Search
Search Results
-
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,...
-
Multi-agent Simulation of Intelligent Energy Regulation in Vehicle-to-Grid
The vehicle-to-grid feature of today’s electric vehicles suggests using them as batteries for stabilizing the power grid besides using them to...
-
Aspects of Modeling Human Behavior in Agent-Based Social Simulation – What Can We Learn from the COVID-19 Pandemic?
Proper modeling of human behavior is crucial when develo** agent-based models to investigate the effects of policies, such as the potential...