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Nikos Karaiskos

@nukappa.bsky.social
267 followers 573 following 11 posts

Spatial Transcriptomics • Bioinformatics • Comp Biology Research Scientist @mdc-berlin.bsky.social

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Reposted by Nikos Karaiskos
Dani León-Periñán @danilexn.bsky.social · 26/08/2026
Malva out in Nature! 🚀 RNA sequences make cells different from each other. Single-cell data captures much of this, but most stays in the dark because we reduce it to gene counts. We introduce Malva to make the world's single-cell data searchable. What took days is now one query in seconds.
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Reposted by Nikos Karaiskos
Leon Strenger @lstrngr.bsky.social · 19/05/2026
I'm very excited to announce that my PhD work is out on biorxiv! pyTrance is a computational method to predict and quantify subcellular RNA co-localization from spatial transcriptomics data. www.biorxiv.org/content/10.6...
biorxiv.org
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Nikos Karaiskos @nukappa.bsky.social · 27/02/2026
Contract details: freelance, March-December 2026, remote-first. If this sounds like you, drop us a message or reach out at jobs@malva.bio for further information. Know someone who'd be a fit? Help us spread the word 🙏 (4/4)
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Nikos Karaiskos @nukappa.bsky.social · 27/02/2026
‍Open positions: Senior Cloud/Infrastructure Engineer tinyurl.com/mryj2cjm Backend Engineer tinyurl.com/2n9xepus Data Engineer tinyurl.com/2mvkbs9m (3/4)
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Nikos Karaiskos @nukappa.bsky.social · 27/02/2026
From the @mdc-berlin.bsky.social in Berlin, Malva is currently part of the @bihatcharite.bsky.social Digital Health Accelerator, with clinical partners at Charité - Universitätsmedizin Berlin. (2/4)
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Nikos Karaiskos @nukappa.bsky.social · 27/02/2026
🚀 We're looking for people to join Malva! 🧬 @danilexn.bsky.social Malva is the first search engine for single-cell genomics: we process massive amounts of sequencing data to enable ultrafast analysis of millions of cells. (1/4)
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Reposted by Nikos Karaiskos
Kamil Lisek @klisek.bsky.social · 22/07/2025
We’re happy to share our new preprint form @N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat lab! 🎉 🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation. 🔗 biorxiv.org/content/10.1...
biorxiv.org
Spatiotemporal dynamics of tumor microenvironment remodeling
During tumorigenesis, interactions between tumor and stromal cells progressively remodel the tumor microenvironment (TME) towards pro-tumoral functions. Understanding early TME remodeling dynamics is ...
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Reposted by Nikos Karaiskos
Tancredi M Pentimalli @tmpentimalli.bsky.social · 16/04/2025
Our 3D study of the tumor microenvironment is finally out! Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 ) Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!
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Reposted by Nikos Karaiskos
Dani León-Periñán @danilexn.bsky.social · 10/01/2025
🧬 Want to implement Open-ST in your lab? We've published a detailed guide that takes you from tissue sections to 3D molecular maps star-protocols.cell.com/protocols/3922
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Nikos Karaiskos @nukappa.bsky.social · 18/12/2024
5/ As large-scale clinical studies are urgently needed to link spatial biomarkers with patient outcomes, we discuss key considerations for the design of clinical ST projects from sample preservation and method choice to panel design and power analysis.
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Nikos Karaiskos @nukappa.bsky.social · 18/12/2024
4/ Several challenges exist to their swift clincal translation: What is the ‘best’ ST method? How do we turn complex molecular data into meaningful insights for patient care? How do we integrate in clinical routines?
Current challenges in the clinical translation of high-resolution spatial Transcriptomics methods
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Nikos Karaiskos @nukappa.bsky.social · 18/12/2024
3/ In the clinic, spatial biomarkers and patient-specific molecular mechanisms identified by ST hold great potential to inform patient care and help the discovery of novel drug targets, as showcased in early preclinical studies
Clinical applications of high-resolution ST methods
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Nikos Karaiskos @nukappa.bsky.social · 18/12/2024
2/ With high-resolution ST we can study tissue organization in 2D and 3D virtual tissue blocks, analyzing the organization of cells in multicellular niches and identifying which receptor–ligand interactions orchestrate their function in situ.
Investigating tissue organization in 2D and 3D virtual tissue blocks
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Nikos Karaiskos @nukappa.bsky.social · 18/12/2024
1/ High-resolution ST omics work as molecular microscopes, digitalizing gene expression and tissue morphology at subcellular resolution. This enables the interactive exploration of millions of transcripts and their comparison with routine histology and pathologist annotations.
Exploring clinical samples with molecular microscopes
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Nikos Karaiskos @nukappa.bsky.social · 18/12/2024
Check our review on the 'Challenges & Opportunities in Clinical Translation of High-Resolution Spatial Transcriptomics (ST)' now online ahead of publication! annualreviews.org/content/journa…
annualreviews.org
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Nikos Karaiskos @nukappa.bsky.social · 18/12/2024
#SpatialTranscriptomics is revolutionizing gene expression profiling at subcellular resolution! 🔬These 'molecular microscopes' can unlock disease mechanisms & guide therapies... But how to bring ST to the clinic? Our thoughts with T. Pentimalli and N. Rajewsky out @annualreviews.bsky.social 🧵👇
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