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Malak S. Abedalthagafi

Publications and source records attributed to Malak S. Abedalthagafi.

3 recordsLinked to original sources

Challenges and Recommendations in Establishing National Human Diversity Genomic Projects

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 challenge for advancing biomedical discovery and accessible health solutions worldwide. Establishing a national genomic project is not a one-size-fits-all endeavor, as each country presents distinct challenges and opportunities. We identify challenges in the way of obtaining and publishing data from Whole Genome Sequencing (WGS) of people in various countries, discuss the progress made by some in their efforts to study their genetic diversity, and assess the most common issues. We recognize that a successful national genome database requires addressing several major issues, including the variable awareness of the recent developments in genomics among government officials, healthcare administrators, and policymakers, the absence of regulations, and ethical considerations, the challenges in securing funding, establishing legal frameworks, and building the necessary infrastructure. By assembling a diverse team of experts across 19 countries, we aim to provide a balanced approach in our recommendations to establish national projects. Our study acknowledges and addresses major intricacies and nuances specific to various settings and regions while presenting diverse opinions of scientists from both high-resource and low-resource countries contributing to a more inclusive and globally relevant framework for advancing genomic research and its applications.

q-bio.OT↗

Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities

Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging, virtualization, and containerization are different approaches to satisfy this need by wrapping omics tools in additional software that makes the omics tools easier to install and use. Here, we systematically review practices across prominent packaging, virtualization, and containerization platforms. We outline the challenges, advantages, and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers, and system administrators. We also propose principles to make packaging, virtualization, and containerization of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.

q-bio.GN↗

Diversity in immunogenomics: the value and the challenge

With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become an increasingly important tool to characterize T and B cell responses in settings of interest. However, the majority of AIRR-seq studies conducted so far were performed in individuals of European ancestry, restricting the ability to identify variation in human adaptive immune responses across populations and limiting their applications. As AIRR-seq studies depend on the ability to assign VDJ sequence reads to the correct germline gene segments, efforts to characterize the genomic loci that encode adaptive immune receptor genes in different populations are urgently needed. The availability of comprehensive germline gene databases and further applications of AIRR-seq studies to individuals of non-European ancestry will substantially enhance our understanding of human adaptive immune responses, promote the development of effective diagnostics and treatments, and eventually advance precision medicine.

q-bio.GN↗