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Reposted by Maria Puschhof

Saez-Rodriguez Group @saezlab.bsky.social · Jun 27

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

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · Jun 23

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...

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...

www.nature.com

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

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 🧵

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Manu Saraswat @manusaraswat.bsky.social · May 16

🧠 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🧵👇

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Moritz Mall @moritzmall.bsky.social · Feb 28

🎗️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?...

Gemeinsam stark: Perspektiven für Kinder mit dem seltenen MYT1L-Gendefekt

YouTube video by Deutsches Krebsforschungszentrum (DKFZ)

youtu.be

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Moritz Mall @moritzmall.bsky.social · Feb 13

#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

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Pau Badia i Mompel @paubadiam.bsky.social · Dec 23

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 😅🥳

Saez-Rodriguez Group @saezlab.bsky.social · Dec 23

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

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Saez-Rodriguez Group @saezlab.bsky.social · Dec 23

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

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Schapiro Lab @schapirolab.bsky.social · Dec 18

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! 🥳

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Maria Puschhof @mariapuschhof.bsky.social · Dec 12

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...

Saez-Rodriguez Group @saezlab.bsky.social · Dec 12

We will be at the inaugural #ESSB conference this week in Berlin: @mariapuschhof.bsky.social a talk on multi-modal brain tumor profiling, @psl-schaefer.bsky.social @tanevski.bsky.social a poster on analyzing condition/temporal spatial data, @changlu9.bsky.social @tanevski.bsky.social [1/2]

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Schapiro Lab @schapirolab.bsky.social · Dec 4

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...

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

karriere.klinikum.uni-heidelberg.de

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Joshua Bull @joshuabull.bsky.social · Dec 9

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!

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Josh Moore @josh-moore.bsky.social · Dec 9

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)

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Maria Puschhof @mariapuschhof.bsky.social · Dec 8

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.

Varun Venkataramani @venkataramanilab.bsky.social · Dec 6

🧵Just in time for
: New research from the Venkataramani lab @CellCellPress
maps how brain tumor cells create extensive neural networks in glioblastoma. Check out our paper here: authors.elsevier.com/sd/article/S...
@ekinreyhan.bsky.social

@svenjaktetzlaff.bsky.social

1/15

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Constantin Pape @cppape.bsky.social · Dec 6

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.

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

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Maria Puschhof @mariapuschhof.bsky.social · Nov 27

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

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Maria Puschhof @mariapuschhof.bsky.social · Nov 27

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

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Saez-Rodriguez Group @saezlab.bsky.social · Nov 26

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

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Jens Puschhof @jenspuschhof.bsky.social · Nov 25

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...

Research Technician

jobs.dkfz.de

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Health + Life Science Alliance Heidelberg Mannheim @hlsalliance.bsky.social · Nov 25

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...

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

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Aino-Maija Leppä @amleppa.bsky.social · Nov 25

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...

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.

www.nature.com

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Jens Puschhof @jenspuschhof.bsky.social · Nov 24

#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

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Saez-Rodriguez Group @saezlab.bsky.social · Nov 20

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

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Maria Puschhof @mariapuschhof.bsky.social · Nov 24

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

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