Matthew Russell
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matteomics.bsky.social
Matthew Russell
@matteomics.bsky.social
170 followers 430 following 200 posts
Measurements want to be accurate;
Experiments want to be elegant;
Data wants to be beautiful and Data wants to be free
#proteomics
#rstats

Posts Replies Media Videos
Reposted by Matthew Russell
ronbeavis.bsky.social
To me, science is about trying to figure out WTF is going on.
January 4, 2026 at 3:25 PM
Reposted by Matthew Russell
matthewcollins.bsky.social
Experience in #archaeological #proteomics?
Interested in #Roman economy / organic artefacts?
Background in data analysis for #ZooMS?

Then apply for a 3-year RA post working to join PELLIS project with the wonderful @gtaylortu.bsky.social to investigate Roman leather economy

Apply by 12/01/2026
T: 01642 342201 E: [email protected]
tuwpapps.tees.ac.uk
December 16, 2025 at 2:39 PM
Reposted by Matthew Russell
alisonchaves.bsky.social
#proteomics people, this figure has been around for some years. I'm trying to track the original source to give credit. Any idea? Found this publication pubs.rsc.org/en/content/a...
www.crownbio.com/hs-fs/hubfs/...
December 13, 2025 at 2:52 PM
matteomics.bsky.social
The @eleanormorton.bsky.social‬ Tolkien - CS Lewis skits are some of the best things on the internet.
December 12, 2025 at 2:36 PM
Reposted by Matthew Russell
benneely.com
#AminoAcidAdvent Day 7: Argenine (Arg; R)

What's a pirate's favorite amino acid? ARRRgenine!

This basic residue is a fav for heavy isotope fans, with a storied history from SILAC to SRM, and of course most famous for trypsin cutting after it giving us the 175 m/z y1 we all know and love.
December 10, 2025 at 1:46 PM
Reposted by Matthew Russell
pedrobeltrao.bsky.social
We are hiring for a web developer position, ideally with some experience in bioinformatics. This position is aimed at helping us turn our research in human genetics into useful tools. A background in either bioinformatics or web development is required.

jobs.ethz.ch/job/view/JOP...
Full Stack Web Developer for Life Science Research
jobs.ethz.ch
December 9, 2025 at 5:10 PM
Reposted by Matthew Russell
historysmith.bsky.social
"It’s hard, but struggling is the only way to learn anything.

Once you’ve gotten these skills, you have enough knowledge and expertise to use LLMs & fight & argue with them & speed things up. But before that point, you’re in danger-land."

I love that this is from the perspective of stats & coding.
andrew.heiss.phd Andrew Heiss @andrew.heiss.phd · 27d
Some closing thoughts for my students this semester on LLMs and learning #rstats datavizf25.classes.andrewheiss.com/news/2025-12...
Will you incorporate LLMs and AI prompting into the course in the future? No. Why won’t you incorporate LLMs and AI prompting into the course? These tools are useful for coding (see this for my personal take on this). However, they’re only useful if you know what you’re doing first. If you skip the learning-the-process-of-writing-code step and just copy/paste output from ChatGPT, you will not learn. You cannot learn. You cannot improve. You will not understand the code. In that post, it warns that you cannot use it as a beginner: …to use Databot effectively and safely, you still need the skills of a data scientist: background and domain knowledge, data analysis expertise, and coding ability. There is no LLM-based shortcut to those skills. You cannot LLM your way into domain knowledge, data analysis expertise, or coding ability. The only way to gain domain knowledge, data analysis expertise, and coding ability is to struggle. To get errors. To google those errors. To look over the documentation. To copy/paste your own code and adapt it for different purposes. To explore messy datasets. To struggle to clean those datasets. To spend an hour looking for a missing comma. This isn’t a form of programming hazing, like “I had to walk to school uphill both ways in the snow and now you must too.” It’s the actual process of learning and growing and developing and improving. You’ve gotta struggle. This Tumblr post puts it well (it’s about art specifically, but it applies to coding and data analysis too): Contrary to popular belief the biggest beginner’s roadblock to art isn’t even technical skill it’s frustration tolerance, especially in the age of social media. It hurts and the frustration is endless but you must build the frustration tolerance equivalent to a roach’s capacity to survive a nuclear explosion. That’s how you build on the technical skill. Throw that “won’t even start because I’m afraid it won’t be perfect” shit out the window. Just do it. Just start. Good luck. (The original post has disappeared, but here’s a reblog.) It’s hard, but struggling is the only way to learn anything. You might not enjoy code as much as Williams does (or I do), but there’s still value in maintaining codings skills as you improve and learn more. You don’t want your skills to atrophy. As I discuss here, when I do use LLMs for coding-related tasks, I purposely throw as much friction into the process as possible: To avoid falling into over-reliance on LLM-assisted code help, I add as much friction into my workflow as possible. I only use GitHub Copilot and Claude in the browser, not through the chat sidebar in Positron or Visual Studio Code. I treat the code it generates like random answers from StackOverflow or blog posts and generally rewrite it completely. I disable the inline LLM-based auto complete in text editors. For routine tasks like generating {roxygen2} documentation scaffolding for functions, I use the {chores} package, which requires a bunch of pointing and clicking to use. Even though I use Positron, I purposely do not use either Positron Assistant or Databot. I have them disabled. So in the end, for pedagogical reasons, I don’t foresee me incorporating LLMs into this class. I’m pedagogically opposed to it. I’m facing all sorts of external pressure to do it, but I’m resisting. You’ve got to learn first.
December 9, 2025 at 9:20 PM
matteomics.bsky.social
Totally agree. Better than endnote, better than Mendeley.
jenvictor.bsky.social Jennifer N. Victor @jenvictor.bsky.social · Dec 6
I cannot evangelize enough for @zotero.org for citation management. It's a game changer. If you're a student, and you're writing a paper right now, and you're NOT using Zotero, I ask you...why? Why are you making things harder than they need to be?
a woman is sitting at a desk with her arms outstretched in front of a map on the wall .
ALT: a woman is sitting at a desk with her arms outstretched in front of a map on the wall .
media.tenor.com
December 7, 2025 at 1:37 PM
Reposted by Matthew Russell
vadim-demichev.bsky.social
We are delighted to release 𝐃𝐈𝐀-𝐍𝐍 𝟐.𝟑.𝟏, with a groundbreaking 𝐈𝐧𝐟𝐢𝐧𝐃𝐈𝐀 module for fast searches against huge databases and support for 𝐃𝐃𝐀 data.

Release notes: github.com/vdemichev/Di...
December 5, 2025 at 11:51 AM
matteomics.bsky.social
#notion I have loved you as a notebook but load times are getting too long. My notebook has to be available faster than I can think. Don’t know if its growing sophistication of my connected databases, formula or integrated AI. But it's getting to be unusable.
December 4, 2025 at 12:34 PM
matteomics.bsky.social
I've been "nearly there" with a paper submission to bioRxiv and accompanying data submission to pride for about a week. It's the tension between wanting to check everything is correct (good) and not wanting to let go (bad).
December 4, 2025 at 12:25 PM
Reposted by Matthew Russell
keithfrankish.com
The philosophers were so preoccupied with whether they should that they didn't stop to think if they could.
December 3, 2025 at 9:35 PM
matteomics.bsky.social
An important list of things that are nessisary, but no sufficient, and not magic!
dingdingpeng.the100.ci Julia M. Rohrer @dingdingpeng.the100.ci · Dec 3
1. Transparency is necessary for credibility
2. Transparency is hard to change
3. Require transparency*
4. Transparency is not magic
5. Journals are part of problem
6. Expect more from journals
7. Peer review is not magic
8. A crisis can look a lot like „normal“ science
9. Meta-analysis is not magic
peercommunityin.bsky.social Peer Community In @peercommunityin.bsky.social · Dec 2
In case you have missed Simine Vazire's excellent webinar yesterday, here is the link to watch it online: youtu.be/_vb1CNwC3CM Thanks again @simine.com for staying up so late and thanks to the audience for the great questions!
December 3, 2025 at 11:39 AM
Reposted by Matthew Russell
ageofoddish.bsky.social
Does anyone want a survivorship bias shortbread
My hand holding a shortbread cookie in the shape of an airplane. There are red sprinkles in the pattern of the survivorship bias plane. A plate of the same cookies.
November 29, 2025 at 4:50 AM
Reposted by Matthew Russell
synbio1.bsky.social
Americans make great biologists because we are forged by the hardest challenge in all of biotech: getting flavor from a turkey
November 27, 2025 at 2:35 PM
matteomics.bsky.social
This post says it very well. I guess transparancy is supposed to enable the quality of work to be better judged after the fact, but agree that may do little to improve quality of the work in the first place.
devezer.bsky.social Berna Devezer @devezer.bsky.social · Nov 26
Transparency about poor inferential practices does not relieve us of the responsibility of not engaging in such practices in the first place. Wish we stopped attributing higher moral value on transparency than doing diligent work and explicitly aiming to minimize the reporting of invalid inferences.
November 26, 2025 at 10:54 PM
Reposted by Matthew Russell
albertvilella.bsky.social
@jameshiggins on UK budget news for what it concerns to #biotech and #diagnostics
November 26, 2025 at 6:40 PM
Reposted by Matthew Russell
rcolesworthy.bsky.social
that list of four potential peer reviewers you gave your acquisitions editor? one of them is retired, another is chairing their department and simply can't, the third is on leave and has an autoreply up for months, and the fourth replied within 20 seconds to say "no."
November 25, 2025 at 1:46 PM
matteomics.bsky.social
So much this, I have long wondered why jounals what spesific citations formats. Also, if they do, why not just ask for the doi / pubmed IDs and automate citation formatting to their taste during typsetting.
whysharksmatter.bsky.social David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · Nov 24
I have published more than 70 peer reviewed scientific journal articles. I am a reviewer at 50+ journals, and an editor at one journal.

I cannot for the life of me fathom why some journals care so much about reference formatting style. If I can find the paper, you've cited it fine.
a man in a tuxedo is asking why are you booing me i 'm right
ALT: a man in a tuxedo is asking why are you booing me i 'm right
media.tenor.com
November 24, 2025 at 7:31 PM
Reposted by Matthew Russell
williamripple.bsky.social
And we warned them with our new 2025 State of the Climate Report which you can check out here: doi.org/10.1093/bios...
November 14, 2025 at 7:31 AM
Reposted by Matthew Russell
olivierduss.bsky.social
Thinking Like a Scientist, Part Two: The Omics Illusion network.febs.org/posts/thinki... #FEBSnet
Thinking like a Scientist: The Limits of Genome Editing and Omics
Second part of Thinking like a Scientist, reflecting on how genome editing and multi-omics, while powerful, can introduce conceptual flaws that distort our understanding of gene function and biologica...
network.febs.org
November 7, 2025 at 1:10 PM
matteomics.bsky.social
One little bonus of using #git for version control with #quarto for scientific writing is the psycological boost from seeing the git graph fill up as a little progress chart.
November 5, 2025 at 12:10 PM
matteomics.bsky.social
I had a wonderful run this morning and beautiful walk this afternoon in the north of England. Both of course were curtasy of the ongoing catastraphy of climate change.
extremetemps.bsky.social Extreme Temperatures Around the World @extremetemps.bsky.social · Nov 1
EUROPE EXCEPTIONAL NOVEMBER WARMTH

An extraordinary warm spell is affecting all North Africa and Europe,only excluding Italy.
42C in Mauritania, 39 Algeria,>25 in the Balkans (mins up to 19C).

Next days hundreds of records with up to 34C in Turkey.
November 2, 2025 at 5:02 PM
matteomics.bsky.social
Oh, amzing tool in #Positron with #Quarto for #Rstats scientific publishing. The gitlense extention allows you to compare any pair of previous commits in a single diff view. Am currently rescuing a few ideas lost to an earlier over zelious condensing effort.
October 31, 2025 at 4:39 PM
matteomics.bsky.social
Amazing Halloween decoration up in #Manchester #UK near the Gay Village. A giant pink spider climbing down wall! The wall belongs to an Alice in Wonderland / Through the Looking Glass themed tea room. I love this city.
A Halloween decoration comprising a giant pink spider climbing down the side of a red brick building.
October 31, 2025 at 10:28 AM