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Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets
Finding related individuals in genomic datasets is a necessary step in many genetic analysis workflows and has broader societal value as a tool for... -
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition
RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA... -
Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency
DNA methylation data plays a crucial role in estimating chronological age in mammals, offering real-time insights into an individual’s aging process.... -
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts
An annotation is a set of genomic intervals sharing a particular function or property. Examples include genes, conserved elements, and epigenetic... -
Computing Robust Optimal Factories in Metabolic Reaction Networks
Perhaps the most fundamental model in synthetic and systems biology for inferring pathways in metabolic reaction networks is a metabolic factory: a... -
SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes
Nucleosome landscapes across the genome are typically characterized using micrococcal nuclease sequencing (MNase-seq). MNase is an endo-exonuclease... -
Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape
Machine learning (ML) is revolutionizing our ability to model the fitness landscape of protein sequences. Recently, the protein language model (pLM)... -
ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation
Metagenomic Hi-C (metaHi-C) enables the recognition of relationships between contigs in terms of their physical proximity within the same cell,... -
An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks
Executable models of biological circuits offer the ability to simulate their behavior under different settings with important biomedical... -
Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics
A key challenge in cancer research is to reconstruct the somatic evolution within a tumor over time and across space. Spatially resolved... -
Disease Risk Predictions with Differentiable Mendelian Randomization
Predicting future disease onset is crucial in preventive healthcare, yet longitudinal datasets linking early risk factors to subsequent health... -
Protein Domain Embeddings for Fast and Accurate Similarity Search
Recently developed protein language models have enabled a variety of applications of the protein contextual embeddings. Per-protein representations... -
Map** the Topography of Spatial Gene Expression with Interpretable Deep Learning
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of this... -
Processing-Bias Correction with DEBIAS-M Improves Cross-Study Generalization of Microbiome-Based Prediction Models
Microbiome profiling exhibits strong study- and batch-specific effects, impeding the identification of signals that are reproducible across studies... -
Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching
Substitution matrices, which are crafted to quantify the functional impact of substitutions or deletions in biomolecules, are central component of... -
Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes
In this study, we demonstrated that SARS-CoV-2 emerging variants can be detected or predicted by examining the community structure of viral... -
Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography
Biomedical data is often distributed between a network of custodians, causing challenges for researchers wishing to securely compute aggregate... -
DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors
D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. We introduce DexDesign,... -
User Needs for Home Robotic Devices: A Comparison Between Middle-Aged and Older Adults
Robotic devices are being introduced to support active aging and enhance the lives of older adults at home. To effectively design and implement such... -
Research on Interactive Design of Guangxi Bronze Drum Tourism and Cultural Creative Products Based on AR Technology
Guangxi is one of the birthplaces of bronze drum culture, and bronze drum culture is rich in resources, which provides precious cultural genes for...