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
· 2d
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.
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...
This proteomics banger from @compomics.com and @ebi.embl.org folks looks great. It is one of those titles that makes some people really excited and others let out an audible groan (I’m in the former).
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Unlocking the Next Decade of Proteomics with Standardized, Structured Metadata
The proteomics community has fully embraced data sharing, yet data set metadata provision remains limited, especially at the level of the biological samples and experimental design. This hampers large...
pubs.acs.org
January 25, 2026 at 12:56 PM
This proteomics banger from @compomics.com and @ebi.embl.org folks looks great. It is one of those titles that makes some people really excited and others let out an audible groan (I’m in the former).
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Machine perception liquid biopsy: is proteomics; is not proteomics (sung to Soul Coughing). I really don't know how I feel about this on many levels, but I just learned about it so 🤷♂️.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Machine perception liquid biopsy identifies brain tumours via systemic immune and tumour microenvironment signature - Nature Nanotechnology
Engineered carbon nanotube sensors enable the detection of intracranial tumours in blood, identify low-abundance biomarkers and amplify cancer detection by capturing secreted factors from the entire t...
www.nature.com
January 23, 2026 at 1:44 PM
Machine perception liquid biopsy: is proteomics; is not proteomics (sung to Soul Coughing). I really don't know how I feel about this on many levels, but I just learned about it so 🤷♂️.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ben Neely
Preventing Proteomics Data Tombs Through Collective Responsibility and Community Engagement www.nature.com/artic...
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#proteomics #prot-paper
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#proteomics #prot-paper
January 23, 2026 at 1:01 PM
Preventing Proteomics Data Tombs Through Collective Responsibility and Community Engagement www.nature.com/artic...
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#proteomics #prot-paper
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#proteomics #prot-paper
Really not science: when I was a kid we (and everyone else) had these rooftop carriers from Sears (ours on our small Bronco II). I just remember the snail on it. Recently I’ve seen them around and saw it was X-cargo… totally the worst pun ever. 35 years later I’m just now laughing at the joke.
January 23, 2026 at 12:27 PM
Really not science: when I was a kid we (and everyone else) had these rooftop carriers from Sears (ours on our small Bronco II). I just remember the snail on it. Recently I’ve seen them around and saw it was X-cargo… totally the worst pun ever. 35 years later I’m just now laughing at the joke.
Dario is all over the media. He said (summarized by @axios.com) “10 million people — 7 million in Silicon Valley, with the rest scattered — could "decouple" from the rest of society, enjoying as much as 50% GDP growth while others were left behind.”
www.wsj.com/tech/ai/anth...
www.wsj.com/tech/ai/anth...
Anthropic CEO Says Government Should Help Ensure AI’s Economic Upside Is Shared
In a WSJ interview, Dario Amodei says the public isn’t prepared for the potential inequality that the technology might create.
www.wsj.com
January 21, 2026 at 2:23 PM
Dario is all over the media. He said (summarized by @axios.com) “10 million people — 7 million in Silicon Valley, with the rest scattered — could "decouple" from the rest of society, enjoying as much as 50% GDP growth while others were left behind.”
www.wsj.com/tech/ai/anth...
www.wsj.com/tech/ai/anth...
Reposted by Ben Neely
We’re delighted to report a global structural proteome analysis within living cells!
doi.org/10.1038/s443...
#proteomics #structuralproteomics #massspectrometry #structuralbiology #ethz @imsb-eth.bsky.social
doi.org/10.1038/s443...
#proteomics #structuralproteomics #massspectrometry #structuralbiology #ethz @imsb-eth.bsky.social
January 13, 2026 at 5:29 PM
We’re delighted to report a global structural proteome analysis within living cells!
doi.org/10.1038/s443...
#proteomics #structuralproteomics #massspectrometry #structuralbiology #ethz @imsb-eth.bsky.social
doi.org/10.1038/s443...
#proteomics #structuralproteomics #massspectrometry #structuralbiology #ethz @imsb-eth.bsky.social
Reposted by Ben Neely
🧪 Online (Zoom)
📅 23 April 2026
⏰ 14:00–16:00 CEST
✅ Free registration is mandatory!
👉More information in comments!
🔗 ECR Day Registration: docs.google.com/forms/d/e/1F...
🔗 Science Slam Registration: docs.google.com/forms/d/e/1F...
#Proteomics #EarlyCareerResearchers #YPIC #EuPA#EuBIC
📅 23 April 2026
⏰ 14:00–16:00 CEST
✅ Free registration is mandatory!
👉More information in comments!
🔗 ECR Day Registration: docs.google.com/forms/d/e/1F...
🔗 Science Slam Registration: docs.google.com/forms/d/e/1F...
#Proteomics #EarlyCareerResearchers #YPIC #EuPA#EuBIC
January 21, 2026 at 9:26 AM
🧪 Online (Zoom)
📅 23 April 2026
⏰ 14:00–16:00 CEST
✅ Free registration is mandatory!
👉More information in comments!
🔗 ECR Day Registration: docs.google.com/forms/d/e/1F...
🔗 Science Slam Registration: docs.google.com/forms/d/e/1F...
#Proteomics #EarlyCareerResearchers #YPIC #EuPA#EuBIC
📅 23 April 2026
⏰ 14:00–16:00 CEST
✅ Free registration is mandatory!
👉More information in comments!
🔗 ECR Day Registration: docs.google.com/forms/d/e/1F...
🔗 Science Slam Registration: docs.google.com/forms/d/e/1F...
#Proteomics #EarlyCareerResearchers #YPIC #EuPA#EuBIC
Reposted by Ben Neely
very happy that the iq 2.0 paper is published.
Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics
Protein quantification is a crucial data processing step that combines quantitative values at the peptide or fragment level into protein levels in mass spectrometry-based proteomics. However, many of ...
pubs.acs.org
January 20, 2026 at 11:36 PM
very happy that the iq 2.0 paper is published.
Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
Reposted by Ben Neely
Applications are now open for @olgavitek.bsky.social 's May Intitute on computation and statistics for mass spectrometry and proteomics at @northeasternu.bsky.social !
--> computationalproteomics.khoury.northeastern.edu
--> computationalproteomics.khoury.northeastern.edu
May Institute – Computation and statistics for mass spectrometry and proteomics
computationalproteomics.khoury.northeastern.edu
January 20, 2026 at 11:26 PM
Applications are now open for @olgavitek.bsky.social 's May Intitute on computation and statistics for mass spectrometry and proteomics at @northeasternu.bsky.social !
--> computationalproteomics.khoury.northeastern.edu
--> computationalproteomics.khoury.northeastern.edu
Part of me loves how bad this is, but maybe I’m also terrified someone takes it and runs with it. 😬😱
Found on LinkedIn alongside text describing how PCR works. 😂. #TeamMassSpec #massspectrometry #science #badai
January 19, 2026 at 11:13 PM
Part of me loves how bad this is, but maybe I’m also terrified someone takes it and runs with it. 😬😱
Reposted by Ben Neely
Especially given "an emerging conflict between individual and collective incentives to adopt AI in science, where scientists receive expanded personal reach and impact, but the knowledge extent of entire scientific fields tends to shrink".
January 15, 2026 at 4:38 PM
Especially given "an emerging conflict between individual and collective incentives to adopt AI in science, where scientists receive expanded personal reach and impact, but the knowledge extent of entire scientific fields tends to shrink".
Not science: one of my favorite cold weather dishes is peas over cornbread (my cold weather window here is fleetingly random). These specific peas were sea island red peas that took over and had a late season bumper crop (👀 @iondoctor.bsky.social). Maybe not the best picture but you get the idea.
January 13, 2026 at 1:23 PM
Not science: one of my favorite cold weather dishes is peas over cornbread (my cold weather window here is fleetingly random). These specific peas were sea island red peas that took over and had a late season bumper crop (👀 @iondoctor.bsky.social). Maybe not the best picture but you get the idea.
My best idea is that since no one is writing the show's email address, we give an LLM a prompt like "based on our show's transcripts, ask me or Orsburn short snarky/sarcastic/fun questions about anything", but given my new disdain for LLMs, maybe that is too on the nose. Would be hilarious though.
Some productive procrastination today planing the next iteration of #THEProteomicsShow with Ben @proteomicsnews.bsky.social, “all the parts”, and it’s exciting.
BUT, we’ve got a 100th episode to plan. Bad ideas only please.
BUT, we’ve got a 100th episode to plan. Bad ideas only please.
January 12, 2026 at 1:45 PM
My best idea is that since no one is writing the show's email address, we give an LLM a prompt like "based on our show's transcripts, ask me or Orsburn short snarky/sarcastic/fun questions about anything", but given my new disdain for LLMs, maybe that is too on the nose. Would be hilarious though.
Reposted by Ben Neely
None of RNA’s remarkably versatile forms are built to last — not even within the cell that they came from. www.quantamagazine.org/cells-across...
January 11, 2026 at 4:46 PM
None of RNA’s remarkably versatile forms are built to last — not even within the cell that they came from. www.quantamagazine.org/cells-across...
Reposted by Ben Neely
Read the full article & preview all pieces in Issue 09: www.asimov.press/p/nature
How Nature Became a 'Prestige' Journal
Since launching in 1869, Nature has evolved from a periodical offering commentary on pigeons to the prestige journal in science. But how did Nature build its reputation, and can it last?
www.asimov.press
January 5, 2026 at 4:14 PM
Read the full article & preview all pieces in Issue 09: www.asimov.press/p/nature