93 Works

Additional file 7 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 7: Table S7. Summary of immune cell changes and differentially methylated CpGs between recovered and dead patients over four time points 7A. Immune cell changes between recovered and dead patients over four time points, 7B. Differential methylation of CpGs between recovered and died patients over four time points. The b_0, b_1, b_2, and b_3 coefficients correspond to the reference model parameters, where survival phenotype is used as a reference. The d_0, d_1, d_2,...

RNA-seq Reveals Dysregulation of Novel Melanocyte Genes upon Oxidative Stress: Implications in Vitiligo Pathogenesis

Konduru Seetharama Sastry, Haroon Naeem, Younes Mokrab & Aouatef Ismail Chouchane
Oxidative stress is known to induce melanocyte death, but the underlying mechanisms are incompletely understood. To identify oxidative stress-induced global gene expression changes in melanocytes, we treated PIG1 melanocytes with H2O2 in a dose- and time-dependent manner and performed RNA-seq. This approach allowed us to capture the events occurring early as well as late phase after treatment with H2O2. Our bioinformatics analysis identified differentially expressed genes involved in various biological processes of melanocytes which are...

Additional file 1 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 1: Mapping of differentially expressed ir-lncRNAs to protein coding genes. (A) Diagram representation of the random walk with restart global propagation network algorithm. (B) Walkscore distribution of protein-coding genes in TCGA-BRCA, with cutoff set at walkscore ≥ 0.01 to generate a ranked list of protein-coding genes in proximity of differentially expressed ir-lncRNAs.

Additional file 3 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 3: Propagation walkscores of 127 proxy protein-coding genes in the TCGA-BRCA cohort.

Additional file 7 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 7: Akaike information criterion (AIC), delta AIC, and HRs for death (overall survival) and corresponding 95%-confidence interval for ICR and 3 ir-lncRNA signature in 18 solid cancer TCGA datasets and RAQA cohort.

Assessing the genetic burden of familial hypercholesterolemia in a large middle eastern biobank

Geethanjali Devadoss Gandhi, Waleed Aamer, Navaneethakrishnan Krishnamoorthy, Najeeb Syed, Elbay Aliyev, Aljazi Al-Maraghi, Muhammad Kohailan, Jamil Alenbawi, Mohammed Elanbari, Borbala Mifsud, Younes Mokrab, Charbel Abi Khalil & Khalid A. Fakhro
Abstract Background The genetic architecture underlying Familial Hypercholesterolemia (FH) in Middle Eastern Arabs is yet to be fully described, and approaches to assess this from population-wide biobanks are important for public health planning and personalized medicine. Methods We evaluate the pilot phase cohort (n = 6,140 adults) of the Qatar Biobank (QBB) for FH using the Dutch Lipid Clinic Network (DLCN) criteria, followed by an in-depth characterization of all genetic alleles in known dominant (LDLR,...

Patterns and distribution of de novo mutations in multiplex Middle Eastern families

Muhammad Kohailan, Waleed Aamer, Najeeb Syed, Sujitha Padmajeya, Sura Hussein, Amira Sayed, Jyothi Janardhanan, Sasirekha Palaniswamy, Nady El hajj, Ammira Al-Shabeeb Akil & Khalid A. Fakhro
While de novo mutations (DNMs) are key to genetic diversity, they are also responsible for a high number of rare disorders. To date, no study has systematically examined the rate and distribution of DNMs in multiplex families in highly consanguineous populations. Leveraging WGS profiles of 645 individuals in 146 families, we implemented a combinatorial approach using 3 complementary tools for DNM discovery in 353 unique trio combinations. We found a total of 27,168 DNMs (median:...

CXCR7 signaling promotes breast cancer survival in response to mesenchymal stromal stem cell-derived factors

Mashael Al-toub, Mohammad Almohawes, Radhakrishnan Vishnubalaji, Musaad Alfayez, Abdullah Aldahmash, Moustapha Kassem & Nehad M. Alajez
The interaction between cancer cells and molecular cues provided by tumor stromal cells plays a crucial role in cancer growth and progression. We have recently reported that the outcome of interaction between tumor cells and stromal cells is dependent on the gene expression signature of tumor cells. In the current study, we observed that several cancer cell lines, e.g., MCF7 breast cancer line, exhibited growth advantage when cultured in the presence of conditioned media (CM)...

Evaluation of cationic channel TRPV2 as a novel biomarker and therapeutic target in Leukemia-Implications concerning the resolution of pulmonary inflammation

Kodappully S. Siveen, Kirti S. Prabhu, Aeijaz S. Parray, Maysaloun Merhi, Abdelilah Arredouani, Mohamed Chikri, Shahab Uddin, Said Dermime, Ramzi M. Mohammad, Martin Steinhoff, Ibrahim A. Janahi & Fouad Azizi
Patients treated during leukemia face the risk of complications including pulmonary dysfunction that may result from infiltration of leukemic blast cells (LBCs) into lung parenchyma and interstitium. In LBCs, we demonstrated that transient receptor potential vanilloid type 2 channel (TRPV2), reputed for its role in inflammatory processes, exhibited oncogenic activity associated with alteration of its molecular expression profile. TRPV2 was overexpressed in LBCs compared to normal human peripheral blood mononuclear cells (PBMCs). Additionally, functional full...

Fibrillar form of α-synuclein-specific scFv antibody inhibits α-synuclein seeds induced aggregation and toxicity

Vijay Gupta, Safa Salim, Issam Hmila, Nishant N. Vaikath, Indulekha P. Sudhakaran, Simona S. Ghanem, Nour K. Majbour, Sara A. Abdulla, Mohamed M. Emara, Houari B. Abdesselem, Tamas Lukacsovich, Daniel Erskine & Omar M. A. El-Agnaf
Synucleinopathies including Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA) are characterized by pathological accumulation of α-synuclein (α-syn). Amongst the various approaches attempting to tackle the pathological features of synucleinopathies, antibody-based immunotherapy holds much promise. However, the large size of antibodies and corresponding difficulty in crossing the blood-brain barrier has limited development in this area. To overcome this issue, we engineered single-chain variable fragments (scFvs) against fibrillar α-syn, a putative...

The use of technology in tracking soccer players’ health performance: a scoping review

Jassim Almulla, Abdulrahman Takiddin & Mowafa Househ
Background Quantifying soccer players’ performance using different types of technologies helps coaches in making tactical decisions and maintaining players’ health. Little is known about the relation between the performance measuring technologies and the metrics they measure. The aim of this study is to identify and group the different types of technologies that are used to track the health-related performance metrics of soccer players. Methods We conducted a systematic search for articles using IEEE Xplore, PubMed,...

Additional file 2 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 2: Table S2. Summary of different models tested for estimating differences between controls and COVID-19 patients for immune cell proportions. Adjusted R2, residual standard error (sigma), AIC, and p.value for each tested model for each cell type are shown. The following models were tested, mod1; Age and ethnicity as covariates, mod2; age as a covariate, mod3; ethnicity as a covariate, mod4; no covariates.

Additional file 3 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 3: Table S3. Summary of identified differentially methylated CpGs between COVID-19 patients and controls. A. All significant CpGs B. Variable description from Table S2A. C. Significant CpGs from genes previously described as COVID-19 important [1]. D. Functional annotation of genes from Supplemental table 3C.

Additional file 4 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 4: Table S4. Summary of differentially methylated pathways detected between COVID-19 patients and controls based on CpG sites.

Additional file 9 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 9: Table S9. Summary of univariate Cox proportional hazard analysis of the previously identified CpGs. Column variables represent Name; chr; chromosome number, pos; position, CpG name, relation_to_Island; where is CpG located in relationship to island, UCSC RefGene Name; UCSC gene name, UCSC RefGene Accession; UCSC gene accession, UCSC RefGene Group; where in respect to gene is CpG located, Beta; estimated coefficient beta from the model, StandardError; standard error, Z; z-score, LRT; likelihood ratio...

DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Abstract Background COVID-19 infections could be complicated by acute respiratory distress syndrome (ARDS), increasing mortality risk. We sought to assess the methylome of peripheral blood mononuclear cells in COVID-19 with ARDS. Methods We recruited 100 COVID-19 patients with ARDS under mechanical ventilation and 33 non-COVID-19 controls between April and July 2020. COVID-19 patients were followed at four time points for 60 days. DNA methylation and immune cell populations were measured at each time point. A...

Developing an online hate classifier for multiple social media platforms

Joni Salminen, Maximilian Hopf, Shammur A. Chowdhury, Soon-gyo Jung, Hind Almerekhi & Bernard J. Jansen
The proliferation of social media enables people to express their opinions widely online. However, at the same time, this has resulted in the emergence of conflict and hate, making online environments uninviting for users. Although researchers have found that hate is a problem across multiple platforms, there is a lack of models for online hate detection using multi-platform data. To address this research gap, we collect a total of 197,566 comments from four platforms: YouTube,...

Developing an online hate classifier for multiple social media platforms

Joni Salminen, Maximilian Hopf, Shammur A. Chowdhury, Soon-gyo Jung, Hind Almerekhi & Bernard J. Jansen
The proliferation of social media enables people to express their opinions widely online. However, at the same time, this has resulted in the emergence of conflict and hate, making online environments uninviting for users. Although researchers have found that hate is a problem across multiple platforms, there is a lack of models for online hate detection using multi-platform data. To address this research gap, we collect a total of 197,566 comments from four platforms: YouTube,...

Additional file 1 of An integrated multi-omic approach demonstrates distinct molecular signatures between human obesity with and without metabolic complications: a case–control study

Fayaz Ahmad Mir, Raghvendra Mall, Ehsan Ullah, Ahmad Iskandarani, Farhan Cyprian, Tareq A. Samra, Meis Alkasem, Ibrahem Abdalhakam, Faisal Farooq, Shahrad Taheri & Abdul-Badi Abou-Samra
Additional file 1: Figure S1. Flowchart highlighting different number of MiRNAs, PCGs, Metabolites analyzed in our dataset and steps taken to identify key MiRNAs, PCGs, Metabolites involved in significantly enriched metabolic pathways between OBM vs OBO. Figure S2. Correlation between clinical traits and enriched metabolic pathways. Here each block represents correlation between the enrichment profile of a metabolic pathway and a clinical characteristic based on their values across the 39 participant profiles. Here we only...

RNA-seq Reveals Dysregulation of Novel Melanocyte Genes upon Oxidative Stress: Implications in Vitiligo Pathogenesis

Konduru Seetharama Sastry, Haroon Naeem, Younes Mokrab & Aouatef Ismail Chouchane
Oxidative stress is known to induce melanocyte death, but the underlying mechanisms are incompletely understood. To identify oxidative stress-induced global gene expression changes in melanocytes, we treated PIG1 melanocytes with H2O2 in a dose- and time-dependent manner and performed RNA-seq. This approach allowed us to capture the events occurring early as well as late phase after treatment with H2O2. Our bioinformatics analysis identified differentially expressed genes involved in various biological processes of melanocytes which are...

MSLP: mRNA subcellular localization predictor based on machine learning techniques

Saleh Musleh, Mohammad Tariqul Islam, Rizwan Qureshi, Nihad Alajez & Tanvir Alam
Abstract Background Subcellular localization of messenger RNA (mRNAs) plays a pivotal role in the regulation of gene expression, cell migration as well as in cellular adaptation. Experiment techniques for pinpointing the subcellular localization of mRNAs are laborious, time-consuming and expensive. Therefore, in silico approaches for this purpose are attaining great attention in the RNA community. Methods In this article, we propose MSLP, a machine learning-based method to predict the subcellular localization of mRNA. We propose...

Additional file 1 of MSLP: mRNA subcellular localization predictor based on machine learning techniques

Saleh Musleh, Mohammad Tariqul Islam, Rizwan Qureshi, Nehad M. Alajez & Tanvir Alam
Additional file 1: File S1. List of physicochemical properties related to DPCP and TPCP. File S2. Name of the features and their mapping. File S3. Selected top features and their importance based on SHAP analysis for locations.

Additional file 3 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 3: Propagation walkscores of 127 proxy protein-coding genes in the TCGA-BRCA cohort.

Additional file 4 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 4: Canonical pathways, diseases and functions associated with the 127 proxy protein-coding genes.

Additional file 6 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 6: Prognostic value of ICR classifier across solid cancers. Forest plot showing HRs for death (overall survival) and corresponding 95%-confidence interval for the continuous ICR score and number of patients for each TCGA cancer cohort and RAQA breast cancer cohort. Significant positive HRs are visualized in blue and significant negative HRs are visualized in red. ICR enabled (HR < 1, p-value < 0.05) cancer types are indicated with orange asterisks and ICR disabled...

Registration Year

  • 2023
    45
  • 2022
    48

Resource Types

  • Text
    56
  • Dataset
    24
  • Collection
    11
  • Audiovisual
    2

Affiliations

  • Hamad bin Khalifa University
    93
  • Hamad Medical Corporation
    58
  • Weill Cornell Medical College in Qatar
    48
  • Qatar Foundation
    36
  • Cornell University
    36
  • Sidra Medical and Research Center
    32
  • St. Jude Children's Research Hospital
    28
  • Centre Hospitalier Universitaire de Clermont-Ferrand
    24
  • Memorial Sloan Kettering Cancer Center
    24
  • University of Genoa
    22