Karl Makepeace

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker An experimental and computational approach for identification of protein-protein interactions by ex vivo chemical crosslinking and mass spectrometry (…

Feature-engineered rescoring is a big help.

We saw a similar big jump in IDs when we applied this logic to XL-MS:
www.sciencedirect.com/science/arti...

#proteomics

quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments. https://www.biorxiv.org/content/10.64898/2026.01.12.698877v1

Feature-engineered rescoring is a big help.

We saw a similar big jump in IDs when we applied this logic to XL-MS: www.sciencedirect.com/science/arti...

#proteomics

Proteome-wide Monitoring of Drug Action in Living Cells using a Novel Label-free Solvent-based Shift Assay Biophysical proteomics assays allow for proteome-wide, label-free monitoring of ligand-induced changes in protein structure and stability, offering insights into protein-ligand interactions and modula...

Proteome-wide Monitoring of Drug Action in Living Cells using a Novel Label-free Solvent-based Shift Assay - Molecular & Cellular Proteomics www.mcponline.org/article/S153...

SPICE (Solvent Proteome Profiling In Cells)🧪💡

#MCP #Proteomics #DrugDiscovery

Robot metabolism: Toward machines that can grow by consuming other machines Robots grow bigger, faster, and more capable by absorbing and integrating material in their environment.

Robot metabolism: Toward machines that can grow by consuming other machines | Science Advances www.science.org/doi/10.1126/...

👏👏👏👏

🔬 BioMCP: Open-source MCP server for biomedical research AI - connects to clinical trials, PubMed & genomic variants APIs.
Overview video: youtu.be/bKxOWrWUUhM
#BiomedicalAI #OpenSource #MCP #proteogenomics

Show Your Stripes Visualising how the climate has changed for every country across the globe

430 ppm 😮‍💨 #heatwave #nyc
showyourstripes.info/c/northameri...

Research Workflow with Quarto + {targets} – Kazuharu Yanagimoto

New Blog Post: "Research Workflow with Quarto + {targets}"

Let {targets} take the lead and compile your research with Quarto!

#QuartoPub #rstats

kazuyanagimoto.com/blog/2025/04...

GitHub - t-kalinowski/quickr: R to Fortran Transpiler R to Fortran Transpiler. Contribute to t-kalinowski/quickr development by creating an account on GitHub.

#RStats WHAT MAGICKS IS THIS?!?!?! https://github.com/t-kalinowski/quickr

shikokuchuo{net}: mirai 2.3.0 Advancing Async Computing in R

We are delighted to announce mirai 2.3.0 for advanced async computing in #RStats!

Mirai allows event-driven async in Shiny & parallel processing in purrr.

This release brings improvements in serialization & distributed computing. Read more from @shikokuchuo.net: shikokuchuo.net/posts/26-mir...

NIH scientists call on director to protect biomedical research In a public letter, hundreds of scientists expressed their dissent to the Trump administration's policies affecting the National Institutes of Health and called on its director to support the agency.

NPR story about the #BethesdaDeclaration

www.npr.org/sections/sho...

1/n

Discovery + innovation: Accelerating^2

Here, "groundbreaking" or "disruptive" assessed by "CD index" suggests otherwise... questionable. 🤔

#science

Great visualization of NSF cuts to science funding (which doesn't even include cancelled grants) 🧪 nytimes.com/interactive/... h/t to @jhelvy.bsky.social

I’m the Canadian who was detained by Ice for two weeks. It felt like I had been kidnapped I was stuck in a freezing cell without explanation despite eventually having lawyers and media attention. Yet, compared with others, I was lucky

👀 Wow.
www.theguardian.com/us-news/2025...
#Canada #Travel

👀 #proteogenomics

The War on Science

New episode out! 🧪

The Trump administration has thrown the science world into chaos. We talk to @maxkozlov.bsky.social at @nature.com and Jocelyn Kaiser at @science.org about what's going on.

On Spotify or wherever you listen 👇

open.spotify.com/episode/56Co...

iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments Thanks to the plummeting costs of continuously evolving omics analytical platforms, research centers collect multiomics data more routinely. They are, however, confronted with the lack of a versatile software solution to harmoniously analyze single-omics and interpret multiomics data. We have developed iSODA, a web-based application for the analysis of single- and multiomics data. The tool emphasizes intuitive interactive visualizations designed for user-driven data exploration. Researchers can access a variety of functions ranging from simple visualization like volcano plots and PCA to advanced functional analyses like enrichment analysis and lipid saturation analysis. For integrated multiomics, iSODA incorporates multi-omics factor analysis and similarity network fusion. The ability to adapt the data on-the-fly allows for tasks, such as the removal of outlier samples or failed features, imputation, or normalization. All results are presented through interactive plots, the modular design supports extensions, and tooltips and tutorials provide comprehensive guidance for users. iSODA is accessible under http://isoda.online/.

iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments #AC pubs.acs.org/doi/10.1021/...

🍁

Open AI > OpenAI 🤔
#deepseek

Remembering what I did this week with LLMs – Garrick Aden-Buie Using the GitHub API and {ellmer} to remember what I did this week.

LLMs + #RStats are a powerful combo. I wrote a little post about using R to curate GitHub data and {ellmer} to program with LLMs to automate one of my least favorite tasks: remembering what I did this week.

www.garrickadenbuie.com/blog/llm-wor...

The UVic "Edge" 🪦 2015-2024

The UVic logo: how it’s going, and where it started UVic unveiled a new logo collection, or “mark,” last month, signifying the start of a new design era for the university.

Not convinced by the new #UVic logo.🤔

The "Edge" was visually distinct + captured our unique identity through multiple layers of meaning - location, innovation, dynamism.

The new "quasi-Google Drive" logo feels reductive by comparison. + Why?

martlet.ca/the-uvic-log... via @themartlet.bsky.social

π-HuB: the proteomic navigator of the human body Nature - We introduce a major scientific endeavour called π-HuB (proteomic navigator of the human body), its aim being to generate and harness multimodality proteomic datasets to enhance our...

`π-HuB` <- `proteomics` + `big-science`
rdcu.be/d3Lfo

You had me at Data Viewer enhancements. 🎉
youtu.be/8uRcB34Hhsw?...

#Positron #RStudio #R

pak::pak("tidyverse/elmer") # ✅🤩