Mervin Fansler

Postdoc @Mayr_Christine Lab | @cbm_student | Study mRNA 3' end regulation. Reproducible research. Help with @condaforge #bioconda.

[Mervin Fansler @MervinFansler]

Finally out! My first-coauthor work together with the brilliant Sibylle Mitschka. Went through many iterations of substantial improvements. 👌

And just in time for commencement this week! 🎉

I’ll share a 🧵soon…

[Christine Mayr @Mayr_Christine]

New paper!
We provide a scRNA-seq pipeline for simultaneous gene expression and 3′UTR length analysis.
We quantified 3′UTRs in 474 cell types and found that 3′UTR length provides information that is independent of gene expression.
https://t.co/hZto8xdfzE

[Wolf Vollprecht @wolfvollprecht]

Our mission is to make it super smooth to publish @condaproject packages to our platform. We also did a bunch of work recently to add CDN to all channels, serve sharded repodata and more - for a very fast experience. 🚀🚀🚀

[Alejo Rodriguez-Fraticelli @AlejoFraticelli]

Curious about quantitative stem cell analysis?

Join our lab as a PhD student with one of this super prestigious (and generously funded) IRB PhD fellowships!

Call is open NOW!

[MSK Library @MSKLibrary]

Featured today by @MSKLibrary: Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression
#scRNAseq #3UTRLength #GeneExpression #Transcriptomics #RNASequencing #GenomicsResearch #MolecularBiology

@MervinFansler @SMitschka @Mayr_Christine

https://t.co/ZUqjKv9KsX

[Nils Blüthgen @molsysbio]

How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? Together with
@landthaler_m's group , we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB https://t.co/ycYZdb6Axt

[Rui Yang @RuiYang53922541]

Out in @NatureComms ! ChromaFold predicts 3D contact maps using single-cell ATAC-seq alone. https://t.co/54MIrOSwCr

[Itai Yanai @ItaiYanai]

There are ~40k postdocs in the US, according to the NIH. While PhD students generally have good support (their committees, external advisors, and classmates), the postdocs do not. To help with this, we're starting the 'Postdoc Night Science' club with a first branch in NYC. ⬇️

[Wolf Vollprecht @wolfvollprecht]

All the dev tools from @condaforge at your fingertips :)

[Karthik Guruvayurappan @somet3000]

Happy to share that the paper on enhancer interactions led by @zrcjessica and I from my time in the @GrahamMcVicker lab is now published in Cell Genomics!

https://t.co/dfAbONwjTu

A thread on some of the new analyses below: (1/n)

[The Nobel Prize @NobelPrize]

BREAKING NEWS
The 2024 #NobelPrize in Physiology or Medicine has been awarded to Victor Ambros and Gary Ruvkun for the discovery of microRNA and its role in post-transcriptional gene regulation.

[Itai Yanai @ItaiYanai]

Doing good science is 90% finding a science buddy to constantly talk to about the project.

[zack chiang @z_chiang]

7 years ago, I met a junior fellow named @JD_Buenrostro who blew me away with a vision of futuristic genomic technologies

Today, we (@ajaylabade31, @carolinecomenho) are excited to share our first steps into that future: Expansion in situ genome sequencing

1/

[Andrew Marderstein @amarderstein]

🧵 Thrilled to share our latest in @Nature! We’ve mapped fetal blood development in Down syndrome (DS) using single-cell multi-omics, studying why children with DS face a 150-fold higher leukemia risk and blood abnormalities at birth.

https://t.co/ZNeujvmZ2z

[Dan Landau @landau_lab]

PATH (phylogenetic analysis of trait heritability) is out @NatureGenet! Excited about tackling the fundamentals of somatic evolution:
*measuring cell state heritability
*a quantitative definition for cell plasticity (1-heritability)
*cell-state transition dynamics
👀🧵👇

[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

[Hanabi @Hanabi_NYC]

September 17,
Astoria the Roosevelt Island Turkey.

Thank you very much for my signs!!

#birdcpp

[ShorterLab @ShorterLab]

Disorder-mediated interactions target proteins to specific condensates: Molecular Cell https://t.co/TE60Xq5bOC

[Ewan Birney @ewanbirney]

This is increasing the number of accurate genetic diagnoses one can make (in this case quite modestly) but also emphaises the importance of unbiased research discovery via WGS and suggests there might be more to be found in the non-coding RNA space.

[NimwegenLab @NimwegenLab]

How to rigorously identify distinguishable gene expression states in scRNA-seq data. Our Cellstates paper has now been published:
https://t.co/sdpRLDQYOE
See the quoted thread for a description of this work.
What are the main revisions in the final paper? 1/n

[prof-g @prof_g]

spent a few hours with Claude 3.5 sonnet doing some mathematics research. you are underestimating the impact AI will have on research. yes, you. yes, I'm serious. no, it does not replace mathematicians. but the augmentation is about to take off.

[Christine Mayr @Mayr_Christine]

Our new paper!
mRNAs play structural roles in the cytoplasm.
The longest mRNAs bound to FXR1 generate an mRNA-protein assembly that plays an essential role in cellular signaling by enabling proximity of proteins without RNA binding domains.
https://t.co/UtNTjM0LGX