Related papers: The big challenge for livestock genomics is to mak…

Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data…

Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive. One of the biggest challenges to whole-cell models is assembling the large and diverse array of data needed to model an…

The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…

In recent years, we have witnessed a dramatic data explosion in genomics, thanks to the improvement in sequencing technologies and the drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each…

Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…

Next Generation Sequencing can sample the whole genome (WGS) or the 1-2% of the genome that codes for proteins called the whole exome (WES). Machine learning approaches to variant calling achieve high accuracy in WGS data, but the reduced…

Buffaloes are farm animals that contribute to food security by providing high quality meat and milk. They can better tolerate the adverse effects of global climate change on their meat and milk production. Despite their advantages,…

Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel…

How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to…

In this article, we propose an approach to breeding which focuses on mating instead of truncation selection, our method uses genome-wide marker information in a similar fashion to genomic selection so we refer it to as genomic mating. Using…

Genomic selection (GS), as a critical crop breeding strategy, plays a key role in enhancing food production and addressing the global hunger crisis. The predominant approaches in GS currently revolve around employing statistical methods for…

Genomic approaches have revolutionized medical research, providing valuable insights into human physiology and disease. Despite major benefits from large collections of genomes, the lack of diversity in genomic data represents a significant…

We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…

Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing. As genomes represent the entirety of an organism's hereditary…

Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…

Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…

Leveraging the vast genetic diversity within microbiomes offers unparalleled insights into complex phenotypes, yet the task of accurately predicting and understanding such traits from genomic data remains challenging. We propose a framework…

Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…

Genomic prediction can be a powerful tool to achieve greater rates of genetic gain for quantitative traits if thoroughly integrated into a breeding strategy. In rice as in other crops, the interest in genomic prediction is very strong with…

Human genomic data carry unique information about an individual and offer unprecedented opportunities for healthcare. The clinical interpretations derived from large genomic datasets can greatly improve healthcare and pave the way for…