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Kiarash Jamali

@kjamali.bsky.social
1.9K followers 1.5K following 24 posts

Group Leader at the Generative Biology Institute, EIT, Oxford, UK. Researching machine learning approaches applied to biology, specifically protein design. Lab website: jamalilab.com

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Reposted by Kiarash Jamali
Sjors Scheres @sjorsscheres.bsky.social · 8h
Our adventures into #proteinfolding: GuideFlip designs flexible molecular interactions by discrete flow matching to design sequence & structure together! Grateful for funding by Love Tito's (@titosvodka.bsky.social) and the @ukri.org. 🥳
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Kiarash Jamali @kjamali.bsky.social · 22h
Please check out our cool new method, GuideFlip! Optimised for binders against disordered proteins
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Kai Yi @kaiyi94.bsky.social · 22h
6/7 We further apply GuideFlip to a curated set of 285 human DisProt targets. For 177 (62.1%), at least one design passed our computational filters. These are predicted candidates. Explore complexes and download sequences: huggingface.co/spaces/ykiii...
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Kai Yi @kaiyi94.bsky.social · 22h
1/7 Excited to share GuideFlip! We use guided discrete flow matching to co-design protein sequences and structures for flexible interactions, with experimental validation across three systems: α-synuclein, RBX1 and active-state GPCR nanobodies.
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Tanmay Bharat @tbharat-lab.bsky.social · 15/07/2026
Structural basis of biofilm formation mediated by the Pseudomonas aeruginosa fibrillar adhesin CdrA led by @olivia--smith.bsky.social Collaboration with @alexbateman1.bsky.social , Andres Floto and @geiselbiofilm.bsky.social labs
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Kiarash Jamali @kjamali.bsky.social · 28/04/2026
Thrilled with this result, tune in for more soon!
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Kai Yi @kaiyi94.bsky.social · 28/04/2026
Thrilled with the our results with @kjamali.bsky.social and @sjorsscheres.bsky.social from the recent binder competition! 🎉 2 of our 7 designs successfully bound to the target, with affinities ranking 2nd and 3rd overall. All of these designs targeted the disordered region of the protein.
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Sjors Scheres @sjorsscheres.bsky.social · 28/04/2026
The #ADFLIP approach by @kaiyi94.bsky.social and @kjamali.bsky.social, combined with their approach to backpropagation through #AlphaFold2, is really powerful. Keep tuned for more exciting results! 🥳
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Joe Greener @jgreener64.bsky.social · 01/04/2026
On this 1st April I'm happy to release a technical report from our startup MirageBio, describing a new protein structure model with state-of-the-art performance. jgreener64.github.io/posts/techni...
jgreener64.github.io
MirageBio technical report
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Reposted by Kiarash Jamali
Kelly Nguyen @kellythd-nguyen.bsky.social · 26/03/2026
Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍. www.science.org/doi/10.1126/... www.youtube.com/watch?v=gFE4...
youtube.com
Cryo-EM structure of yeast telomerase
YouTube video by MRC Laboratory of Molecular Biology
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 24/02/2026
Are you a structural biologist pushing the boundaries of molecular science with an ambitious research programme? Join our Structural Studies Division as a tenure-track Group Leader, with core funding, world-leading facilities & enthusiastic colleagues. Apply by 16 MAR www.nature.com/naturecareer...
Job opening for Research Group Leader in Structural Studies at MRC Laboratory of Molecular Biology, focusing on macromolecular structures.
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bioRxivpreprint @biorxivpreprint.bsky.social · 24/02/2026
A portable orthogonal replication system enables continuous gene evolution near the biological speed limit www.biorxiv.org/content/10.64898/20…
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Sjors Scheres @sjorsscheres.bsky.social · 16/02/2026
Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. 🥳 mrc.tal.net/vx/mobile-0/...
mrc.tal.net
Research Group Leader Tenure Track - Structural Studies - LMB 2775 - Medical Research Council
Location: Cambridge. Vacancy: Research Group Leader Tenure Track - Structural Studies - LMB 2775. Closing Date: 16/03/2026, 23:55
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Sjors Scheres @sjorsscheres.bsky.social · 09/12/2025
Star student & postdoc Kiarash Jamali is setting up his own group at the Ellison institute in Oxford. Join him for the most exciting machine learning research in structural biology and beyond!! 🤩 #ProudPI
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Bogdan Toader @btoader.com · 09/12/2025
Join ML wizard Kiarash to develop BioML methods that work
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Joe Greener @jgreener64.bsky.social · 09/12/2025
Kiarash is starting his research group on computational enzyme design, get in touch with him if you want to be part of it.
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Kiarash Jamali @kjamali.bsky.social · 09/12/2025
I’m excited to announce that I will be starting my research group on computational enzyme design at the Generative Biology Institute, Oxford, UK (@eitoxford.bsky.social)! PhD applications are open, deadline is Jan 8th (www.chem.ox.ac.uk/genbio-dtp). Email kiarash.jamali@eit.org with any questions!
chem.ox.ac.uk
GenBio DTP
Optional supporting text
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Gautam Dey @gautamdey.bsky.social · 07/11/2025
And just when you thought things were settling down, the enigmatic Asgard archaea have another surprise in store! Cell cycle/life cycle stage-specific internal compartments with almost no eukaryote-derived clues as to how they might function. Beautiful tomography and microscopy - congrats all 🤩
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Kiarash Jamali @kjamali.bsky.social · 07/11/2025
Incredible work!
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Reposted by Kiarash Jamali
Tanmay Bharat @tbharat-lab.bsky.social · 07/11/2025
An Asgard archaeon with internal membrane compartments Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors! www.biorxiv.org/content/10.1...
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Max Wilkinson @maxewilkinson.bsky.social · 31/10/2025
The Wilkinson Lab is open for science! @mskcancercenter.bsky.social 🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬 annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
wilkinsonlab.bio
Wilkinson Lab
We discover and study reverse transcriptases
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John Rubinstein @johnrubinstein.bsky.social · 30/10/2025
New lab preprint! @zestytoast.bsky.social tagged a scarce mycobacterial protein in M. smegmatis with TwinStep but got… something? @kjamali.bsky.social's ModelAngelo built models & @martinsteinegger.bsky.social's FoldSeek IDed them as the biotin-containing MCC & LCC complexes 🧵 tinyurl.com/ukny4ptz
Cryo-EM maps and atomic models of the biotin-containing 3-methylcrotonyl-CoA carboxylase (MCC) complex and long-chain acyl-CoA carboxylase (LCC) complex
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Sjors Scheres @sjorsscheres.bsky.social · 29/10/2025
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated. mrc.tal.net/vx/appcentre...
mrc.tal.net
Quick Check Needed
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Sjors Scheres @sjorsscheres.bsky.social · 05/10/2025
If you are interesting in developing new algorithms for #cryoEM as a #PhD student or as a #postdoc, then do email or DM me. We have exciting opportunities coming up.
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Annika Inampudi @annikainampudi.bsky.social · 06/08/2025
Researchers found that low lithium levels are linked to Alzheimer's disease in humans, and restoring it can reverse cognitive decline in mice. For a field still searching for cure, this paper may offer a clever new approach 🧠 Read more about it in @science.org www.science.org/content/arti...
science.org
Could lithium stave off Alzheimer’s disease?
The metal is depleted in brains of people with disease and can reverse memory symptoms in mice, new study shows
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 01/08/2025
Rewriting the language of life: Jason Chin’s group in the LMB’s PNAC Division have synthesised E. coli with just 57 codons instead of the usual 64. Syn57 required 101000+ codon changes & represents a bold step towards programmable life. Read more: www2.mrc-lmb.cam.ac.uk/syn57-repres... #LMBResearch🧪
Glowing E. coli bacteria in green and blues on a background of DNA bases
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Martin Pacesa @martinpacesa.bsky.social · 25/07/2025
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
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Kieran Didi @kdidi.bsky.social · 19/07/2025
Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!
research.nvidia.com
La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
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Julien Capin @ju-cap.bsky.social · 17/07/2025
You designed binders for your favourite protein and wish there was a way to experimentally screen them within 24h w/ only a set of pipettes and a plate reader? Check out our Cell-Free 2-Hybrid approach (CF2H) Full post: tinyurl.com/48cz5nb6 Preprint: www.biorxiv.org/cgi/content/...
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Sjors Scheres @sjorsscheres.bsky.social · 15/07/2025
Our entrance into protein design! Inverse folding steered by external sources of information, and for multiple conformations. By the amazing @kaiyi94.bsky.social and @kjamali.bsky.social! Download our code and try it yourself. 🥳
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Sjors Scheres @sjorsscheres.bsky.social · 07/07/2025
Many congratulations to Dr Kiarash Jamali @kjamali.bsky.social for successfully defending his PhD thesis today! 🥳 Also many thanks to Jonas Adler and Randy Read for examining him. I expect great things from Dr Jamali in his career, so do keep an eye on him. #ModelAngelo
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Elizabeth Villa @thevillalab.bsky.social · 10/06/2025
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Joe Parham @joeparham19.bsky.social · 29/05/2025
We are excited to share our preprint describing how Sulfolobus cells coordinate DNA segregation with cell division! In eukaryotes this type of regulation involves checkpoints and CDK-cyclins. But how does this work in archaea? This is the question we ask in our paper: www.biorxiv.org/content/10.1...
biorxiv.org
Temporal and spatial coordination of DNA segregation and cell division in an archaeon.
Cells must coordinate DNA segregation with cytokinesis to ensure that each daughter cell inherits a complete genome. Here, we explore how DNA segregation and division are mechanistically coupled in ar...
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Arjen Jakobi @cryotud.bsky.social · 26/05/2025
LocScale-SURFER is now also available for quick install via the ChimeraX toolshed: cxtoolshed.rbvi.ucsf.edu
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Diego del Alamo @delalamo.xyz · 15/05/2025
"Adapting ProteinMPNN for antibody design without retraining" Our several-years-old fix to ProteinMPNN's tendency to make weird antibody CDR sequences is finally preprinted
biorxiv.org
Adapting ProteinMPNN for antibody design without retraining
The neural network ProteinMPNN designs protein sequences capable of folding into predefined tertiary structures and quaternary assemblies. It has become widely used due to its high success rates when ...
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Reposted by Kiarash Jamali
Dawid Zyla @dzyla.bsky.social · 27/04/2025
1/5: Over the last few months, I have been working on an update for the #FollowRelionGracefully dashboard, which offers improved real-time job previews for #cryoEM #Relion jobs.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 27/04/2025
AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...
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Kelly Nguyen @kellythd-nguyen.bsky.social · 16/04/2025
We are looking for a postdoctoral fellow to join us to explore telomerase regulation by histones. Please get in touch if this may interest you.
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Brian Kelch @briankelch.bsky.social · 18/04/2025
Postdoc @emma.sedivy.bsky.social determined the structure of the Neck complex that joins the capsid head to the tail. We only knew the identity of 4 out of 8 of the proteins in the Neck, but we were able to identify the remaining 4 using ModelAngelo by @kjamali.bsky.social. /3
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Brian Kelch @briankelch.bsky.social · 18/04/2025
Did you know that there is so much DNA packed inside a phage capsid that the pressure is 10X higher than in a bottle of champagne? In our latest preprint, we wondered how that is contained in a phage that lives at extremely high temperatures. /1 www.biorxiv.org/content/10.1...
Meme describing types of headaches, with the most all encompassing headache being the stress of holding copious amounts of DNA in a phage head.
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Felix Randow @felixrandow.bsky.social · 09/04/2025
RNF213, a host E3 ligase, ubiquitylates LPS to mark cytosol-invading bacteria for autophagy. But how do cytosol-adapted bacteria escape? We found that Shigella's E3 ligase IpaH1.4 blocks LPS ubiquitylation by degrading RNF213 via the proteasome. www.nature.com/articles/s41...
nature.com
Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213 - Nature Structural & Molecular Biology
Naydenova, Boyle and Pathe et al. report that Shigella uses the ubiquitin E3 ligase IpaH1.4 to evade lipopolysaccharide ubiquitylation in infected cells by degrading the host E3 ligase RNF213. Using c...
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 09/04/2025
How do cytosol-invading bacteria evade LPS ubiquitylation by the host's defence machinery? @felixrandow.bsky.social's group determined that Shigella flexneri uses IpaH1.4 to degrade the LPS ligase RNF213, inhibiting the cell's ubiquitylation abilities. Read more: tinyurl.com/3y4kv2bp #LMBResearch🧪
Comparison of Salmonella and Shigella host cell invasion. Salmonella are targeted by the host E3 ligase RNF213, which ubiquitylates bacterial lipopolysaccharide (LPS), marking bacteria for autophagic destruction. Shigella employs its effector proteins IpaH1.4 - an E3 ubiquitin ligase itself - to ubiquitylate RNF213, leading to its proteasomal degradation and thus preventing the host from tagging Shigella for destruction.Cryo-EM structure showing how the leucine-rich repeat (LRR) domain of IpaH1.4 binds to the RING domain of RNF213
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Joe Greener @jgreener64.bsky.social · 08/04/2025
This has been a long journey, but it's now out in final form. @kjamali.bsky.social academic.oup.com/bioinformati...
academic.oup.com
Fast protein structure searching using structure graph embeddings
Abstract . Comparing and searching protein structures independent of primary sequence has proved useful for remote homology detection, function annotation,
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Lucas Farnung @lucas.farnunglab.com · 06/04/2025
🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome
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Dr Abeba Birhane @abeba.blacksky.app · 05/11/2024
saw this piece being shared around on the bird site and sharing it here cuz it's so good genomebiology.biomedcentral.com/articles/10....
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Suyang Zhang @suyangzhang.bsky.social · 24/03/2025
Excited to share our new preprint on co-transcriptional splicing! U1 snRNP is recruited to RNA polymerase II through multiple interaction sites, with elongation factor SPT6 binding directly to the U1 snRNP protein. www.biorxiv.org/content/10.1... #cryoEM #transcription #splicing
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Science Magazine @science.org · 20/03/2025
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion. Learn more in this week's issue: scim.ag/3FA3Ygq
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Sylvie Callegari @sylviecallegari.bsky.social · 13/03/2025
Thrilled to share the structure of dimerised human PINK1 docked to an endogenous translocase array on the mitochondrial surface, composed of two TOM complexes, bridged by a VDAC2 dimer! Published today in Science www.science.org/doi/10.1126/... @wehi-research.bsky.social @komanderlab.bsky.social
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Joe Peters Lab @joepeterslab.bsky.social · 06/03/2025
Our preprint is now published www.science.org/doi/10.1126/...
science.org
Telomeric transposons are pervasive in linear bacterial genomes
Eukaryotes have linear DNA and their telomeres are hotspots for transposons, which in some cases took over telomere maintenance. Here we identify several families of independently evolved telomeric tr...
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George Ghanim @automnenine.bsky.social · 07/03/2025
Did you know that two jumping sequences (LINE-1 and Alu) make up nearly 30% of our genomes? Ever wonder how they jump into new genomic sites? We have some exciting discoveries to share new in @science.org on the structural mechanisms of LINE-1 retrotransposition (aka jumping 🧬➡️🧬) 🧪 #ScienceResearch
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