1005 papers
This paper introduces and evaluates a new iterative inference framework that combines random forests with multivariate Gaussian mixture models to improve the coverage properties of confidence intervals and estimator precision in population genetic simulations compared to non-iterative ABC-RF and sequential neural likelihood methods.
This paper introduces TOGGLE, a self-supervised graph diffusion framework that leverages deep learning and reinforcement-guided clustering to delineate fine-grained functional heterogeneity and predict cell fate within transcriptionally similar populations, successfully identifying distinct neuronal states in ischemic stroke and epigenetic memory in neural stem cells without prior labels.
This study reveals that in *Caenorhabditis elegans*, strain-specific structural variant architectures significantly influence mutation retention dynamics following mutagenesis, with higher outcrossing rates paradoxically leading to greater structural variant burdens and reduced purging of deleterious mutations.
This study introduces EscapeMap, a modular framework that integrates deep mutational scanning and generative modeling to predict SARS-CoV-2 escape variants, validate antibody resilience through designed RBD mutants, and identify optimal antibody combinations for therapeutic strategies.
This paper introduces the Tiling Algorithm, a reference-free method for characterizing the structural diversity and minor species of Adeno-associated virus (AAV) genomes using accurate long-read sequencing data, thereby overcoming the limitations of alignment-based approaches in handling AAV-specific challenges like inverted terminal repeats and replication artifacts.
The paper introduces siMILe, a weakly-supervised multiple instance learning method enhanced by adversarial erasing that enables the discriminative identification of condition-specific oligomeric protein structures from 3D single-molecule localization microscopy data without requiring structure-level supervision.
RNApdbee 3.0 is a unified web server that provides comprehensive RNA secondary structure annotation by integrating 2D and 3D data to classify diverse nucleotide interactions, handle structural inconsistencies, and generate standardized outputs and visualizations from 3D coordinates.
This paper presents a validated, standardized framework that bridges the platform gap between array-based and high-throughput sequencing data, enabling the robust adaptation of legacy epigenetic clocks for cell-free DNA analysis through optimized parameters and transfer learning.
This study reveals that organ-specific autoimmune diseases are driven by altered antigen processing that exposes previously "cryptic" self-proteins to the immune system, distinguishing them from systemic diseases caused by a breakdown of tolerance toward normally presented self-antigens.
This paper presents a novel genotype-only computational framework that achieves near-perfect classification of half-sibling versus niece/nephew pairs by leveraging across-chromosome phasing and haplotype-level sharing features, thereby resolving a critical ambiguity in large-scale genomic biobanks without requiring pedigree information.