Cigdem Ak, PhD

Calling all cancer researchers!

Join us, @ohsuknight.bsky.social and @stanford.edu at this year's Early Detection of Cancer Conference for the cutting-edge, cross-disciplinary science that is shaping the future of cancer early detection.

Check out the agenda and register: cruk.ink/3UR67Zu

Paper: nature.com/articles/s4200…
Code: github.com/ohsu-cedar-com���

#InterpretableML #AIinCancer #SingleCell #MultiOmics #InterpretableAI #CancerGenomics #OpenScience #Bioinformatics #ComputationalBiology #MachineLearning
@commsbio.nature.com @ohsunews.bsky.social @ohsuknight.bsky.social

Unlike black-box models that rely on post hoc interpretation, scMKL is designed to highlight the regulatory mechanisms that drive its predictions from the beginning.

We developed scMKL, a framework that integrates single-cell multiomics data using biologically informed kernels by leveraging decades of knowledge on gene sets and transcription factor motifs.

Our work is highlighted on the Communications Biology homepage!

www.nature.com/commsbio/

Congratulations!

Last year I got to present at the #SpatialBiology Summit at #Stanford. It was one of the most energizing events I’ve been part of.

Attending remotely this year, but looking forward to reconnecting and seeing what’s new.

📄 lnkd.in/gPv2cXCv
🎥 lnkd.in/gBMWB_gU
📝 Register for #SBS25: lnkd.in/g5yaxEwE

Made it to #AACR2025 Let me know if you’re around or come to my presentation, let’s connect!

AxonFinder: Automated segmentation of tumor innervating neuronal fibers Neurosignaling is increasingly recognized as a critical factor in cancer progression, where neuronal innervation of primary tumors contributes to the disease's advancement. This study focuses on segmenting individual axons within the prostate tumor microenvironment, which have been challenging to detect and analyze due to their irregular morphologies. We present a novel deep learning-based approach for the automated segmentation of axons, AxonFinder, leveraging a U-Net model with a ResNet-101 encoder, based on a multiplexed imaging approach.

Neurosignaling is recognized as a key factor in cancer progression, yet current spatial profiling approaches are unable to detect neuronal innervation in the TME. www.cell.com/heliyon/full...