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
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
Reposted by YC Lin
After years in making, I am glad to be able to share our attempt on establishing a framework for combined functional and computational assessment of variant pathogenicity in the sodium leak channel NALCN:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 17, 2025 at 3:30 PM
After years in making, I am glad to be able to share our attempt on establishing a framework for combined functional and computational assessment of variant pathogenicity in the sodium leak channel NALCN:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by YC Lin
Writing this piece for Science AAAS gave me a chance to pause and think about what truly matters - to me as a scientist and as a person. If you’re curious, I share my journey of building a new life overseas and the lessons it brought.
www.science.org/content/arti...
www.science.org/content/arti...
I thought science hinged on prestige. Moving abroad made me reassess my priorities
In Denmark, this Ph.D. student fell in love with an egalitarian society that values work-life balance
www.science.org
September 16, 2025 at 6:53 AM
Writing this piece for Science AAAS gave me a chance to pause and think about what truly matters - to me as a scientist and as a person. If you’re curious, I share my journey of building a new life overseas and the lessons it brought.
www.science.org/content/arti...
www.science.org/content/arti...
Reposted by YC Lin
Stability vs flexibility: reshaping archaeal membranes in silico
This ‘fundamental’ study characterises the mechanics and stability of bolalipids from archaeal membranes using a minimalist, physics-based computational model.
buff.ly/jCnRfkO
This ‘fundamental’ study characterises the mechanics and stability of bolalipids from archaeal membranes using a minimalist, physics-based computational model.
buff.ly/jCnRfkO
September 16, 2025 at 10:02 AM
Stability vs flexibility: reshaping archaeal membranes in silico
This ‘fundamental’ study characterises the mechanics and stability of bolalipids from archaeal membranes using a minimalist, physics-based computational model.
buff.ly/jCnRfkO
This ‘fundamental’ study characterises the mechanics and stability of bolalipids from archaeal membranes using a minimalist, physics-based computational model.
buff.ly/jCnRfkO
Reposted by YC Lin
Delighted that our FtsEX-EnvC paper is now live at mBio!
FtsEX-EnvC is a bacterial Type VII ABC transporter that activates key periplasmic enzymes during cell division.
We found mutations that disrupt FtsEX-EnvC activity and a disulfide that leaves it permanently active.
doi.org/10.1128/mbio...
FtsEX-EnvC is a bacterial Type VII ABC transporter that activates key periplasmic enzymes during cell division.
We found mutations that disrupt FtsEX-EnvC activity and a disulfide that leaves it permanently active.
doi.org/10.1128/mbio...
September 16, 2025 at 3:29 PM
Delighted that our FtsEX-EnvC paper is now live at mBio!
FtsEX-EnvC is a bacterial Type VII ABC transporter that activates key periplasmic enzymes during cell division.
We found mutations that disrupt FtsEX-EnvC activity and a disulfide that leaves it permanently active.
doi.org/10.1128/mbio...
FtsEX-EnvC is a bacterial Type VII ABC transporter that activates key periplasmic enzymes during cell division.
We found mutations that disrupt FtsEX-EnvC activity and a disulfide that leaves it permanently active.
doi.org/10.1128/mbio...
Reposted by YC Lin
🚨🧠🔬 A major breakthrough in molecular neuroscience:
I am excited to share a new story from our lab, published in accelerated format today by @nature.com:
"Delta-type glutamate receptors are ligand-gated ion channels"
Read more here (free article link): rdcu.be/eGIKz
I am excited to share a new story from our lab, published in accelerated format today by @nature.com:
"Delta-type glutamate receptors are ligand-gated ion channels"
Read more here (free article link): rdcu.be/eGIKz
September 16, 2025 at 4:47 PM
🚨🧠🔬 A major breakthrough in molecular neuroscience:
I am excited to share a new story from our lab, published in accelerated format today by @nature.com:
"Delta-type glutamate receptors are ligand-gated ion channels"
Read more here (free article link): rdcu.be/eGIKz
I am excited to share a new story from our lab, published in accelerated format today by @nature.com:
"Delta-type glutamate receptors are ligand-gated ion channels"
Read more here (free article link): rdcu.be/eGIKz
extremely cool!!!!
1/14
Happy (but mostly relieved) to share my dream project with @boudkerlab.bsky.social, now published in @natsmb.nature.com! We used evolution, protein engineering & cryoEM to uncover how ion coupling in glutamate transporters works, and how it evolved.🧵
Free article: go.nature.com/4oRUC1q
Happy (but mostly relieved) to share my dream project with @boudkerlab.bsky.social, now published in @natsmb.nature.com! We used evolution, protein engineering & cryoEM to uncover how ion coupling in glutamate transporters works, and how it evolved.🧵
Free article: go.nature.com/4oRUC1q
Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters - Nature Structural & Molecular Biology
Reddy et al. used ancestral protein reconstruction, cryo-electron microscopy and functional assays to elucidate how a secondary active transporter evolved to harness the energy of sodium gradients to ...
go.nature.com
September 12, 2025 at 3:08 AM
extremely cool!!!!
Reposted by YC Lin
Second author asking the PI to be co-first
September 11, 2025 at 7:08 AM
Second author asking the PI to be co-first
Reposted by YC Lin
Seriously, not every paper needs to be an epic novel, modeled on Anna Karenina...
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Brief but not bland | EMBO reports
EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.
www.embopress.org
September 10, 2025 at 4:22 PM
Seriously, not every paper needs to be an epic novel, modeled on Anna Karenina...
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Reposted by YC Lin
Ultramarathons being a Group 1 carcinogen would be so freaking weird. www.nytimes.com/2025/08/19/h...
Are Marathons and Extreme Running Linked to Colon Cancer?
www.nytimes.com
September 10, 2025 at 2:09 PM
Ultramarathons being a Group 1 carcinogen would be so freaking weird. www.nytimes.com/2025/08/19/h...