Related papers: KEGGexpressionMapper allows for analysis of pathwa…
We present the design and implementation of a RAG-based AI system benchmarking (RAGPerf) framework for characterizing the system behaviors of RAG pipelines. To facilitate detailed profiling and fine-grained performance analysis, RAGPerf…
Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology…
Ecologists and evolutionary biologists are relying on an increasingly sophisticated set of statistical tools to describe complex natural systems. One such tool that has gained increasing traction in the life sciences is structural equation…
Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…
Genome-Scale Metabolic Models (GEMs) describe the interactions between genes, proteins, and the biochemical reactions that underpin an organism's metabolism aiming to computationally simulate functions at the cellular level. While many…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
Multi Expression Programming (MEP) is a Genetic Programming variant that uses a linear representation of chromosomes. MEP individuals are strings of genes encoding complex computer programs. When MEP individuals encode expressions, their…
Differential gene expression (DGE) analysis is foundational to transcriptomic research, yet tool selection can substantially influence results. This study presents a comprehensive comparison of two widely used DGE tools, edgeR and DESeq2,…
Gene co-expression network differential analysis is designed to help biologists understand gene expression patterns under different condition. By comparing different gene co-expression networks we may find conserved part as well as…
The search for symbolic regression models with genetic programming (GP) has a tendency of revisiting expressions in their original or equivalent forms. Repeatedly evaluating equivalent expressions is inefficient, as it does not immediately…
RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the…
Discovering important genes that account for the phenotype of interest has long been challenging in genomewide expression analysis. Analyses such as Gene Set Enrichment Analysis (GSEA) that incorporate pathway information have become…
Symbolic regression seeks to uncover physical laws from experimental data by searching for closed-form expressions, which is an important task in AI-driven scientific discovery. Yet the exponential growth of the search space of expression…
High-throughput pheno-, geno-, and envirotyping allows characterization of plant genotypes and the trials they are evaluated in, producing different types of data. These different data modalities can be integrated into statistical or…
Biomedical knowledge graphs (KGs) encode rich, structured information critical for drug discovery tasks, but extracting meaningful insights from large-scale KGs remains challenging due to their complex structure. Existing biomedical…
We develop a model-based methodology for integrating gene-set information with an experimentally-derived gene list. The methodology uses a previously reported sampling model, but takes advantage of natural constraints in the…
High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of…
The matched case-control design, up until recently mostly pertinent to epidemiological studies, is becoming customary in biomedical applications as well. For instance, in omics studies, it is quite common to compare cancer and healthy…
Estimating the effort of software systems is an essential topic in software engineering, carrying out an estimation process reliably and accurately for a software forms a vital part of the software development phases. Many researchers have…