Related papers: MOSGA: Modular Open-Source Genome Annotator
Properly annotated multimedia content is crucial for supporting advances in many Information Retrieval applications. It enables, for instance, the development of automatic tools for the annotation of large and diverse multimedia…
Medical image quality assessment (MIQA) is a vital prerequisite in various medical image analysis applications. Most existing MIQA algorithms are fully supervised that request a large amount of annotated data. However, annotating medical…
High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…
The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive…
Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for…
The task of understanding and interpreting the complex information encoded within genomic sequences remains a grand challenge in biological research and clinical applications. In this context, recent advancements in large language model…
Multimodal learning, while contributing to numerous success stories across various fields, faces the challenge of prohibitively expensive manual annotation. To address the scarcity of annotated data, a popular solution is unsupervised…
Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…
Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an…
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…
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…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
Generalized Additive Models (GAMs) balance predictive accuracy and interpretability, but manually configuring their structure is challenging. We propose using the multi-objective genetic algorithm NSGA-II to automatically optimize GAMs,…
We present SODA, a lightweight and open-source visualization library for biological sequence annotations that enables straightforward development of flexible, dynamic, and interactive web graphics. SODA is implemented in TypeScript and can…
Organic solar cells (OSCs) hold great promise for sustainable energy, but discovering high-performance materials is time-consuming and costly. Existing molecular generation methods can aid the design of OSC molecules, but they are mostly…
In industries such as healthcare, finance, and manufacturing, analysis of unstructured textual data presents significant challenges for analysis and decision making. Uncovering patterns within large-scale corpora and understanding their…
With the rapid proliferation of scientific literature, versatile academic knowledge services increasingly rely on comprehensive academic graph mining. Despite the availability of public academic graphs, benchmarks, and datasets, these…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
High-resolution mapping of cells and tissue structures provides a foundation for developing interpretable machine-learning models for computational pathology. Deep learning algorithms can provide accurate mappings given large numbers of…