Khalimat Murtazalieva

Can't wait to read this!

How can we tap into the enormous functional diversity of microbes on this planet?

Join us at EMBL Heidelberg (8–10 Dec 2026) to learn about ongoing efforts to decode gene function and organisation in human gut microbes, and present your science.

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2 Nature Methods - AF2BIND is a logistic regression model trained on AlphaFold2 pair features to predict small-molecule binding-site residues in proteins, without multiple sequence alignments,...

Our paper with @sokrypton.org using AlphaFold2 to predict small-molecule binding sites in proteins is now out in Nature Methods! 🧵
rdcu.be/e7SnX
www.nature.com/articles/s41...

First day wearing vision glasses! Seeing everything clearly, especially from a distance, makes such a big difference. It also made me realise how much my vision has deteriorated over the last few years and how important healthy habits are: good posture, the right work setup, and regular exercise.

After >10 years of our lab studying bacterial cGAS-like enzymes, @hobbslabutah.bsky.social finally reconstitutes viral sensing in vitro and discovers how these ancient receptors sense phage protease enzymes to detect virion assembly and activate antiviral immunity

www.biorxiv.org/content/10.6...

New AI in genomics fellowship with the sanger institute and Google DeepMind A new research fellowship will explore the application of AI in genomics, funded by Google DeepMind.

Postdoc on AI/biology funded by asanger and DeepMind!

www.sanger.ac.uk/news_item/ne...

Preprint: www.biorxiv.org/content/10.6...

Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions.

We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.

How to learn gene regulation patterns from multimodal single-cell data? To answer this question, we at OpenProblems organised the Kaggle competition on modality prediction. It ran back in 2022 but still remains the world's largest competition in the single-cell field. 1/17

Phage–host interactions are a key driver of microbial ecology, but observing them in nature is hard!
With metaHi-C, we detect freshwater phage–host pairs and link their infection dynamics to evolution.

Together with @nadal-molero.bsky.social & Ana Martin-Cuadrado

www.biorxiv.org/content/10.6...

1/5
Happy by a recent biorxiv pre-print about DARNA (PD-T7-3) anti-phage defense system. This system is activated by binding to ssDNA, presented by phage SSB, to cleave tRNA in the anti-codon loop.
www.biorxiv.org/content/10.6...

‘An AlphaFold 4’ – scientists marvel at DeepMind drug spin-off’s exclusive new AI Nature - Isomorphic Lab’s proprietary drug-discovery model is a major advance, but scientists developing open-source tools are left guessing how to achieve similar results.

“It’s a major advance, on the scale of an AlphaFold4. The problem, of course, is that we know nothing of the details.”

Isomorphic Lab’s proprietary drug-discovery model is a major advance
go.nature.com/4kHrHeR

Finding one mutation that improves a protein is hard. Finding five that work together is exponentially harder.

Today in @science.org, Hsu and Konermann labs present MULTI-evolve, a lab-in-the-loop framework that does it in just one machine learning-guided round.

Structure and mechanism of antiphage retron Eco2 Nature Structural & Molecular Biology - This study shows how the bacterial retron Eco2 defends against viruses. Phage nucleases trigger activation of Eco2, which cuts RNAs, shuts down protein...

1/6) Hot off the press @natsmb.nature.com 🔥! Jasnauskaite et al. reveal how the minimal bacterial retron Eco2 defends against #phage 🛡️. Phage nucleases trigger Eco2, which cuts RNA, shuts down protein production and stops phage replication 🦠🚫. #phagesky #immunity #microbiology #cryo-em rdcu.be/e4AyH

Koonin's lab in NIH is looking for postdocs. If you know someone who is interested, please spread the word. The details about the position are below: www.training.nih.gov/jobs/pdf-ecb...

Annotating genomes at increased scale and resolution Nature Reviews Genetics - In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and...

Our new review on genome annotation just appeared in @naturerevgenet.bsky.social, with a particular focus on the human genome, with Hayden Ji and Mihaela Pertea: rdcu.be/e4mI1

Inferring context-specific site variation with evotuned protein language models Abstract. Multiple sequence alignments (MSAs) have been traditionally used for making inferences about site-specific diversity in proteins. Recent advancem

Our paper on inferring context dependent entropy using protein language models is officially out in NAR Genomics & Bioinformatics! 🧬🤖

with Adam Strange, Jumpei Ito, and @systemsvirology.bsky.social

academic.oup.com/nargab/artic...

details below...

#NARGAB

Abstract submission is now OPEN for the 2026 Symposium on the Immune System of Bacteria!

sisb2026.rockefeller.edu
🗓 May 5–7, 2026
📍 Rockefeller University, New York City
⏰ Abstract deadline: March 16, 2026

Attendance will be capped, be sure to register early and secure your spot.

See you in NYC!

A fun little idea that worked surprisingly well, using a structure-informed yet structure-independent alphabet for de novo protein design: www.biorxiv.org/content/10.6...
🧵(1/n)

Are you hungry? We are curious about how people think about hunger while going about their daily routine. Remember there are no right or wrong answers, there are only your answers. Responses are anonymous.

I'm doing a market research about eating habits and appetite control. Are you hungry? 🙃

If you have 2 minutes, please fill in the Google form below (anonymous, unless you want to have a follow up chat): forms.gle/Mpc86LbhGSyH...

Spread the word!

Thank you!

On the balance of knowledge - Nature Reviews Immunology Ruslan Medzhitov shares his thoughts on the balance between generating data and developing theories in immunology, with a focus on exploring the rules that govern complex systems.

Too much data, too little thinking.
A important essay from Ruslan Medzhitov on the importance of understanding data, not just generating it. A must read.
@Yale
www.nature.com/articles/s41...

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

The immune systems paradox

Some widespread prokaryotic immune systems are absent in eukaryotes, whereas relatively rare ones became central to eukaryotic innate immunity

@audeber.bsky.social & E. Koonin hypothesize the answer is #HGT

shareable link: rdcu.be/e2EmD

www.nature.com/articles/s41...

Filament-mediated repurposing of toxic dITP for immunity in the Kongming system Feng et al. uncover how a bacterial immune effector, KomBC, is activated by the toxic nucleotide dITP. A preassembled filament converts sparse, non-cyclic dITP signals into cooperative NADase activation, revealing a distinct ultrasensitive immune mechanism.

Online Now: Filament-mediated repurposing of toxic dITP for immunity in the Kongming system Online now:

The plot thickens! Exciting new discoveries in the NAD⁺ centric battlefield between bacteria and phages. Congrats, Ilya!

EMBL-EBI Training. Sustainable computing in science: an introduction to the environmental impacts of computational research. This course has been developed in collaboration with the Cambridge Sustainable Computing Lab at the University of Cambridge. It was supported by funding from the Wellcome Trust Foundation and the University of Cambridge.

Have you ever paused and wondered about the many different ways in which computing infrastructure and activities impact the environment?

@loiclnlg.bsky.social and our own Flaminia Zane have created a free guide dedicated to sustainable computing in science: www.ebi.ac.uk/training/onl...

🧬🖥️📊🌱

Dimensions of cancer

In this @cp-cell.bsky.social review, Doug Hanahan shows how the Hallmarks of cancer framework has evolved over the last 25 years: http://dlvr.it/TQkrl9

We'll discuss this in depth @CellSymposia #CSHallmarks2026 http://dlvr.it/TQkrlF

DNA-protein cross-links promote cGAS-STING–driven premature aging and embryonic lethality DNA-protein cross-links (DPCs) are highly toxic DNA lesions that block replication and transcription, but their impact on organismal physiology is unclear. We identified a role for the metalloprotease...

Our Science paper is out! 😃

www.science.org/doi/10.1126/...

Chemical inhibition of a bacterial immune system Bacteriophages are promising alternatives to antibiotics for treating bacterial infections. However, bacteria possess immune systems that neutralize bacteriophages. Zang et al. discover small molecule...

Chemical inhibition of a bacterial immune system

Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. One compound, IP6C, improves phage-therapy against P. aeruginosa & is effective against Thoeris in polymicrobial communities
www.cell.com/cell-host-mi...

One of the best parts of travelling home is getting amazing gifts from my nieces 🎁

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...