Welcome to our first-year Integrated Physiology students on campus!

Wow, this seems a very draconian and impractical stance for #NIH to take for its grants involving foreign partners! 👇

Article below haa a full takedown. #academicchatter #funding @academicchatter

"Beginning October 1, 2023, foreign subaward recipients will be required to provide the U.S. prime grantee “copies of all lab notebooks, all data and all documentation that support the research outcomes…no less than every six months, or more frequently based on risks”"

https://www.nejm.org/doi/full/10.1056/NEJMp2307543?query=WB&cid=NEJM%20Weekend%20Briefing,%20September%209,%202023%20DM2282798_NEJM_Non_Subscriber&bid=1788903581

It was a pleasure having summer students Abigiya Abate and Gabe Wu work with us in the lab. Both did a stellar job and will be an asset to any graduate programs!

@RonBeavis Elaborate? Do you mean most are "text-mining associations" (lime green) rather than physical interactions?

Based on these 2 images, which region of SPARCL1:p corresponds to the nicely folded set of α-helices and β-sheets & which region is a gnarly freak show of E/D-dominated low complexity domains?

Fun conference at @us_hupo last week. Congrats again to Jordan who received the HUPO Travel Award and gave an excellent oral presentation on his project!

Excited for @us_hupo conference next week. Come check out the talk by Jordan Currie (OA07.01) on protein turnover and localization analysis in Parallel Session 07: Protein Dynamics and Turnover on Tuesday 3/7 11:30-12:50!

Seems sensible to me right now, but with the speed of change, how long will this hold true? What properties or abilities would you expect an AI to have for it to qualify for authorship in a scholarly context?

Personal responsibility, consent and agency come to mind, but I have no idea how one would validate these properties.

I suspect scientific editors will be confronting this soon. 2/

RT @ChemistryNews@twitter.com

Enhancement of a prime editing system via optimal recruitment of the pioneer transcription factor P65 https://www.nature.com/articles/s41467-023-35919-0

🐦🔗: https://twitter.com/ChemistryNews/status/1615336654264492038

dplyr 1.1.0 is out now! 🎉

This is a huge release, so we split the announcement into 4 posts to be released throughout the week. #rstats

Today we'll focus on joins, including:
- join_by()
- Inequality and rolling joins
- Two new quality control arguments

https://www.tidyverse.org/blog/2023/01/dplyr-1-1-0-joins/

We have integrated semi-supervised PSM rescoring in the ANN-SoLo open modification spectral library search engine.

Open modification searching = identify modified peptides without explicitly having to specify PTMs.

PSM rescoring = more accurate and sensitive spectrum identification results.

Open modification searching + PSM rescoring = Win! 💪

Now published in JPR: https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00616
Try ANN-SoLo: https://github.com/bittremieux/ANN-SoLo

PSM rescoring is transparently integrated into ANN-SoLo using the mokapot package by @wfondrie.

Bonus: ANN-SoLo is a spectral library tool, allowing us to use PSM features derived from fragment intensities directly. No need for complex deep learning-based spectrum predictions as used by alternative tools.

PSM rescoring was originally introduced by Percolator, and is increasingly being used to post-process spectrum annotation results from standard searching. But does it also work with open modification searching results?

Yes! We identify a large number of additional modified peptides, including from phosphoproteomics and glycoproteomics datasets.

Ok, so.

Tweets look really good when you send them in Messages on iOS/macOS. Mastodon posts… don’t. So I built a little tool that makes them much nicer to look at:

https://mstdn.link

Add ?to={any Mastodon post URL} to the end of that domain and when you send it to a friend, you get the nice looking preview. Of course the page makes it easy to paste a URL in. And there’s a Shortcut to make it even easier on iOS or macOS.

RT @NCIEytanRuppin@twitter.com

Immune signatures predict development of autoimmune toxicity in patients with cancer treated with immune checkpoint inhibitors https://www.cell.com/med/fulltext/S2666-6340(22)00523-2#.Y89gtmoZNPE.twitter

🐦🔗: https://twitter.com/NCIEytanRuppin/status/1617754695354941442

Congrats to Jordan Currie, who won our local "3 Minute Talk" competition discussing his project on spatiotemporal proteomics, and will be invited to compete in the regional round 🎉

Excited about the release of AdA, led by @FeryalMP@twitter.com & @edwardfhughes@twitter.com, on training an adaptive agent capable of hypothesis-driven exploration to solve challenging unseen tasks in minutes. There is a wealth of insights in this paper👇

https://arxiv.org/abs/2301.07608
https://www.youtube.com/watch?v=U93bUQ1roiw

I wonder what it says about the proteomics field to have a new paper discussing the target decoy method for PSM false discovery rates some 21 years after decoy databases were first introduced:

https://pubs.acs.org/doi/abs/10.1016/S1044-0305%2802%2900352-5

Sequence-reversed, concatenated target/decoy databases were already established by the Elias and Gygi 2007 paper. Are we, as a field, still getting this wrong 2 decades later? Do we formalize basic concepts to such a degree in papers that no one understands them?

#TeamMassSpec

I'll admit to being skeptical about "synthetic biology", wondering if it's just buzz words, but this recent paper from Daniels et al. blew me away with its combination of novel insights into cell signaling circuitry & its clinical potential #ScienceSunday 1/n
https://pubmed.ncbi.nlm.nih.gov/36480602/

How Crocs Can Go Hours Without Air: Crocodilian Hemoglobin

The crocodilian edition of hemoglobins work so well that crocs can go hours without air. The hyper-efficiency of that adaptation has led some biologists to wonder why, of all the jawed vertebrates, crocodilians were the lone group to hit on such an optimal solution to making the most of a breath. After resurrecting the hemoglobin of ancient crocodilian ancestors, a team may have an answer
#hemoglobinopathy #cellbiology #molecularbiology