YC Lin
@yiechanglin.bsky.social
Boya Postdoctoral Fellow @PKU | formally @corrylab.bsky.social, ANU
MD simulations of lipids and membrane proteins
Like PIP2, I am negatively charged in the head
MD simulations of lipids and membrane proteins
Like PIP2, I am negatively charged in the head
Pinned
YC Lin
@yiechanglin.bsky.social
· Mar 17
1/ In my final project as part of the @corrylab.bsky.social, we show the bacterial TAM complex facilitates the spontaneous flow of phospholipids from the IM to the OM in MD simulations..
www.biorxiv.org/content/10.1101/2025.03.12.642747v1
www.biorxiv.org/content/10.1101/2025.03.12.642747v1
Reposted by YC Lin
Relying on ChatGPT to teach you about a topic leaves you with shallower knowledge than Googling and reading about it, according to new research that compared what more than 10,000 people knew after using one method or the other.
Shared by @gizmodo.com: buff.ly/yAAHtHq
Shared by @gizmodo.com: buff.ly/yAAHtHq
November 26, 2025 at 9:06 AM
Relying on ChatGPT to teach you about a topic leaves you with shallower knowledge than Googling and reading about it, according to new research that compared what more than 10,000 people knew after using one method or the other.
Shared by @gizmodo.com: buff.ly/yAAHtHq
Shared by @gizmodo.com: buff.ly/yAAHtHq
Reposted by YC Lin
Super collaboration with @raffaeleieva.bsky.social and @fronzeslab.bsky.social on the LptDEMY complex.
rdcu.be/eRxNf here our new study on the characterization of the lipopolysaccharide holotranslocon, LptDE and the newly identified subunits LptM and LptY. Great collaboration with @fronzeslab.bsky.social @pstansfeld.bsky.social @JulienMarcoux @YvesQuentin
Structural basis of lipopolysaccharide assembly by the outer membrane translocon holo-complex
Nature Communications - The asymmetric distribution of lipopolysaccharide (LPS) on the surface of the bacterial outer membrane is essential and crucial for antibiotic resistance. Here, authors...
rdcu.be
November 24, 2025 at 4:56 PM
Super collaboration with @raffaeleieva.bsky.social and @fronzeslab.bsky.social on the LptDEMY complex.
Reposted by YC Lin
ARC says they’ll announce DECRA and LIEF outcomes tomorrow (Tuesday 25th Nov).
In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first).
In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first).
November 23, 2025 at 11:40 PM
ARC says they’ll announce DECRA and LIEF outcomes tomorrow (Tuesday 25th Nov).
In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first).
In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first).
Reposted by YC Lin
"We thank the reviewers for their helpful suggestions"
November 23, 2025 at 11:19 AM
"We thank the reviewers for their helpful suggestions"
Reposted by YC Lin
Latest RFDiffusion3 from the Baker lab.
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present RFd...
www.biorxiv.org
November 20, 2025 at 10:32 PM
Latest RFDiffusion3 from the Baker lab.
Reposted by YC Lin
Toxoplasma gondii carefully balances calcium between its organelles. This study shows the ER, via the SERCA pump, is central to controlling Ca²⁺ in the cytosol and mitochondria.
🔗 buff.ly/RFgcZgE
🔗 buff.ly/RFgcZgE
November 20, 2025 at 11:28 PM
Toxoplasma gondii carefully balances calcium between its organelles. This study shows the ER, via the SERCA pump, is central to controlling Ca²⁺ in the cytosol and mitochondria.
🔗 buff.ly/RFgcZgE
🔗 buff.ly/RFgcZgE
Reposted by YC Lin
Just ported @ryanfeigenbaum.com's amazing color logic into a standalone, MIT-licensed library. Perceptually uniform palettes for your next generative art or design project. 🎨 meodai.github.io/pro-color-ha...
November 20, 2025 at 9:51 PM
Just ported @ryanfeigenbaum.com's amazing color logic into a standalone, MIT-licensed library. Perceptually uniform palettes for your next generative art or design project. 🎨 meodai.github.io/pro-color-ha...
Reposted by YC Lin
Biology of bridge-like lipid transfer proteins continues to be uncovered at a rather brisk pace. These things are important... Cool paper, congratulations!
Thrilled to share our latest work showing that the bridge lipid transport protein ATG2A transfers diacylglycerol (DAG), and some TAG/PA, from the ER to LDs, thereby recruiting DGAT2 to drive local TAG synthesis, promoting LD expansion while protecting ER membranes.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ATG2A-mediated DAG transfer recruits DGAT2 for lipid droplet growth - Nature Structural & Molecular Biology
Elhan et al. show that ATG2A acts with DGAT2, the enzyme producing triacylglycerol (TAG), in lipid droplet growth. By delivering diacylglycerol to lipid droplets, ATG2A not only fuels TAG production b...
www.nature.com
November 18, 2025 at 6:20 AM
Biology of bridge-like lipid transfer proteins continues to be uncovered at a rather brisk pace. These things are important... Cool paper, congratulations!
Reposted by YC Lin
[Resources]
#AlphaFold protein and PPI prediction databases
1️⃣ Predictomes (genome maintenance & H2A/H2b) predictomes.org
2️⃣ Flypredictome www.flyrnai.org/tools/fly_pr...
3️⃣ Human interactome prodata.swmed.edu/humanPPI
4️⃣ BFVD (viral proteins) bfvd.steineggerlab.workers.dev
1/2
#AlphaFold protein and PPI prediction databases
1️⃣ Predictomes (genome maintenance & H2A/H2b) predictomes.org
2️⃣ Flypredictome www.flyrnai.org/tools/fly_pr...
3️⃣ Human interactome prodata.swmed.edu/humanPPI
4️⃣ BFVD (viral proteins) bfvd.steineggerlab.workers.dev
1/2
July 30, 2025 at 11:25 AM
[Resources]
#AlphaFold protein and PPI prediction databases
1️⃣ Predictomes (genome maintenance & H2A/H2b) predictomes.org
2️⃣ Flypredictome www.flyrnai.org/tools/fly_pr...
3️⃣ Human interactome prodata.swmed.edu/humanPPI
4️⃣ BFVD (viral proteins) bfvd.steineggerlab.workers.dev
1/2
#AlphaFold protein and PPI prediction databases
1️⃣ Predictomes (genome maintenance & H2A/H2b) predictomes.org
2️⃣ Flypredictome www.flyrnai.org/tools/fly_pr...
3️⃣ Human interactome prodata.swmed.edu/humanPPI
4️⃣ BFVD (viral proteins) bfvd.steineggerlab.workers.dev
1/2
Reposted by YC Lin
A handy translation guide for non-academic speakers.
November 13, 2025 at 2:19 PM
A handy translation guide for non-academic speakers.
Reposted by YC Lin
Kat Blow has developed CCD2MD, a suite of packages for preparing co-folded outputs for MD simulations.
Created for protein–lipid interactions in integral membrane proteins, it also works for peripheral and lipid-anchored proteins too.
pubs.acs.org/doi/full/10....
github.com/keb721/ccd2md
Created for protein–lipid interactions in integral membrane proteins, it also works for peripheral and lipid-anchored proteins too.
pubs.acs.org/doi/full/10....
github.com/keb721/ccd2md
CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations
Protein–lipid interactions play a crucial role in the stability and function of membrane proteins. While experimental approaches to characterize these interactions in a native-like membrane environmen...
pubs.acs.org
November 12, 2025 at 11:53 AM
Kat Blow has developed CCD2MD, a suite of packages for preparing co-folded outputs for MD simulations.
Created for protein–lipid interactions in integral membrane proteins, it also works for peripheral and lipid-anchored proteins too.
pubs.acs.org/doi/full/10....
github.com/keb721/ccd2md
Created for protein–lipid interactions in integral membrane proteins, it also works for peripheral and lipid-anchored proteins too.
pubs.acs.org/doi/full/10....
github.com/keb721/ccd2md
Reposted by YC Lin
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Reposted by YC Lin
"After 16 years in academia, I’ve become more selective about collaboration. It remains a joy and a blessing, but I’ve also learned how quickly 'we' can turn wicked." #ScienceWorkingLife https://scim.ag/43ibPrT
November 12, 2025 at 11:14 PM
"After 16 years in academia, I’ve become more selective about collaboration. It remains a joy and a blessing, but I’ve also learned how quickly 'we' can turn wicked." #ScienceWorkingLife https://scim.ag/43ibPrT
Reposted by YC Lin
What is the most profitable industry in the world, this side of the law? Not oil, not IT, not pharma.
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
November 12, 2025 at 10:31 AM
What is the most profitable industry in the world, this side of the law? Not oil, not IT, not pharma.
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
Reposted by YC Lin
Astonishing and in a way heartening to see what people are prepared to put up with to get the education they want.
The number of foreign students in the U.S. decreased by less than 1 percent this fall, according to new federal data, despite predictions that their enrollment would plummet this year due to a crackdown by the Trump administration.
Trump’s crackdown on foreign students barely impacts enrollment, data shows
About 1.3 million students in the U.S. had active visas in October, down less than 1 percent from a year ago.
www.washingtonpost.com
November 12, 2025 at 6:03 AM
Astonishing and in a way heartening to see what people are prepared to put up with to get the education they want.
Reposted by YC Lin
Beautiful “action potential” stained glass made by @laurenatlas.bsky.social
Picked 🔵 because it reminds me of our #ChR2 optotagging experiments 🤓🧪
Picked 🔵 because it reminds me of our #ChR2 optotagging experiments 🤓🧪
November 6, 2025 at 2:51 PM
Beautiful “action potential” stained glass made by @laurenatlas.bsky.social
Picked 🔵 because it reminds me of our #ChR2 optotagging experiments 🤓🧪
Picked 🔵 because it reminds me of our #ChR2 optotagging experiments 🤓🧪
Reposted by YC Lin
Our paper on the Bacteroidota BAM complex is out in @natmicrobiol.nature.com! With @madejmar.bsky.social
We found that BAM in Bacteroides and Porphyromonas gingivalis has a distinct architecture from BAM in Proteobacteria.
doi.org/10.1038/s415...
We found that BAM in Bacteroides and Porphyromonas gingivalis has a distinct architecture from BAM in Proteobacteria.
doi.org/10.1038/s415...
Structure of a distinct β-barrel assembly machinery complex in the Bacteroidota - Nature Microbiology
Structural and functional characterization of the β-barrel assembly machinery complex in Bacteroidota reveals a distinct, seven-component complex with a large extracellular domain that may enable β-barrel–surface lipoprotein complex assembly.
doi.org
October 2, 2025 at 6:20 AM
Our paper on the Bacteroidota BAM complex is out in @natmicrobiol.nature.com! With @madejmar.bsky.social
We found that BAM in Bacteroides and Porphyromonas gingivalis has a distinct architecture from BAM in Proteobacteria.
doi.org/10.1038/s415...
We found that BAM in Bacteroides and Porphyromonas gingivalis has a distinct architecture from BAM in Proteobacteria.
doi.org/10.1038/s415...
Reposted by YC Lin
“In a research paper from the @australiainstitute.org.au called *Cooking the books at the Australian National University*, David Richardson and @richarddenniss.bsky.social said the ANU's argument about its unhealthy financial position was "flimsy".”
www.canberratimes.com.au/story/907948...
www.canberratimes.com.au/story/907948...
'Cooking the books': national think tank questions ANU finances
'They should make clear how they use such donations.'
www.canberratimes.com.au
October 1, 2025 at 9:14 PM
“In a research paper from the @australiainstitute.org.au called *Cooking the books at the Australian National University*, David Richardson and @richarddenniss.bsky.social said the ANU's argument about its unhealthy financial position was "flimsy".”
www.canberratimes.com.au/story/907948...
www.canberratimes.com.au/story/907948...
Reposted by YC Lin
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
September 29, 2025 at 3:01 PM
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
Reposted by YC Lin
Elizabeth Hinde and Jorge Alegre-Cebollada to Receive 2026 Michael and Kate Bárány Award buff.ly/n6RrjdO
September 24, 2025 at 7:30 PM
Elizabeth Hinde and Jorge Alegre-Cebollada to Receive 2026 Michael and Kate Bárány Award buff.ly/n6RrjdO
Reposted by YC Lin
Join us for the next CryoEM Current Practices Webinar on 9/25/2025 at 12 PM ET / 9 AM PT with Dr. Sarah Clark who will sharing her research on the "Architecture of a Bridge-like Lipid Transfer Protein."
Register here:
us02web.zoom.us/webinar/regi...
Register here:
us02web.zoom.us/webinar/regi...
September 22, 2025 at 10:43 PM
Join us for the next CryoEM Current Practices Webinar on 9/25/2025 at 12 PM ET / 9 AM PT with Dr. Sarah Clark who will sharing her research on the "Architecture of a Bridge-like Lipid Transfer Protein."
Register here:
us02web.zoom.us/webinar/regi...
Register here:
us02web.zoom.us/webinar/regi...
Reposted by YC Lin
September 20, 2025 at 11:34 PM
Reposted by YC Lin
Check out our preprint in which we determine how a class of potent protein antibiotics specifically kill P. aeruginosa without a need to enter the cell.
doi.org/10.1101/2025...
This is work from my PhD in the lab of @rhyswg.bsky.social and many collaborators who contributed amazing data!
doi.org/10.1101/2025...
This is work from my PhD in the lab of @rhyswg.bsky.social and many collaborators who contributed amazing data!
A Protein Antibiotic Inhibits the BAM Complex to Kill Without Cell Entry
Many antibiotics are ineffective against Gram-negative pathogens such as Pseudomonas aeruginosa because they cannot penetrate the bacterial outer membrane. Here, we show that protein antibiotics calle...
doi.org
September 22, 2025 at 5:08 AM
Check out our preprint in which we determine how a class of potent protein antibiotics specifically kill P. aeruginosa without a need to enter the cell.
doi.org/10.1101/2025...
This is work from my PhD in the lab of @rhyswg.bsky.social and many collaborators who contributed amazing data!
doi.org/10.1101/2025...
This is work from my PhD in the lab of @rhyswg.bsky.social and many collaborators who contributed amazing data!
Reposted by YC Lin
Only single cell sequencing of the all these post docs will reveal why
September 19, 2025 at 8:54 AM
Only single cell sequencing of the all these post docs will reveal why
Reposted by YC Lin
Lipid droplets: Open questions and conceptual advances around a unique organelle. New review from Mike Henne (@hennelab.bsky.social), Emma Reynolds, and William: rupress.org/jcb/article/...
#Biochemistry #CellMetabolism #LipidDroplets
#Biochemistry #CellMetabolism #LipidDroplets
September 18, 2025 at 2:15 PM
Lipid droplets: Open questions and conceptual advances around a unique organelle. New review from Mike Henne (@hennelab.bsky.social), Emma Reynolds, and William: rupress.org/jcb/article/...
#Biochemistry #CellMetabolism #LipidDroplets
#Biochemistry #CellMetabolism #LipidDroplets