Related papers: Agalma: an automated phylogenomics workflow
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
Thematic Analysis (TA) is a fundamental method in healthcare research for analyzing transcript data, but it is resource-intensive and difficult to scale for large, complex datasets. This study investigates the potential of large language…
Developing artificial intelligence (AI) for clinical research requires a comprehensive data foundation that supports model training and rigorous evaluation. Here, we introduce TrialPanorama, a large-scale structured resource that aggregates…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain…
Application of phylogenetic methods to textual traditions has traditionally treated all changes as equivalent even though it is widely recognized that certain types of variants were more likely to be introduced than others. While it is…
The General Automated Machine learning Assistant (GAMA) is a modular AutoML system developed to empower users to track and control how AutoML algorithms search for optimal machine learning pipelines, and facilitate AutoML research itself.…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent…
Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…
Increasing clinical trial protocol complexity, amendments, and challenges around knowledge management create significant burden for trial teams. Structuring protocol content into standard formats has the potential to improve efficiency,…
Audio Question Answering (AQA) constitutes a pivotal task in which machines analyze both audio signals and natural language questions to produce precise natural language answers. The significance of possessing high-quality, diverse, and…
Automated machine learning (AutoML) accelerates AI development by automating tasks in the development pipeline, such as optimal model search and hyperparameter tuning. Existing AutoML systems often require technical expertise to set up…
Taking its point of departure in the recent developments in the field of digital humanities and the increasing automatisation of scholarly workflows, this study explores the implications of digital approaches to textual traditions for the…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
This paper introduces LLAssist, an open-source tool designed to streamline literature reviews in academic research. In an era of exponential growth in scientific publications, researchers face mounting challenges in efficiently processing…
We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster,…