Our new paper on long-read barcode clustering is now available at #Bioinformatics: https://doi.org/10.1093/bioinformatics/btae182
#Barcode #BarSeq #DMS #mave
TIL: GitHub supports callout boxes in their markdown rendering 🙌
Optimization of a deep mutational scanning workflow to improve quantification of mutation effects on protein-protein interactions https://www.biorxiv.org/content/10.1101/2023.10.23.563542v1?med=mas
BioRxiv has joined forces with Company of Biologists to expand our presence on Mastodon.
Mastodon accounts now available for every subject category https://connect.biorxiv.org/news/2023/09/27/biorxiv_expands_on_social_platforms
“In a large study published in September 2022 ..researchers developed a tool that’s essentially a library of every conceivable change to the N-protein over time. They used deep mutational scanning to predict how each of those changes would affect the ability of 17 antibodies used in 11 commercially available rapid tests to latch onto the virus… can cross-reference changes in each new variant of the virus to quickly assess whether a given test will still work. “
Our new #git #cheatsheet is ready for use, thanks to @SciCompAalto: https://aaltoscicomp.github.io/cheatsheets/git-the-way-you-need-it-cheatsheet.pdf
It's designed for beginners/intermediates to introduce things slowly, recognizing that most use is simple, and grouping advanced uses together how they are used. It'll be used in our workshop next week. #RSEng #HPC #teaching
@yokofakun For 2FA I invested in a pair of hardware security keys recently and I'm very happy with it. No more looking up codes in an app, just press the button on the key instead.
For all the folks starting their #PhD (or their master thesis) today - a reminder why your PhD advisor can solve a problem so "easily" ...
Docking With AlphaFold Structures: Oops | Science | AAAS
#StructuralBiology #Alphafold @strucbio
https://www.science.org/content/blog-post/docking-alphafold-structures-oops
Writing or reviewing a manuscript? Watch out for these ten common statistical mistakes ⬇️ 6/n
#AcademicChatter #Writing #Academia #PhDlife #PhD #ECR #SciComm #ScholComm #Reproducibility #DataScience #DataAnalysis #Data #Research #Statistics
https://elifesciences.org/articles/48175?utm_source=mastodon&utm_medium=social&utm_campaign=organic
Code sharing increases citations but remains uncommon
https://doi.org/10.21203/rs.3.rs-3222221/v1
'We examine temporal trends in code sharing in ecology and evolution publications since 2010.
We find that scientists are overwhelmingly (95%) failing to publish their code.
We also find code sharing can considerably improve citations.'
My favorite paper that I've read this year — a look at how confusion between inferential uncertainty and outcome variability creates all sorts of problems — is now out in PNAS.
Here's the paper: https://www.pnas.org/doi/abs/10.1073/pnas.2302491120
Here's the thread I wrote about the preprint last April: https://fediscience.org/@ct_bergstrom/110267907188002904
Optimizing #RShiny applications with webR is a game-changer 🤯 By leveraging browser-based computation, we witness a significant reduction in server load and enhanced responsiveness.
Dive deeper into the technical insights: https://appsilon.com/bringing-webr-into-shiny/
alright #rstats , no cheating -- without running it beforehand, what would you expect this code to do?
add <- function(a, b) {
a + b
} / 2
add(2, 4)
Just discovered there is an extension of #Inkscape to quickly edit scientific figures (change axis ratio, font sizes, etc) 🤩
The approach itself is implemented in multidms software package, which is available at https://github.com/matsengrp/multidms
We think it should also be useful to other labs performing deep mutational scanning across protein variants or selection conditions.
In new study, we develop rigorous method to jointly analyze deep mutational scanning of different protein homologs or conditions
We use it to identify mutations w effects on spike-mediated viral entry that differ by >1,000-fold among #SARSCoV2 strains.
Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries.
Our pre-print is now available: https://www.biorxiv.org/content/10.1101/2023.02.22.529427v1
@fritzroth
#pacbio #Bioinformatics #DeepMutationalScanning #BarSeq #VariantEffectMapping #longread #mave
Is it left handed or this some sort of optical illusion? 🧐
---
RT @hajirasouliha
A DNA double helix molecule made of drones! #AGBT23
https://twitter.com/hajirasouliha/status/1623107978613211140
Announcing papertooter. Papertooter is a simple script that takes the URL of a biorxiv preprint, and posts the title and link to the paper on Mastodon using the Mastodon Python API. It also posts a unique hashtag it generates from the paper's DOI.
Feature requests and bug reports welcome.
Research Associate in the Roth Lab at the Donnelly Centre, University of Toronto
--
Computational Biology, Bioinformatics, Systems Biology
--
:flag-ca: :de: