A5056259054- RNA modifications and cancer
- Genomic variations and chromosomal abnormalities
- Acute Myeloid Leukemia Research
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Genomics and Rare Diseases
- Hematological disorders and diagnostics
- Immunodeficiency and Autoimmune Disorders
- Genetics and Neurodevelopmental Disorders
- Autism Spectrum Disorder Research
- Metabolomics and Mass Spectrometry Studies
- Cancer Genomics and Diagnostics
- Pluripotent Stem Cells Research
- Health, Environment, Cognitive Aging
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Salivary Gland Disorders and Functions
- Tendon Structure and Treatment
- Receptor Mechanisms and Signaling
- HIV-related health complications and treatments
- CRISPR and Genetic Engineering
- Folate and B Vitamins Research
- Viral Infectious Diseases and Gene Expression in Insects
- Oral microbiology and periodontitis research
Qatar Foundation
2017-2024
Hamad bin Khalifa University
2016-2024
King's College London
2024
MRC London Institute of Medical Sciences
2024
Imperial College London
2024
Howard Hughes Medical Institute
2012
Wellcome Sanger Institute
2012
Royal Veterinary College
2007-2010
Kingston University
2009
Alterations in cancer genomes strongly influence clinical responses to treatment and many instances are potent biomarkers for response drugs. The Genomics of Drug Sensitivity Cancer (GDSC) database (www.cancerRxgene.org) is the largest public resource information on drug sensitivity cells molecular markers response. Data freely available without restriction. GDSC currently contains data almost 75 000 experiments, describing 138 anticancer drugs across 700 cell lines. To identify response,...
Stress Granules (SGs) are dynamic ribonucleoprotein aggregates, which have been observed in cells subjected to environmental stresses, such as oxidative stress and heat shock (HS). Although pluripotent stem (PSCs) highly sensitive stress, the role of SGs regulating PSC self-renewal differentiation has not fully elucidated. Here we found that sodium arsenite (SA) HS, but hydrogen peroxide (H2O2), induce SG formation human induced (hi) PSCs. Particularly, these granules contain well-known...
Abstract Summary Transposable elements (TEs) influence the evolution of novel transcriptional networks yet specific and meaningful interpretation how TE-derived initiation contributes to transcriptome has been marred by computational methodological deficiencies. We developed LIONS for analysis RNA-seq data specifically detect quantify TE-initiated transcripts. Availability implementation Source code, container, test instruction manual are freely available at www.github.com/ababaian/LIONS....
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by deficits in social communication, restricted interests, and repetitive behaviors. Despite considerable research efforts, the genetic complexity of ASD remains poorly understood, complicating diagnosis treatment, especially Arab population, with its diversity linked to migration, tribal structures, high consanguinity. To address scarcity data Middle East, we conducted genome sequencing (GS) on 50 subjects their...
Retrotransposons (RTEs) have been postulated to reactivate with age and contribute aging through activated innate immune response inflammation. Here, we analyzed the relationship between RTE expression using published transcriptomic methylomic datasets of human blood. Despite no observed correlation activity chronological age, most classes families except short interspersed nuclear elements (SINEs) correlated biological age-associated gene signature scores. Strikingly, found that SINEs was...
Allele-specific transcriptional regulation, including of imprinted genes, is essential for normal mammalian development. While the regulatory regions controlling genes are associated with DNA methylation (DNAme) and specific histone modifications, interplay between transcription these epigenetic marks at allelic resolution typically not investigated genome-wide due to a lack bioinformatic packages that can process integrate multiple epigenomic datasets resolution. In addition, existing...
Abstract The relationship between salivary α-amylase activity (psAAa) or AMY1 copy number and the risk of obesity remains controversial. We aimed to assess this in a cohort from Qatar, where affects 43% adults. was investigated cross-sectionally 923 Qatari adults Qatar biobank cohort. CN estimated form whole genome sequencing data. associations with prevalence were assessed by linear logistic regressions. found no difference obese normal-weight individuals. However, psAAa significantly lower...
Abstract Retrotransposons (RTEs) have been postulated to reactivate with age and contribute aging through activated innate immune response inflammation. Here, we analyzed the relationship between RTE expression using published transcriptomic methylomic datasets of human blood. Despite no observed correlation activity chronological age, most classes families except short interspersed nuclear elements (SINEs) correlated biological age-associated gene signature scores. Strikingly, found that...
Introduction The unprecedented impact of the coronavirus pandemic (COVID-19) has had profound implications on ASD community, including disrupting daily life, increasing stress and emotional dysregulation in autistic children, worsening individual family well-being. Methods This study used quantitative qualitative survey data from parents Qatar (n=271), to understand COVID-19 children their families Qatar. questionnaire was a combination open-ended (qualitative) closed-ended (quantitative)...
Retrotransposons (RTEs) have been postulated to reactivate with age and contribute aging through activated innate immune response inflammation. Here, we analyzed the relationship between RTE expression using published transcriptomic methylomic datasets of human blood. Despite no observed correlation activity chronological age, most classes families except short interspersed nuclear elements (SINEs) correlated biological age-associated gene signature scores. Strikingly, found that SINEs was...
The association of salivary α-amylase activity (SAA) or low copy number its coding gene AMY1 with diabetes remains controversial. We aimed to reinvestigate the these factors in Qatar, where prevalence is about 16%. obtained cross-sectional data 929 Qataris (age > 18 years) from Qatar Biobank. estimated variants (CNV) whole-genome data, and quantified SAA plasma (pSAA). used adjusted logistic regression examine between pSAA CNV odds. found a significant high activity, but not CNV, reduced...
It is now evident that DNA forms an organized nuclear architecture, which essential to maintain the structural and functional integrity of genome. Chromatin organization can be systematically studied due recent boom in chromosome conformation capture technologies (e.g., 3C its successors 4C, 5C Hi-C), accompanied by development computational pipelines identify biologically meaningful chromatin contacts such data. However, not all tools are applicable experimental designs features. Capture...
Abstract Background Successful treatment of HIV-positive patients is fundamental to controlling the progression AIDS. Causes failure are either related drug resistance and/or insufficient levels in blood. Severe side effects, coupled with intense nature many regimens, can lead fatigue and consequently periodic or permanent non-adherence. Although non-adherence a recognised problem HIV treatment, it still poorly detected both clinical practice research often based on unreliable information...
The relationship between salivary α-amylase activity (ssAAa) and the risk of metabolic disorders remains equivocal. We aimed to assess this in adults from Qatar, where obesity type 2 diabetes are highly prevalent. cross-sectionally quantified ssAAa saliva estimated AMY1 CN whole-genome sequencing data 1499 participants. Linear regression was used adiposity glycemic markers. Logistic examine association occurrence or diabetes. mean median were significantly lower obese individuals. There...
The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus at consensus sub-consensus levels over three-year period (2015–2017) its implications on disease severity. A total 90 nasal samples positive for the pH1N1 virus were deep-sequenced analyzed to detect low-frequency variants (LFVs) haplotypes. Parallel LFVs was seen hemagglutinin (HA) gene across three scales: among patients (33%), years...
Abstract Abnormal eye gaze is a hallmark characteristic of autism spectrum disorder (ASD). The primary aim the present research was to develop an Arabic version objective measure ASD, “autism index” (AI), based on tracking social and nonsocial stimuli validated initially in United States. initial phase this study included translation English language eye‐tracking into appropriate for Arabic‐speaking culture. During second phase, we tested it total 144 children with 96 controls. AI had...
Traumatic brain injury (TBI) can be defined as a disorder in the function of after bump, blow, or jolt to head, penetrating head injury. Mild traumatic (mTBI) cause devastating effects, such initiation long-term neurodegeneration tissue. In current study, effects mTBI were investigated on rat regions; cortex (Co) and corpus callosum (CC) 24 h (subacute trauma) by Fourier transform infrared (FTIR) imaging immunohistochemistry (IHC). IHC studies showed formation amyloid-β (Aβ) plaques region...
Abstract Summary Transposable Elements (TEs) influence the evolution of novel transcriptional networks yet specific and meaningful interpretation how TE-initiation events contribute to transcriptome has been marred by computational methodological deficiencies. We developed LIONS for analysis paired-end RNA-seq data specifically detect quantify TE-initiated transcripts. Availability Source code, container, test instruction manual are freely available at www.github.com/ababaian/LIONS . Contact...
Somatic cells are reprogrammed with reprogramming factors to generate induced pluripotent stem (iPSCs), offering a promising future for disease modeling and treatment by overcoming the limitations of embryonic cells. However, this process remains inefficient since only small percentage transfected can undergo full reprogramming. Introducing miRNAs, such as miR-294 miR302/3667, factors, has shown increase iPSC colony formation. Previously, we identified five transcription GBX2, NANOGP8, SP8,...
Abstract Mutational profiles of Myelodysplastic syndromes (MDS) have established that a relatively small number genetic aberrations, including SF3B1 and SRSF2 spliceosome mutations, lead to specific phenotypes prognostic subgrouping. We performed Multi-Omics Factor Analysis (MOFA) on two published MDS cohorts bone marrow mononuclear cells (BMMNCs) CD34+ with three data modalities (clinical, genotype, transcriptomics). Seven different views, immune profile, inflammation/aging, Retrotransposon...
Retrotransposons (RTEs) have been postulated to reactivate with age and contribute aging through activated innate immune response inflammation. Here, we systematically analyzed the relationship between RTEs expression using published transcriptomic methylomic datasets of human blood. Despite no observed correlation activity chronological age, most RTE classes families except short interspersed nuclear elements (SINEs) correlate age-associated gene signature scores. Strikingly, found that...