Fool

Code 🐒 Lab 🐁

[Niko McCarty. @NikoMcCarty]

This is an interesting (and short) paper about biases in forensic evidence.

It argues that "an error in statistical reasoning," found in a 2023 paper, is leading to "highly inflated claims" and potentially biasing evidence against a defendant in an ongoing homicide case.

[Andrew White 🐦‍⬛ @andrewwhite01]

We’ve just finished writing the missing 15,616 Wikipedia articles to get complete coverage of all 19,255 human genes. We used PaperQA2, which has higher accuracy than existing human-written Wikipedia articles, as judged by blinded biology PhD students and postdocs. 1/5

[Fool @methylrot]

@kieranrcampbell Seems useful!
Have you noticed discrepancies between the the specificity or abundance of markers in RNA compared to antibody intensities?

[The Journal of Immaterial Science @JImmatSci]

BREAKING NEWS: The 2024 Noble Prize for Medicine has been awarded to Jack the Rat for his contribution to research on phallogigantism and the JAK/STAT signalling pathway.
You can read how Jack used AI to conduct his research here: https://t.co/zeC7OwydTu

[Fool @methylrot]

@nr_claudio If it is Visium CellXGene is nice.
EMBL's BioImageArchive has expressed interest in hosting spatial transcriptomics dataset. They can give you a link that you can use with Vitessce/Samui for GUI data exploration in the browser which is nice

[Stephen Turner 🦋 @stephenturner.us @strnr]

Conotoxins (cone snail venom) are one of the most deadly neurotoxins found in nature.

Here's ConoDL/ConoGen: "an end-to-end conotoxin generation model" https://t.co/jKgCYrZ1wJ https://t.co/iPkBS6OfCr

[Eugene Katrukha 🇺🇦 @katpyxa]

While hanging out at https://t.co/dEQbQX6q43, a resource mostly for microscopy image analysis, sometimes I see people using #ImageJ @FijiSc @napari_imaging for "outside science" unusual interesting applications. Here is a small thread of things I saw (1/N)

[Constantin Ahlmann-Eltze (@const-ae.bsky.social) @const_ae]

There's a lot of excitement about foundation models and their ability to learn biology 🧬💻

But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.

https://t.co/lTJM7ghk2r

[Pete Bankhead @petebankhead]

Let me introduce: InstanSeg 🦠🔬💻👩‍🔬

This *would* have been a short thread about Thibaut Goldsborough’s PhD work… but he solved too many problems.

Now it's a long thread about 2 preprints, a whole new approach to cell segmentation & #opensource software to make it easy to use

[Fool @methylrot]

@benoitbruneau @SethBlackshaw @WallaceUcsf Got a link?
I am interested in classifying some cardiomyocytes :)

[Fool @methylrot]

@GenomicsCow 10x ones are pretty good, down to how many times you are supposed to shake samples 🤪

[Nick Banovich @NeBanovich]

Earlier this week we carried out a preliminary analysis of our first @10xGenomics Xenium prime (5,000 gene) run. We had designed this experiment to get a sense of how the prime chemistry performed compared to the Xenium V1 chemistry.

[Fool @methylrot]

@shyam_lab @VairavanL @iaintan_mdphd @villanilab @astar_gis Hi @shyam_lab @VairavanL ,great work!
When do you plan to relase a package?
I would love to try it out with some of my samples that have been difficult to QC

[bioRxiv Bioinfo @biorxiv_bioinfo]

Pertpy: an end-to-end framework for perturbation analysis https://t.co/pqQgQvUxhC #biorxiv_bioinfo

[Lukas Heumos @LukasHeumos]

I'm so excited for the very first scverse conference from September 10-12 in Munich, Germany. We are very close to reaching 100+ participants.
We still have spots so please consider joining us: https://t.co/xklVJPXQHD

[Niko McCarty. @NikoMcCarty]

This "frugal CRISPR kit" costs about $2.

It includes a cell-free extract (no living cells), plasmids encoding colorful proteins, and Cas9 + guide RNAs.

Students express colorful proteins in the extract & then use CRISPR to cut the protein-coding genes, leading to loss of color.

[Fool @methylrot]

@ScienceScottT Cool, thanks a lot!

I really like that more and more algorithms for improved clustering are coming out

[Fool @methylrot]

Hi @ScienceScottT

Is there a simple way to apply your cluster validation algorithm from https://t.co/F6YLYhDK3f to my anndata to improve clustering?

[Fool @methylrot]

@ScienceScottT @lpachter Could you elaborate on that a little bit? The new 10X flex kits can multiplex 16 fixed samples at once. How would you include replicates and include that in an analysis?