Nils Eling

I am happy to share that we are looking for a computational postdoc to join the Schapiro Lab (schapirolab.com) and the Translational Spatial Profiling Center (tspc-hd.com). Please apply or share :) karriere.klinikum.uni-heidelberg.de/index.php?ac=j…

The genomics core in Aberdeen is seeking a talented bioinformagician: abdnjobs.co.uk/vacancy/bioi... They work on projects from ChIP-seq to metagenomics to single-cell multi-omics. Aberdeen is amazing - the biggest national park in the UK is just a short drive away. Reach out!

Check out the pre-print to see how we tackled these challenges and what we came up with to reproducibly detect cell types in their tissue context for all images analysed within @IMMUcan biorxiv.org/content/10.110…

The challenges - samples have been collected at different hospitals over the course of years - the throughput in data acquisition and analysis had to be massively scaled (talking about tens of thousands of images) - we had to select representative and informative regions for IMC

After years of optimisation (both experimentally and computationally), we now present a robust pipeline to profile thousands of cancer patient samples using multiplexed imaging. Huge team effort lead by @DanielS33860077 as part of @BodenmillerLab and @IMMUcan

After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳 nature.com/articles/s4158… LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space. Some highlights⬇️

Excited to share our atlas build&use guide, out @naturemethods today. Led by @KHrovatin & @SikkemaLisa w @MDLuecken, our review highlights best practices for building, sharing, and leveraging atlases to unlock new biological discoveries. 🌍@humancellatlas nature.com/articles/s4159…

The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳 For more on Spatial Proteomics and a road map to this special issue, please see this month’s Editorial or read on in this thread. nature.com/articles/s4159…

NiCo is out! Our new algorithm for spatial transcriptome data analysis predicts the crosstalk of cell types co-localized in tissue niches and sheds light on the downstream effects of cell-cell interactions by inferring covarying gene programs. nature.com/articles/s4146…

What gets erased when you integrate single cell data, and can you recover it? Finally, we know what happens and how to recover the lost signals. So excited to share CellANOVA, published online today in NBT! go.nature.com/4hZnzW5

An integrated neural organoid atlas helps us all stand on the shoulders of great scientists! We explore coverage and fidelity, provide tools to assess new protocols, and use the diverse cohort to assess disease models. nature.com/articles/s4158…

News! @louisaslett @durham_uni and I are excited to announce that SPARRAv4 (Scottish Patients At Risk of Readmission and Admission version 4) is published in @npjDigitalMed – a long-term collaboration with @P_H_S_Official supported by @turinginst and @HDR_UK @EdinUni_IGC 1/N

Really enjoyed writing this piece for @NatureRevGenet Journal Club and reflecting on the path that modern in situ-based single-cell expression profiling methods have taken over the last few decades!

STAMP is OUT! Sequencing-free #singlecell RNA and Protein profiling. Game-changing approach for scalable and cost-efficient analysis of single cells. The future starts today! Amazing ⁦@LGMartelotto⁩ ⁦@DrJasPlummer⁩ biorxiv.org/content/10.110…

👉Consider joining us for a post-doc at @emblebi & @ASTRAZENECAUK as part of the EAZPOD program to study multicellular mechanisms associated with #cancer treatment resistance! #postdoc ebi.ac.uk/research/postd…

The recording for today's webinar will soon be available from @EBItraining. Meanwhile here are the notebooks 🤓 github.com/PMBio/spatiald… Thanks again for inviting me and @WVierdag, and thanks to the @scverse_team for the collaborative effort in preparing the notebook.

Exciting opportunity! I am hiring a postdoc to join the group and to develop computational methods for the analysis of biomedical data including imaging and genomics data at a single-cell or spatial resolution 🧬 stephaniehicks.com/join

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. biorxiv.org/content/10.110…

Job alert! We have an open position in our team. Looking for a data scientist to analyze clinical and preclinical data to advance our early drug discovery efforts. novartis.com/careers/career…