Happy to see out our latest work on studying animal body size variations using single cell transcriptomics to measure gene expression of individual cells. Learned my fair bit of statistics here, and most importantly I learned how to build wrapper functions for "complex" tasks in R (such as differntial gene expression) in a modular way. Thanks to all the authors involved! https://www.science.org/doi/10.1126/sciadv.adm7042 #singlecell #scrna #allometry #splitseq #planarians #generegulation

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

Pipeline release! nf-core/scrnaseq v3.0.0 - 3.0.0!

Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/3.0.0

Pleased to share a review I contributed to, now published in Nature Neuroscience: Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system.

The article highlights how lineage tracing sheds light on cell fate decisions and molecular mechanisms in development and disease. Read here: https://doi.org/10.1038/s41593-024-01827-9

Reminder for people doing single-cell sequencing work: where possible, try to validate your single-cell data before reporting on it.

#HiveMind
#Genomics
#SingleCell

Looking for suggestions for publicly available single-cell RNA-Seq data from human skin that are 1) raw fastq files for a standard prep like chromium or 2) analyzed data (per cell per gene normalized expression) that *includes* non-coding RNA *not* just coding RNA.

I've looked before and found a number of possibilities that were poorly annotated, didn't include original data, had only processed data with choices I disagreed with, etc.

Bgee has a new look! We have officially switched to the new Bgee website. Check us out at https://www.bgee.org/ @SIB #scRNAseq #RNAseq #singlecell #GeneExpression #bgee #biocuration #bioinformatics

Proteomic researcher and #mdcBerlin group leader Fabian Coscia combines mass spectrometry, #AI, #microscopy, and #robotics to search for the #proteins that drive diseases such as #cancer at the #SingleCell level.

Read more: https://www.mdc-berlin.de/news/news/surveyor-cellular-proteins

"My mother used to joke that my favorite question was really 'why'? Curiosity is what has driven me throughout my life and also driven me towards a path in #science," says lab leader Ashley Sanders.

Her lab is part of the joint #research focus “#SingleCell Approaches for Personalized Medicine” of the @bih_charite, @ChariteBerlin and #mdcBerlin
https://www.youtube.com/watch?v=tHPkaGjA5xw

More about Ashley Sanders: https://lnkd.in/eP9bJCBX

I've accepted a Graduate Research internship offer from Ozette for this summer! Looking forward to working with Fritz Lekschas and team at the intersection of #DataVisualization #SingleCell #Genomics #Oncology #NGS #AI #ML

Learn more about Ozette's research here: https://www.ozette.com/technology-and-applications/

New #Nematostella single-cell reference atlas, from Alison Cole and the Technau lab https://www.researchsquare.com/article/rs-3854371/v1 #cnidaria #singleCell #biology

Cross-posting from the @AllenInstitute feed on Threads:

As you age, so does your immune system.

Our study in Nature Immunology finds that as people age, their T cells undergo molecular changes. The study used TEA-seq, a new method that analyzes immune cells at high detail, to compare immune systems.

https://alleninstitute.org/news/how-your-immune-system-changes-over-time/

New Single Cell dataset, new UMAP plot. I'm calling this one "Exploded Car":

Exciting News!
This week has been a whirlwind of milestones and achievements that I'm thrilled to share with all of you!(1/5)

Spatial transcriptomics of plant-fungal interactions

New Preprint with Karen Serrano, Margot Bezrutczyk, Henrik Scheller, and @bcoli

"Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis"

https://www.biorxiv.org/content/10.1101/2023.08.02.551648v1

@LBNLBioSci #plantmicrobial #symbiosis #microbiome #singlecell #transcriptomes #plants #fungi

Significance analysis for clustering with single-cell RNA-sequencing data

https://www.nature.com/articles/s41592-023-01933-9

Is your #UMAP lying to you? First post on
@scifind where we look at ways to quantify distortions in 2D embeddings of high dimensional data, a favourite #dataviz technique in #singlecell, all done in #RStats!

https://scifind.io/posts/is-your-umap-lying-to-you-qp6k3rwuny8444z

We are recruiting a #postdoc to work on the #bioinformatics / #biostatistics of new types of #GeneExpression data in @bgeedb: new #SingleCell, isoform-specific #RNAseq, etc. We integrate all data types into summary scores and calls of expression, so there are a lot of challenges in integrating each new data type. And a lot of opportunities both for methodological research, and for downstream biology using these newly integrated data. #academicjobs @dee_unil #SIB https://bit.ly/3G7DUGD

A post by my colleague Ally Hawkins about one of the projects we’ve been working on lately at the Childhood Cancer Data Lab: Creating an open source workflow to uniformly process data for the Single-cell Pediatric Cancer Atlas portal

#nextflow #singlecell #workflows https://www.ccdatalab.org/blog/creating-an-open-source-workflow-to-uniformly-process-data-for-the-single-cell-pediatric-cancer-atlas-portal

Re-posting an #introduction after moving server:

My research group at the Wellcome Centre for Human Genetics in Oxford uses #SingleCell techniques and Genome Architecture Mapping to study #epigenetics #Chromatin and #GenomeFolding in rare #NeurodevelopmentalDisorders.

I (He/Him) love to be outside #Hiking or #Cycling and I’m a big fan of #FlightFree travel. Interested in #Equity issues in STEM, trying to read and educate myself to be a better ally.

Toot at me with your #Andor theories!