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
· 6d
Ep 94 - Alt Proteomics - Dr. Timothy Cleland by The Proteomics Show
For the final episode of the US HUPO sponsored "Alt Proteomics" series highlighting alternative proteomics things, Ben and Ben sit down to talk with Dr. Timothy Cleland, Smithsonian Institution.Keywor...
creators.spotify.com
We wrapped up #THEProteomicsShow Alt Proteomics season with Tim Cleland @paleoproteomicist.bsky.social talking paleoproteomics with me and Ben @proteomicsnews.bsky.social. Won't lie, this season was a blast talking about less typical "proteomics". Find it wherever you find fine podcasts or here.
Listening to In Our Time on slime moulds and all I can think about is proteomics and of course @edwardmarcotte.bsky.social.
www.bbc.co.uk/programmes/m...
www.bbc.co.uk/programmes/m...
BBC Radio 4 - In Our Time, Slime Moulds
Melvyn Bragg and guests discuss the remarkable world of slime mould.
www.bbc.co.uk
November 25, 2025 at 5:21 AM
Listening to In Our Time on slime moulds and all I can think about is proteomics and of course @edwardmarcotte.bsky.social.
www.bbc.co.uk/programmes/m...
www.bbc.co.uk/programmes/m...
Tell me more!
a close up of a squirrel 's face with a blurry background .
ALT: a close up of a squirrel 's face with a blurry background .
media.tenor.com
November 24, 2025 at 10:22 PM
Tell me more!
This “major update to ProteomicsDB” is definitely worth a look. academic.oup.com/nar/advance-...
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale
Abstract. Proteomic and phenotypic cell sensitivity datasets are increasingly important for understanding chemoproteomics and the underlying drug mechanism
academic.oup.com
November 22, 2025 at 4:49 AM
This “major update to ProteomicsDB” is definitely worth a look. academic.oup.com/nar/advance-...
First off, excellent and will be reading.
Second, totally off topic, but I dig the gear looking Venn. It’s like a serpentine on the front of an engine.
Second, totally off topic, but I dig the gear looking Venn. It’s like a serpentine on the front of an engine.
November 20, 2025 at 11:15 AM
First off, excellent and will be reading.
Second, totally off topic, but I dig the gear looking Venn. It’s like a serpentine on the front of an engine.
Second, totally off topic, but I dig the gear looking Venn. It’s like a serpentine on the front of an engine.
I hated when lost smoky oak, and tbh, this iteration never made sense. I sincerely hope something fun moves back in. Things next door in the former glass company space aren’t cutting it.
November 18, 2025 at 11:00 PM
I hated when lost smoky oak, and tbh, this iteration never made sense. I sincerely hope something fun moves back in. Things next door in the former glass company space aren’t cutting it.
We wrapped up #THEProteomicsShow Alt Proteomics season with Tim Cleland @paleoproteomicist.bsky.social talking paleoproteomics with me and Ben @proteomicsnews.bsky.social. Won't lie, this season was a blast talking about less typical "proteomics". Find it wherever you find fine podcasts or here.
Ep 94 - Alt Proteomics - Dr. Timothy Cleland by The Proteomics Show
For the final episode of the US HUPO sponsored "Alt Proteomics" series highlighting alternative proteomics things, Ben and Ben sit down to talk with Dr. Timothy Cleland, Smithsonian Institution.Keywor...
creators.spotify.com
November 18, 2025 at 7:13 PM
We wrapped up #THEProteomicsShow Alt Proteomics season with Tim Cleland @paleoproteomicist.bsky.social talking paleoproteomics with me and Ben @proteomicsnews.bsky.social. Won't lie, this season was a blast talking about less typical "proteomics". Find it wherever you find fine podcasts or here.
Reposted by Ben Neely
From the @narjournal.bsky.social #NARDatabaseIssue | EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025 | #Bioinformatics #OpenData #OpenScience #Proteomics #Genomics #Bioimaging 🧬 🖥️🧪🔓
⬇️
academic.oup.com/nar/advance-...
⬇️
academic.oup.com/nar/advance-...
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2025
Abstract. The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolec
academic.oup.com
November 15, 2025 at 2:38 PM
From the @narjournal.bsky.social #NARDatabaseIssue | EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025 | #Bioinformatics #OpenData #OpenScience #Proteomics #Genomics #Bioimaging 🧬 🖥️🧪🔓
⬇️
academic.oup.com/nar/advance-...
⬇️
academic.oup.com/nar/advance-...
Reposted by Ben Neely
Since I didn't get anything back yesterday, I'll ask again:
Is there an existing terminology to refer to the two proximal flanking IDRs associated with a named structured domain?
Is there an existing terminology to refer to the two proximal flanking IDRs associated with a named structured domain?
November 16, 2025 at 2:00 PM
Since I didn't get anything back yesterday, I'll ask again:
Is there an existing terminology to refer to the two proximal flanking IDRs associated with a named structured domain?
Is there an existing terminology to refer to the two proximal flanking IDRs associated with a named structured domain?
At least one (or two) of these are more “lifetime” achievement type things, but the Cotter is for the early researchers. There’s been efforts to make the descriptions and qualifications broader for each award while keeping the intention. Others know better than me.
Still, good perspective.
Still, good perspective.
November 15, 2025 at 4:49 PM
At least one (or two) of these are more “lifetime” achievement type things, but the Cotter is for the early researchers. There’s been efforts to make the descriptions and qualifications broader for each award while keeping the intention. Others know better than me.
Still, good perspective.
Still, good perspective.
Ugh, never forget. And this got picked up by so much pop sci outlets too.
November 15, 2025 at 2:34 PM
Ugh, never forget. And this got picked up by so much pop sci outlets too.
Core: yeah that RIN value really is too low for us to get anything meaningful.
… mammoth you say, no problem!
… mammoth you say, no problem!
Scientists have extracted the oldest RNA molecules out of a wooly mammoth, gaining a snapshot into the processes at work in the extinct mammal's body just before it died. n.pr/4patABW
Scientists pull ancient RNA from a wooly mammoth's body
Scientists have extracted the oldest RNA molecules out of a wooly mammoth, gaining a snapshot into the processes at work in the extinct mammal's body just before it died.
n.pr
November 14, 2025 at 9:12 PM
Core: yeah that RIN value really is too low for us to get anything meaningful.
… mammoth you say, no problem!
… mammoth you say, no problem!
Say what we will about the feds right now, but I am pretty sure they realized how much we paid in publication fees and subscription fees and noped them pretty hard. Unsure how this is shaking out in real policy so far.
November 14, 2025 at 7:56 PM
Say what we will about the feds right now, but I am pretty sure they realized how much we paid in publication fees and subscription fees and noped them pretty hard. Unsure how this is shaking out in real policy so far.
In case you missed the live #THEProteomicsShow with me and Ben Orsburn @proteomicsnews.bsky.social, it was pretty fun. HUGE thanks to the organizers of #HUPO2025 for inviting us, and for Ken Weke (Univ. of Victoria) for being our guest. Definitely check it out wherever you get podcasts, or here:
The Proteomics Show • A podcast on Spotify for Creators
Ben Orsburn and Ben Neely co-host a podcast series in a “fireside chat” format with prestigious proteomics researchers. The guests are great, the hosts are questionable.
anchor.fm
November 14, 2025 at 2:03 PM
In case you missed the live #THEProteomicsShow with me and Ben Orsburn @proteomicsnews.bsky.social, it was pretty fun. HUGE thanks to the organizers of #HUPO2025 for inviting us, and for Ken Weke (Univ. of Victoria) for being our guest. Definitely check it out wherever you get podcasts, or here:
So I love this scene at the end of Casino Royale, but then someone pointed out Mr. White's knee pads and I can't unsee them. Still, easily one of my favs, and 100% my fav trilogy.
November 14, 2025 at 1:00 PM
So I love this scene at the end of Casino Royale, but then someone pointed out Mr. White's knee pads and I can't unsee them. Still, easily one of my favs, and 100% my fav trilogy.
You motivated me to click through. Turns out not many actual emails of substance (without a time limit, like review invitation), maybe less than 20. I’ve unsubscribed from a lot now.
November 13, 2025 at 7:30 PM
You motivated me to click through. Turns out not many actual emails of substance (without a time limit, like review invitation), maybe less than 20. I’ve unsubscribed from a lot now.
I’ve never understood it. Like is it really as self congratulatory as it seems or surely there is more to it and I’m doing it wrong.
November 13, 2025 at 7:29 PM
I’ve never understood it. Like is it really as self congratulatory as it seems or surely there is more to it and I’m doing it wrong.
Of course authors seem to be on bluesky. Thanks Dungeon Crawler Matt @mattdinniman.bsky.social.
November 13, 2025 at 2:44 PM
Of course authors seem to be on bluesky. Thanks Dungeon Crawler Matt @mattdinniman.bsky.social.
Personalize auto emails... never!
I feel like mad libs were way ahead of their time. I bet you could easily create a more fun form letter + random word picker from dictionary to create way better content.
I feel like mad libs were way ahead of their time. I bet you could easily create a more fun form letter + random word picker from dictionary to create way better content.
November 13, 2025 at 1:42 PM
Personalize auto emails... never!
I feel like mad libs were way ahead of their time. I bet you could easily create a more fun form letter + random word picker from dictionary to create way better content.
I feel like mad libs were way ahead of their time. I bet you could easily create a more fun form letter + random word picker from dictionary to create way better content.
Not science: after months of not really reading (aka stress), I am late to the Dungeon Crawler Carl series and loving it. Squid Games + Hunger Games + Hitchhiker's Guide + DnD + who knows what else = this LitRPG masterpiece, and I can't put it down (read book 1 on trip). Lotsa stars/thumbs from me.
November 13, 2025 at 1:40 PM
Not science: after months of not really reading (aka stress), I am late to the Dungeon Crawler Carl series and loving it. Squid Games + Hunger Games + Hitchhiker's Guide + DnD + who knows what else = this LitRPG masterpiece, and I can't put it down (read book 1 on trip). Lotsa stars/thumbs from me.
Good news: only 370 emails made it through to my inbox. That is still alot of emails.
Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.
Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.
![alot [of emails] monster](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:gl7bvz3uo4ym2fnmvgkjzeb3/bafkreiafi3qk6gq7kociv7fxixq4rrbbzozfuleihj3kmm7ighpbxucxty@jpeg)
November 13, 2025 at 12:54 PM
Good news: only 370 emails made it through to my inbox. That is still alot of emails.
Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.
Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.
Reposted by Ben Neely
"Biomarker studies are the greatest reproducibility crisis in science" (M. Uhlén, 2025).
November 11, 2025 at 6:02 PM
"Biomarker studies are the greatest reproducibility crisis in science" (M. Uhlén, 2025).
Since I’ve heard I may be back at work soon, I’ll file this in the “to read” pile. www.nature.com/articles/s41...
Koina: Democratizing machine learning for proteomics research - Nature Communications
Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...
www.nature.com
November 12, 2025 at 12:28 PM
Since I’ve heard I may be back at work soon, I’ll file this in the “to read” pile. www.nature.com/articles/s41...
Have you heard about the podcast live show on Monday? No snow then!
November 8, 2025 at 10:34 PM
Have you heard about the podcast live show on Monday? No snow then!
And by 41 hours you’ll be a master!
November 7, 2025 at 9:18 PM
And by 41 hours you’ll be a master!