Mohamed Helmy

Mohamed Helmy
BenchSci.com · Science cluster

M.Sc and Ph.D in Systems Biology

About

56
Publications
25,696
Reads
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2,237
Citations
Additional affiliations
September 2017 - present
BenchSci
Position
  • Bioinformatician
September 2013 - August 2017
University of Toronto
Position
  • PostDoc Position
April 2013 - August 2013
Al-Azhar University
Position
  • Visiting Faculty Member

Publications

Publications (56)
Article
Background World population growth, climate change, food distribution and the current pandemic are some of the main factors that affect food security. Traditional farming techniques, although a vital lifeline for our survival, are increasingly generating large amounts of harmful greenhouse emissions as the global population expands significantly. I...
Article
Full-text available
The majority of human genome are non-coding genes. Recent research have revealed that about half of these genome sequences make up of transposable elements (TEs). A branch of these belong to the endogenous retroviruses (ERVs), which are germline viral infection that occurred over millions of years ago. They are generally harmless as evolutionary mu...
Article
Full-text available
The study of gene expression variability, especially for cancer and cell differentiation studies, has become important. Here, we investigate transcriptome-wide scatter of 23 cell types and conditions across different levels of biological-complexity. We focused on genes that act like toggle-switches between pairwise replicates of the same cell type,...
Article
Full-text available
Gene expression profiling techniques, such as DNA microarray and RNA-Sequencing, have provided significant impact on our understanding of biological systems. They contribute to almost all aspects of biomedical research, including studying developmental biology, host-parasite relationships, disease progression and drug effects. However, the high-thr...
Article
Full-text available
Background : Vaccine hesitancy can limit the benefits of available vaccines in halting the spread of COVID-19 pandemic. Previously published studies paid little attention to Arab countries, which has a population of over 440 million. In this study, we present the results of the first large-scale multinational study that measures vaccine hesitancy a...
Preprint
Full-text available
In this study, we present the results of the first large-scale multinational study (36,220 participants) that measures vaccine hesitancy among Arab-speaking subjects. Our analysis shows a significant rate of vaccine hesitancy among Arabs in and outside the Arab region (83% and 81%, respectively). The most cited reasons for hesitancy are concerns ab...
Article
Full-text available
Many proteins involved in signal transduction contain peptide recognition modules (PRMs) that recognize short linear motifs (SLiMs) within their interaction partners. Here, we used large-scale peptide-phage display methods to derive optimal ligands for 163 unique PRMs representing 79 distinct structural families. We combined the new data with previ...
Article
Full-text available
Metabolic engineering aims to maximize the production of bio-economically important substances (compounds, enzymes, or other proteins) through the optimization of the genetics, cellular processes and growth conditions of microorganisms. This requires detailed understanding of underlying metabolic pathways involved in the production of the targeted...
Article
Full-text available
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG...
Article
Full-text available
Palynological investigation relays on morphology and seed coat characters. It's a well-known approach to be used in discrimination between related plants. While the DNS barcoding used specific regions in the plant genome to identify the plant species/sub-species. Here, we compared pollen grain taxonomy and DNA barcoding taxonomy of 12 taxa belongin...
Research
Full-text available
Palynological investigation relays on morphology and seed coat characters. It's a well-known approach to be used in discrimination between related plants. While the DNS barcoding used specific regions in the plant genome to identify the plant species/sub-species. Here, we compared pollen grain taxonomy and DNA barcoding taxonomy of 12 taxa belongin...
Chapter
Full-text available
Plants are significantly subject of diverse environmental stresses. Abiotic stresses are mainly due to nonliving environmental factors such as drought, heat, cold, and salinity, whereas biotic stresses are mainly caused by other living organisms in the surrounding environment such as bacteria, fungi, viruses, nematodes, and insects. A long series o...
Poster
DNA barcoding was proposed to facilitate systematic species identification, biodiversity monitoring, and conservation. Un-like animals, the application of DNA barcoding is more complicated in plants because of the larger number of regions that need to be sequenced, compared to the single mitochondrial COX gene used in animals. After identifying the...
Article
The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated and sequenced 15 rbcL and six mat...
Chapter
Plant stress is a state where the plant is growing in non-ideal growth conditions that increase the demands made upon it. The effects of stress can lead to deficiencies in growth, crop yields, permanent damage or death if the stress exceeds the plant tolerance limits. Plant stress factors are mainly categorized into two main groups; abiotic factors...
Chapter
Recently, multiple “omics” sciences such as genomics, transcriptomics, proteomics, and bioinformatics have been introduced. These sciences can be applied and effectively used in the area of biotic stresses, particularly microbial pathogeny studies. In this chapter, we provide deeper insight and discussion on the important applications of the divers...
Chapter
Recent development in omics technologies such as genomics, proteomics, transcriptomics, metabolomics as well as functional genomics has helped the identification and functional characterization of a large number of gene families and mechanisms associated with abiotic stress tolerance in plants. In this chapter, we will mainly discuss gene expressio...
Chapter
The continuous development of analytical and experimental technologies as well as instruments resulted in the development of very specialized experimental approaches that can identify, measure and quantify particular types of cellular molecules. These technologies are known as “Omics Technologies”. Most of the omics technologies are high throughput...
Article
Reversible protein-tyrosine phosphorylation is catalyzed by the antagonistic actions of protein-tyrosine kinases (PTKs) and phosphatases (PTPs), and represents a major form of cell regulation. Acute myeloid leukemia (AML) is an aggressive hematological malignancy that results from the acquisition of multiple genetic alterations, which in some insta...
Book
Providing a comprehensive overview of cutting-edge research on Omics applications in plant sciences field,“Plant Stress Tolerance” focuses on different approaches towards plant stress tolerance including both biotic stresses and abiotic stresses. This book outlines the challenges facing this area of research, with solid, up-to-date information for...
Article
Full-text available
Global mechanization, urbanization and various natural processes have led to the increased release of toxic compounds into the biosphere. These hazardous toxic pollutants include a variety of organic and inorganic compounds, which pose a serious threat to the ecosystem. The contamination of soil and water are the major environmental concerns in the...
Article
Full-text available
The differences between countries in national income, growth, human development and many other factors are used to classify countries into developed and developing countries. There are several classifications systems that use different sets of measures and criteria. The most common classifications are the United Nations (UN) and the World Bank (WB)...
Conference Paper
DNA Barcoding is widely used for biodiversity studies based on standard DNA regions. While many loci have been proposed as a DNA barcodes in plants, standardizing regions as a DNA barcode poses a challenge in many plant families. The Egyptian flora is rich with a huge number of Poaceae plants differs on their morphological characteristics in advanc...
Article
Full-text available
Sequencing and restriction analysis of genes like 16S rRNA and HSP60 are intensively used for molecular identification in the microbial communities. With aid of the rapid progress in bioinformatics, genome sequencing became the method of choice for bacterial identification. However, the genome sequencing technology is still out of reach in the deve...
Data
The supplementary materials include seven supplementary figures and 12 supplementary tables. Supplementary figure 1 is an illustration of expected restriction results of two Lactobacillus strains. Supplementary figures 2 and 3 are the Identification schemes of Lactobacillus using fragments numbers or fragments numbers and fragments size of HSP60 ge...
Book
As part of the SpringerBriefs series, this book presents a brief overview of the history, development, methods, applications, and challenges of NGS, and is divided into three parts. Part I provides an introduction to the basics of molecular biology, algorithms, and data structures required to assist readers in understanding the more technical porti...
Chapter
There are several assemblers employed in next-generation environment. These may be classified according to their respective graph construction approaches (see Chap. 9) or their targeted data sets. In this chapter, we will present select examples of next-generation sequence assemblers and discuss their implementation approaches. The assemblers we di...
Chapter
In the previous chapters, we described the most common and well-established next-generation sequencing technologies and platforms. However, several methodologies and sequencers with outstanding features have also been released in the last few years. Furthermore, additional technologies demonstrating great promise are currently in development. In th...
Chapter
This chapter provides an overview of prevalent data structures and algorithms that are commonly utilized in bioinformatics. In particular, we place emphasis on data structures and algorithms that are employed in bioinformatic techniques during next-generation sequence assembly.
Chapter
The next-generation sequencing field has developed at such a rapid pace that the achievements of today exceed the challenges and limitations of the last few years. We have previously described how next-generation sequencing has advanced DNA sequencing from low throughput to high throughput and minimized labor-intensive practices to more automated p...
Chapter
The next-generation sequencing methods that we described in Chap. 3 were implemented into several commercial instruments in order to make the sequencing technologies available to individual laboratories. In this chapter, we will overview the major DNA sequencing platforms and present several comparisons for their advantages, disadvantages, sequenci...
Chapter
Organisms can be divided into simple (or unicellular) organisms and complex (or multicellular) organisms. Both simple and complex organisms share major cellular and biological processes that are mediated through proteins and nucleic acids. Proteins are the molecules responsible for every structural or biological process achieved inside living cells...
Chapter
Full-text available
Next-generation sequencing technologies have pushed the envelope beyond the primary goal of identifying the sequence of nucleotides within a given DNA molecule to a whole new multitude of applications. In this chapter, we describe select novel applications of next-generation sequencing in relation to large-scale sequencing-based projects, cell and...
Chapter
Next-generation sequence assembly can be viewed as a five-stage process of data processing and computational challenges. These stages are error correction, graph construction, graph simplification, scaffolding, and the assembly assessment stage. These stages communicate with each other to produce the final assembled sequences. Each stage receives a...
Chapter
The process of sequence assembly in the next-generation environment is broken down into five stages. We introduced all these stages in Chap. 8. Here, we will discuss four of these stages in detail and present the different approaches followed in each of them. Additionally, we will debate the challenges that face each stage and their stage-specific...
Chapter
Although there are different measures to evaluate assembler performance and assembly quality, developing assessment tools that incorporate present measures and defining new ones for the various assembly types (genomic, transcriptomic, and metagenomic) still remain a major challenge in the next-generation environment. In this chapter, we will introd...
Chapter
Ever since the double helix structure of DNA was first described by James Watson and Francis Crick, decoding the sequence of DNA nucleotides has been a primary focus for biologists. Therefore, methodology for DNA sequencing has undergone rapid development, particularly since the 1970s. In this chapter, we will provide an overview of the majority of...
Article
Full-text available
Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research. Despite the many advantages of next-generation sequencers, e.g., the high-throughput sequencing rate and relatively low cost of sequencing, the assembly of the reads produced by these sequencers still remains a major challenge. In this review, we add...
Article
We have developed a novel bioinformatics method called mass spectrum sequential subtraction (MSSS) to search large peptide spectra datasets produced by liquid chromatography/mass spectrometry (LC-MS/MS) against protein and large-sized nucleotide sequence databases. The main principle in MSSS is to search the peptide spectra set against the protein...
Article
Full-text available
Our recently developed rice proteogenomics database (OryzaPG-DB) is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid chromatography-tandem mass spectrometry (LC-MS/MS), and mapping of the peptides to their genomic origins...
Data
Supplementary Materials and Methods. Details of materials and experimental procedures used to produce the utilized dataset.
Article
Full-text available
Proteogenomics aims to utilize experimental proteome information for refinement of genome annotation. Since mass spectrometry-based shotgun proteomics approaches provide large-scale peptide sequencing data with high throughput, a data repository for shotgun proteogenomics would represent a valuable source of gene expression evidence at the translat...
Article
Full-text available
The Toll-like receptor (TLR) 3 plays a critical role in mammalian innate immune response against viral attacks by recognizing double-stranded RNA (dsRNA) or its synthetic analog polyinosinic-polycytidylic acid (poly (IratioC)). This leads to the activation of MAP kinases and NF-kappaB which results in the induction of type I interferons and proinfl...
Data
In silico TLR4 model reactions and parameter values. (0.13 MB DOC)
Data
In silico simulation of NF-κB and MAP kinase activation. (A) p38, (B) ERK, (C) JNK and (D) NF-κB. Blue solid lines indicate wildtype (WT) and red dotted lines indicate MyD88 KO conditions. The x-axis represents simulation time in minutes and the y-axis represents relative activity, with the maximum value normalized to 1. (2.17 MB TIF)
Data
Enhanced TRAM-dependent pathway in the absence of TRAF6. (A) Ifit1 and (B) Ifit2 transcripts in wildtype (Traf6+/+) and Traf6−/− macrophages unstimulated (filled bar) or LPS (gray bar) for 60 min were analyzed by qRT-PCR and normalized to Gapdh. The values represent the average of six independent cultures and are shown as means±SEM. (1.73 MB TIF)
Data
In silico simulation of AP-1 and NF-κB activation. (A) NF-κB, (B) JNK. Blue solid lines indicate wildtype (WT) and green dotted lines indicate MyD88 overexpressed twice WT levels. The x-axis represents simulation time in minutes and the y-axis represents relative activity, with the maximum value normalized to 1. (1.92 MB TIF)
Article
Full-text available
Various receptors on cell surface recognize specific extracellular molecules and trigger signal transduction altering gene expression in the nucleus. Gain or loss-of-function mutations of one molecule have shown to affect alternative signaling pathways with a poorly understood mechanism. In Toll-like receptor (TLR) 4 signaling, which branches into...
Conference Paper
Full-text available
We constructed dynamic in silico Toll-like receptor (TLR) 4 models constituting the Myeloid Differentiation factor 88 (MyD88)-dependent and –independent pathways and investigated the experimental induction of MyD88-dependent pathway genes Tnf, Il1, Cxcl1 and the MyD88-independent pathway genes Ccl5, Cxcl10, Ifit1 in wildtype and several knock-out...

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