @artemisaev.bsky.social · 09/07/2026
Happy to share a preview of recent work from E. Koonin & colleagues, revealing the widespread presence of reparative helicases as central components of prokaryotic immune systems. Written by our talented PhD student Oksana. www.cell.com/cell-host-mi...
cell.com
A repair helicase unravels the tangled web of bacterial immunity
DNA repair proteins are repeatedly repurposed for antiviral immunity. In this issue of Cell Host & Microbe, Bell et al. utilized phylogenetic reconstruction of the evolutionary routes of the YprA repa...
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Reposted by Khalimat Murtazalieva
Protein Society @proteinsociety.bsky.social · 27/06/2026
📄 *Magnesium as a conformational gatekeeper of KRAS: Structural dynamics and therapeutic implications* (Fig. 6b) Read the full study in Protein Science: onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
Magnesium as a conformational gatekeeper of KRAS: Structural dynamics and therapeutic implications
Magnesium serves as an essential cofactor for small GTPases, yet its structural role in regulating KRAS conformational dynamics and nucleotide exchange remains poorly understood. Here, we combine hyd....
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Reposted by Khalimat Murtazalieva
Cambridge Diary @cambridgediary.bsky.social · 26/06/2026
The 2027 Cambridge Diary Calendar. It’s calendar time again when you have the opportunity to help decide which images make up the Cambridge Diary 2027 Calendar. This year we will be building the calendar live online at cambridgebooks.co.uk.
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AI Proteins @aiproteins.com · 25/06/2026
Three weeks ago, we welcomed the local scientific community to join us at our headquarters in Kenmore Square for the inaugural lecture in the AI Proteins Seminar Series. Our speaker Neil King from @uwproteindesign.bsky.social delivered a superb seminar. Check it out 👇 youtu.be/OPRMfRnlx1k
youtu.be
Neil King: ML-based design of nanoparticle vaccines (AI Proteins Seminar Series)
YouTube video by AI Proteins
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Reposted by Khalimat Murtazalieva
Arc Institute @arcinstitute.org · 23/06/2026
Imagine programming protein, DNA, and RNA systems like you would write computer code, or even by natural language prompting of an AI agent. @brianhie.bsky.social and team just made this a reality with Proto: a high-level programming language for generative biology.
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Nature Biotechnology @natbiotech.nature.com · 23/06/2026
Efficient generation of epitope-targeted antibodies with Germinal - @brianhie.bsky.social @synbiogaolab.bsky.social @stanford.edu @arcinstitute.org www.nature.com/articles/s41...
nature.com
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.
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Malcolm White @mfwhite2.bsky.social · 23/06/2026
The floodgates open…
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Grantham Research Institute at LSE @granthamlse.bsky.social · 23/06/2026
We regret that our event on Extreme Heat: Improving governance and strengthening action around the world has been cancelled due to the red extreme heat warning issued by the UK Met Office. Our apologies to everyone who was planning to attend the event.
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Ákos T Kovács @evolvedbiofilm.bsky.social · 12/06/2026
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity @natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino www.nature.com/articles/s41...
nature.com
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity - Nature Microbiology
The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of...
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Reposted by Khalimat Murtazalieva
David Ho @davidho.bsky.social · 21/06/2026
Norway is banning generative AI for schoolchildren under 13 starting in September.
techradar.com
Norway says math, reading, and writing come first as it introduces AI restrictions for under-13s
Norway is taking steps to limit how generative AI can be used in schools from the start of the next school year.
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Yunha Hwang @microyunha.bsky.social · 17/06/2026
Excited to share the latest version of FlashPPI published with @pnas.org ! And stay tuned for updates soon…👀
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Sergey Ovchinnikov @sokrypton.org · 15/06/2026
New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)
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artemisaev.bsky.social @artemisaev.bsky.social · 09/06/2026
The CRISPR-Cas system in E. coli K-12 is considered inactive. We questioned whether mobile elements encode anti-CRISPRs against this system and found a highly abundant AcrIE9-AcrIE10 tandem and a novel AcrIE13 — an HTH protein more similar to Aca than known Acrs. www.pnas.org/doi/10.1073/...
pnas.org
A census of anti-CRISPR proteins reveals AcrIE9 and AcrIE13 as inhibitors of the Escherichia coli K12 type IE CRISPR-Cas system | PNAS
CRISPR-Cas adaptive immunity systems provide defense against mobile genetic elements and are often countered by diverse anti-CRISPR (Acr) proteins....
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 06/06/2026
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 search.foldseek.com/folddisco
nature.com
Structural motif search across the protein universe with Folddisco - Nature Biotechnology
Folddisco enables protein structural motif search in million scale databases.
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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...
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Alex Crits-Christoph @acritschristoph.bsky.social · 27/05/2026
Looks promising at first glance, ... "A preprint describing the full results is available here and will be posted on bioRxiv" biohub.ai/papers/esm_p... ESMC (pLM): biohub.ai/models/esmc ESMFold2 (ESMC for prediction): biohub.ai/models/esmfo... Released at the ESM github: github.com/Biohub/esm/
biohub.ai
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Biohub @biohub.org · 27/05/2026
Proteins are the machinery of life. Billions of their sequences have been cataloged—but the biology behind most is still unknown. Today we're releasing ESMFold2, ESMC and ESM Atlas to help change that. Open source, open to every scientist. biohub.ai/esm/protein
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Khalimat Murtazalieva @khalimat.bsky.social · 21/05/2026
Absolute food obsession ❤️
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 11/05/2026
Genie3: all-atom SE3-equivariance for fast and performant protein design. @yeqinglin.bsky.social @moalquraishi.bsky.social www.biorxiv.org/content/10.6...
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Mart Krupovic @mkrupovic.bsky.social · 11/05/2026
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...
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Khalimat Murtazalieva @khalimat.bsky.social · 10/05/2026
it’s absolutely the best weather for hikes at Seven Sisters!
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Mohammed AlQuraishi @moalquraishi.bsky.social · 08/05/2026
Equivariance is dead! 😢 Or is it? 😈 Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa. It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇
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Sam Horsfield @samuelhorsfield.bsky.social · 05/05/2026
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
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Science Magazine @science.org · 04/05/2026
Bangladesh is in the grip of an explosive measles epidemic, stemming from a catastrophic breakdown in vaccine procurement following the country’s 2024 revolution. The result was nationwide vaccine shortages and plummeting immunization rates. scim.ag/4tM2lAr
scim.ag
Measles explodes in Bangladesh after vaccination breakdown, killing hundreds of children
Changes to government’s vaccine purchase system after 2024 revolution led to nationwide shortages, gaps in immunity
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Sar Crespi @boron110.bsky.social · 01/05/2026
"... that challenge only seems to motivate Farid and his team, who are constantly probing the programs that generate AI video, audio, and images, looking for new weaknesses." Fantastic story by @kakape.bsky.social @science.org www.science.org/content/arti...
science.org
Deepfakes are everywhere. The godfather of digital forensics is fighting back
Hany Farid, who's spent his career building tools to detect fake images, is facing his biggest challenge yet: AI
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Veesler lab @veeslerlab.bsky.social · 29/04/2026
Can we use #proteindesign to develop countermeasures before viruses cause pandemics? We describe the computational design of an ultrapotent and broadly neutralizing deltacoronavirus miniprotein in our latest work led by Nathan Avery @hhmi-science.bsky.social 1/12 www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Nature Microbiology @natmicrobiol.nature.com · 27/04/2026
Out Now! Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity #MicroSky
go.nature.com
Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity
Nature Microbiology, Published online: 27 April 2026; doi:10.1038/s41564-026-02312-8A large-scale, comparative cell biology and biochemical screen defines the molecular features controlling antiphage defence systems that encode nuclease effectors and accessory NTPase proteins.
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Lisa Guerrero @lisaguerrero.bsky.social · 26/04/2026
Sanity break: My 87-year-old dad, Walter Coles, walks along the beach almost every day armed with his camera and an eye for beauty. (Huntington Beach in Orange County, CA.) He shot these images the other day and I wanted to share them with you. 🫶🏽
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Inga Songailiene @ingasongailiene.bsky.social · 25/04/2026
slide from my science outreach talk last week, - some books for those interested in life sciences, microbiology, phages 🧫🧬
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Nature Reviews Microbiology @natrevmicro.nature.com · 23/04/2026
New online! Phage host range: determinants, dynamics and applications
dlvr.it
Phage host range: determinants, dynamics and applications
Nature Reviews Microbiology, Published online: 23 April 2026; doi:10.1038/s41579-026-01306-xComprehensive assessment of the host range of phages is a prerequisite for their safe and effective use in multiple applications but is rarely undertaken. This Review outlines the molecular and ecological determinants of phage host range and discusses the importance of these determinants for developing phage-based applications.
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