"Scalable image-based visualization and alignment of spatial transcriptomics datasets", by Preibisch et al. 2025 @preibischs
https://www.sciencedirect.com/science/article/pii/S2405471225000973
#transcriptomics #BioimageInformatics

Pipeline release! nf-core/molkart v1.1.0 - 1.1.0 - Resolution Road!

Please see the changelog: https://github.com/nf-core/molkart/releases/tag/1.1.0

Aujourd'hui, Gwenaelle nous partage l'histoire des technologies de transcriptomique : comment faisait-on avant l'ère bénie du séquençage haut débit
https://bioinfo-fr.net/expression-de-gene-evolution
#bioinfofr #transcriptomics

I am very happy to announce that our work on hemichordate gene expression and chromatin accessibility dynamics is now published on Nature Ecology and Evolution! https://www.nature.com/articles/s41559-024-02562-x

"Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis", by Wan et al. 2024
https://www.biorxiv.org/content/10.1101/2024.08.27.609868v1

STATGEN 2024 talk
Statistical Methods for Single-Cell RNA-Seq Analysis and Spatial Transcriptomics
Rafael Irizarry

tSNE and UMAP plots:
"They really aren't informative, but they are really pretty."

Negative control scRNAseq data set: the percent of zeros is very high, and contributes strongly to the first PCA. tSNE plot 'discovers' new cells.

Transformed to log2(1 + CPM): looks zero-inflated.

Raw counts: Poisson

1/

Sophisticated swarming: #Bacteria support each other across generations
https://phys.org/news/2023-11-sophisticated-swarming-bacteria-generations.html

Simultaneous spatiotemporal #transcriptomics and #microscopy of #Bacillus subtilis swarm development reveal cooperation across generations: Hannah Jeckel et al. https://www.nature.com/articles/s41564-023-01518-4

"Living in communities provides many advantages to individual #microbes. They are more resilient against adverse environmental conditions, conquer new territories, and benefit from each other."

Very happy that our review paper "A primer on #correlation-based #dimension #reduction methods for #multi-omics analysis" is out. Thanks to the reviewers & journal too for their help.

https://royalsocietypublishing.org/doi/10.1098/rsif.2023.0344

#genomics #omics #systems #data #model #modelling #biology #transcriptomics

Yo #bioinformatics peeps, besides the #cmap dataset, are there are examples of good examples of Sample metadata organization?

I'm thinking specifically of ways to capture different experimental variables which can then be used for differential gene expression, but not only, in #Transcriptomics. E.g. fields are multiple treatments and concentrations, genotypes, siRNA Target, time point, etc.

I have a pretty good idea but I fear that I might be reinventing the wheel.

A #job! my friend Nicole Ackermans is hiring a postdoc to study #neurogenomics and #transcriptomics of headbutting in goats! ​

Official ad will be up soon, but:
Salary: $51k with benefits (NIH standard)
​Tuscaloosa cost of living/m $1598
​​ 2-year contract starting as soon as January 2024, but flexible
​ You get to pet goats
Project is flexible

Contact via: https://bsc.ua.edu/people/nicole-l-ackermans/
​

Hey there!
I'm a French researcher in developmental biology, focusing on mammalian sex determination and gonadal development at the genetic level. I have a PhD in bioinformatics but I do wet and dry lab.
I am a free (as in freedom) and open source software advocate, formerly actively involved in FOSS groups.
I love dataviz, photography, classic rock music, and playing video games.
I moved from another Mastodon instance.
#introductions #stem #DevBio #genetics #genomics #transcriptomics #SexDet

I forgot to do this, so here it is:
Hello #mastodon! I'm Luca, a #PhD student in #complexsystems at the University of Turin (#unito).

I mainly work in #genomics and #transcriptomics. My project involves the study of the #cancer #transportome, and its role in the overall #cellbiology.
I code in #python and #R, but i'm trying to (slowly) learn about #rustlang. I use #archlinux, btw.

I also play a ton of #boardgames and #videogames. I love #mechanicalkeyboard (s) and own a #corne myself.

Includes my interview with 10xGenomics! #neuroscience #transcriptomics #spatialtranscriptomics #datascience #bioinformatics #developmentalbiology #SfN22 #SfN2022

Where neuroscientists go to connect: Recapping Society for Neuroscience 2022
https://www.10xgenomics.com/blog/where-neuroscientists-go-to-connect-recapping-society-for-neuroscience-2022

My #introduction - I work at the Roslin Institute, University of Edinburgh on improving #aquaculture #sustainability (especially #shellfish ) by studying #disease, #innate #immunology and #sequencing (#genomics, #metagenomics, #transcriptomics).

I also love #Surfing , paddleboarding, #CoastalRowing , #Forests , #Foraging , #Homebrew , learning languages and good tunes
in

Forgot to add #Introduction to our first post!

IMPACTT is a Canadian microbiome research core focused on supporting the Canadian and International microbiome research communities.

We run #workshops, #webinars, a #mentorship program, and an annual #symposium dedicated to furthering #microbiome #research.

We also highlight job opportunities within the research sphere, so tag us in your posts!

Hey #rstats folks, do you think it's OK to use arithmetic mean to characterise (zero inflated) count data? Apparently it's the de facto standard in #SingleCellAnalysis #transcriptomics, but I'm not the only one who thinks it's dodgy https://github.com/satijalab/seurat/issues/5542 #Seurat