Alternative polyadenylation (APA) has a central role in regulation of the fate of mRNA and exhibits high variability in the brain and in neurons. However, brain APA regulation has not been mapped at cell type resolution, and the genetic control of APA in brain cell types and its contribution to genetic disease have rem...
Jiu-Hong Nan, Carles A. Boix, Shao-Hui Shi et al.· Nature Genetics· 0 citations
Advancing precision medicine requires accurate prediction of disease liability across populations and contexts. A major challenge is the limited transferability of polygenic scores (PGS) across genetic ancestry groups. We present GeneSIS (GENE and Sex Interaction Score), a supervised statistical learning framework for...
Through multiplex, single-cell enhancer assays, HAQERs are identified as active enhancers in the developing brain and cardiomyocytes, and their potential contributions to human-specific gene regulation across multiple tissues are highlighted.
Yan-Ting Luo, Riley J. Mangan, S. Weaver et al.· Cell Genomics· 0 citations
An extended PRS (ePRS) framework for type 2 diabetes (T2D) that incorporates locus-by-locus non-additive effects beyond those captured by additive single-locus PRS or linkage disequilibrium (LD) tagging is developed, with potential for clinical use pending prospective validation.
K. Multerer, P. Atkinson, L. Woods et al.· medRxiv· 0 citations
A distributional theory in which evidence shifts the receiver's distribution of initial answers, driven by a receiver prior weight and a candidate evidence tilt, leading to three predictions: candidates more probable to the receiver are more persuasive, receivers more readily integrate characteristic errors of their ow...
Using single-nucleus RNA sequencing across 109 human and 22 mouse samples spanning dorsal and ventral striatum, a comprehensive atlas of subregional neuronal specialization is provided, suggesting divergent pharmacological targets, connectivity, and disease mechanisms.
Raleigh M. Linville, Benjamin T. James, K. Galani et al.· Cell· 2 citations· ⚡1
Under realistic dark-protein deployment conditions where relational modalities are unavailable, ProtJEPA significantly outperforms naive concatenation of remaining modalities and cross-domain evaluations on drug–target interaction and disorder prediction confirm transfer beyond training modalities.
Vaibhava Lakshmi Ravideshik, Jinha Kim, M. Kellis· bioRxiv· 0 citations
This work evaluates embedding retrieval where surface form and meaning are pulled apart on purpose: retrieving items that share underlying structure but not wording, in two unrelated domains under one protocol, competition mathematics and embodied-agent trajectories.
Deciphering the regulatory consequences of sequence divergence across human evolution is essential to understanding the molecular basis of human-specific traits and disease. Although millions of derived alleles distinguish humans from great apes, only a small fraction are likely to influence human-specific traits. Prev...
Riley J. Mangan, Nikitha Thoduguli, Dimitar Ivanov et al.· bioRxiv· 0 citations
An encyclopedia of enhancer–gene regulatory interactions in the human genome is built, revealing global properties of enhancer networks, identifying differences in regulatory complexity across genes, and improving analyses linking noncoding variants to target genes and cell types for common, complex diseases.
A. Gschwind, Kristy S. Mualim, Alireza Karbalayghareh et al.· Nature· 6 citations
Phenoverse is introduced, an interpretable deep learning framework that learns sample-level disease state representations through cell type-aware residual encoding, prototype learning, and Perceiver-based aggregation that demonstrates that trajectory-derived genes reveal cross-cohort molecular programs and show consist...
Manoj M Wagle, Yongheng Wang, Soham Samanta et al.· bioRxiv· 0 citations
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