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The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and wide...

Materias / palabras clave: computational biology, biological systems, biological modelling; Science: Biology (General)

ABSTRACT The rapid advancement of medicine, fueled by big data and interdisciplinary research, has significantly transformed the landscape of computational oncology research. In this evolving environment, effective time ...

The rapid expansion of whole-genome sequencing (WGS) has highlighted the important contribution of noncoding variants to human disease, yet their pathogenic mechanisms remain difficult to resolve. Traditional statistical...

Abstract Background N6-methyladenosine ( $$m^{6}A$$ ) plays a crucial role in enriching RNA functional and genetic information. While deep learning has advanced $$m^{6}A$$ site identification, current state-of-the-art me...

In recent years， quantitative microbial risk assessment （QMRA） for food safety has developed rapidly both domestically and internationally. QMRA integrates multidisciplinary theoretical knowledge and technical meth...

Abstract The latent features of RNA sequences are crucial for our understanding of their functions. Thus, Transformer-based nucleotide language models have received widespread attention; however, the O(n²) complexity of...

A common feature in biological neuromuscular systems is the redundancy in joint actuation. Understanding how these redundancies are resolved in typical joint movements has been a long-standing problem in biomechanics, ne...

Tumor growth involves a dynamic interplay between cancer cells and host cells, which collectively form a tumor microenvironmental network that either suppresses or promotes tumor growth under different conditions. The tr...

Abstract Human social behaviors involve complex interactions between individuals, and understanding how interbrain neural activity reflects and predicts these interactions is critical for advancing social cognitive neuro...

Abstract Cell–cell communication regulates complex biological processes in multicellular systems. Existing scRNA-seq-based methods typically aggregate gene expression by clusters, overlooking within-cluster heterogenei...

Background: Deep learning has transformed medical imaging by enabling earlier and more accurate disease diagnosis. Lesion and tumor segmentation, essential for analyzing and tracking morphological changes, is commonly do...

Social determinants of health (SDOH) are the conditions in which people live, work, and play, and the wider set of factors (e.g., social and economic systems and policies) that shape a person's daily life. SDOH can diffe...

Protein structure determines biological function. Accurately conceptualizing 3D protein/ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereosc...

Materias / palabras clave: Biology; Suite; Software; Software suite; Scale (ratio); Software development; Sequence (biology); Computational biology; Data science; Bioinformatics; Computer science; Genetics

Materias / palabras clave: Biology; Organism; Gene; Computational biology; Ontology; Function (biology); Gene ontology; Vocabulary; Controlled vocabulary; Genetics; World Wide Web; Computer science

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagen...

The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platfor...

Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it ...

The hallmarks of cancer conceptualization is a heuristic tool for distilling the vast complexity of cancer phenotypes and genotypes into a provisional set of underlying principles. As knowledge of cancer mechanisms has p...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated ...

The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each...

MOTIVATION: Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end librarie...