iiinova — where your digital self keeps evolving

Sinem Saka @sinemsaka.bsky.social · 21/06/2026

#5 Big thanks to all co-authors -- project leads Valeriy Pak and Yulia Ermakova, and contributors Christina Schniederjohann, Berkan Kanmaz, Robert Reinhardt, Felix Schneider, Tomas Martak, Sascha Dietrich, and Peter-Martin Bruch.

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Sinem Saka @sinemsaka.bsky.social · 21/06/2026

#4 We validated the approach across both subcellular Immuno-SABER and tissue-based CODEX workflows for multiplexed protein imaging, yielding high-performance panels.

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Sinem Saka @sinemsaka.bsky.social · 21/06/2026

#3 Key features: - One universal reagent for site-directed conjugation of any DNA barcode - Rapid generation of custom barcoded panels - Minimal antibody input requirements - Compatibility with off-the-shelf antibodies - Reduced cost, time, and effort during panel development

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Sinem Saka @sinemsaka.bsky.social · 21/06/2026

#2 In our new preprint, we introduce UnO (Universal Oligo Adapter). UnO is a dual-photoreactive adapter that enables rapid covalent and site-directed attachment of user-defined DNA barcodes to small quantities of off-the-shelf antibodies by a simple illumination step in a parallelizable fashion.

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Sinem Saka @sinemsaka.bsky.social · 21/06/2026

Many multiplexed detection approaches rely on DNA-barcoded antibodies. But every new barcode typically requires a separate conjugation reaction, making panel development resource-intensive and low-throughput.

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Sinem Saka @sinemsaka.bsky.social · 21/06/2026

If you’ve built DNA-barcoded antibody panels, you know the pain: every barcode means another conjugation. In our new preprint we introduce UnO, which transforms antibody conjugation problem into a universal barcode conversion workflow, enabling rapid panel generation. www.biorxiv.org/content/10.6...

biorxiv.org

Universal oligo adapters for high-efficiency DNA-barcoded antibody panel generation

DNA-barcoded antibodies are central to a broad range of spatial and dissociative assays and applications, including multiplexed imaging, single-cell profiling, and proximity detection. Direct modifica...

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Sinem Saka @sinemsaka.bsky.social · 27/04/2026

Cells are not just bags of molecules. Function depends on spatial interactions: RNAs and/or proteins come together with interaction partners to drive regulation and function. In our new preprint, we introduce ProPER, a novel method for in situ proximity detection. Preprint: tinyurl.com/muju86s6

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Sinem Saka @sinemsaka.bsky.social · 21/03/2026

We haven't got into lifetime in this work. By signal amplification we tune the signal level to balance the intensity in overlapping channels and improve the unmixing accuracy.

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Sinem Saka @sinemsaka.bsky.social · 20/03/2026

Spectral multiplexing is typically limited to 4-5 channels. Our new preprint introduces a framework that utilizes DNA barcoding and signal tuning to enable robust spectral unmixing and ground-truth benchmarking to achieve 15-plex subcellular profiling without cycling www.biorxiv.org/content/10.6...

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Sinem Saka @sinemsaka.bsky.social · 12/07/2025

I am delighted to co-organize the 2nd #ESSB meeting as an #EMBL Conference, with incredible support of @events.embl.org. Abstract submission deadline is July 15! #ESSB members submitting an abstract are eligible for one of 100 registration subsidy awards (up to 50%). #ESSB2025 #EMBLSpatialBiology

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Sinem Saka @sinemsaka.bsky.social · 23/06/2025

We had a lovely week in Heidelberg teaching ins and outs of #spatialbiology, and providing hands-on training for custom protocols like #immuno-saber, #ibex, #hybRISS. Massive thanks to my co-organizers, our dedicated trainers and excellent speakers, and #EMBO, #EMBL & sponsors. #EMBOSpatialOmics

embl.org

Imaging-based spatial-omics

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Sinem Saka @sinemsaka.bsky.social · 31/05/2025

We are happy to participate in the ARISE program and have a range of collaborative opportunities for various backgrounds including biochemistry, imaging, omics or lab automation. Get in touch if interested!

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Sinem Saka @sinemsaka.bsky.social · 03/03/2025

Seems to be available in Amazon Germany: www.amazon.de/Teekanne-Pre...

amazon.de

Amazon.de

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Sinem Saka @sinemsaka.bsky.social · 03/03/2025

We are repeating our EMBO Practical course for imaging-based spatial omics this June in Heidelberg. We will cover sample preparation, multiplexed IF (IBEX and Immuno-SABER), antibody-DNA conjugation, in situ sequencing, data analysis and visualization. Lots of fun and in-depth discussions!

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Sinem Saka @sinemsaka.bsky.social · 01/01/2025

The beautiful DNA-microart created by the wonderful Jennifer Heck and Kristina Jevdokimenko in our group to celebrate the festive season: Using Light-Seq, pixels of a DNA canvas was "painted" on a microscope by photocrosslinking DNA barcodes with 3 different fluorophores @embl.org's PhD course '24

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Sinem Saka @sinemsaka.bsky.social · 13/12/2024

The 1st European Society for Spatial Biology (#ESSB) meeting has been a blast! Great talks, exciting posters, new tech platforms and a budding vibrant community - made this a joy beyond our expectations. See you all again next year's edition at @embl.org Heidelberg on 14-17 Oct 2025!

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