Jan Felix
@janfelix.bsky.social
Structural Biologist from Gent. Former Post-Doc @ Gutsche group, IBS, Grenoble, FR and @ Savvides Lab, IRC, Gent, BE.
Currently part of the VIB Bioimaging Core Gent Team.
Interested in ❄️🔬 #CryoEM and #Cytokines.
Currently part of the VIB Bioimaging Core Gent Team.
Interested in ❄️🔬 #CryoEM and #Cytokines.
Pinned
Jan Felix
@janfelix.bsky.social
· Sep 2
Now published @cp-cellreports.bsky.social! Antibody-mediated TGF-β1 activation for the treatment of diseases caused by deleterious T cell activity: www.cell.com/cell-reports...
Fantastic collaboration & massive effort from Sophie Lucas Lab @ de Duve Institute. #CryoEM with @savvideslab.bsky.social.
Fantastic collaboration & massive effort from Sophie Lucas Lab @ de Duve Institute. #CryoEM with @savvideslab.bsky.social.
Reposted by Jan Felix
A longread on why Cofnas is doing pseudoscience, by yours truly. Many thanks to @forbetterscience.bsky.social for hosting the text!
September 15, 2026 at 6:41 AM
A longread on why Cofnas is doing pseudoscience, by yours truly. Many thanks to @forbetterscience.bsky.social for hosting the text!
Reposted by Jan Felix
RE: freedom of speech, academic freedom, and race science. In this (long) thread, I’m going to 1) establish my bona fides on academic freedom and race science, 2) show why academic freedom and freedom of speech are different and… 1/34
August 25, 2026 at 6:31 PM
RE: freedom of speech, academic freedom, and race science. In this (long) thread, I’m going to 1) establish my bona fides on academic freedom and race science, 2) show why academic freedom and freedom of speech are different and… 1/34
Reposted by Jan Felix
🚀 Preprint alert: cFAR and Relative Signal: Diagnosing Preferred Orientation in Single-Particle #CryoEM
Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev
Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev
August 17, 2026 at 12:00 PM
🚀 Preprint alert: cFAR and Relative Signal: Diagnosing Preferred Orientation in Single-Particle #CryoEM
Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev
Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev
Reposted by Jan Felix
In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn
June 11, 2026 at 6:02 PM
In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn
Reposted by Jan Felix
🛠️💉It's time for engineering contractile injection systems! @chipericson.bsky.social & @davidschaumann.bsky.social introduce programmable CIS - PROCIS, combining tail length control, non-native cargo loading, and cell retargeting all in one system! www.biorxiv.org/content/10.6... 🧵 1/5
June 1, 2026 at 8:29 AM
🛠️💉It's time for engineering contractile injection systems! @chipericson.bsky.social & @davidschaumann.bsky.social introduce programmable CIS - PROCIS, combining tail length control, non-native cargo loading, and cell retargeting all in one system! www.biorxiv.org/content/10.6... 🧵 1/5
Reposted by Jan Felix
Thermo Fisher has now made public the company line, which is ?!??!?!??!?!?! you really gotta read it.
cen.acs.org/research-int...
cen.acs.org/research-int...
May 28, 2026 at 8:37 PM
Thermo Fisher has now made public the company line, which is ?!??!?!??!?!?! you really gotta read it.
cen.acs.org/research-int...
cen.acs.org/research-int...
Reposted by Jan Felix
We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better.
Preprint: www.biorxiv.org/content/10.6...
Code: github.com/warpem/miss-...
🧶 Thread:
Preprint: www.biorxiv.org/content/10.6...
Code: github.com/warpem/miss-...
🧶 Thread:
May 3, 2026 at 6:11 AM
We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better.
Preprint: www.biorxiv.org/content/10.6...
Code: github.com/warpem/miss-...
🧶 Thread:
Preprint: www.biorxiv.org/content/10.6...
Code: github.com/warpem/miss-...
🧶 Thread:
Reposted by Jan Felix
1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).
March 23, 2026 at 5:54 PM
1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).
Reposted by Jan Felix
It took a while but it’s finally published!
The GAP activity of SEAC (GATOR) is a metabolic switch that allows cells to quickly respond to changes in amino acid levels, both for inhibition and reactivation.
The GAP activity of SEAC (GATOR) is a metabolic switch that allows cells to quickly respond to changes in amino acid levels, both for inhibition and reactivation.
New online: Structure and function of the yeast amino acid-sensing SEAC–EGOC supercomplex
Structure and function of the yeast amino acid-sensing SEAC–EGOC supercomplex
Nature Structural & Molecular Biology, Published online: 12 February 2026; doi:10.1038/s41594-026-01746-2Tafur et al. determined the cryo-electron microscopy structure of the SEA complex (GATOR) bound to its substrate, the EGO complex (Ragulator–Rag), and showed that its GAP activity is essential for both rapid inactivation and reactivation of TORC1.
dlvr.it
February 13, 2026 at 12:56 PM
It took a while but it’s finally published!
The GAP activity of SEAC (GATOR) is a metabolic switch that allows cells to quickly respond to changes in amino acid levels, both for inhibition and reactivation.
The GAP activity of SEAC (GATOR) is a metabolic switch that allows cells to quickly respond to changes in amino acid levels, both for inhibition and reactivation.
Reposted by Jan Felix
🚀 CryoSPARC v5.0 BETA is here!
We’re excited to deploy another major #CryoSPARC release to help enable and accelerate #cryoEM data analysis. v5 has a redesigned underlying software system and many new features - highlights in thread!
Full changelog: cryosparc.com/updates/v5.0.0
We’re excited to deploy another major #CryoSPARC release to help enable and accelerate #cryoEM data analysis. v5 has a redesigned underlying software system and many new features - highlights in thread!
Full changelog: cryosparc.com/updates/v5.0.0
January 27, 2026 at 8:36 PM
🚀 CryoSPARC v5.0 BETA is here!
We’re excited to deploy another major #CryoSPARC release to help enable and accelerate #cryoEM data analysis. v5 has a redesigned underlying software system and many new features - highlights in thread!
Full changelog: cryosparc.com/updates/v5.0.0
We’re excited to deploy another major #CryoSPARC release to help enable and accelerate #cryoEM data analysis. v5 has a redesigned underlying software system and many new features - highlights in thread!
Full changelog: cryosparc.com/updates/v5.0.0
Reposted by Jan Felix
CCP-EM Spring Symposia have become key venues for methods-focused cryo-EM advances and an annual fixture for structural biologists worldwide. Their early adoption of online talks set the bar for inclusive meetings, and even as they have grown over the years, they have kept a family feel. Kudos!
Giles and Burnley: Ten years of the CCP-EM Spring Symposium ##Cryoem##ElectronCryoMicroscopy##CCPEM... ##IUCrhttps://journals.iucr.org/paper?S2059798325010496
Ten years of the CCP-EM Spring Symposium
This article reviews the growth over the last ten years of the CCP-EM Spring Symposium. The conference is now established as a popular meeting for practitioners of life-science cryoEM and highlights new methods and exemplar applications.
journals.iucr.org
November 29, 2025 at 7:06 PM
CCP-EM Spring Symposia have become key venues for methods-focused cryo-EM advances and an annual fixture for structural biologists worldwide. Their early adoption of online talks set the bar for inclusive meetings, and even as they have grown over the years, they have kept a family feel. Kudos!
Reposted by Jan Felix
📢 New preprint:
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇
October 18, 2025 at 6:59 PM
📢 New preprint:
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇
Reposted by Jan Felix
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
September 26, 2025 at 2:28 AM
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
Reposted by Jan Felix
We finally wrote up the paper for LocScale-2.0.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
September 15, 2025 at 7:39 AM
We finally wrote up the paper for LocScale-2.0.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
Reposted by Jan Felix
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
September 13, 2025 at 12:05 AM
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
Now published @cp-cellreports.bsky.social! Antibody-mediated TGF-β1 activation for the treatment of diseases caused by deleterious T cell activity: www.cell.com/cell-reports...
Fantastic collaboration & massive effort from Sophie Lucas Lab @ de Duve Institute. #CryoEM with @savvideslab.bsky.social.
Fantastic collaboration & massive effort from Sophie Lucas Lab @ de Duve Institute. #CryoEM with @savvideslab.bsky.social.
September 2, 2025 at 11:25 AM
Now published @cp-cellreports.bsky.social! Antibody-mediated TGF-β1 activation for the treatment of diseases caused by deleterious T cell activity: www.cell.com/cell-reports...
Fantastic collaboration & massive effort from Sophie Lucas Lab @ de Duve Institute. #CryoEM with @savvideslab.bsky.social.
Fantastic collaboration & massive effort from Sophie Lucas Lab @ de Duve Institute. #CryoEM with @savvideslab.bsky.social.
Reposted by Jan Felix
We are excited to announce the first in-cell structure of a LINC complex within a native nuclear envelope at subnanometer resolution!! #In-cell cryo-ET + #atomistic MD simulations! @tomdendooven.bsky.social et al!!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
August 5, 2025 at 12:41 PM
We are excited to announce the first in-cell structure of a LINC complex within a native nuclear envelope at subnanometer resolution!! #In-cell cryo-ET + #atomistic MD simulations! @tomdendooven.bsky.social et al!!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Finally out @natcomms.nature.com
"Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses".
Great collab between @savvideslab.bsky.social (we performed #CryoEM) and Xavier Saelens Lab, spearheaded by Arne Matthys.
www.nature.com/articles/s41...
"Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses".
Great collab between @savvideslab.bsky.social (we performed #CryoEM) and Xavier Saelens Lab, spearheaded by Arne Matthys.
www.nature.com/articles/s41...
July 10, 2025 at 8:45 AM
Finally out @natcomms.nature.com
"Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses".
Great collab between @savvideslab.bsky.social (we performed #CryoEM) and Xavier Saelens Lab, spearheaded by Arne Matthys.
www.nature.com/articles/s41...
"Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses".
Great collab between @savvideslab.bsky.social (we performed #CryoEM) and Xavier Saelens Lab, spearheaded by Arne Matthys.
www.nature.com/articles/s41...
Reposted by Jan Felix
If this is true, it’s abysmally shortsighted for #NIH. The new tools nurtured by the long series of #CASP challenges probably contribute far more in one year to the scientific and industrial economies than the entire funds that have supported it.
Exclusive: An international scientific competition widely credited with spurring the development of artificial intelligence for biology appears to be on its deathbed. scim.ag/44ukS90
Exclusive: Famed protein structure competition nears end as NIH grant money runs out
Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold
scim.ag
July 3, 2025 at 8:08 AM
Reposted by Jan Felix
We have a preprint for you
EHD2 forms rings on caveolae necks, in contrast to most EHDs forming helices. We determined its structure on membranes and show that N-term acts as a spacer
By Elena, Vasya @vasiliimikirtumov.bsky.social, Jeff &Oli Daumke www.biorxiv.org/content/10.1...
EHD2 forms rings on caveolae necks, in contrast to most EHDs forming helices. We determined its structure on membranes and show that N-term acts as a spacer
By Elena, Vasya @vasiliimikirtumov.bsky.social, Jeff &Oli Daumke www.biorxiv.org/content/10.1...
June 8, 2025 at 11:22 AM
We have a preprint for you
EHD2 forms rings on caveolae necks, in contrast to most EHDs forming helices. We determined its structure on membranes and show that N-term acts as a spacer
By Elena, Vasya @vasiliimikirtumov.bsky.social, Jeff &Oli Daumke www.biorxiv.org/content/10.1...
EHD2 forms rings on caveolae necks, in contrast to most EHDs forming helices. We determined its structure on membranes and show that N-term acts as a spacer
By Elena, Vasya @vasiliimikirtumov.bsky.social, Jeff &Oli Daumke www.biorxiv.org/content/10.1...
Reposted by Jan Felix
I’m very happy to share my first paper on the effects of AWI interactions and flexibility on SPA data quality! Thank you to everyone on the team 🤩
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Untangling the effects of flexibility and the AWI in cryoEM sample preparation: A case study using KtrA
Single particle cryo-electron microscopy (cryoEM) is a powerful tool for elucidating the structures of biological macromolecules without requiring cry…
www.sciencedirect.com
June 2, 2025 at 5:18 PM
I’m very happy to share my first paper on the effects of AWI interactions and flexibility on SPA data quality! Thank you to everyone on the team 🤩
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Jan Felix
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
May 22, 2025 at 10:10 AM
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Reposted by Jan Felix
Reports of diverse stoichiometries have complicated our understanding of the complex between ALK kinase and its #cytokine ligand ALKAL2. @janfelix.bsky.social @savvideslab.bsky.social &co reanalyze #cryoEM data to clarify the situation @plosbiology.org 🧪 plos.io/4lvRfvu
April 14, 2025 at 5:34 PM
Reports of diverse stoichiometries have complicated our understanding of the complex between ALK kinase and its #cytokine ligand ALKAL2. @janfelix.bsky.social @savvideslab.bsky.social &co reanalyze #cryoEM data to clarify the situation @plosbiology.org 🧪 plos.io/4lvRfvu
Reposted by Jan Felix
Delighted to share our reanalysis of cryo-EM data in EMPIAR-10930, now at:
journals.plos.org/plosbiology/... ;
revealing the ALK-ALKAL2 assembly with 2:1 stoichiometry and resolving the conundrum introduced by the originally reported 2:2 complex. ALK/LTK-cytokine signalling getting clearer!
journals.plos.org/plosbiology/... ;
revealing the ALK-ALKAL2 assembly with 2:1 stoichiometry and resolving the conundrum introduced by the originally reported 2:2 complex. ALK/LTK-cytokine signalling getting clearer!
Reanalysis of cryo-EM data reveals ALK-cytokine assemblies with both 2:1 and 2:2 stoichiometries
The mechanistic understanding of the complex between ALK kinase and its cytokine ligand ALKAL2 has been complicated by reports of diverse stoichiometries (2:1 vs 2:2). This study reanalyzes cryo-EM da...
journals.plos.org
April 13, 2025 at 7:04 PM
Delighted to share our reanalysis of cryo-EM data in EMPIAR-10930, now at:
journals.plos.org/plosbiology/... ;
revealing the ALK-ALKAL2 assembly with 2:1 stoichiometry and resolving the conundrum introduced by the originally reported 2:2 complex. ALK/LTK-cytokine signalling getting clearer!
journals.plos.org/plosbiology/... ;
revealing the ALK-ALKAL2 assembly with 2:1 stoichiometry and resolving the conundrum introduced by the originally reported 2:2 complex. ALK/LTK-cytokine signalling getting clearer!
Reposted by Jan Felix
#CryoSPARC v4.7 is out! 🚀
Featuring a new automatic Micrograph Junk Detector that labels and rejects contaminants, new tools for curating subsets of particles, performance and stability fixes, and more!
Full changelog: cryosparc.com/updates
#cryoEM
Featuring a new automatic Micrograph Junk Detector that labels and rejects contaminants, new tools for curating subsets of particles, performance and stability fixes, and more!
Full changelog: cryosparc.com/updates
#cryoEM
April 9, 2025 at 2:14 PM
#CryoSPARC v4.7 is out! 🚀
Featuring a new automatic Micrograph Junk Detector that labels and rejects contaminants, new tools for curating subsets of particles, performance and stability fixes, and more!
Full changelog: cryosparc.com/updates
#cryoEM
Featuring a new automatic Micrograph Junk Detector that labels and rejects contaminants, new tools for curating subsets of particles, performance and stability fixes, and more!
Full changelog: cryosparc.com/updates
#cryoEM