Gopalan
@arulmari.bsky.social
A Chemical biologist, dabbling in neuro-glycobiology, glyco-immunology, and glycoproteomics; Viveka (86-91)→IISc (91-98)→ETHZ (98-99)→NIH (2000-2003)→JHU (2003-2007)→NII (2007----). Opinionated, one way or the other.
Reposted by Gopalan
This is a better summary than anything I've seen in mainstream or alternative media. Essential reading.
I’ve unfortunately needed to add more material to my post from yesterday. The re-election of Donald Trump is looking like the biggest act of American self-destruction since the Civil War.
Same link, new title and some updates.
Same link, new title and some updates.
Revised and Extended: What's Happening Inside the NIH and NSF
www.science.org
February 6, 2025 at 1:30 AM
This is a better summary than anything I've seen in mainstream or alternative media. Essential reading.
Reposted by Gopalan
"Kids might die, but Robert Kennedy can keep cashing in," Sen. Elizabeth Warren says during a heated exchange with #RFK Jr. over whether he would agree to not taking fees from suing drug companies.
January 29, 2025 at 7:13 PM
"Kids might die, but Robert Kennedy can keep cashing in," Sen. Elizabeth Warren says during a heated exchange with #RFK Jr. over whether he would agree to not taking fees from suing drug companies.
Reposted by Gopalan
Literally every time I have filed this story (4x this week), something happened to change it before my editor had a chance to look.
But here’s WTF happened at NIH this week (so far)
cen.acs.org/policy/US-fu...
But here’s WTF happened at NIH this week (so far)
cen.acs.org/policy/US-fu...
US funding freeze memo rescinded, NIH confusion persists
Acting NIH director Memoli clarifies communication restrictions as White House moves to freeze US government grants
cen.acs.org
January 29, 2025 at 8:57 PM
Literally every time I have filed this story (4x this week), something happened to change it before my editor had a chance to look.
But here’s WTF happened at NIH this week (so far)
cen.acs.org/policy/US-fu...
But here’s WTF happened at NIH this week (so far)
cen.acs.org/policy/US-fu...
Reposted by Gopalan
MS protein analysis—I’m one of many to follow in his footsteps. Great NIH program officers are the backbone of the extramural system. I owe much to several of them over the years.
January 26, 2025 at 11:14 PM
MS protein analysis—I’m one of many to follow in his footsteps. Great NIH program officers are the backbone of the extramural system. I owe much to several of them over the years.
Reposted by Gopalan
Just because a paper is highly cited, it doesn’t mean it is correct or truthful. This paper (www.nature.com/articles/nat...) was cited 4504 times and yet it was retracted.
There is no penalty for non-compliance. It’s just that someone someday will probably report it to the editors. 1/2
There is no penalty for non-compliance. It’s just that someone someday will probably report it to the editors. 1/2
RETRACTED ARTICLE: Pluripotency of mesenchymal stem cells derived from adult marrow - Nature
Nature - RETRACTED ARTICLE: Pluripotency of mesenchymal stem cells derived from adult marrow
www.nature.com
January 26, 2025 at 1:59 PM
Just because a paper is highly cited, it doesn’t mean it is correct or truthful. This paper (www.nature.com/articles/nat...) was cited 4504 times and yet it was retracted.
There is no penalty for non-compliance. It’s just that someone someday will probably report it to the editors. 1/2
There is no penalty for non-compliance. It’s just that someone someday will probably report it to the editors. 1/2
Reposted by Gopalan
Mark, with all due respect. Sit down and visit with some folks who are intimately familiar with the NIH, the scientific process, how grants are handled and funded.
The NIH is not a business. There are no shareholders. There is no mandate for profit. This is not a business model and should not be.
The NIH is not a business. There are no shareholders. There is no mandate for profit. This is not a business model and should not be.
Trump is doing what you do after you acquire a company. Crazy I know. But reality. The Dir of NIH should reach out to DOGE and offer to bring them in to remove inefficiencies.
There are always some and the Director know what they are.
DOGE gets a win. NIH gets back to work.
There are always some and the Director know what they are.
DOGE gets a win. NIH gets back to work.
Hi Mark, how do you feel about cancer research being canceled.
January 25, 2025 at 2:27 PM
Mark, with all due respect. Sit down and visit with some folks who are intimately familiar with the NIH, the scientific process, how grants are handled and funded.
The NIH is not a business. There are no shareholders. There is no mandate for profit. This is not a business model and should not be.
The NIH is not a business. There are no shareholders. There is no mandate for profit. This is not a business model and should not be.
Reposted by Gopalan
I fear there is deep truth here.
January 11, 2025 at 8:47 PM
I fear there is deep truth here.
Reposted by Gopalan
Skimming through the latest paper journals plays a catalytic role in a fascinating decades-long friendship that Roald Hoffmann had with two Chinese chemists, Tang Ao-Qing and Lu Jiaxi. I recommend watching his recounting of a story of geopolitics and chemistry: www.sciencehistory.org/visit/events...
January 3, 2025 at 1:38 PM
Skimming through the latest paper journals plays a catalytic role in a fascinating decades-long friendship that Roald Hoffmann had with two Chinese chemists, Tang Ao-Qing and Lu Jiaxi. I recommend watching his recounting of a story of geopolitics and chemistry: www.sciencehistory.org/visit/events...
Reposted by Gopalan
Us: "Hey we wrote a spirited defense of basic science funding, showing how it drives startup creation and ultimately GDP. Would you like to publish it as an OpEd?"
Major Media Outlets: "No."
Major Media Outlets: "No."
December 12, 2024 at 1:54 PM
Us: "Hey we wrote a spirited defense of basic science funding, showing how it drives startup creation and ultimately GDP. Would you like to publish it as an OpEd?"
Major Media Outlets: "No."
Major Media Outlets: "No."
Reposted by Gopalan
Your regular reminder that you can cite unrefereed editorials, reviews, data, news, websites, books, even tweets. Citing preprints isn’t doing anything controversial 1/2
December 14, 2024 at 1:58 PM
Your regular reminder that you can cite unrefereed editorials, reviews, data, news, websites, books, even tweets. Citing preprints isn’t doing anything controversial 1/2
Reposted by Gopalan
This is what happens when you let computer scientists design molecules 🤯 Oral presentation @neuripsconf.bsky.social #NeurIPS2024 #chemsky
December 14, 2024 at 2:32 AM
This is what happens when you let computer scientists design molecules 🤯 Oral presentation @neuripsconf.bsky.social #NeurIPS2024 #chemsky
Reposted by Gopalan
The applying of immuno-RCA for the high-sensitivity detection of the ABO blood group antibodies on the printed glycoarray https://www.biorxiv.org/content/10.1101/2024.12.11.625986v1
December 14, 2024 at 10:16 AM
The applying of immuno-RCA for the high-sensitivity detection of the ABO blood group antibodies on the printed glycoarray https://www.biorxiv.org/content/10.1101/2024.12.11.625986v1
Reposted by Gopalan
Beautiful work - I love the analysis of organelle rearrangement in response to changes in lipid flux.
Preprint alert!! How zonated hepatocytes adapt to changes in lipid influx due to fasting or a Western diet (WD). We developed a microscopy-based phenotyping method called single-cell phenomics (scPhenomics) to measure the features of mitochondria and lipid droplets (LDs).
December 13, 2024 at 6:57 AM
Beautiful work - I love the analysis of organelle rearrangement in response to changes in lipid flux.
Reposted by Gopalan
i do find it interesting in a bleak way that silicon valley is basically recapitulating 1920s-style american reactionary politics.
The tech bro fascination with eugenics is so on brand. The idea that you could make accurate, actionable predictions from individual genotypes (with all their complex, non-linear interactions) from averaged, linearly modeled population-level genomic statistics is just another big data fantasy
December 12, 2024 at 5:25 PM
i do find it interesting in a bleak way that silicon valley is basically recapitulating 1920s-style american reactionary politics.
Reposted by Gopalan
The journey of breakthrough medical treatments is long and tortuous. Loved hearing about the pioneering work of Pieter Cullis and the development of lipid nanoparticles!
Note on his slide “basic research is important”!
Note on his slide “basic research is important”!
December 11, 2024 at 10:49 PM
The journey of breakthrough medical treatments is long and tortuous. Loved hearing about the pioneering work of Pieter Cullis and the development of lipid nanoparticles!
Note on his slide “basic research is important”!
Note on his slide “basic research is important”!
Reposted by Gopalan
Back by popular demand, I present PPI Prediction Challenge #2.
My claim: I AM SKEPTICAL COMPUTATIONAL APPROACHES CAN PREDICT WHETHER TWO PROTEINS INTERACT.
Someone prove me wrong (take two).
docs.google.com/forms/d/e/1F...
1/n
My claim: I AM SKEPTICAL COMPUTATIONAL APPROACHES CAN PREDICT WHETHER TWO PROTEINS INTERACT.
Someone prove me wrong (take two).
docs.google.com/forms/d/e/1F...
1/n
PPI Prediction Challenge #2
For this protein-protein interaction prediction challenge, we present three target proteins: KRAS, RAF (the KRAS binding domain), and Mdm2. For each target protein, we are providing you a list of 8 po...
docs.google.com
December 10, 2024 at 9:45 PM
Back by popular demand, I present PPI Prediction Challenge #2.
My claim: I AM SKEPTICAL COMPUTATIONAL APPROACHES CAN PREDICT WHETHER TWO PROTEINS INTERACT.
Someone prove me wrong (take two).
docs.google.com/forms/d/e/1F...
1/n
My claim: I AM SKEPTICAL COMPUTATIONAL APPROACHES CAN PREDICT WHETHER TWO PROTEINS INTERACT.
Someone prove me wrong (take two).
docs.google.com/forms/d/e/1F...
1/n
Reposted by Gopalan
It reminds me to point out that Pauling’s PhD Thesis (PDF linked at the bottom of this page: thesis.library.caltech.edu/1791/) is literally a cover page followed by reprints of 5 JACS papers…
a man in a suit and tie is saying " boom easy as that "
Alt: a man in a suit and tie is saying “boom easy as that”
media.tenor.com
December 10, 2024 at 12:49 PM
It reminds me to point out that Pauling’s PhD Thesis (PDF linked at the bottom of this page: thesis.library.caltech.edu/1791/) is literally a cover page followed by reprints of 5 JACS papers…
Reposted by Gopalan
Yet another amazing and captivating story by @jeremymberg.bsky.social ⬇️🧵 ++ great (I agree) advice,
Prof Pauling, how do you come up with so many good ideas?
"I try to come up with many ideas and I throw away the bad ones" LC Pauling 👍🏻😎
Prof Pauling, how do you come up with so many good ideas?
"I try to come up with many ideas and I throw away the bad ones" LC Pauling 👍🏻😎
Bluetorial: What’s the worst that can happen? Meeting a scientific hero
(Lots of chemical history today)
(Lots of chemical history today)
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
December 10, 2024 at 1:27 PM
Yet another amazing and captivating story by @jeremymberg.bsky.social ⬇️🧵 ++ great (I agree) advice,
Prof Pauling, how do you come up with so many good ideas?
"I try to come up with many ideas and I throw away the bad ones" LC Pauling 👍🏻😎
Prof Pauling, how do you come up with so many good ideas?
"I try to come up with many ideas and I throw away the bad ones" LC Pauling 👍🏻😎
Reposted by Gopalan
I remain impressed that this got published in a high-profile journal. Most med chemists have a visceral, well-founded negative reaction to those structures. I wish we could teach our bio colleagues the structural spidey sense. Tip of the iceberg here when it comes to setting the record straight.
December 4, 2024 at 1:00 AM
I remain impressed that this got published in a high-profile journal. Most med chemists have a visceral, well-founded negative reaction to those structures. I wish we could teach our bio colleagues the structural spidey sense. Tip of the iceberg here when it comes to setting the record straight.
Reposted by Gopalan
That awkward moment when someone publishes a paper saying that they can’t find any evidence that your compounds bind to what your own series of papers say that they bind to. . .
Do They Even Bind?
www.science.org
December 3, 2024 at 7:02 PM
That awkward moment when someone publishes a paper saying that they can’t find any evidence that your compounds bind to what your own series of papers say that they bind to. . .
Reposted by Gopalan
I think I have not developed a thick skin of academia, yet. Manuscript getting desk rejected stings and it is not a great feeling to be in. Ugh!
a little girl is sitting in a car seat holding a lollipop
ALT: a little girl is sitting in a car seat holding a lollipop
media.tenor.com
December 8, 2024 at 12:26 PM
I think I have not developed a thick skin of academia, yet. Manuscript getting desk rejected stings and it is not a great feeling to be in. Ugh!
Reposted by Gopalan
Now this is a paper I had long been waiting for! NanoSPLITS is out! Parallel single cell proteomic and transcriptomic measurements from the same cell! Great work from @cajunscience.bsky.social and @nanopots.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting - Nature Communications
Single-cell multiomics can provide broad insights into gene/protein regulatory networks and cellular diversity. Here, authors develop nanoSPLITS, a nanodroplet splitting approach for global profiling ...
www.nature.com
December 6, 2024 at 12:17 AM
Now this is a paper I had long been waiting for! NanoSPLITS is out! Parallel single cell proteomic and transcriptomic measurements from the same cell! Great work from @cajunscience.bsky.social and @nanopots.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Gopalan
You'll notice proteomics has tighter CVs and higher correlation between the cells. Also the average proteome to transcriptome correlation is low (~0.35). Really nice to see this quantified clearly
December 6, 2024 at 12:22 AM
You'll notice proteomics has tighter CVs and higher correlation between the cells. Also the average proteome to transcriptome correlation is low (~0.35). Really nice to see this quantified clearly