Made a minor update to my {doilinker} 📦 to replace {corpus}, which is currently not on CRAN github.com/lazappi/doilin….

Check it out if you want to find the preprint associated with a paper or vice versa. Available on GitHub and r-universe.

1/7 Want to know which spatial patterns correlate with your disease of interest? Check out our preprint introducing GraphCompass, a Python-based framework for the differential analysis of spatial organization across conditions! bioRxiv: biorxiv.org/content/10.110…

Curious about how Self-Supervised Learning (SSL) is reshaping Single-Cell Genomics (SCG)? 🧬🤖 Our latest paper, 'Delineating the Effective Use of Self-Supervised Learning in Single-Cell Genomics,' offers an in-depth analysis. Thread [1/n]
bioRxiv:
doi.org/10.1101/2024.0…

I'm super excited to announce our new framework for exploratory electronic health record analysis 'ehrapy'. Although analysis is standardized for single-cell by seurat, bioconductor and scanpy, EHR analysis was until now the wild west. medrxiv.org/content/10.110…

1/5 Integration of scRNA-seq data is key for cross-dataset comparison. Yet, substantial batch effects can't be sufficiently removed without losing too much biological information. We show how to improve the integration of substantial batch effects tinyurl.com/3efh585v

To ease understanding of diabetes, which is complicated by bio and technical factors affecting the regulators of blood glucose – the pancreatic islets, we created a comprehensive mouse islet atlas (MIA) by integrating multiple single-cell transcriptomic (scRNA-seq) datasets.

Presenting mubind, a new method at Fabian Theis lab to learn scATAC-seq using seq features and graph representations e.g. kNN-graphs for cell-cell communication. With it, we can learn motif features linked with local cell transitions #ISMBECCB2023 [1/3]
github.com/theislab/mubin…

Introducing inVAE: Leveraging domain variability to learn conditionally invariant representations to unwanted biases. inVAE captures biological variations in single-cell datasets obtained from diverse conditions and labs. Helmholtz Munich | @HelmholtzMunich Ferdi Kapl Soroor Hediyeh-zadeh Fabian Theis (1/7)🧵

We are also excited to announce to have passed over 1500 tools in the database! 🎉

This happened a few months later than we predicted in our 1000 tools paper but we are still excited to see the growth in the field since then.

📣 Abstract submission is open for #EuroBioC2023 conference in Ghent 🇧🇪 Sep 20-22 eurobioc2023.bioconductor.org !

Submit an abstract by April 14 for

Short talk
Software demo
Poster
Contributed session
BOF session

👉 Submit here openreview.net/group?id=bioco…

#rstats #Bioinformatics

Excited to announce that we are significantly expanding the computational biology program at Peter Mac Research.

Applications now open for 2 group leader positions! Come and work with me! Please share widely. Closing June 1.

careers.petermac.org/job/MELBOURNE-…

One challenge of single-cell integration is that true biological variation is treated as batch effect. My new video compares 5 different methods against 3 datasets with known yet subtle biological variation. #R #Python #Bioinformatics youtu.be/NFA2YGshATs

We made an explainer on the power of single cell technology to help understand biology and disease at a single cell level. Thanks Illumina for production support.

Clip below and full video at: youtube.com/watch?v=-nty4s…

Need a #virus or #phage bioinformatics tool?

Have a #virus or #phage bioinformatics tool?

Check out this google sheet and add your new tools

docs.google.com/spreadsheets/d…

I want to talk today about a methodological issue in #genomics research that has been around a long time but is still a major problem.
The reason is that today I reviewed another manuscript that has this exact problem.

Andreas Halman decided the community needed a free and effective software tool for screening literature for systematic reviews.

Here we present Catchii
catchii.org

I have reopened this PhD scholarship, closing 20 February 2023! Details below

Please reach out if interested 💯