Maria Puschhof

The final version of our multi-omics study on kidney fibrosis is out now (tinyurl.com/kidneyfibMSB). Together w/ Pepperkok + Savitski labs @embl.org, we present a time-resolved #multiomics + computational network modeling approach in combination w/ phenotypic assays to study #kidneyfibrosis

Leveraging data as a patient–scientist: frustrations and opportunities - Nature Reviews Nephrology The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability h...

I wrote a short piece on how becoming an IgA Nephropathy patient has changed my perspective on biomedical research, developing an appreciation for the challenges in data interpretability & availability and the importance of patient engagement www.nature.com/articles/s41...

How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

YouTube video by Deutsches Krebsforschungszentrum (DKFZ) Gemeinsam stark: Perspektiven für Kinder mit dem seltenen MYT1L-Gendefekt

🎗️On #RareDiseaseDay, we raise awareness for #MYT1L Syndrome, a rare #autism-associated disorder disrupting brain development. Our research at DKFZ, ZI, and Heidelberg University Hospital shows an epilepsy drug may help—future trials ahead!
📑 www.nature.com/articles/s41...
🎥 youtu.be/nYqNEPIOc-8?...

#CellPlasticity—the ability of cells to change their identity—is vital for tissue growth and repair. But when it goes unchecked, it can fuel #cancer. Our latest study examines how to block #LiverCancer by actively suppressing plasticity. www.nature.com/articles/s41... #CancerBiology

The final chapter of my PhD thesis is now out! 🎉 We compared the latest gene regulatory network (#GRN) inference methods for #single-cell multimodal datasets and evaluated their performance across various tasks. Hard to believe this journey started in March 2021 and has finally reached this point 😅🥳

GRETA graphical abstract

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta

Interested in our research? We've created a starter pack so you can now follow our current lab members and alumni. Be sure to check it out! 🥳

Hyped to be at the #ESSB #spatial #biology conference together with some of my colleagues from the @saezlab.bsky.social . Great science, beautiful venue, looking forward to the next 1.5 days...

Postdoc – Computational Tissue Analysis (m/f/d)

We are looking for a Postdoc with a strong computational background to join our team. Want to work on the development and application of computational methods in the field of translational spatial biology? Apply now!
karriere.klinikum.uni-heidelberg.de/index.php?ac...

Very pleased to announce that our package for Multiscale Spatial Analysis - MuSpAn - has landed!

The preprint is on biorxiv now, but you can find a lot more details at www.muspan.co.uk, including documentation, worked tutorials (an ever-expanding list), install guides, and how to get the code!

A poster giving an overview of MuSpAn.

We’re thrilled to introduce MuSpAn!
For researchers in biological imaging, MuSpAn provides tools for Multiscale Spatial Analysis with advanced mathematical methods.

🌟 For more information: www.muspan.co.uk
📝 Preprint: doi.org/10.1101/2024...

We hope you find it as useful as we do! (Poster below)

Great to see the study published! Congrats to all co-authors and thanks very much for having us @juliosaezrod.bsky.social @saezlab.bsky.social on the team. A nice example of how the @aihcluster.bsky.social makes new collaborations possible.

Electron micrograph of a mossy fiber synapse with many synaptic vesicles.

Want to know how many vesicles there are in a mossy fibre synapse, without counting thousands of vesicles by hand in electron micrographs?
Our new tool SynapseNet has you covered and is now available as a preprint www.biorxiv.org/content/10.1... .
Read on for a short overview of our paper.

Many thanks for this nice starter pack, Andreas. Any chance you could include me please?

Thanks so much for the starter pack! Any chance you could add me to it?

We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io

Research Technician

Looking for a job as a #Research #Technician in #Cancer #Microbiome?
We offer a collaborative team, diversity of methods, opportunity for further training and a stimulating & fun work place at DKFZ @dkfz.bsky.social!
Apply now to our group (or share with your network):
jobs.dkfz.de/en/jobs/1671...

Health and Life Science Alliance Explore!Tech Program open till January 24, 2025

Our Alliance provides seed-funds for testing innovative ideas develop high-end technologies.
Call for all Alliance members to apply jointly with Core Facility / Technology Platform members.
Apply by January 24, 2025.
More details on our webpage:
www.health-life-sciences.de/opportunitie...

Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype - Nature Genetics An integrated single-cell multiomic analysis of complex karyotype acute myeloid leukemia characterizes intratumoral heterogeneity and highlights links to therapeutic sensitivities.

Extremely proud to see my PhD project exploring intra-tumor heterogeneity in complex karyotype AML finally out in @NatureGenet! 🎉 👩🏻‍🔬

They say that 10,000 hours make you an expert, so I guess after more than five years of work I’m half-way there 😅 ⬇️1/5

www.nature.com/articles/s41...

#Organoid research starter pack.
I didn't find many researchers from the field yet, please comment/text me to be added!
go.bsky.app/RmXgs6d

We have created a starterpack to make it easier to follow current members and alumni from our lab, check it out 👇 (DM us if we forgot about you)
Also juliosaezrod.bsky.social has recently joined Bluesky
go.bsky.app/5ZtPHPz

I would love to be added to this starter pack as well, if possible. Thanks :-)