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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated proteins (Cas) systems have revolutionized genome editing by providing high precision and versatility. However, most genome editing applications rely on a limited number of well-characterized Cas9 and Cas12 variants, constraining the potential for broader genome engineering applications. In this study, we extensively explored Cas9 and Cas12 proteins and developed CasGen, a novel transformer-based deep generative model with margin-based latent space regularization to enhance the quality of newly generative Cas9 and Cas12 proteins.
View Article and Find Full Text PDFIncorporation of Epstein-Barr viral variation implicates significance of Latent Membrane Protein 1 in survival prediction and prognostic subgrouping in Burkitt lymphoma.
Int J Cancer
March 2025
Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA.
Although Epstein-Barr virus (EBV) plays a role in Burkitt lymphoma (BL) tumorigenesis, it is unclear if EBV genetic variation impacts clinical outcomes. From 130 publicly available whole-genome tumor sequences of EBV-positive BL patients, we used least absolute shrinkage and selection operator (LASSO) regression and Bayesian variable selection models within a Cox proportional hazards framework to select the top EBV variants, putative driver genes, and clinical features associated with patient survival time. These features were incorporated into survival prediction and prognostic subgrouping models.
View Article and Find Full Text PDFBayesian-Guided Generation of Synthetic Microbiomes with Minimized Pathogenicity.
Annu Int Conf IEEE Eng Med Biol Soc
July 2024
Synthetic microbiomes offer new possibilities for modulating microbiota, to address the barriers in multidtug resistance (MDR) research. We present a Bayesian optimization approach to enable efficient searching over the space of synthetic microbiome variants to identify candidates predictive of reduced MDR. Microbiome datasets were encoded into a low-dimensional latent space using autoencoders.
View Article and Find Full Text PDFCarp edema virus surveillance in the koi trade: early detection through shipping environment sampling and longitudinal monitoring of CEV outbreaks in a wholesaler facility.
Vet Res
March 2025
IHAP, Université de Toulouse, INRAE, ENVT, 31300, Toulouse, France.
Carp edema virus (CEV), a member of the Poxviridae family, has been a significant pathogen in koi and common carp since its initial identification in Japan during the 1970s. CEV, the causative agent of Koi Sleepy Disease (KSD), can cause high mortality rates and has been reported in many countries and is often linked to the fish trade. The virus is typically detected through DNA analysis of gill tissues, where the highest viral loads are found.
View Article and Find Full Text PDFModeling the link between the plausibility of statements and the truth effect.
Psychon Bull Rev
March 2025
Department of Psychology, University of Marburg, Gutenbergstraße 18, 35032, Marburg, Germany.
People judge repeated statements as more true than new ones. This repetition-based truth effect is a robust phenomenon when statements are ambiguous. However, previous studies provided conflicting evidence on whether repetition similarly affects truth judgments for plausible and implausible statements.
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