@VingronLab

regulatory sequence motifs, epigenetic regulation, sequence analysis, single cell transcriptomics, haplotyping, 3D chromatin structure, biological networks

 Berlin, Germany
molgen.mpg.de/28935/vingron-lab
Joined January 2019
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  • Followers635
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We are excited to share 𝘀𝗰𝗔𝗧𝗔𝗰𝗮𝘁, a great new tool for annotating #scATACseq data! Check out the thread for more details ⬇️
Aybuge Altay@aybuge_altay16 Oct 2024
I am happy to share that my PhD work, 𝘀𝗰𝗔𝗧𝗔𝗰𝗮𝘁🐈, is now out in #nargab @VingronLab academic.oup.com/nargab/arti… #scATAcat #epigenomics #singlecell Here is a 🧵👇

scATAcat: cell-type annotation for scATAC-seq data

Abstract. Cells whose accessibility landscape has been profiled with scATAC-seq cannot readily be annotated to a particular cell type. In fact, annotating

academic.oup.com
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Excited to share our new paper “CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics” and accompanying R package by @young_Yanie_Z and @ClemensKohl which was just published in @NAR_Open ! academic.oup.com/nar/advance…

CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics

Abstract. A fundamental analysis task for single-cell transcriptomics data is clustering with subsequent visualization of cell clusters. The genes responsi

academic.oup.com
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Identifying cell populations by the expression of their marker genes often requires manual analysis. The biMAP instead embeds cells & genes in a single plot, which not only simplifies cell type annotation but also lets you interactively explore the marker genes of the clusters!
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You can try out CAbiNet by simply installing it from our GitHub: github.com/VingronLab/CAbiNe…

GitHub - VingronLab/CAbiNet

Contribute to VingronLab/CAbiNet development by creating an account on GitHub.

github.com
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Our collaboration paper with @fubcp and @MundlosLab is out! Congrats to all the authors 🥳 Learn more 👇🏼
Jerome Jatzlau@JeromeJatzlau23 Jul 2023
I'm very happy to share that our collaborative study between @fubcp and @StefanMundlos & @vingron is finally published online @iScience_CP. cell.com/iscience/fulltext/S… We show the mechano-dependency of BMP9 SMAD-signaling in the vasculature. #BMP #ATACseq #genomics #vasculature

Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial...

Biological sciences; Molecular biology; Molecular interaction

cell.com
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Association plots paper is out! Congrats to @ela_gralinska 🥳 Read the 🧵to learn more 🤓
Elzbieta Gralinska@ela_gralinska11 Jul 2023
**Association Plots** and cluster-specific genes in high-dimensional data (1/7) Very happy to share that our manuscript on Association Plots from @VingronLab (@MPI_MolGen) , summarizing the basic concepts of my PhD project, is finally out. Below the key points from our paper:
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Join us for today’s Institute Social Hour - Easter edition! Egg themed games, chocolates and homemade pizza is waiting for you! @MPI_MolGen
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And karaoke 🎤 🎶
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Our new study “Prediction of protein-protein interactions using sequences of intrinsically disordered regions” published in Proteins journal, reveals that intrinsically disordered regions can aid in predicting specific features of eukaryotic PPI network! Check out our paper!
Gözde Kibar@gozdekibar424 Mar 2023
(1/4) I am happy to share that my PhD work on predicting protein-protein interactions using intrinsically disordered regions is now published in Proteins : Structure, Function, and Bioinformatics ! @VingronLab onlinelibrary.wiley.com/doi/… #PPIs #IntrinsicallyDisorderedRegions #IDPs

Prediction of protein–protein interactions using sequences of intrinsically disordered regions

Protein–protein interactions (PPIs) play a crucial role in numerous molecular processes. Despite many efforts, mechanisms governing molecular recognition between interacting proteins remain poorly...

onlinelibrary.wiley.com
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📢 #JobAlert: Wir haben eine Postdoc Stelle in Bioinformatik an der Freien Universität zu besetzen! @FU_Berlin @MPI_MolGen 📅 Bewerben bis 20.03.2023! Bitte verbreiten Sie die Nachricht: fu-berlin.de/universitaet/be…
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How can anyone survive a shattered genome? Our @VingronLab @MundlosLab @MeloUira & R. Schöpflin found that the answer lies in the "dark matter" of our genome. molgen.mpg.de/4594088/

The architecture of shattered genomes

Scientists have reconstructed the chromosomes of patients with an extremely high number of aberrations in their genome that could alter the expression of nearby genes and potentially cause disease....

molgen.mpg.de
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Our new work 'CAbiNet: Joint visualization of cells and genes based on a gene-cell graph' by Yan Zhao @young_Yanie_Z, Clemens Kohl @ClemensKohl, Martin Vingron @VingronLab, et. al. has been released at bioRxiv ( biorxiv.org/content/10.1101/… ).Looking forward to your comments!

CAbiNet: Joint visualization of cells and genes based on a gene-cell graph

In routine single-cell RNA-sequencing (scRNA-seq) analysis workflows, cells are commonly visualized in 2D to show the patterns in the data. However, these visualization approaches do not give any...

biorxiv.org
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CAbiNet: Joint visualization of cells and genes based on a gene-cell graph biorxiv.org/cgi/content/shor… #bioRxiv
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We Put Up Our Christmas Tree 🎄 🎅 🤶 Thanks to all Vingron lab members for their collaborative efforts! Come and visit the Pikachu on top of tree 🎊 @MPI_MolGen
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Our new #bioconductor R package 'APL' by @ela_gralinska, @ClemensKohl, and Martin Vingron @VingronLab is out! 'APL' implements the concept of Association Plots for #SingleCell data. bioconductor.org/packages/re…
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(1/8) Interested in the identification of #markergenes from single-cell data? Now it’s possible using our “Association Plots” adapted to SC data! sciencedirect.com/science/ar… @JmolBiol by @ela_gralinska, @ClemensKohl, Bita Sokhandan Fadakar, and Martin Vingron #scRNA #Rpackage
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(7/8) Finally, we also present how to visualize genes detected using other tools for differential expression in the Association Plots.
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(8/8) Interested? Check out our paper and the #bioconductor R package implementing this concept! Paper: sciencedirect.com/science/ar… R package: bioconductor.org/packages/re… Questions? @ela_gralinska
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