Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely addres...
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes. These approaches often use graphical models of the pangenome to support algorithms for sequence alignment, visualization, functional genomics, and association studies. The additional information provided to these methods by the pangenome allows them to achieve superior performance on a variety of bioinformatic tasks, including read alignment, variant calling, and genotyping. Pangenome graphs stand to become a ubiquitous tool in genomics. Although it is unclear whether they will replace linearreference genomes, their ability to harmoniously relate multiple sequence and coordinate systems will make them useful irrespective of which pangenomic models become most common in the future.
In clinical artificial intelligence (AI), graph representation learning, mainly through graph neural networks and graph transformer architectures, stands out for its capability to capture intricate relationships and s...
In clinical artificial intelligence (AI), graph representation learning, mainly through graph neural networks and graph transformer architectures, stands out for its capability to capture intricate relationships and structures within clinical datasets. With diverse data—from patient records to imaging—graph AI models process data holistically by viewing modalities and entities within them as nodes interconnected by their relationships. Graph AI facilitates model transfer across clinical tasks, enabling models to generalize across patient populations without additional parameters and with minimal to no retraining. However, the importance of human-centered design and model interpretability in clinical decision-making cannot be overstated. Since graph AI models capture information through localized neural transformations defined on relational datasets, they offer both an opportunity and a challenge in elucidating model rationale. Knowledge graphs can enhance interpretability by aligning model-driven insights with medical knowledge. Emerging graph AI models integrate diverse data modalities through pretraining, facilitate interactive feedback loops, and foster human–AI collaboration, paving the way toward clinically meaningful predictions.
Analysis of cancer genomes has shown that a large fraction of chromosomal changes originate from catastrophic events including whole-genome duplication, chromothripsis, breakage-fusion-bridge cycles, and chromoplexy. ...
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Analysis of cancer genomes has shown that a large fraction of chromosomal changes originate from catastrophic events including whole-genome duplication, chromothripsis, breakage-fusion-bridge cycles, and chromoplexy. Through sophisticated computational analysis of cancer genomes and experimental recapitulation of these catastrophic alterations, we have gained significant insights into the origin, mechanism, and evolutionary dynamics of cancer genome complexity. In this review, we summarize this progress and survey the major unresolved questions, with particular emphasis on the relative contributions of chromosome fragmentation and DNA replication errors to complex chromosomal alterations.
In chemoinformatics and medicinal chemistry, machine learning has evolved into an important approach. In recent years, increasing computational resources and new deep learning algorithms have put machine learning onto...
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In chemoinformatics and medicinal chemistry, machine learning has evolved into an important approach. In recent years, increasing computational resources and new deep learning algorithms have put machine learning onto a new level, addressing previously unmet challenges in pharmaceutical research. In silico approaches for compound activity predictions, de novo design, and reaction modeling have been further advanced by new algorithmic developments and the emergence of big data in the field. Herein, novel applications of machine learning and deep learning in chemoinformatics and medicinal chemistry are reviewed. Opportunities and challenges for new methods and applications are discussed, placing emphasis on proper baseline comparisons, robust validation methodologies, and new applicability domains.
Clinical genetic laboratories must have access to clinically validated biomedicaldata for precision medicine. A lack of accessibility, normalized structure, and consistency in evaluation complicates interpretation of...
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Clinical genetic laboratories must have access to clinically validated biomedicaldata for precision medicine. A lack of accessibility, normalized structure, and consistency in evaluation complicates interpretation of disease causality, resulting in confusion in assessing the clinical validity of genes and genetic variants for diagnosis. A key goal of the Clinical Genome Resource (ClinGen) is to fill the knowledge gap concerning the strength of evidence supporting the role of a gene in a monogenic disease, which is achieved through a process known as Gene–Disease Validity curation. Here we review the work of ClinGen in developing a curation infrastructure that supports the standardization, harmonization, and dissemination of Gene–Disease Validity data through the creation of frameworks and the utilization of common data standards. This infrastructure is based on several applications, including the ClinGen GeneTracker, Gene Curation Interface, data Exchange, GeneGraph, and website.
The rapidly growing scale and variety of biomedicaldata repositories raise important privacy concerns. Conventional frameworks for collecting and sharing human subject data offer limited privacy protection, often nec...
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The rapidly growing scale and variety of biomedicaldata repositories raise important privacy concerns. Conventional frameworks for collecting and sharing human subject data offer limited privacy protection, often necessitating the creation of data silos. Privacy-enhancing technologies (PETs) promise to safeguard these data and broaden their usage by providing means to share and analyze sensitive data while protecting privacy. Here, we review prominent PETs and illustrate their role in advancing biomedicine. We describe key use cases of PETs and their latest technical advances and highlight recent applications of PETs in a range of biomedical domains. We conclude by discussing outstanding challenges and social considerations that need to be addressed to facilitate a broader adoption of PETs in biomedicaldatascience.
Cardiovascular diseases (CVDs) are responsible for more deaths than any other cause, with coronary heart disease and stroke accounting for two-thirds of those deaths. Morbidity and mortality due to CVD are largely pre...
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Cardiovascular diseases (CVDs) are responsible for more deaths than any other cause, with coronary heart disease and stroke accounting for two-thirds of those deaths. Morbidity and mortality due to CVD are largely preventable, through either primary prevention of disease or secondary prevention of cardiac events. Monitoring cardiac status in healthy and diseased cardiovascular systems has the potential to dramatically reduce cardiac illness and injury. Smart technology in concert with mobile health platforms is creating an environment where timely prevention of and response to cardiac events are becoming a reality.
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