Ci Ji (CJ) Lim's Avatar

Ci Ji (CJ) Lim

@cijilim

Associate Professor @ UW-Madison Biochemistry. www.limlab.org Telomeres, Cryo-EM, Single-molecule Biophysics. Opinions are my own. πŸ‡ΈπŸ‡¬

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26.09.2023
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Latest posts by Ci Ji (CJ) Lim @cijilim

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Meet UW-Madison’s Reinier Hernandez Reinier is at the forefront of the development of radiotherapeutics working in his lab and together with WARF Therapeutics. From this collaboration we have a CAIX compound poised to move to the clinic.

Meet Reinier Hernandez, assistant professor of @wiscmedphys.bsky.social @uwiscradiology.bsky.social, whose Advanced Radiotheranostics Laboratory aims to harness the power of radionuclides to tackle problems in diverse areas of biomedical research.

09.03.2026 15:34 πŸ‘ 1 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0

Development of a photostable pH biosensor based on mStayGold https://www.biorxiv.org/content/10.64898/2026.03.06.710027v1

09.03.2026 02:49 πŸ‘ 6 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0
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A proteome-wide dependency map of protein interaction motifs Nature Structural & Molecular Biology, Published online: 06 March 2026; doi:10.1038/s41594-026-01762-2AmbjΓΈrn and Meeusen et al. functionally characterize all reported and a comprehensive set of predicted short linear motifs (SLiMs) using base-editing screens, identifying 450 reported and 264 predicted SLiMs required for normal cell proliferation.

ICYMI: New online: A proteome-wide dependency map of protein interaction motifs

07.03.2026 20:51 πŸ‘ 10 πŸ” 5 πŸ’¬ 0 πŸ“Œ 0
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Research Technician - Zhang Lab Primary Work Address: One Shields Avenue, Davis, CA, 95616 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute (HHMI) advances the discovery and s...

Our lab is hiring a research technician! We are interested in reproduction, stem cells, and development. If you are seeking a robust 2-year career experience before the next chapter of your educational journey, this is the position for you!

hhmi.wd1.myworkdayjobs.com/en-US/Extern...

07.03.2026 15:46 πŸ‘ 8 πŸ” 5 πŸ’¬ 0 πŸ“Œ 0
Job Details

Pls re-post: My department @oxfordbiochemistry.bsky.social are recruiting for several new faculty positions (links below). Broad search in molecular biology/biochemistry, across prokaryotes and eukaryotes. Interested in understanding life at the molecular level, this job might be for you!
1/n

05.03.2026 21:35 πŸ‘ 87 πŸ” 125 πŸ’¬ 2 πŸ“Œ 3

I was on Capitol Hill today with @asbmb.bsky.social urging lawmakers to support strong federal investment in
scientific research and training. Also to support : predictable and sustained funding.
#ASBMBAdvocates #ScienceServesUsAll

06.03.2026 21:54 πŸ‘ 9 πŸ” 5 πŸ’¬ 0 πŸ“Œ 1
Figure 1. Cryo-EM of abundant protein complexes in native membranes.

Figure 1. Cryo-EM of abundant protein complexes in native membranes.

Figure 2. Cryo-EM of membrane proteins in vesicles.

Figure 2. Cryo-EM of membrane proteins in vesicles.

Figure 3. 3D reconstruction of V-ATPase in native synaptic vesicle membranes.

Figure 3. 3D reconstruction of V-ATPase in native synaptic vesicle membranes.

Figure 4. Generation of membrane vesicles for structure determination of proteins in their native lipid bilayer.

Figure 4. Generation of membrane vesicles for structure determination of proteins in their native lipid bilayer.

I've written a review on what I think is an extremely exciting direction in cryo-EM:

Cryo-EM of endogenous membrane proteins in their native lipid bilayer

Open access in Quarterly Reviews of Biophysics:
doi.org/10.1017/S003...

06.03.2026 12:40 πŸ‘ 152 πŸ” 56 πŸ’¬ 3 πŸ“Œ 1
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The results are finally in! πŸ†πŸ’»πŸ§¬

I'm thrilled to announce that the manuscript for the Bits to Binders protein design competition is out on bioRxiv! Here's a summary of our findings, including some simple criteria that nearly *double* success rates when applied as a filter 🧡

04.03.2026 15:01 πŸ‘ 31 πŸ” 17 πŸ’¬ 1 πŸ“Œ 2
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Meet UW-Madison’s Brian Fox β€œBrian looks for enzymes that have evolved to harness them for new, industrial uses, like the deconstruction of biomass for use in biorenewable chemicals and fuels. The resulting discoveries will allow for sustainable alternatives through processes already partially optimized by nature.”

"Brian looks for enzymes that have evolved to harness them for new, industrial uses, like the deconstruction of biomass for use in biorenewable chemicals and fuels," says Jennifer Gottwald, WARF director of licensing.

04.03.2026 21:57 πŸ‘ 4 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0

Huge congratulations, Yasu!!! Well-deserved for the outstanding program that you are running! πŸ’ͺπŸŽ‰

03.03.2026 03:54 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
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Dorothy Crowfoot Hodgkin, biochemist & a trailblazer in crystallography, she established the biomolecular structures of insulin, vitamin B12, & penicillin winning the Nobel in Chemistry in 1964 #WomensHistoryMonthΒ #WomenInStem #WomenInScience

01.03.2026 11:06 πŸ‘ 50 πŸ” 24 πŸ’¬ 1 πŸ“Œ 0
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Paper alert from @codyz.bsky.social y.social and Yang Liu. New mechanism for chromatin remodeling by ATRX. Super cool story. Congrats to #lugerlab alumni.
www.biorxiv.org/content/10.6...

28.02.2026 01:39 πŸ‘ 27 πŸ” 8 πŸ’¬ 0 πŸ“Œ 0
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Senior Scientist, Protein Sciences in South San Francisco, California, United States of America | Research & Development at Genentech Apply for Senior Scientist, Protein Sciences job with Genentech in South San Francisco, California, United States of America. Research & Development at Genentech

Our department at Genentech is hiring. We're looking for a freshly-minted PhD (0-3 years) protein biochemist / structural biologist to join as a Sr Scientist. A rare opportunity to join our group leader job family at a more junior level than we usually hire.

24.02.2026 16:55 πŸ‘ 55 πŸ” 57 πŸ’¬ 2 πŸ“Œ 0
RNA Society

The most important #RNA conference of the year with lots of amazing science and a really friendly atmosphere. This year in beautiful Montreal πŸ‡¨πŸ‡¦ !

www2.rnasociety.org

24.02.2026 12:05 πŸ‘ 20 πŸ” 13 πŸ’¬ 0 πŸ“Œ 0
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πŸ‘€ At #BPS but haven’t stopped by booth 401 yet? Meet the team to discover how you can unlock the ultimate #single-molecule resolution at your benchtop, generating high-impact insights into #biomolecular interactions and dynamics. See you there! @biophysicalsoc.bsky.social #biophysics #lifescience

24.02.2026 08:45 πŸ‘ 4 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0
Job opening for Research Group Leader in Structural Studies at MRC Laboratory of Molecular Biology, focusing on macromolecular structures.

Job opening for Research Group Leader in Structural Studies at MRC Laboratory of Molecular Biology, focusing on macromolecular structures.

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...

24.02.2026 09:45 πŸ‘ 36 πŸ” 48 πŸ’¬ 0 πŸ“Œ 2
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Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...

22.02.2026 20:10 πŸ‘ 84 πŸ” 28 πŸ’¬ 4 πŸ“Œ 0
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Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization Pathogenic Bordetella bacteria use protein adhesins to infect the ciliated respiratory epithelia of vertebrate hosts. In this work, we show that the filamentous hemagglutinin FhaB adhesin of Bordetell...

Just published in @science.org with related Perspective by FranΓ§oise Jacob-Dubuisson.
Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization | Science www.science.org/doi/10.1126/...

20.02.2026 11:04 πŸ‘ 34 πŸ” 10 πŸ’¬ 1 πŸ“Œ 0
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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.

19.02.2026 19:50 πŸ‘ 55 πŸ” 20 πŸ’¬ 1 πŸ“Œ 0
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🚨New preprint! We built a cell-free genomics platform (GATO-seq) to probe transcriptional regulation and discovered a β€œsuper pause” sequence that triggers a new Pol II active-site conformation. Huge shout-out to @robertovn.bsky.social for pulling off this monster of a project. tinyurl.com/superpause

19.02.2026 14:24 πŸ‘ 49 πŸ” 12 πŸ’¬ 0 πŸ“Œ 1
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Evolution of error correction through a need for speed Kinetic proofreading is a class of error-correcting mechanisms in biology that expend energy to avoid mistakes during replication, transcription, and translation. Proofreading is typically assumed to ...

@science.org Evolution of error correction through a need for speed | Science #evolution πŸ§¬πŸ”¬ www.science.org/doi/10.1126/...

19.02.2026 19:07 πŸ‘ 41 πŸ” 13 πŸ’¬ 0 πŸ“Œ 1

Papers are like buses... You wait for ages, then two come along at once.

Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published!

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

19.02.2026 03:30 πŸ‘ 86 πŸ” 35 πŸ’¬ 6 πŸ“Œ 2
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Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related β€˜proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...

Our paper is now out in Nature:

β€œAncient co-option of LTR retrotransposons as yeast centromeres”

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

A short thread on how retrotransposons helped give rise to yeast point centromeres.

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18.02.2026 16:03 πŸ‘ 227 πŸ” 115 πŸ’¬ 8 πŸ“Œ 10
Top:  A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5β€² (blue) to 3β€² (red) end.

Top: A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5β€² (blue) to 3β€² (red) end.

Accurate RNA structure prediction remains a challenge, despite recent computational advances. This study presents DRFold2, a #DeepLearning framework that significantly enhances accuracy of de novo #RNAstructure prediction by increasing contact prediction precision @plosbiology.org πŸ§ͺ plos.io/4aoOQiX

18.02.2026 17:25 πŸ‘ 15 πŸ” 10 πŸ’¬ 1 πŸ“Œ 0
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Awesome seminar today by UCSF's @willowcoyote.bsky.social! He is not afraid to blaze his own trail, redefining paradigms along the way!

17.02.2026 02:23 πŸ‘ 20 πŸ” 4 πŸ’¬ 1 πŸ“Œ 0
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

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. πŸ₯³

mrc.tal.net/vx/mobile-0/...

16.02.2026 12:09 πŸ‘ 83 πŸ” 106 πŸ’¬ 1 πŸ“Œ 2
Biology Open | The Company of Biologists Biology Open | The Company of Biologists Fast & Fair peer review A new initiative offering high-quality peer review within 7 working days of submission Biology Open (BiO) has embar...

Have you applied to be a reviewer @biologyopen.bsky.social ? pays Β£220/manuscript journals.biologists.com/bio/pages/fa...

15.02.2026 15:33 πŸ‘ 7 πŸ” 3 πŸ’¬ 1 πŸ“Œ 1

Congratulations!!!

15.02.2026 01:27 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
The Structura logo with dates for the workshop listed. The bottom reads "Hosted by SickKids and Structura Biotechnology"

The Structura logo with dates for the workshop listed. The bottom reads "Hosted by SickKids and Structura Biotechnology"

Deadline approaching to register for the @structurabio.bsky.social & @sickkidsto.bsky.social CryoSPARC workshop in Toronto!
Open to all, this is a unique opportunity to learn CryoSPARC from the experts at Structura.
April 30/May, 2026.
For more information and to register:
tinyurl.com/y42pf4wy

13.02.2026 16:40 πŸ‘ 8 πŸ” 9 πŸ’¬ 0 πŸ“Œ 1

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.

13.02.2026 12:56 πŸ‘ 11 πŸ” 7 πŸ’¬ 0 πŸ“Œ 1