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
· 13d
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.
This super fun proteomics article from @davidteschner.bsky.social et al. came out last spring in JPR, but just found the repo thanks to @magnuspalmblad.bsky.social. Definitely need to poke around a bit more in this.
pubs.acs.org/doi/full/10....
github.com/theGreatHerr...
pubs.acs.org/doi/full/10....
github.com/theGreatHerr...
Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data
Mass spectrometry is essential for analyzing and quantifying biological samples. The timsTOF platform is a prominent commercial tool for this purpose, particularly in bottom-up acquisition scenarios. ...
pubs.acs.org
December 1, 2025 at 3:31 PM
This super fun proteomics article from @davidteschner.bsky.social et al. came out last spring in JPR, but just found the repo thanks to @magnuspalmblad.bsky.social. Definitely need to poke around a bit more in this.
pubs.acs.org/doi/full/10....
github.com/theGreatHerr...
pubs.acs.org/doi/full/10....
github.com/theGreatHerr...
Reposted by Ben Neely
Dungeon Crawler Carl Hardcover
62% off, only $11.38
Find out what the hype is all about, or share the love!
#ad amzn.to/4a7gX6z
62% off, only $11.38
Find out what the hype is all about, or share the love!
#ad amzn.to/4a7gX6z
December 1, 2025 at 12:02 PM
Dungeon Crawler Carl Hardcover
62% off, only $11.38
Find out what the hype is all about, or share the love!
#ad amzn.to/4a7gX6z
62% off, only $11.38
Find out what the hype is all about, or share the love!
#ad amzn.to/4a7gX6z
Really not science: so I adored prairie home companion but had never seen anything like it live. Until right now.
www.shortwavekitsch.com
www.shortwavekitsch.com
November 30, 2025 at 10:18 PM
Really not science: so I adored prairie home companion but had never seen anything like it live. Until right now.
www.shortwavekitsch.com
www.shortwavekitsch.com
Not science: this college football season has been a wild ride, from coaches leaving to rivalry games this weekend to how conference championships shaped up. Toss in some Kiffin and it’s insane, and we aren’t even at CFP yet. Great time for [some] fans and all neutrals. Of course, GO DAWGS!!!
November 30, 2025 at 5:32 PM
Not science: this college football season has been a wild ride, from coaches leaving to rivalry games this weekend to how conference championships shaped up. Toss in some Kiffin and it’s insane, and we aren’t even at CFP yet. Great time for [some] fans and all neutrals. Of course, GO DAWGS!!!
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...
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-...
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?
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!
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:
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...
Reposted by Ben Neely
#Palaeoproteomics of Middle and Late Pleistocene hominin fossils and associated zooarchaeological assemblages from Central Eurasia with @fridowelker.bsky.social!
Postdoc: jobportal.ku.dk/videnskabeli...
Research Assistant: jobportal.ku.dk/videnskabeli...
Postdoc: jobportal.ku.dk/videnskabeli...
Research Assistant: jobportal.ku.dk/videnskabeli...
Postdoc in Paleoproteomics
jobportal.ku.dk
October 30, 2025 at 2:43 AM
#Palaeoproteomics of Middle and Late Pleistocene hominin fossils and associated zooarchaeological assemblages from Central Eurasia with @fridowelker.bsky.social!
Postdoc: jobportal.ku.dk/videnskabeli...
Research Assistant: jobportal.ku.dk/videnskabeli...
Postdoc: jobportal.ku.dk/videnskabeli...
Research Assistant: jobportal.ku.dk/videnskabeli...
Reposted by Ben Neely
We are #hiring! 🚀
#PRIDE team is looking for a developer to build its future infrastructure. Our focus in a nutshell: #bigdata, single cell proteomics #SCP, & an #AI-oriented platform. Join us to shape the future of open proteomics data!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
#PRIDE team is looking for a developer to build its future infrastructure. Our focus in a nutshell: #bigdata, single cell proteomics #SCP, & an #AI-oriented platform. Join us to shape the future of open proteomics data!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Software Developer
You will contribute to the development of core database applications, web services, data ingestion workflows, and the PRIDE Web platform as part of the PRIDE ecosystem. Working closely with the team, ...
embl.wd103.myworkdayjobs.com
October 23, 2025 at 1:38 PM
We are #hiring! 🚀
#PRIDE team is looking for a developer to build its future infrastructure. Our focus in a nutshell: #bigdata, single cell proteomics #SCP, & an #AI-oriented platform. Join us to shape the future of open proteomics data!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
#PRIDE team is looking for a developer to build its future infrastructure. Our focus in a nutshell: #bigdata, single cell proteomics #SCP, & an #AI-oriented platform. Join us to shape the future of open proteomics data!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Reposted by Ben Neely
Are you going to the International Human Proteomics Organization World Congress? Are you traveling with your (electric?) guitar? Do you have a few free minutes on Monday early afternoon? I have a great idea! Please reach out. Bonus points if you tune down to drop C.
October 22, 2025 at 4:25 PM
Are you going to the International Human Proteomics Organization World Congress? Are you traveling with your (electric?) guitar? Do you have a few free minutes on Monday early afternoon? I have a great idea! Please reach out. Bonus points if you tune down to drop C.
I listened to something the other day that described 4 attributes of a dream job (paraphrased):
1) autonomy
2) creativity
3) colleagues
4) impact
Part of this is also your ability to identify these traits in your job. Ex. A person selling food is impacting the world by feeding others.
1) autonomy
2) creativity
3) colleagues
4) impact
Part of this is also your ability to identify these traits in your job. Ex. A person selling food is impacting the world by feeding others.
October 21, 2025 at 1:23 PM
I listened to something the other day that described 4 attributes of a dream job (paraphrased):
1) autonomy
2) creativity
3) colleagues
4) impact
Part of this is also your ability to identify these traits in your job. Ex. A person selling food is impacting the world by feeding others.
1) autonomy
2) creativity
3) colleagues
4) impact
Part of this is also your ability to identify these traits in your job. Ex. A person selling food is impacting the world by feeding others.
Reposted by Ben Neely
🚀 Registration is open for EuBIC-MS Winter School 2026! ❄️🧬
📍 Harrachov, Czechia
🎙️ Keynotes | 🛠️ Workshops | 🤝 Networking
Supported by @denbi.bsky.social
This event is a must for anyone in #Bioinformatics, #Proteomics, or #Metabolomics.
🔗 eubic-ms.org/events/2026-...
#EuBIC2026 #MassSpec @eubic-ms.org
📍 Harrachov, Czechia
🎙️ Keynotes | 🛠️ Workshops | 🤝 Networking
Supported by @denbi.bsky.social
This event is a must for anyone in #Bioinformatics, #Proteomics, or #Metabolomics.
🔗 eubic-ms.org/events/2026-...
#EuBIC2026 #MassSpec @eubic-ms.org
October 20, 2025 at 2:44 PM
🚀 Registration is open for EuBIC-MS Winter School 2026! ❄️🧬
📍 Harrachov, Czechia
🎙️ Keynotes | 🛠️ Workshops | 🤝 Networking
Supported by @denbi.bsky.social
This event is a must for anyone in #Bioinformatics, #Proteomics, or #Metabolomics.
🔗 eubic-ms.org/events/2026-...
#EuBIC2026 #MassSpec @eubic-ms.org
📍 Harrachov, Czechia
🎙️ Keynotes | 🛠️ Workshops | 🤝 Networking
Supported by @denbi.bsky.social
This event is a must for anyone in #Bioinformatics, #Proteomics, or #Metabolomics.
🔗 eubic-ms.org/events/2026-...
#EuBIC2026 #MassSpec @eubic-ms.org
Reposted by Ben Neely
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
qedscience.com
October 15, 2025 at 12:22 PM
Reposted by Ben Neely
Registration is now open for the EuBIC-MS Winter School 2026!
Join us in Harrachov, Czechia for a week of keynotes, workshops, and networking on computational MS.
Info and registration: eubic-ms.org/events/2026-...
#EuBIC2026 #MassSpectrometry #MassSpec #Bioinformatics #Proteomics #Metabolomics
Join us in Harrachov, Czechia for a week of keynotes, workshops, and networking on computational MS.
Info and registration: eubic-ms.org/events/2026-...
#EuBIC2026 #MassSpectrometry #MassSpec #Bioinformatics #Proteomics #Metabolomics
October 16, 2025 at 9:36 AM
Registration is now open for the EuBIC-MS Winter School 2026!
Join us in Harrachov, Czechia for a week of keynotes, workshops, and networking on computational MS.
Info and registration: eubic-ms.org/events/2026-...
#EuBIC2026 #MassSpectrometry #MassSpec #Bioinformatics #Proteomics #Metabolomics
Join us in Harrachov, Czechia for a week of keynotes, workshops, and networking on computational MS.
Info and registration: eubic-ms.org/events/2026-...
#EuBIC2026 #MassSpectrometry #MassSpec #Bioinformatics #Proteomics #Metabolomics
In Our Time (yes, that one) has a companion episode to our Ep 76 of #THEProteomicsShow w/ @originalastacus.bsky.social, since they had Dr. Jane Hurst on (talking about darcin). Also check out Kathryn Lilley in Ep 80 for the companion companion.
www.bbc.co.uk/programmes/p...
www.bbc.co.uk/programmes/p...
October 15, 2025 at 5:50 PM
In Our Time (yes, that one) has a companion episode to our Ep 76 of #THEProteomicsShow w/ @originalastacus.bsky.social, since they had Dr. Jane Hurst on (talking about darcin). Also check out Kathryn Lilley in Ep 80 for the companion companion.
www.bbc.co.uk/programmes/p...
www.bbc.co.uk/programmes/p...
Not science: after 2 weeks home I can confirm my dogs do a lot of sleeping during the day.
October 15, 2025 at 3:10 PM
Not science: after 2 weeks home I can confirm my dogs do a lot of sleeping during the day.