Karl Makepeace
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makepeace.bsky.social
Karl Makepeace
@makepeace.bsky.social
Proteomics 🩸 Mass Spectrometry ✨ Structural Biology 🧬 Network Biology 🕸️ Bioinformatics 💻 Canada 🍁 Columbia University 🗽 @ionsbyfriday 𝕏
Pinned
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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
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...
www.mcponline.org
November 11, 2025 at 3:49 PM
Robot metabolism: Toward machines that can grow by consuming other machines | Science Advances www.science.org/doi/10.1126/...
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.
www.science.org
August 1, 2025 at 9:04 PM
🔬 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
July 11, 2025 at 4:14 PM
Reposted by Karl Makepeace
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...
Research Workflow with Quarto + {targets} – Kazuharu Yanagimoto
kazuyanagimoto.com
April 26, 2025 at 8:41 AM
Reposted by Karl Makepeace
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...
shikokuchuo{net}: mirai 2.3.0
Advancing Async Computing in R
shikokuchuo.net
June 6, 2025 at 2:43 PM
Discovery + innovation: Accelerating^2

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

#science
A feature in Nature examines the debate among researchers over whether ‘disruptive’ or ‘novel’ science is waning and how to remedy the problem. 🧪
Are groundbreaking science discoveries becoming harder to find?
Researchers are arguing over whether ‘disruptive’ or ‘novel’ science is waning – and how to remedy the problem.
go.nature.com
May 24, 2025 at 11:59 PM
Reposted by Karl Makepeace
Great visualization of NSF cuts to science funding (which doesn't even include cancelled grants) 🧪 nytimes.com/interactive/... h/t to @jhelvy.bsky.social
May 24, 2025 at 7:03 PM
Tumors hijack RNA splicing, creating public neoantigens across cancer types. These neojunctions are processed, HLA-presented, and recognized by T cells—offering universal immunotherapy targets.
Tumour-wide RNA splicing aberrations generate actionable public neoantigens
www.nature.com/articles/s41...
Tumour-wide RNA splicing aberrations generate actionable public neoantigens - Nature
A study identifies public neoantigens generated by tumor-wide aberrant mRNA splicing activity across distinct cancer types.
www.nature.com
February 23, 2025 at 4:41 PM
Reposted by Karl Makepeace
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...
The War on Science
open.spotify.com
February 19, 2025 at 10:43 PM
Reposted by Karl Makepeace
iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments #AC pubs.acs.org/doi/10.1021/...
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/.
pubs.acs.org
January 31, 2025 at 3:49 PM
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February 2, 2025 at 10:32 PM
Open AI > OpenAI 🤔
#deepseek
January 28, 2025 at 2:10 AM
Reposted by Karl Makepeace
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...
Remembering what I did this week with LLMs – Garrick Aden-Buie
Using the GitHub API and {ellmer} to remember what I did this week.
www.garrickadenbuie.com
January 25, 2025 at 12:27 AM
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
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.
martlet.ca
December 23, 2024 at 4:25 AM
You had me at Data Viewer enhancements. 🎉
youtu.be/8uRcB34Hhsw?...

#Positron #RStudio #R
December 10, 2024 at 4:05 PM
pak::pak("tidyverse/elmer") # ✅🤩
posit.co Posit @posit.co · Dec 2
✨ posit::glimpse() is back! ✨

Get a glimpse of our tools in our newsletter.

This edition features Positron news, packages for AI & LLMs, the brand.yml launch, #Quarto workshop recordings, and more.

We’re positive you’ll find something valuable! #RStats #Python

Read here: posit.co/blog/posit-g...
posit::glimpse() Newsletter - December 2024 - Posit
posit.co
December 3, 2024 at 11:43 PM