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Ben Neely

@benneely.com

1.9K followers 700 following 2.2K posts

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

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Ben Neely @benneely.com · Nov 16

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

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Ben Neely @benneely.com · 10h

Yeah, definitely more of a “I can do that and maybe even know why and what rules not to break” but I 100% don’t intuitively understand it.

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Reposted by Ben Neely

Adam Phillippy @aphillippy.bsky.social · 12h

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

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Ben Neely @benneely.com · 1d

It’s been constant light rain for us, so not a deluge, but tossing on a king tide has made it super fun in the Lowcountry. Good news is the astronomical effects are decreasing. water.noaa.gov/gauges/chts1

Cooper River at Charleston Harbor (IN MLLW)

water.noaa.gov

Reposted by Ben Neely

Timothée Poisot @ctrlalttim.com · 2d

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.

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Reposted by Ben Neely

Will Fondrie @handle.invalid · 3d

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

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Ben Neely @benneely.com · 3d

Ha, I definitely helped with that!

Ben Neely @benneely.com · 3d

I mean, there was that paper (paleoproteomics?) where they had the dog naw on bones in the lab.

So it’s not something you’ve concern for or seen evidence of? I figured asking you was the quickest way to an answer. Thanks.

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Ben Neely @benneely.com · 3d

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!

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Ben Neely @benneely.com · 3d

Yeah, absolutely imo. Primm- just comes across as pretentious or awkward to me.

Ben Neely @benneely.com · 3d

But what about the movie or the nucleotide sequence? Come on dictionary people, give me real info!

Ben Neely @benneely.com · 4d

I also liked it when it came out! though it was incredibly unpopular at the time.

Ben Neely @benneely.com · 4d

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

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Ben Neely @benneely.com · 5d

Ha, I guess for all my genomics skywalkers. Hopefully it’s better than Peptide: a protein building game (which I do own).

TabletopGamingDeals @tabletopgamedeals.bsky.social · 5d

While not as big a deal as the other two our favourite Genius Games Game Genotype is also on sale.

It's 19% off, a Prime Big Deal

#ad amzn.to/4h0Ktw1

This is a great dice drafting worker placement game about Mendelian genetics and growing pea plants.

Ben Neely @benneely.com · 6d

I definitely got a couple games not on my list because of you. Big thanks.

Ben Neely @benneely.com · 6d

It was a legit AI collab variety show, but the escalating tension was also part of the show, but done so people thought it was real.

www.instagram.com/p/DPenupQEgn...

Welcome back to Instagram. Sign in to check out what your friends, family & interests have been capturing & sharing around the world.

www.instagram.com

Ben Neely @benneely.com · 8d

I was playing a pre-determined part, which was for the guests.

Ben Neely @benneely.com · 8d

Since I’ve started this thread: “feedback” was 3 people legit tried to fight us, and one guy was coming to work the event (gigpro) but quit to protest with us. He got super pissed when he found out we were fake, like security had to escort him away and report him.

Point: AI emotions run hot.

Ben Neely @benneely.com · 8d

Nearly every patron both nights was taping us out of safety, annoyance or laughter. This is from night one with matching shirts. Second night we looked more legit in normal clothes and had more “feedback” from guests. And all those uber drivers were freaked out!

www.instagram.com/reel/DPZFTUa...

Welcome back to Instagram. Sign in to check out what your friends, family & interests have been capturing & sharing around the world.

www.instagram.com

Ben Neely @benneely.com · 8d

… which I guess is the point of performance art and this event specifically. AI is great, but even satirically it does have a dark underside to the promised future.

Ben Neely @benneely.com · 8d

So… for two nights I was a paid extra, first protesting outside the event, then a patron yelling at hecklers inside, and got to see the show 3 times. Seeing people’s reaction for and against, I can 100% see real (large and violent too) protest being a thing in the near future.

synthetic-theatre.ai

This is not part of the show but is a recent thread on bluesky that feels pretty close to a sentiment I see.

Only one half of our protest, which was like 50 people with signs and bullhorns making our voices known. Lots of stories here.

The ad for the gig. I was brought in late after they realized they wanted more people inside. This was posted Tuesday night when I realized I wasn’t gonna be working Wednesday.

Reposted by Ben Neely

Ruth Huttenhain @rhuttenhain.bsky.social · 11d

My lab @stanfordmedicine.bsky.social is recruiting! We are looking for a postdoc at the interface of quantitative proteomics and G protein-coupled receptor (GPCR) biology:
postdocs.stanford.edu/prospective/...
#TeamMassSpec #Proteomics #GPCR #Postdoc

Open Postdoctoral position, faculty mentor Ruth Huttenhain | Office of Postdoctoral Affairs

postdocs.stanford.edu

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Ben Neely @benneely.com · 9d

It felt pretty on brand for the meeting, especially with their announcement from Germany involving hockey uniforms. When in Rome!

But you know, the show is a bit all over, so no promises what you’ll find.

a man in a suit sits on a park bench with two older people

ALT: a man in a suit sits on a park bench with two older people

media.tenor.com

Ben Neely @benneely.com · 10d

I think just moving to “proteomes”, as in a complete annotated proteome, is paramount. The whole tr v sp thing needs to be gone, especially for human searches, but also for any other species. BUT, you can still gain or lose genes between assemblies and annotations, which is a bit of a can of worms.

Ben Neely @benneely.com · 10d

I’m late to this news, but Melvyn Bragg is stepping down as host of In Our Time. I can’t emphasize enough how much this show has meant to me, and Melvyn’s style is what makes it awesome. Definitely hit the back catalog, or one of my fav recent ones is this one on lungs… there’s so much more to it.

BBC Radio 4 - In Our Time, The Evolution of Lungs

From the mechanics of the first breaths on Earth to the reason we hiccup.

www.bbc.co.uk

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Ben Neely @benneely.com · 11d

This morning instead of proteomic-ing, I went to a rehearsal for what I guess will be performance art. I have a very small role but it’s gonna be a blast to do this for real Friday and Saturday night… and get paid to do it! The show itself is great btw.

Ben Neely @benneely.com · 12d

First step for shutdown Ben was to apply to some local calls for extras in a live show this week. I would recommend reading the article as it describes the upcoming experiment of creativity with AI, which is front and center in our science world.

charlestoncitypaper.com/2025/08/01/s...

'Synthetic Theatre' will be colorful mix of McBride, Beeple - Charleston City Paper

Imagine, if you will, an unassuming warehouse in a no-frills industrial strip on the outskirts of a South Carolina town.

charlestoncitypaper.com