Ben Neely
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benneely.com
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
Pinned
As of right now, it is not an exaggeration that I am getting many fold better science/proteomics content and interactions here, as well as some of my pop culture (eventually sports) and local info! A good time to get mine folks that *you* make the algorithm.

bsky.social/about/blog/7...
Algorithmic Choice with Custom Feeds - Bluesky
Our implementation of algorithmic choice lets users customize one of the most important parts of their social media experience: their feed.
bsky.social
Core: yeah that RIN value really is too low for us to get anything meaningful.

… mammoth you say, no problem!
npr.org NPR @npr.org · 7h
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
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
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
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.
November 13, 2025 at 12:54 PM
Reposted by Ben Neely
"Biomarker studies are the greatest reproducibility crisis in science" (M. Uhlén, 2025).
November 11, 2025 at 6:02 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...
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
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 in Paleoproteomics
jobportal.ku.dk
October 30, 2025 at 2:43 AM
October 23, 2025 at 3:34 PM
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...
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
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
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.
October 21, 2025 at 1:23 PM
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
October 20, 2025 at 2:44 PM
Reposted by Ben Neely
Here's the link to the system, try it! qedscience.com
@qedscience.bsky.social
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
October 16, 2025 at 9:36 AM
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...
October 15, 2025 at 5:50 PM
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
Reposted by Ben Neely
Struggling to compare Bruker timsTOF methods or extract window schemes from raw .d files? I developed a free desktop tool to solve this: timsCompare! 🚀

It automates the manual work of extracting method parameters, presenting them in a structured and comparable view.

(A thread 🧵)
October 15, 2025 at 11:01 AM
Big news for you #HUPO2025 folks from @proteomicsnews.bsky.social, it seems there’s gonna be some #THEProteomicsShow action there. Our other shows at EuBIC and US HUPO were fun, so definitely mark your calendars for Monday after noon.

proteomicsnews.blogspot.com/2025/10/its-...
It's official! The Proteomics Show will be live at International HUPO!
Since no one asked for it (and ASMS ignored me)!  THE Proteomics Show will record live at International HUPO on Monday, November 10th. Mai...
proteomicsnews.blogspot.com
October 14, 2025 at 10:51 PM
Reposted by Ben Neely
Come join us! We’re seeking a tenure-track colleague in Organic Chemistry. Our department is solely-undergraduate, and well-equipped for a PUI- 400 MHz NMR, six mass specs (including MALDI AND HRMS ESI), and more. DM me with questions!
#chemsky

@chemjobber.bsky.social

jobs.cofc.edu/postings/17277
Assistant Professor of Organic Chemistry
Tenure-Track Assistant Professor in Organic Chemistry. The Department of Chemistry and Biochemistry at the College of Charleston invites applications for a tenure-track faculty position beginning in F...
jobs.cofc.edu
October 10, 2025 at 10:01 PM
My 13 year old is blasting Weezer’s Blue album in his room on old Bose shelf speakers that may be older than me… from his Apple Watch to a bluetooth amp. It’s not quite a full circle but I for one dig it.
October 14, 2025 at 10:02 PM
Reposted by Ben Neely
The pangenome resources and genome assembly/inference approaches we are building will eventually enable complete, personalized “T2T” genomes for everyone. This is the thesis of the Q100 project (www.biorxiv.org/content/10.1...) and what my group is currently working towards. Stay tuned... [10/10]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
October 13, 2025 at 8:17 PM
Reposted by Ben Neely
Inspired by an event I attended this week: the number one issue for adoption of data sharing practices is that part of the open science community is unable to conceptualize that incentives won't ever fix the fact that some people just don't want to share.
October 12, 2025 at 1:46 AM
Reposted by Ben Neely
I'm a huge fan of this proposal!

If we can get vendor buy-in to an open, common format, it could bring more computational folks into the field. How can these folks be excited about #proteomics when its hard to even read the already complicated data?

pubs.acs.org/doi/10.1021/...
mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format
Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.
pubs.acs.org
October 10, 2025 at 5:53 PM
Hey @ronbeavis.bsky.social, me and @proteomicsnews.bsky.social were chatting about your cRAP and I recall you saying you could identify certain European labs by their wool sweaters. Did you ever see if you could identify labs that had cats or dogs as pets, and include those keratins in cRAP? Thanks!
October 10, 2025 at 12:42 PM
Live footage of me taking kids to school next couple days.

Charleston is a glimpse into the future. King Tide means flood, and a little rain or onshore wind makes it real big. But tides go up and down quick. Still, planning trips to avoid high tide downtown. @chswx.com

water.noaa.gov/gauges/chts1
two people are standing on a boat in the ocean .
ALT: two people are standing on a boat in the ocean .
media.tenor.com
October 9, 2025 at 11:05 AM