Marwa Abdelhakim
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View article: Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology
Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology Open
Background Retinoblastoma is the most common intraocular malignancy of childhood, yet its genomic landscape remains incompletely defined, particularly in understudied populations. Beyond RB1 loss, the contribution of additional somatic and…
View article: Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing Open
Methicillin-resistant Staphylococcus aureus (MRSA) surveillance in regions with mass gatherings presents unique challenges for public health systems. Saudi Arabia, hosting millions of pilgrims annually, provides a distinctive setting for s…
View article: Genomic surveillance of Methicillin Resistant <i>Staphylococcus aureus</i> in Saudi Arabia
Genomic surveillance of Methicillin Resistant <i>Staphylococcus aureus</i> in Saudi Arabia Open
Methicillin-resistant Staphylococcus aureus (MRSA) surveillance in regions with mass gatherings presents unique challenges for public health systems. Saudi Arabia, hosting millions of pilgrims annually, provides a distinctive setting for s…
View article: Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia Open
The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple in…
View article: Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project Open
Background A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-…
View article: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Open
Computational methods for identifying gene–disease associations can use both genomic and phenotypic information to prioritize genes and variants that may be associated with genetic diseases. Phenotype-based methods commonly rely on compari…
View article: Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project
Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project Open
Background A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average “diagnostic odyssey” lasts over five years, and causal variants are identified in under 50%. The Rare Genomes Project (RGP) is a direc…
View article: A personal, reference quality, fully annotated genome from a Saudi individual
A personal, reference quality, fully annotated genome from a Saudi individual Open
We have used multiple sequencing approaches to sequence the genome of a volunteer from Saudi Arabia. We use the resulting data to generate a de novo assembly of the genome, and use different computational approaches to refine the assembly.…
View article: Non-surgical Treatment of Central Venous Occlusion in Haemodialysis Patients
Non-surgical Treatment of Central Venous Occlusion in Haemodialysis Patients Open
Background: Central venous stenosis (CVS) is often found in patients on hemodialysis.Prior ipsilateral central venous catheterization and cardiac rhythm insertion are major risk factors, however the lack of this history may potentially lea…
View article: Diversity of Phenotype and Genetic Etiology of 23 Cystinuria Saudi Patients: A Retrospective Study
Diversity of Phenotype and Genetic Etiology of 23 Cystinuria Saudi Patients: A Retrospective Study Open
Background: Cystinuria is an inborn error of metabolism that manifests with renal stones due to defective renal epithelial cell transport of cystine which resulted from pathogenic variants in the SLC3A1 and/or SLC7A9 genes. Among nephrolit…
View article: Phenotypic and molecular spectrum of pyridoxamine‐5′‐phosphate oxidase deficiency: A scoping review of 87 cases of pyridoxamine‐5′‐phosphate oxidase deficiency
Phenotypic and molecular spectrum of pyridoxamine‐5′‐phosphate oxidase deficiency: A scoping review of 87 cases of pyridoxamine‐5′‐phosphate oxidase deficiency Open
Pyridoxamine‐5′‐phosphate oxidase (PNPO) deficiency is an autosomal recessive pyridoxal 5′‐phosphate (PLP)‐vitamin‐responsive epileptic encephalopathy. The emerging feature of PNPO deficiency is the occurrence of refractory seizures in the…
View article: <scp><i>EMC10</i></scp> homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay
<span><i>EMC10</i></span> homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay Open
In recent years, several genes have been implicated in the variable disease presentation of global developmental delay (GDD) and intellectual disability (ID). The endoplasmic reticulum membrane protein complex (EMC) family is known to be i…
View article: What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations Open
Background Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied t…
View article: DDIEM: Drug Database for Inborn Errors of Metabolism
DDIEM: Drug Database for Inborn Errors of Metabolism Open
Background Inborn errors of metabolism (IEM) represent a subclass of rare inherited diseases caused by a wide range of defects in metabolic enzymes or their regulation. Of over a thousand characterized IEMs, only about half are understood …
View article: Additional file 3 of What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
Additional file 3 of What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations Open
Additional file 3.
View article: Additional file 3 of What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
Additional file 3 of What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations Open
Additional file 3.
View article: MOESM2 of Combining lexical and context features for automatic ontology extension
MOESM2 of Combining lexical and context features for automatic ontology extension Open
Additional file 2 The evaluation of analyzing NCBI abstracts annotated using Whatizit tool.
View article: PathoPhenoDB: a database of pathogen-phenotype associations
PathoPhenoDB: a database of pathogen-phenotype associations Open
PathoPhenoDB is a database containing pathogen-to-phenotype associations mined from the scientific literature. PathoPhenoDB relies on manual curation of pathogen-disease relations, and on ontology-based text mining to associate phenotypes …
View article: PathoPhenoDB: a database of pathogen-phenotype associations
PathoPhenoDB: a database of pathogen-phenotype associations Open
PathoPhenoDB is a database containing pathogen-to-phenotype associations mined from the scientific literature. PathoPhenoDB relies on manual curation of pathogen-disease relations, and on ontology-based text mining to associate phenotypes …
View article: PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research Open
Understanding the relationship between the pathophysiology of infectious disease, the biology of the causative agent and the development of therapeutic and diagnostic approaches is dependent on the synthesis of a wide range of types of inf…
View article: PathoPhenoDB: a database of pathogen-phenotype associations
PathoPhenoDB: a database of pathogen-phenotype associations Open
PathoPhenoDB is a database containing pathogen-to-phenotype associations mined from the scientific literature. PathoPhenoDB relies on manual curation of pathogen-disease relations, and on ontology-based text mining to associate phenotypes …