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Abstract Although an established model organism, Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datasets and outdated algorithms. Here, we report a new approach to consolidating RNA-seq and microarray data based on a systematic exploration of parameters and computational controls, enabling us to infer functional gene associations from their co-expression patterns. To illustrate the power of this approach, we took advantage of new data regarding a previously studied pathway, the biogenesis of a secretory organelle called the mucocyst. Our untargeted clustering approach recovered over 80% of the genes that were previously verified to play a role in mucocyst biogenesis. Furthermore, we tested four new genes that we predicted to be mucocyst-associated based on their co-expression and found that knocking out each of them results in mucocyst secretion defects. We also found that our approach succeeds in clustering genes associated with several other cellular pathways that we evaluated based on prior literature. We present the Tetrahymena Gene Network Explorer (TGNE) as an interactive tool for genetic hypothesis generation and functional annotation in this organism and as a framework for building similar tools for other systems. 

Yttrium iron garnet (YIG) magnonics has garnered significant research interest because of the unique properties of magnons (quasiparticles of collective spin excitation) for signal processing. In particular, hybrid systems based on YIG magnonics show great promise for quantum information science due to their broad frequency tunability and strong compatibility with other platforms. However, their broad applications have been severely constrained by substantial microwave loss in the gadolinium gallium garnet (GGG) substrate at cryogenic temperatures. In this study, we demonstrate that YIG thin films can be spalled from YIG/GGG samples. Our approach is validated by measuring hybrid devices comprising superconducting resonators and spalled YIG films, which exhibit anti-crossing features that indicate strong coupling between magnons and microwave photons. Such new capability of separating YIG thin films from GGG substrates via spalling and the integrated superconductor-YIG devices represent a significant advancement for integrated magnonic devices, paving the way for advanced magnon-based coherent information processing.