Our paper (with Julie Cartier, Johanna Lagoas, Youmna Ayadi, Adeline Fermanian and @flomass) on the use of statistical knockoffs for the differential analysis of transcriptomics data just came out, very appropriately as it nicely illustrates my point:
https://academic.oup.com/bib/article/27/3/bbag148/8687371
Using simulated outcomes on real transcriptomics data, we've shown that KOs (and in particular, the KOPI approach) do retrieve important variables with better power than classical approaches (Wilcoxon, Lasso), while controlling FDR.
However, all methods perform poorly when the relationship between gene expressions and outcome is nonlinear.
On real outcomes, the method is overly conservative (having no discoveries is a surefire way of controlling your number of false discoveries), and we had to turn the false discovery rate threshold to 50% to select any gene at all.
#machineLearning #genomics #featureSelection #biomarkerDiscovery #transcriptomics
🧬 Is your metabolism quietly signaling the earliest signs of future disease?
🔗 Metabolic phenotypes: Molecular bridges between health homeostasis and disease imbalance. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.057
📚 CSBJ: https://www.csbj.org/
#MetabolicPhenotyping #Metabolomics #PrecisionMedicine #MultiOmics #BiomarkerDiscovery #TranslationalMedicine #DiseasePrevention #AIinHealthcare
Nghiên cứu mới giới thiệu phương pháp "lựa chọn cảm biến động" dựa trên lý thuyết quan sát để khám phá dấu ấn sinh học (biomarker). Phương pháp này giúp xác định và diễn giải các tín hiệu sinh học một cách hiệu quả từ lượng lớn dữ liệu, tối ưu hóa việc chọn biomarker theo thời gian. Ứng dụng rộng rãi trong y tế, nông nghiệp, sản xuất sinh học và hệ thần kinh.
#BiomarkerDiscovery #DynamicSensorSelection #ObservabilityTheory #SinhHoc #NghienCuuKhoaHoc #YTe
Esoteric Testing: Going Beyond Standard Testing Approaches
Esoteric Testing involves deliberately designing unconventional test cases aimed at finding hard-to-discover flaws. Rather than following typical usage patterns or common scenarios, esoteric tests push the system to its logical extremes and boundaries to expose weaknesses.
Esoteric Testing-https://themediumblog.com/read-blog/158536
#CoherentMarketInsights #ChronicDiseaseManagement #GenomicTesting #BiomarkerDiscovery #PointofCareTesting
Proteomics Today Where Genomics Was in the 80s: Margaret Donovan and Asim Siddiqui of Seer on Landmark Study
@seer_bio @mkrdonovan #proteomics #biomarkerdiscovery #proteoform
It’s a thrilling time to be in proteomics. Today we discuss a recent paper in PLOS One demonstrating how new technology has revealed a novel biomarker for non-small cell lung cancer previously undetected by other methods. The paper could be a model for new proteomics research going forward. Our guests are Margaret Donovan, Product Marketing Manager, and Asim Siddiqui, Senior VP of Research, both at proteomics company, Seer. “Historically the way in which we’ve been able to analyze the proteome has essentially meant you’re making trade-offs.
Chloé Azencott
CSBJ
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