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Benefiting from the advancements in deep learning, various genomic analytical techniques, such as survival analysis, classification of tumors and their subtypes, and exploration of specific pathways, have significantly enhanced our…
Isoform quantification is an important goal of RNA-seq experiments, yet it remains prob- lematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental…
Portable genome sequencing technology is revolutionizing genomic research by providing a faster, more flexible method of sequencing DNA and RNA [1, 2]. The unprecedented shift from bulky stand-alone benchtop equipment confined in a…
Recent advances in deep generative models have greatly expanded the potential to create realistic synthetic health datasets. These synthetic datasets aim to preserve the characteristics, patterns, and overall scientific conclusions derived…
Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for comparative analyses of RNA levels at…
The intricate relationship between genetic variation and human diseases has been a focal point of medical research, evidenced by the identification of risk genes regarding specific diseases. The advent of advanced genome sequencing…
Complex diseases are multifactorial traits caused by both genetic and environmental factors. They represent the most part of human diseases and include those with largest prevalence and mortality (cancer, heart disease, obesity, etc.).…
Genetic analysis methods are foundational to advancing personalized and preventative medicine, accelerating disease diagnostics, and monitoring the health of organisms and ecosystems. Current nucleic acid technologies such as polymerase…
As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data…
Data visualization is a fundamental tool in genomics research, enabling the exploration, interpretation, and communication of complex genomic features. While machine learning models show promise for transforming data into insightful…
Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cells without sample pooling or RNA extraction. Currently, there is no algorithm optimized…
Complete genome sequences contain valuable information about natural selection, but extracting this information for short, widely scattered noncoding elements remains a challenging problem. Here we introduce a new computational method 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…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
The discovery of genetic risk factors has transformed human genetics, yet the pace of new gene identification has slowed despite the exponential expansion of sequencing and biobank resources. Current approaches are optimized for the…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we…
Genome annotation is an important issue in biology which has long been addressed with gene prediction methods and manual experiments requiring biological expertise. The expanding Next Generation Sequencing technologies and their enhanced…
Consent is an ethical cornerstone of clinical research and healthcare in general. Although the ethical principles of consent - providing information, ensuring comprehension, and ensuring voluntariness - are well-defined, the technological…
Identifying cancer driver genes is crucial for understanding tumor biology and developing precision therapies. However, existing computational methods often rely on single biological networks or population-level mutation patterns, limiting…