Kiarash Jamali
@kjamali.bsky.social
PhD student machine learning in cryo-EM, Scheres group, MRC Laboratory of Molecular Biology, Cambridge, UK.
Reposted by Kiarash Jamali
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 🤩
Beautiful tomography and microscopy - congrats all 🤩
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...
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...
November 7, 2025 at 10:56 AM
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 🤩
Beautiful tomography and microscopy - congrats all 🤩
Incredible work!
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...
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...
November 7, 2025 at 7:42 PM
Incredible work!
Reposted by Kiarash Jamali
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...
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...
November 7, 2025 at 10:44 AM
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...
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...
Reposted by Kiarash Jamali
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)
🧬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)
Wilkinson Lab
We discover and study reverse transcriptases
wilkinsonlab.bio
October 31, 2025 at 7:00 PM
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)
🧬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)
Reposted by Kiarash Jamali
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
@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
October 30, 2025 at 3:21 AM
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
@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
Reposted by Kiarash Jamali
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/vx/appcentre...
Quick Check Needed
mrc.tal.net
October 29, 2025 at 9:17 AM
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/vx/appcentre...
Reposted by Kiarash Jamali
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...
Read more about it in @science.org
www.science.org/content/arti...
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
www.science.org
August 6, 2025 at 4:09 PM
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...
Read more about it in @science.org
www.science.org/content/arti...
Reposted by Kiarash Jamali
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🧪
Syn57 required 101000+ codon changes & represents a bold step towards programmable life.
Read more: www2.mrc-lmb.cam.ac.uk/syn57-repres...
#LMBResearch🧪
August 1, 2025 at 8:28 AM
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🧪
Syn57 required 101000+ codon changes & represents a bold step towards programmable life.
Read more: www2.mrc-lmb.cam.ac.uk/syn57-repres...
#LMBResearch🧪
Reposted by Kiarash Jamali
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!
July 25, 2025 at 7:48 AM
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!
Reposted by Kiarash Jamali
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!
July 19, 2025 at 8:46 PM
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!
Reposted by Kiarash Jamali
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/...
Check out our Cell-Free 2-Hybrid approach (CF2H)
Full post: tinyurl.com/48cz5nb6
Preprint: www.biorxiv.org/cgi/content/...
July 17, 2025 at 11:42 AM
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/...
Check out our Cell-Free 2-Hybrid approach (CF2H)
Full post: tinyurl.com/48cz5nb6
Preprint: www.biorxiv.org/cgi/content/...
Reposted by Kiarash Jamali
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. 🥳
Download our code and try it yourself. 🥳
Excited to share our paper at #ICML: All-atom inverse protein folding through discrete flow matching with @kjamali.bsky.social and @sjorsscheres.bsky.social : openreview.net/forum?id=8tQdw…. If you are at ICML, let’s connect and talk generative models&protein design!
OpenReview
Promoting openness in scientific communication and the peer-review process
https://openreview.net/forum?id=8tQdw…
July 15, 2025 at 7:18 AM
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. 🥳
Download our code and try it yourself. 🥳
Reposted by Kiarash Jamali
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
July 7, 2025 at 8:23 PM
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
Reposted by Kiarash Jamali
Reposted by Kiarash Jamali
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...
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...
www.biorxiv.org
May 29, 2025 at 3:36 PM
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...
Reposted by Kiarash Jamali
LocScale-SURFER is now also available for quick install via the ChimeraX toolshed:
cxtoolshed.rbvi.ucsf.edu
cxtoolshed.rbvi.ucsf.edu
LocScale-2.0 is deliberately designed to optimise contrast for both high-resolution detail & weak contextual densities such as membrane/micelle or flexible/low-occupancy regions
LocScale-SURFER is a ChimeraX plugin aiding w/ visualisation of contextual structure.
cryotud.github.io/locscale-sur...
LocScale-SURFER is a ChimeraX plugin aiding w/ visualisation of contextual structure.
cryotud.github.io/locscale-sur...
May 26, 2025 at 11:10 AM
LocScale-SURFER is now also available for quick install via the ChimeraX toolshed:
cxtoolshed.rbvi.ucsf.edu
cxtoolshed.rbvi.ucsf.edu
Reposted by Kiarash Jamali
"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
Our several-years-old fix to ProteinMPNN's tendency to make weird antibody CDR sequences is finally preprinted
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 ...
www.biorxiv.org
May 15, 2025 at 4:30 PM
"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
Our several-years-old fix to ProteinMPNN's tendency to make weird antibody CDR sequences is finally preprinted
Reposted by Kiarash Jamali
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.
April 27, 2025 at 8:49 PM
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.
Reposted by Kiarash Jamali
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...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
April 27, 2025 at 12:13 AM
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...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
Reposted by Kiarash Jamali
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.
Excellent opportunity available for a motivated #postdoc to join @kellythd-nguyen.bsky.social’s group investigating the roles of histones in regulating telomerase using a multi-disciplinary approach.
More details: www.nature.com/naturecareer...
Apply by 04 MAY
#PostdocJobs #ScienceJobs
More details: www.nature.com/naturecareer...
Apply by 04 MAY
#PostdocJobs #ScienceJobs
April 16, 2025 at 5:25 PM
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.
Reposted by Kiarash Jamali
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
April 18, 2025 at 2:12 PM
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
Reposted by Kiarash Jamali
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...
www.biorxiv.org/content/10.1...
April 18, 2025 at 2:09 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Kiarash Jamali
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...
www.nature.com/articles/s41...
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...
www.nature.com
April 9, 2025 at 9:44 PM
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...
www.nature.com/articles/s41...
Reposted by Kiarash Jamali
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🧪
@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🧪
April 9, 2025 at 9:09 AM
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🧪
@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🧪