Ben Neely
@benneely.com
Analytical biochemist attempting molecular cartography across the tree of life, powered by MS-based proteomics. Opinions expressed are solely my own. he/him
benjaminneely.com
Charleston, SC, USA
benjaminneely.com
Charleston, SC, USA
Pinned
Ben Neely
@benneely.com
· 15d
Ben @proteomicsnews.bsky.social and I did our big 100th episode of #THEProteomicsShow, but our guest was an extremely snarky AI overlord super fan. Not sure where it ranks on our dumb ideas list, but fun as always. Find it wherever you find fine podcasts. Upcoming live episode has real guests.
Final audible choices made:
1) Last audible credit to @aptshadow.bsky.social reading Service Model. Murderbot + Redshirts? Totes
2) Hainish Cycle 1-3 (love Le Guin) - $5
3) Emperor of Silence (rec for Red Rising fans; bounced off it when reading) - $6
4) Storm Front (never read Dresden Files!) - $4
1) Last audible credit to @aptshadow.bsky.social reading Service Model. Murderbot + Redshirts? Totes
2) Hainish Cycle 1-3 (love Le Guin) - $5
3) Emperor of Silence (rec for Red Rising fans; bounced off it when reading) - $6
4) Storm Front (never read Dresden Files!) - $4
February 19, 2026 at 12:53 PM
Final audible choices made:
1) Last audible credit to @aptshadow.bsky.social reading Service Model. Murderbot + Redshirts? Totes
2) Hainish Cycle 1-3 (love Le Guin) - $5
3) Emperor of Silence (rec for Red Rising fans; bounced off it when reading) - $6
4) Storm Front (never read Dresden Files!) - $4
1) Last audible credit to @aptshadow.bsky.social reading Service Model. Murderbot + Redshirts? Totes
2) Hainish Cycle 1-3 (love Le Guin) - $5
3) Emperor of Silence (rec for Red Rising fans; bounced off it when reading) - $6
4) Storm Front (never read Dresden Files!) - $4
Not science (again?!): I did a 3 months for $3 audible promo and got the last DCC book “This Inevitable Ruin”, not realizing Soundbooth Theatre would ruin all my future audiobook choices. I’ve pre-ordered the upcoming DCC book but have one credit remaining and might need suggestions.
All shall fear the might of the Princess Posse!
YouTube video by Soundbooth Theater
youtube.com
February 18, 2026 at 12:24 AM
Not science (again?!): I did a 3 months for $3 audible promo and got the last DCC book “This Inevitable Ruin”, not realizing Soundbooth Theatre would ruin all my future audiobook choices. I’ve pre-ordered the upcoming DCC book but have one credit remaining and might need suggestions.
Reposted by Ben Neely
New preprint! We did a systematic comparison of proteases, digestion conditions, and labeling methods for histone PTM analysis by MS-based proteomics in the Yates lab at @scripps.edu.
TL;DR: you can get great results in ~3 h of sample prep. 🧵
TL;DR: you can get great results in ~3 h of sample prep. 🧵
February 16, 2026 at 10:34 PM
New preprint! We did a systematic comparison of proteases, digestion conditions, and labeling methods for histone PTM analysis by MS-based proteomics in the Yates lab at @scripps.edu.
TL;DR: you can get great results in ~3 h of sample prep. 🧵
TL;DR: you can get great results in ~3 h of sample prep. 🧵
Not science: everything’s cool on the AI front, really. Apparently no more software companies, no more movie industry, totally gonna be fine for my kids’ futures. All this great content, tools and advancements will be paid for by… them working those other jobs. www.techspot.com/news/111338-...
ByteDance's Seedance 2.0 AI video generator sparks Hollywood outcry after viral clip
ByteDance launched Seedance 2.0 in China earlier this week for users of its Jianying app. Currently able to generate 15-second clips, the company says it will soon...
www.techspot.com
February 16, 2026 at 5:56 PM
Not science: everything’s cool on the AI front, really. Apparently no more software companies, no more movie industry, totally gonna be fine for my kids’ futures. All this great content, tools and advancements will be paid for by… them working those other jobs. www.techspot.com/news/111338-...
Not science: when I was a kid, the ads were chewing gum, dog food, soft drinks and the bud v bud lite saga. Watching Olympics now (streaming) and my kids mostly learn about a variety of syndromes and diseases from drug commercials. Bring back gum!
February 15, 2026 at 1:45 PM
Not science: when I was a kid, the ads were chewing gum, dog food, soft drinks and the bud v bud lite saga. Watching Olympics now (streaming) and my kids mostly learn about a variety of syndromes and diseases from drug commercials. Bring back gum!
To all my blood proteomics skywalkers: reviewer was surprised by high Hp levels, even though is an acute phase protein. Blood Atlas has it in top 10, and I can say in ~30+ mammals it is ~top 10. Fun answer is why? Mike Janech pointed out it is a scavenger to keep Fenton reaction in check.
Hemoglobin. A biologic fenton reagent.
Iron and iron compounds may facilitate hydroxyl-radical generation from activated oxygen species. Earlier work on the generation of this radical has b…
www.sciencedirect.com
February 13, 2026 at 5:03 PM
To all my blood proteomics skywalkers: reviewer was surprised by high Hp levels, even though is an acute phase protein. Blood Atlas has it in top 10, and I can say in ~30+ mammals it is ~top 10. Fun answer is why? Mike Janech pointed out it is a scavenger to keep Fenton reaction in check.
Not science: hard to hear about James Van Der Beek. His situation is tragically common in the US, even the fact he had issues paying for cancer treatment.
I wasn't a Dawson's Creek person but dang, I loved "What Would Diplo Do?" and strongly suggest watching it (free on Tubi, etc.).
I wasn't a Dawson's Creek person but dang, I loved "What Would Diplo Do?" and strongly suggest watching it (free on Tubi, etc.).
What Would Diplo Do? (TV Series 2017) ⭐ 7.1 | Comedy
30m | TV-14
www.imdb.com
February 13, 2026 at 12:40 PM
Not science: hard to hear about James Van Der Beek. His situation is tragically common in the US, even the fact he had issues paying for cancer treatment.
I wasn't a Dawson's Creek person but dang, I loved "What Would Diplo Do?" and strongly suggest watching it (free on Tubi, etc.).
I wasn't a Dawson's Creek person but dang, I loved "What Would Diplo Do?" and strongly suggest watching it (free on Tubi, etc.).
AI is killing the magic and love of life's little things. Ex. I swore this undergrad email was AI gen, but then I met with them and they are ridiculously well spoken, exactly as they wrote.
The general suspicion that AI has introduced sucks. We are in the post-truth and post-originality era. Booo!
The general suspicion that AI has introduced sucks. We are in the post-truth and post-originality era. Booo!
Going to make a "things AI killed" list, beyond the obvious: from poorly written emails from undergrads (even professionals) to fun works of creativity I now find sus. I didn't appreciate how jaded we will become to most/all digital interactions. Worse than the post-truth world. Now is IRL or bust.
February 11, 2026 at 1:19 PM
AI is killing the magic and love of life's little things. Ex. I swore this undergrad email was AI gen, but then I met with them and they are ridiculously well spoken, exactly as they wrote.
The general suspicion that AI has introduced sucks. We are in the post-truth and post-originality era. Booo!
The general suspicion that AI has introduced sucks. We are in the post-truth and post-originality era. Booo!
Going to make a "things AI killed" list, beyond the obvious: from poorly written emails from undergrads (even professionals) to fun works of creativity I now find sus. I didn't appreciate how jaded we will become to most/all digital interactions. Worse than the post-truth world. Now is IRL or bust.
February 9, 2026 at 1:20 PM
Going to make a "things AI killed" list, beyond the obvious: from poorly written emails from undergrads (even professionals) to fun works of creativity I now find sus. I didn't appreciate how jaded we will become to most/all digital interactions. Worse than the post-truth world. Now is IRL or bust.
I was reading something about the cost of LLMs, like 500 ml of water for generating an email. Images are a ton more tokens so assume a ton more water and energy. Now let’s make it an internet trend to compound it. How much do these trends cost, literally? Of course no more cheap NVME or RAM, ever.
February 7, 2026 at 2:23 PM
I was reading something about the cost of LLMs, like 500 ml of water for generating an email. Images are a ton more tokens so assume a ton more water and energy. Now let’s make it an internet trend to compound it. How much do these trends cost, literally? Of course no more cheap NVME or RAM, ever.
What the heck is NCBI's SmartBlast?!!! If this is one of those tools that has been around for ages and I just not stumbled on it I am gonna be aggro.
blast.ncbi.nlm.nih.gov/smartblast/s...
blast.ncbi.nlm.nih.gov/smartblast/s...
February 6, 2026 at 1:05 PM
What the heck is NCBI's SmartBlast?!!! If this is one of those tools that has been around for ages and I just not stumbled on it I am gonna be aggro.
blast.ncbi.nlm.nih.gov/smartblast/s...
blast.ncbi.nlm.nih.gov/smartblast/s...
You might recall the concept of expansion microscopy came up on Ep 96 with @lingjunmeng.bsky.social, and turns out even @quantamagazine.bsky.social thinks its mind blowing too. www.quantamagazine.org/expansion-mi...
February 6, 2026 at 12:41 PM
You might recall the concept of expansion microscopy came up on Ep 96 with @lingjunmeng.bsky.social, and turns out even @quantamagazine.bsky.social thinks its mind blowing too. www.quantamagazine.org/expansion-mi...
Big changes coming to UniProt (👀 @pwilmarth.bsky.social), though I feel like this is essentially targeting people who think it is Sprot v. TrEMBL instead of simply Sprot v Proteomes. And yes, you should likely be using proteomes, and in most cases canonical only.
www.uniprot.org/help/refprot...
www.uniprot.org/help/refprot...
UniProt
UniProt is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.
www.uniprot.org
February 5, 2026 at 7:32 PM
Big changes coming to UniProt (👀 @pwilmarth.bsky.social), though I feel like this is essentially targeting people who think it is Sprot v. TrEMBL instead of simply Sprot v Proteomes. And yes, you should likely be using proteomes, and in most cases canonical only.
www.uniprot.org/help/refprot...
www.uniprot.org/help/refprot...
Ben @proteomicsnews.bsky.social and I did our big 100th episode of #THEProteomicsShow, but our guest was an extremely snarky AI overlord super fan. Not sure where it ranks on our dumb ideas list, but fun as always. Find it wherever you find fine podcasts. Upcoming live episode has real guests.
February 4, 2026 at 5:33 AM
Ben @proteomicsnews.bsky.social and I did our big 100th episode of #THEProteomicsShow, but our guest was an extremely snarky AI overlord super fan. Not sure where it ranks on our dumb ideas list, but fun as always. Find it wherever you find fine podcasts. Upcoming live episode has real guests.
For those of you not in the eastern US, it’s been cold lately. The mid-Atlantic to NE is cosplaying Hoth, and we even got snow in the SE (not significant in Chas of course, cause we have a meteorological forcefield to anything not off the ocean).
Assuming groundhogs will warn of white walkers.
Assuming groundhogs will warn of white walkers.
Grading the groundhogs
In honor of Groundhog Day and in the spirit of fun, we pitted groundhogs from all over the United States against each other — and data from NOAA's National Centers for Environmental Information — to s...
www.noaa.gov
February 2, 2026 at 11:50 AM
For those of you not in the eastern US, it’s been cold lately. The mid-Atlantic to NE is cosplaying Hoth, and we even got snow in the SE (not significant in Chas of course, cause we have a meteorological forcefield to anything not off the ocean).
Assuming groundhogs will warn of white walkers.
Assuming groundhogs will warn of white walkers.
The rate of AI stuff is astounding. I’m over here watching the tech demo for Google’s Project Genie, reading about Moltbook (it’s where your AI agents go to chill), and then realizing AI breaks the economy if it fails OR succeeds. It’s exciting and cool, and not worth it, but there’s no reverse.
Project Genie | Experimenting with infinite interactive worlds
YouTube video by Google DeepMind
youtu.be
February 1, 2026 at 4:39 AM
The rate of AI stuff is astounding. I’m over here watching the tech demo for Google’s Project Genie, reading about Moltbook (it’s where your AI agents go to chill), and then realizing AI breaks the economy if it fails OR succeeds. It’s exciting and cool, and not worth it, but there’s no reverse.
Yep, Ben @proteomicsnews.bsky.social and I finally got Bill Noble on #THEProteomicsShow. We had been wanting him on forever so he went and won an award to make it easier for us to meet. Enjoy the rambles (I hope), and mind the monkeys. Find it wherever you find fine podcasts.
January 30, 2026 at 4:46 PM
Yep, Ben @proteomicsnews.bsky.social and I finally got Bill Noble on #THEProteomicsShow. We had been wanting him on forever so he went and won an award to make it easier for us to meet. Enjoy the rambles (I hope), and mind the monkeys. Find it wherever you find fine podcasts.
Reposted by Ben Neely
Episode 98? Finally! (I've been busy) With 2026 Gilman Award for Computational Proteomics Award Winner Bill Noble!
January 30, 2026 at 1:56 PM
Episode 98? Finally! (I've been busy) With 2026 Gilman Award for Computational Proteomics Award Winner Bill Noble!
In other words, I am trying to ask myself more "how can we make this right, or at least usable", since taking hammers to the looms is out of the question at this point, and I worry a lot of our current discussions sound way too elitist and nonconstructive, but we also can't take the other extreme. 🤷♂️
We need FAIR practices in data and code sharing (as always), but with vibe coded tools there must be a benchmark comparison. Remember when new proteomics algorithms compared to Mascot and MS-GF+? We need that now. I would point to proteomicsML, but more is needed, and impetus lies with authors.
7/7
7/7
January 30, 2026 at 1:12 PM
In other words, I am trying to ask myself more "how can we make this right, or at least usable", since taking hammers to the looms is out of the question at this point, and I worry a lot of our current discussions sound way too elitist and nonconstructive, but we also can't take the other extreme. 🤷♂️
On the "vibe coding omics analysis is here" demo paper, and some responses (run for the hills!), a thread for myself:
- we know that LLM-assisted or even driven coding is here. if you haven't tried it even in the last 3 months, you are behind
- yes it is powerful and enabling
1/7
- we know that LLM-assisted or even driven coding is here. if you haven't tried it even in the last 3 months, you are behind
- yes it is powerful and enabling
1/7
January 30, 2026 at 12:59 PM
On the "vibe coding omics analysis is here" demo paper, and some responses (run for the hills!), a thread for myself:
- we know that LLM-assisted or even driven coding is here. if you haven't tried it even in the last 3 months, you are behind
- yes it is powerful and enabling
1/7
- we know that LLM-assisted or even driven coding is here. if you haven't tried it even in the last 3 months, you are behind
- yes it is powerful and enabling
1/7
Reposted by Ben Neely
We start our group meetings with a “safety minute” and today’s speaker chose this paper as his example of a threat du jour 😂. Surprised to see this in JPR which we usually think of as a reliably rigorous journal
Concerning on many levels (publishing and innovation to name a few). The #teammassspec community had a bit of a discussion here:
bsky.app/profile/alis...
bsky.app/profile/alis...
My 5cents on why doing this without knowing the code and statistics is a bad idea. 1 The sample-wise imputation will add noise, and 2 You shouldn't z-scoring abundance for diff abundance analysis
Vibe Coding Omics Data Analysis Applications | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
Vibe Coding Omics Data Analysis Applications | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
January 30, 2026 at 7:34 AM
We start our group meetings with a “safety minute” and today’s speaker chose this paper as his example of a threat du jour 😂. Surprised to see this in JPR which we usually think of as a reliably rigorous journal
Ep 98: bridgerton, cocaine monkeys, and birding… making sure you know we aren’t AI, right @proteomicsnews.bsky.social.
January 29, 2026 at 8:15 PM
Ep 98: bridgerton, cocaine monkeys, and birding… making sure you know we aren’t AI, right @proteomicsnews.bsky.social.
Reposted by Ben Neely
www.nature.com/articles/s41...
@benneely.com was the one who taught me about Jane Richardson, the woman who developed ribbon diagram visualization for the 3D structure of proteins! 👩🔬🧪🍝🧬💻
@benneely.com was the one who taught me about Jane Richardson, the woman who developed ribbon diagram visualization for the 3D structure of proteins! 👩🔬🧪🍝🧬💻
Stories from the scientist who changed how we visualize proteins - Nature Reviews Chemistry
Ahead of her 85th birthday, Jane Richardson, Professor of Biochemistry at Duke University, discussed her life in science from making her own telescope to developing the ribbon diagrams for the 3D stru...
www.nature.com
January 29, 2026 at 3:10 PM
www.nature.com/articles/s41...
@benneely.com was the one who taught me about Jane Richardson, the woman who developed ribbon diagram visualization for the 3D structure of proteins! 👩🔬🧪🍝🧬💻
@benneely.com was the one who taught me about Jane Richardson, the woman who developed ribbon diagram visualization for the 3D structure of proteins! 👩🔬🧪🍝🧬💻
Reposted by Ben Neely
It is my great honor to announce that registration for the 7th ESCP Single Cell Proteomics Conference is now open: lnkd.in/e4iyiQjf
With around 250 participants, it is one of the largest SCP conferences worldwide. We are also proud to announce that there is no participation fee for our conference.
With around 250 participants, it is one of the largest SCP conferences worldwide. We are also proud to announce that there is no participation fee for our conference.
January 28, 2026 at 4:23 PM
It is my great honor to announce that registration for the 7th ESCP Single Cell Proteomics Conference is now open: lnkd.in/e4iyiQjf
With around 250 participants, it is one of the largest SCP conferences worldwide. We are also proud to announce that there is no participation fee for our conference.
With around 250 participants, it is one of the largest SCP conferences worldwide. We are also proud to announce that there is no participation fee for our conference.
Digging around in iOS controls today I found I can limit Siri to not providing writing and/or math help. That's cool.
Another find is a pretty cool paper/post on LLM "thinking" and agents, from the Claude folks.
www.anthropic.com/research/tra...
Another find is a pretty cool paper/post on LLM "thinking" and agents, from the Claude folks.
www.anthropic.com/research/tra...
Tracing the thoughts of a large language model
Anthropic's latest interpretability research: a new microscope to understand Claude's internal mechanisms
www.anthropic.com
January 26, 2026 at 1:07 PM
Digging around in iOS controls today I found I can limit Siri to not providing writing and/or math help. That's cool.
Another find is a pretty cool paper/post on LLM "thinking" and agents, from the Claude folks.
www.anthropic.com/research/tra...
Another find is a pretty cool paper/post on LLM "thinking" and agents, from the Claude folks.
www.anthropic.com/research/tra...