Mohamed Hamed

Mohamed Hamed
University of Rostock · Bioinformatics and Computational biology

PhD in computer science (Bioinformatics-Computational Biology)

About

75
Publications
5,767
Reads
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325
Citations
Citations since 2017
54 Research Items
288 Citations
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20172018201920202021202220230102030405060
20172018201920202021202220230102030405060
Introduction
Mohamed Hamed currently works at the Bioinformatics and Computational biology, University of Rostock. Mohamed does research in Systems Biology, Bioinformatics and Biostatistics. Their most recent publication is 'Combined Casein Kinase II inhibition and epigenetic modulation in acute B-lymphoblastic leukemia'.
Additional affiliations
April 2010 - December 2015
Universität des Saarlandes
Position
  • Researcher
March 2010 - March 2015
Universität des Saarlandes
Position
  • Researcher

Publications

Publications (75)
Article
Full-text available
Little is known about optimally applying chemotherapeutic agents in a specific temporal sequence to rapidly reduce the tumor load and to improve therapeutic efficacy. The clinical optimization of drug efficacy while reducing side effects is still restricted due to an incomplete understanding of the mode of action and related tumor relapse mechanism...
Article
Full-text available
Background Assessment of immune-specific markers is a well-established approach for predicting the response to immune checkpoint inhibitors (ICIs). Promising candidates as ICI predictive biomarkers are the DNA damage response pathway genes. One of those pathways, which are mainly responsible for the repair of DNA damage caused by ultraviolet radiat...
Article
Full-text available
Background Behcet’s disease (BD) is a systemic inflammatory disease of the blood vessels and affects various body parts. This study aimed to determine the association of four single-nucleotide polymorphisms (SNPs) and BD in the Egyptian population using multiple statistical models and show the resulting associations along with previous studies of d...
Preprint
Cytotoxic CD8 ⁺ T lymphocytes (CTL) eliminate infected cells or transformed tumour cells by releasing perforin-containing cytotoxic granules at the immunological synapse. The secretion of such granules depends on Ca ²⁺ -influx through store operated Ca ²⁺ channels, formed by STIM-activated Orai proteins. Whereas molecular mechanisms of the secretio...
Article
Full-text available
Introduction: Ageing-related processes such as cellular senescence are believed to underlie the accumulation of diseases in time, causing (co)morbidity, including cancer, thromboembolism and stroke. Interfering with these processes may delay, stop or reverse morbidity. The aim of this study is to investigate the link between (co)morbidity and agei...
Article
Full-text available
Background: The introduction of combined conventional cytostatics and pathway-specific inhibitors has opened new treatment options for several cancer types including hematologic neoplasia such as leukaemias. As the detailed understanding of the combination-induced molecular effects is often lacking, the identification of combination-induced molecu...
Article
Full-text available
The molecular basis of aging and of aging-associated diseases is being unraveled at an increasing pace. An extended healthspan, and not merely an extension of lifespan, has become the aim of medical practice. Here, we define health based on the absence of diseases and dysfunctions. Based on an extensive review of the literature, in particular for h...
Preprint
Full-text available
Aging-related processes such as cellular senescence are believed to underlie the accumulation of diseases in time, causing (co-)morbidity, including cancer, thromboembolism and stroke. Intervening into these processes may delay, stop or reverse morbidity. To study the link between (co-)morbidity and aging, by exploring biomarkers and molecular mech...
Article
Full-text available
Adipose tissue plays an active role in the regulation of the body´s energy balance. Mesenchymal stem/stromal cells from adipose tissue (adMSC) are the precursor cells for repair and adipogenesis. Since the balance of the differentiation state of adipose tissue-resident cells is associated with the development of various diseases, the examination of...
Article
TFmiR2 is a freely available web server for constructing and analyzing integrated TF and miRNA co-regulatory networks for human and mouse. TFmiR2 generates tissue- and biological process-specific networks for the set of deregulated genes and miRNAs provided by the user. Furthermore, the service can now identify key driver genes and miRNAs in the co...
Article
Full-text available
Mismatch repair deficient (MMR-D) tumors exemplify the prototypic hypermutator phenotype. Owing to the high mutation rates, plenty of neo-antigens are present on the tumor cells’ surface, ideally shared among different cancer types. The MLH1 knock out mouse represents a preclinical model that resembles features of the human MMR-D counterpart. While...
Article
Background MLH1 knock out mice develop mismatch repair deficient (MMR-D) neoplasias spontaneously and reflect the diverse clinical presentation of MMR-D-driven carcinogenesis in men. The tumor spectrum includes a high prevalence of early Non-Hodgkin T cell lymphomas (NHL), lymphoid skin lesions as well as later developing epithelial tumors of the g...
Article
Full-text available
Prostate cancer (PCa) is a genetically heterogeneous cancer entity that causes challenges in pre-treatment clinical evaluation, such as the correct identification of the tumor stage. Conventional clinical tests based on digital rectal examination, Prostate-Specific Antigen (PSA) levels, and Gleason score still lack accuracy for stage prediction. We...
Preprint
Full-text available
MLH1 knock out mice represent a preclinical model that resembles features of the human counterpart. As these mice develop mismatch repair deficient (MMR-D) neoplasias in a sequential twin-peaked manner (first lymphomas, then gastrointestinal tumors) we aimed at identification of the underlying molecular mechanisms. Using whole-exome sequencing, we...
Article
Full-text available
Background The tumor suppressor protein phosphatase and tensin homolog (PTEN) is a key regulator of the PI3K/AKT pathway which is frequently altered in a variety of tumors including a subset of acute B-lymphoblastic leukemias (B-ALL). While PTEN mutations and deletions are rare in B-ALL, promoter hypermethylation and posttranslational modifications...
Preprint
Full-text available
To explore the molecular processes underlying some biological theme of interest based on public data, gene lists are used herein as input for the construction of annotated pathway maps, employing Cytoscape apps, and then high-throughput ("omics") gene expression data are overlaid onto these maps. Seeded with a published set of marker genes of the s...
Article
Full-text available
Endothelial progenitor cells (EPCs) are a group of rare cells that play an important role in the repair of injured vascular endothelial cells and assist in reperfusion of ischemic tissue. Decreased production and/or loss of function of EPCs are associated with diabetic vasculopathy. The molecular mechanisms by which diabetes impairs EPCs remain unc...
Data
Panels A and B. Visualization of all motifs that contain mir-709 and its interactions with central-hubs and other genes. (EPS)
Data
The complete list of detected TF-miRNA co-regulatory motifs. (DOC)
Data
The entire TF-miRNA network (D-EPC-GRN) constructed from the differentially expressed genes, their targets and regulators as well as the enriched miRNAs and their targets and regulators. Nodes in turquoise triangle denote TFs. The miRNAs are represented in orange square shapes. Grey circles represent the target genes. Larger nodes (forming the inne...
Data
The annotated functional terms and diseases in the identified miRNA list. (DOC)
Data
Principal Component Analysis (PCA) for all identified 80 genes in comparison 4 (non-diabetic and diabetic EPCs). Genes are clustered based on relative gene expression and are given a color-coded sphere. Green spheres are genes that are downregulated. Red spheres are genes that are up-regulated. (TIF)
Data
List of all differentially expressed genes. There were 80 genes specific to comparison 4 (non-diabetic EPC vs D-EPC) and they were all annotated in the Mouse WG-6 V2 beadchip. There were only 3 genes that are diabetes related. They are underlined and italic formatted. Genes with positive LFC Diff values are up regulated in D-EPC. (DOC)
Data
Predicted interactions between EPC specific functional DE-genes (Cxcr4, Nos3, Cxcl12) and genes in our D-EPC-GRN. (DOC)
Preprint
Full-text available
The molecular basis of aging and of aging-related diseases is being unraveled at an increas-ing pace. More recently, a long healthspan is seen as an important goal. However, a precise definition of health and healthspan is not straightforward, and the causal molecular basis of health "per se" is largely unknown. Here, we define health based on dise...
Article
Full-text available
The volume of molecular observations on human diseases in public databases is continuously increasing at accelerating rates. A bottleneck is their computational integration into a coherent description, from which researchers may derive new well-founded hypotheses. Also, the need to integrate data from different technologies (genetics, coding and re...
Article
Full-text available
Mismatch-repair deficiency (MMR-D) is closely linked to hypermutation and accordingly, high immunogenicity. Hence, MMR-D-related tumors constitute ideal vaccination targets both for therapeutic and prophylactic approaches. Herein, the prophylactic and therapeutic impact of a cellular vaccine on tumor growth and tumor-immune microenvironment was stu...
Article
Full-text available
Mutations in genomic key elements can influence gene expression and function in various ways, and hence greatly contribute to the phenotype. We developed MutaNET to score the impact of individual mutations on gene regulation and function of a given genome. MutaNET performs statistical analyses of mutations in different genomic regions. The tool als...
Article
The actin-binding protein profilin1 (PFN1) plays a central role in actin dynamics, which is essential for cytotoxic T lymphocyte (CTL) functions. The functional role of PFN1 in CTLs, however still remains elusive. Here, we identify PFN1 as the only member of the profilin family expressed in primary human CD8(+) T cells. Using in vitro assays, we fi...
Article
Full-text available
Natural killer (NK) cells play a central role during innate immune responses by eliminating pathogen-infected or tumorigenic cells. In the microenvironment, NK cells encounter not only target cells but also other cell types including non-target bystander cells. The impact of bystander cells on NK killing efficiency is, however, still elusive. In th...
Article
Full-text available
To identify genes contributing to disease phenotypes remains a challenge for bioinformatics. Static knowledge on biological networks is often combined with the dynamics observed in gene expression levels over disease development, to find markers for diagnostics and therapy, and also putative disease-modulatory drug targets and drugs. The basis of c...
Article
Full-text available
Maintenance of cell pluripotency, differentiation, and reprogramming are regulated by complex gene regulatory networks (GRNs) including monoallelically-expressed imprinted genes. Besides transcriptional control, epigenetic modifications and microRNAs contribute to cellular differentiation. As a model system for studying the capacity of cells to pre...
Data
Figure A. Venn diagram of the 3 gene sets involved in the analysis. Imprinted, pluripotent, and hematopoietic genes. Figure B. A sketch diagram showing the calculation of the similarity score between the two observation groups: 1- the similarity scores between imprinted genes and (pluripotent or hematopoietic) genes and 2- the similarity scores bet...
Article
Full-text available
Background Identifying the gene regulatory networks governing the workings and identity of cells is one of the main challenges in understanding processes such as cellular differentiation, reprogramming or cancerogenesis. One particular challenge is to identify the main drivers and master regulatory genes that control such cell fate transitions. In...
Article
Hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) infections are frequently caused by predominant clusters of closely related isolates that cannot be discriminated by conventional diagnostic typing methods. Whole genome sequencing (WGS) and DNA microarray (MA) now allow for better discrimination within a prevalent clonal comple...
Thesis
Full-text available
The biological functions of the molecular components (genes, proteins, miRNAs, siRNAs,..etc) of biological cells and mutations/perturbations thereof are tightly connected with cellular malfunctions and disease pathways. Moreover, these molecular elements interact with each other forming a complex interwoven regulatory machinery that governs, on one...
Article
Full-text available
Breast cancer is a genetically heterogeneous type of cancer that belongs to the most prevalent types with a high mortality rate. Treatment and prognosis of breast cancer would profit largely from a correct classification and identification of genetic key drivers and major determinants driving the tumorigenesis process. In the light of the availabil...
Article
Full-text available
TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. Since the inner workings of cells rely on the correct functioning of an enormously complex system of activating and repressing interact...
Conference Paper
Full-text available
Although next generation sequencing of diseased traits has unraveled thousands of DNA alterations, the functional relevance of most of these mutations and how they relate to other epigenetic mechanisms are still poorly understood. Here, we present SnvDMiR as a freely–available R pipeline that conducts combinatorial proximity analysis between diseas...
Article
Full-text available
Mebitoo is a bioinformatics tool to embrace computational analysis methods with a uniform graphical user interface. Moreover, the software enables persistent storage with an incorporated database engine, which supports XML files for customized data structures. The framework is based on the Netbeans Rich Client Platform (RCP) and can easily be exten...
Article
Full-text available
By analyzing the cellular functions of genetically imprinted genes as annotated in the Gene Ontology for human and mouse, we found that imprinted genes are often involved in developmental, transport and regulatory processes. In the human, paternally expressed genes are enriched in GO terms related to the development of organs and of anatomical stru...
Data
Enriched GO terms of biological functions for the paternally expressed genes in Human. The table lists the annotation terms, the number of associated genes per each GO term, the ratio of genes annotated with this term relative to the total number of paternally expressed genes, the p-value and the fold enrichment. (DOC)
Data
The most specific enriched GO terms of biological functions for the paternally expressed genes in human. The table lists the annotation terms, the number of the associated genes per each GO term, percentage of the involved genes to the study genes, the p-value, gene names and the fold enrichment. (DOC)
Data
Imprinted Gene list. The last column indicates whether the maternal (M) or paternal (P) allele is expressed. P/M means that the gene exhibits species or isoform-specific patterns of imprinting: human COPG2 and ZIM2 were reported to be paternally expressed, whereas these genes are maternally expressed in the mouse. GRB10 encodes maternally, and pate...
Data
Enriched GO terms of biological functions for the full set of imprinted genes in human. The table lists the annotation terms, the number of associated genes per each GO term, the ratio of genes annotated with this term relative to the total number of imprinted genes, the p-value and the fold enrichment. (DOC)
Data
Enriched GO terms of biological functions for the full set of imprinted genes in mouse. The table lists the annotation terms, the number of associated genes per each GO term, the ratio of genes annotated with this term relative to the total number of imprinted genes, the p-value and the fold enrichment. (DOC)
Data
Enriched GO terms of biological functions for the maternally expressed genes in human and mouse. The table lists the annotation terms, the number of associated genes per each GO term, the ratio of genes annotated with this term relative to the total number of maternally expressed genes, the p-value and the fold enrichment. (DOC)
Data
The enriched Transcription factor target (TFT) families for the full set of imprinted genes in human according to the MSigDB database at significance level 0.01. M and P are the numbers of associated maternally and paternally expressed genes respectively. (DOC)
Data
The enriched Transcription factor target (TFT) families for the full set of imprinted genes in mouse according to the MSigDB database at significance level 0.01. M and P are the numbers of associated maternally and paternally expressed genes respectively. (DOC)
Data
Heat map for the enriched transcription factor targets in the full set of imprinted genes in human (a) and mouse (b) at p-value of 0.01. Marked in red and blue in the top line are the maternally and paternally expressed genes, respectively. (TIFF)