Search
Search Results
-
Integrating transformers and many-objective optimization for drug design
BackgroundDrug design is a challenging and important task that requires the generation of novel and effective molecules that can bind to specific...
-
dgfr: an R package to assess sequence diversity of gene families
BackgroundGene families are groups of homologous genes that often have similar biological functions. These families are formed by gene duplication...
-
bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data
BackgroundBisulfite sequencing (BS-Seq) is a fundamental technique for characterizing DNA methylation profiles. Genotype calling from...
-
RNA-clique: a method for computing genetic distances from RNA-seq data
BackgroundAlthough RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated...
-
GATSol, an enhanced predictor of protein solubility through the synergy of 3D structure graph and large language modeling
BackgroundProtein solubility is a critically important physicochemical property closely related to protein expression. For example, it is one of the...
-
Equivariant score-based generative diffusion framework for 3D molecules
BackgroundMolecular biology is crucial for drug discovery, protein design, and human health. Due to the vastness of the drug-like chemical space,...
-
A guided network estimation approach using multi-omic information
IntoductionIn systems biology, an organism is viewed as a system of interconnected molecular entities. To understand the functioning of organisms it...
-
SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines
BackgroundThe initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence...
-
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution
BackgroundCancers are spatially heterogenous, thus their clonal evolution, especially following anti-cancer treatments, depends on where the mutated...
-
Compression algorithm for colored de Bruijn graphs
A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs...
-
A machine learning approach using conditional normalizing flow to address extreme class imbalance problems in personal health records
BackgroundSupervised machine learning models have been widely used to predict and get insight into diseases by classifying patients based on personal...
-
Improving replicability in single-cell RNA-Seq cell type discovery with
Dune BackgroundSingle-cell transcriptome sequencing (scRNA-Seq) has allowed new types of investigations at unprecedented levels of resolution. Among the...
-
Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators
BackgroundComputational models in systems biology are becoming more important with the advancement of experimental techniques to query the...
-
The biomedical knowledge graph of symptom phenotype in coronary artery plaque: machine learning-based analysis of real-world clinical data
A knowledge graph can effectively showcase the essential characteristics of data and is increasingly emerging as a significant means of integrating...
-
PrCRS: a prediction model of severe CRS in CAR-T therapy based on transfer learning
BackgroundCAR-T cell therapy represents a novel approach for the treatment of hematologic malignancies and solid tumors. However, its implementation...
-
HMMF: a hybrid multi-modal fusion framework for predicting drug side effect frequencies
BackgroundThe identification of drug side effects plays a critical role in drug repositioning and drug screening. While clinical experiments yield...
-
Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads
BackgroundPathogenic infections pose a significant threat to global health, affecting millions of people every year and presenting substantial...
-
Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation
Telomeres are regions of repetitive DNA at the ends of linear chromosomes which protect chromosome ends from degradation. Telomere lengths have been...
-
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance
We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best...
-
Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches
BackgroundThe application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and...
