Related papers: Pathway Tools version 28.0: Integrated Software fo…
Nuanced cancer patient care is needed, as the development and clinical course of cancer is multifactorial with influences from the general health status of the patient, germline and neoplastic mutations, co-morbidities, and environment. To…
One approach to using prior experience in robot motion planning is to store solutions to previously seen problems in a database of paths. Methods that use such databases are characterized by how they query for a path and how they use…
This study integrates PET metabolic information with CT anatomical structures to establish a 3D multimodal segmentation dataset for lymphoma based on whole-body FDG PET/CT examinations, which bridges the gap of the lack of standardised…
For agentic systems to use external tools to solve complex, long-horizon tasks, we need a large set of diverse and controllable tool-use environments. We introduce SynthTools, a fully LLM-based pipeline spanning the entire lifecycle:…
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
The Genomic Data Commons (GDC) provides access to high quality, harmonized cancer genomics data through a unified curation and analysis platform centered around patient cohorts. While GDC users can interactively create complex cohorts…
We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics,…
Graphical models are a powerful tool in modelling and analysing complex biological associations in high-dimensional data. The R-package netgwas implements the recent methodological development on copula graphical models to (i) construct…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
Branch is a web application that provides users with no programming with the ability to interact directly with large biomedical datasets. The interaction is mediated through a collaborative graphical user interface for building and…
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…
Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
Planning is an essential topic in the realm of automated driving. Besides planning algorithms that are widely covered in the literature, planning requires different software tools for its development, validation, and execution. This paper…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large…
Networks provide a meaningful way to represent and analyze complex biological information, but the methodological details of network-based tools are often described for a technical audience. Graphery is a hands-on tutorial webserver…
Alterations in nuclear morphology are useful adjuncts and even diagnostic tools used by pathologists in the diagnosis and grading of many tumors, particularly malignant tumors. Large datasets such as TCGA and the Human Protein Atlas, in…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
In this paper, we present a nonlinear analysis software toolkit, which can help in biomechanical gait data analysis by implementing various nonlinear statistical analysis algorithms. The toolkit is proposed to tackle the need for an…