Ahmed Mansour Alzohairy

Ahmed Mansour Alzohairy
Zagazig University · Department of Genetics

BSc, MSc, Ph.D

About

360
Publications
711,715
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1,283
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Introduction
Published many books and research articles in the field of plant biotechnology, genomics and Bioinformatics. I have been invited and participated in many international scientific meetings and conferences in molecular genetics and bioinformatics around the world. I have participated and organized many training courses in molecular genetics and bioinformatics. I am currently an assistant Professor of Genetics and the director of the Egyptian center of Bioinformatics And Genomics (ECBAG),
Additional affiliations
December 2010 - present
Zagazig University
Position
  • Professor (Assistant)
Description
  • 50% teaching + 50% research
Education
September 2000 - September 2005
Zagazig University
Field of study
  • Plant Signal transduction
September 1997 - September 2000
Faculty of agriculture, Zagazig University
Field of study
  • Molecular Genetics
September 1992 - July 1996
Zagazig University
Field of study
  • Genetics and Agricultural Genetic engineering

Publications

Publications (360)
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Choosing a color scheme is really a matter of taste; most multiple sequence- alignment specialists can spend hours explaining to you why they prefer a special color scheme to every other alternative in the galaxy.
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Jalview has two navigation and editing modes: 1- Normal mode, where editing and navigation is performed using the mouse. 2- Cursor mode where editing and navigation are performed using the keyboard. The F2 key is used to switch between these two modes
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The PSIPRED Protein Structure Analysis Workbench aggregates several UCL structure prediction methods into one location, allowing users to run a number of analyses simultaneously. You can view the input form at the main web page for the PSIPRED Server.
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Jalview provides many ways to load - your own sequences.
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Lec2 Loading your own sequence 2022 Jalview provides many ways to load - your own sequences. - Drag and Drop - From a File - From a URL - Cut and Paste - From a public database
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In the present study, the chemical composition and total phenolic (TPC) and total flavonoid contents (TFC) of eight soybean cultivars (Giza 21, Giza 22, Giza 35, Giza 111, Giza 82, Giza 83, Crawford, and Holliday) were estimated. Moreover, antioxidant activity and in vitro cytotoxic activities against HepG-2 and MCF-7 were evaluated. Giza 21, Giza...
Article
One of the most often used techniques to represent color images is quaternion algebra. This study introduces the quaternion Krawtchouk moments, QKrMs, as a new set of moments to represent color images. Krawtchouk moments (KrMs) represent one type of discrete moments. QKrMs use traditional Krawtchouk moments of each color channel to describe color i...
Preprint
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Cadmium (Cd) is a nonessential and extremely toxic element that destructively impacts agricultural production. Accordingly, developing tolerant-Cd as well as low-grain Cd genotypes is considered a promising approach to cope with the pollution problem. The current study aimed at understanding inheritance nature of Cd tolerance and detect Cd-tolerant...
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The spread of fungal growth causes enormous economic, agricultural, and health problems for humans, such as Aspergillus sp., which produce aflatoxins. Thus, the inhibition of aflatoxin production became a precious target. In this research, the thioesterase (TE) domain from Polyketide synthase enzyme was selected to employ the in silico docking, usi...
Research
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2020): Inhibition analysis of aflatoxin by insilico targeting the thioesterase domain of polyketide synthase enzyme in Aspergillus ssp, Journal of Biomolecular Structure and Dynamics, ABSTRACT The spread of fungal growth causes enormous economic, agricultural, and health problems for humans, such as Aspergillus sp., which produce aflatoxins. Thus,...
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Aflatoxins are toxic and carcinogenic components produced by some Aspergillus species such as Aspergillus flavus. Polyketide synthases enzyme (PKS) plays a central role in aflatoxin‘s biosynthesis of in Aspergillus flavus, especially the product template (PT) domain, which controls the aldol cyclization of the polyketide forerunner during the biosy...
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Biomedical color (BMC) images are being used on a wide scale by physicians, where their diagnosis would be more accurate. Hence, it is recommended to develop new approaches that are able to represent and retrieve the BMC images efficiently. This work proposes two methods to represent BMC images: Quaternion Associated Laguerre. Moments (Q ALMs), and...
Article
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The ability of any retrieval system to extract features by using its feature descriptor is the primary criterion to measure its efficiency. In this paper a novel technique for feature extraction of biomedical images is presented. The mooted system uses the Radial Associated Laguerre Moments (RALMs) as a feature descriptor to obtain features from tw...
Article
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This paper presents a novel software called EGBioImage that is implemented for analyzing gel Electrophoresis images, computing the molecular weights of the bands of the unknown size, detecting the types of the bands, grouping the bands according to their molecular weights and labeled each band with its group number in the gel image and generating t...
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One of the most severe sources of information for a molecular biologist is the gel image generated by using gel electrophoresis during the experiment of issr-pcr, sds-pages, and rapd-pcr. DNA and protein gel images are obtained through the gel electrophoresis separations techniques of DNA and protein fragments. The separation of the polymorphic ban...
Preprint
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Cell differentiation processes of stem cells have unique pathways controlled by certain genes including EYA1 (Eyes Absent), SIX1 (Sine oculis homeobox), and SOX9 (Sry-related high mobility group BOX). It was reported that these genes act as transcriptional factors (TFs) for the repair and regeneration of the progenitor cells as well as of damaged t...
Research
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The purpose of this study is estimating the demand analysis for red meat, poultry and fish by using one of dynamic models which called distributed lag models. Nerlove model is one of these models. As a way to answer the question "Is actual consumption quantity equal to the equilibrium demand or is it different from either increase or decrease?" Thi...
Article
The sine cosine algorithm (SCA), a recently proposed population-based optimization algorithm, is based on the use of sine and cosine trigonometric functions as operators to update the movements of the search agents. To optimize performance, different parameters on the SCA must be appropriately tuned. Setting such parameters is challenging because t...
Chapter
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Pairwise global sequence alignment is a vital process for finding functional and evolutionary similarity between biological sequences. The main usage of it is searching biological databases for finding the origin of unknown sequence. The standard global alignment based on dynamic programming approach which produces the accurate alignment but with e...
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•Ident and Sim accepts a group of aligned sequences (in FASTA or GDE format) and calculates the identity and similarity of each sequence pair. •Identity and similarity values are often used to assess whether or not two sequences share a common ancestor or function.
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GenBank to FASTA accepts a GenBank file as input and returns the entire DNA sequence in FASTA format. Use this program when you wish to quickly remove all of the non-DNA sequence information from a GenBank file.
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Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), th...
Data
Detailed description of the different modules provided in the IBT_2016 course, including learning objectives and learning outcomes. (PDF)
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بعض الأفكار الوارده و الأقوال المأثوره التي تدعو للتأمل والتفكر في ما يدور حولنا من أحداث في الحياه أ.د/أحمد منصور الزهيرى قسم الوراثة- كلية الزراعة- جامعة الزقازيق
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1- Understanding Why multiple sequence alignment is useful for scientists 2-Identifying situations where multiple alignments do not help 3-Main Criteria for Building a Multiple Sequence Alignment 4- Main Applications of Multiple Sequence Alignments 5-What are the kinds of sequences you’re looking for? 6- Tips for Naming sequences 7- Tips for diffic...
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“Before you build your alignment, you must carefully select the sequences you want to align. These sequences are members of the same protein family, and they all share a common ancestor. The family is usually too large to be entirely included in your multiple alignment, and picking the right sequences is an art.”
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The interpretation of a multiple alignment depends very much on its appearance. Some tools on the Net can help you make sense of your multiple alignments by extracting blocks or singling out special positions.
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Preparing Your Multiple Alignment for Publication - You want to show this alignment to your colleagues, you want to include it in publications - In short, you need a high-impact picture to convince people that your research is going well.
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Logos are a terrific way to generate highimpact pictures from MSA - logo Figure is a representation of the alignment. - Notice how the conserved amino acids (e.g cysteines) stick out, indicating regions of potential biological importance.
Article
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Background: Sequence Alignment is a main task in a lot of bioinformatics applications and it is used for aligning residues/nucleotides (for protein/DNA) to measure the similarity between two biological sequences and locates the regions of matching. The alignment operation consumes huge execution time especially for long sequences and so paralleliza...
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- COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information. - Clustal Omega - Aligning sequences and structures with Tcoffee More accurate alignments at the cost of a slightly longer running time - Crunching large datasets with MUSCLE
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أدعية رمضان 2017
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Learning objectives Learning about signaling complexes of cell signaling : - Intracellular signaling positive feedback. - Intracellular signaling negative feedback. - General components of the feedback loop. - The role of each components in diseases in different diseases.
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By the end of this session and practical, students are expected to be able to understand: •- The role of Cyclic AMP in signaling •Some G Proteins Regulate the Production of Cyclic AMP • The synthesis and degradation of cyclic AMP. • An increase in cyclic AMP in response to an extracellular signal.
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By the end of this session and practical, students are expected to be able to understand: - The Relationship Between Signal and Response Varies in Different Signaling Pathways - The Speed of a Response Depends on the Turnover of Signaling Molecules
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In this lecture you will: Learning objectives Learning about signaling complexes of cell signaling : - signaling pathways . - intracellular signaling. - Three types of intracellular signaling complexes - MAP kinases (MAPK) Normal Vs Tumor - insulin receptor (a receptor tyrosine kinase)
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Learning about activation of Environmental stresses Activation of cell signaling : - PRINCIPLES OF CELL SIGNALING. - Universality of Cell signaling. - Quorum sensing in Bacteria. - Communication between eukaryotic cells - SIGNALING THROUGH G-PROTEIN-COUPLED RECEPTORS - SIGNALING THROUGH ENZYMECOUPLED RECEPTORS ALTERNATIVE SIGNALING - ROUTES IN GENE...
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Learning objectives Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate . How are signals transmitted between cells . How are signals transmitted across cell membranes into cell interior . How are signals transmitted within a cell . How do signals affect a cell function . Signal transduction ....
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Learning objectives Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate How are signals transmitted between cells How are signals transmitted across cell membranes into cell interior How are signals transmitted within a cell How do signals affect a cell function Signal transduction Ion...
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Learning objectives Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate . How are signals transmitted between cells . How are signals transmitted across cell membranes into cell interior . How are signals transmitted within a cell . How do signals affect a cell function . Signal transduction ....
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Learning objectives Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate . How are signals transmitted between cells . How are signals transmitted across cell membranes into cell interior . How are signals transmitted within a cell . How do signals affect a cell function . Signal transduction ....
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Learning about more details about DNA transposons and Retrotransposons: - The Transposition mechanisms of DNA transposons and Retrotransposons. - Bacterial Insertion Sequences. - General process of transposition for DNA transposons. - Model for reverse transcription
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Learning objectives Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate . How are signals transmitted between cells . How are signals transmitted across cell membranes into cell interior . How are signals transmitted within a cell . How do signals affect a cell function . Signal transduction ....
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Learning objectives Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate How are signals transmitted between cells How are signals transmitted across cell membranes into cell interior How are signals transmitted within a cell How do signals affect a cell function Signal transduction Ion...
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Learning objectives Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate . How are signals transmitted between cells . How are signals transmitted across cell membranes into cell interior . How are signals transmitted within a cell . How do signals affect a cell function . Signal transduction ....
Presentation
Learning objectives Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate . How are signals transmitted between cells . How are signals transmitted across cell membranes into cell interior . How are signals transmitted within a cell . How do signals affect a cell function . Signal transduction ....
Presentation
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Learning objectives - Learning about activation of Environmental stresses Activation of cell signaling : Why do cells communicate How are signals transmitted between cells How are signals transmitted across cell membranes into cell interior How are signals transmitted within a cell How do signals affect a cell function Signal transduction Ion chann...
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Learning outcomes By the end of this session and practical, students are expected to be able to understand what are: - Biotic and abiotic activation of LTR RTs - Examples of reactivation of LTR RTs - Regulation for excess production of Gag - The RTs’ response depends on the host genomes - Retrotransposon insertions lead to changes in expression of...
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Learning outcomes By the end of this session and practical, students are expected to be able to understand what are: •Phospholipase C (PLC) activity increases rapidly in response to heat stress •Heat-shock-induced activation of HAMK is mediated through PLC •DAG kinase and its product PA play an essential role in the heat-dependent activation of HAM...
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Learning outcomes By the end of this session and practical, students are expected to be able to understand what are: •De novo protein synthesis in response to heat shock •Time course study of HSFs •Membrane fluidity and cytoskeleton remodeling activate of HSF1 •MEK inhibitors inhibit the accumulation of pHSF1 and pHSF2 •In silico prediction of poss...
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- In mammals, HSP27 is associated with the cytoskeleton (Tessier et al. 2003) and plays a role in its stabilization (Lavoie et al., 1995). Mammalian HSP27 is also phosphorylated by MAPK-activated protein kinase2 (MAPKAPK2) (Concannon, C.G, et al., 2003). - In previous investigation we demonstrated that mammalian HSP27 homologue exists in tobacco ce...
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Cell Signalling 2017: Lec1 Cell signaling Molecules Most of the following lectures slides was extracted from the following link. http://www.slideshare.net/musselburghgrammar/cell-signalling All copyright reserved to the original producer of this animation
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Genetic divergence of any essential crop helps to increase the recognition of its breeding programs to improve the harvest and quality of the product as well. Moringa which is the sole genus of family Moringaceae is, recently, considered as a high nutritionally and medicinally important crop allover the tropical regions. In the present study, morph...
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Disclaimer This presentations is based on YouTube video. All copyright reserved to the original producer of this animation
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Retrieving a list of related protein sequences Many questions in molecular biology (your dissertation topic, your own research, or your personal interests) require downloading a large collection of similar protein sequences, all related to the same function, rather than just one sequence. These biological questions typically include 1- The detectio...
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The primary structure is the amino acid sequence of your protein. When you analyze the primary structure, you ignore the potential interactions between amino acids. You conduct a primary structure analysis to try to find segments in your protein that display a special composition with interesting properties such as - Hydrophobic regions that could...
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• Protease digestions (where you use an enzyme to cut your protein in specific ways • This can be useful if you’re only interested in carrying out experiments on a portion of your protein.
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1. Knowing what you must about domains, HMMs, profiles, and the Pfam domain collection. 2. Visiting the three most popular sites for finding domains in your protein. 3. Predicting simple physical properties of your sequences. 4. Predicting protease digestion patterns. 5. Predicting coiled-coil domains. 6. Predicting post-translational modification
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• TMHMM is maintained by the Center for Biological Sequence Analysis (CBS) at the Technical University of Denmark. • The CBS (www.cbs.dtu.dk/services/) offers many interesting services for sequence analysis that we encourage you to explore TMHMM is a state-of-the-art method that uses sophisticated mathematical models (Hidden Markov Models) to predi...
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Predicting that your protein has transmembrane segments tells you much more about its function than almost any other simple prediction you can do.If you find one transmembrane segment at the Nterminus of your sequence, you can predict that the protein is secreted. On the other hand, many transmembrane domains in one protein may indicate a channel.T...
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Coiled-coil regions are portions of a protein formed by the intertwining of two or three alpha-helices. One reason it’s considered interesting to find coiled-coil regions is that they’re often involved in protein-protein interactions. Another (less glorious) reason is that these coiledcoil regions can give false matches when you do a database searc...
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Proteins often need to be modified before they become active in the cell. Biologists call such operations posttranslational modifications because they occur after the translation (synthesis) of the protein. These modifications may involve adding sugars, modifying amino acids, or removing pieces of the newly synthesized protein. If you’re studying a...
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Use this tool to guide your reaction buffer selection when setting up double digests, a common timesaving procedure. Choosing the right buffers will help you to avoid star activity and loss of product. Learn more information about double digests, including how to set up a reaction.
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•Translate accepts a DNA sequence and converts it into a protein in the reading frame you specify. •Translate supports the entire IUPAC alphabet and several genetic codes.
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-ReverseTranslateacceptsaproteinsequenceasinputandusesacodonusagetabletogenerateaDNAsequencerepresentingthemostlikelynon-degeneratecodingsequence. -consensussequencederivedfromallthepossiblecodonsforeachaminoacidisalsoreturned. -UseReverseTranslatewhendesigningPCRprimerstoannealtoanunsequencedcodingsequencefromarelatedspecies
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•EMBOSSWaterusestheSmithWatermanalgorithm(modifiedforspeedenhancements)tocalculatethelocalalignmentoftwosequences. - LALIGNfindsinternalduplicationsbycalculatingnon-intersectinglocalalignmentsofproteinornucleotidesequences.
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•CodonPlotacceptsaDNAsequenceandgeneratesagraphicalplotconsistingofahorizontalbarforeachcodon.Thelengthofthebarisproportionaltothefrequencyofthecodoninthecodonfrequencytableyouenter. •UseCodonPlottofindportionsofDNAsequencethatmaybepoorlyexpressed,ortoviewagraphicrepresentationofacodonusagetable(byusingaDNAsequenceconsistingofoneofeachcodontype).
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DNA Molecular Weight •DNA Molecular Weight accepts one or more DNA sequences and calculates molecular weight. •Sequences can be treated as double-stranded or single-stranded, and as linear or circular. •Single-stranded sequences are assumed to have a 5’ phosphate. Use DNA Molecular Weight when calculating molecule copy number.
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•CpGIslandsreportspotentialCpGislandregionsusingthemethoddescribedbyGardiner-GardenandFrommer(1987).Thecalculationisperformedusinga200bpwindowmovingacrossthesequenceat1bpintervals. •CpGislandsaredefinedassequencerangeswheretheObs/Expvalueisgreaterthan0.6andtheGCcontentisgreaterthan50%. •TheexpectednumberofCpGdimersinawindowiscalculatedasthenumberof...
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The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing. You can easily mirror the Sequence Manipulation Suite on your own web site, or you can use it off-line. Th...
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-EMBL Feature Extractor accepts an EMBL file as input and reads the sequence feature information described in the feature table. -The program extracts or highlights the relevant sequence segments and returns each sequence feature in FASTA format. -EMBL Feature Extractor is particularly helpful when you wish to derive the sequence of a cDNA from a g...
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- GenBank Feature Extractor accepts a GenBank file as input and reads the sequence feature information described in the feature table, according to the rules outlined in the GenBank release notes. The program extracts or highlights the relevant sequence segments and returns each sequence feature in FASTA format. - GenBank Feature Extractor is parti...
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- GenBank Feature Extractor accepts a GenBank file as input and reads the sequence feature information described in the feature table, according to the rules outlined in the GenBank release notes. The program extracts or highlights the relevant sequence segments and returns each sequence feature in FASTA format. - GenBank Feature Extractor is parti...
Article
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Methanolic extracts of leaves and seeds of three Moringa species namely, Moringa oleifera, Moringa peregrina and Moringa stenopetala (grown in Orman Botanical Garden, Giza, Egypt) were evaluated for their antimicrobial activity against 19 human pathogens (8 Gram-ve, 6 Gram+ve bacteria and 5 fungi) using agar-well diffusion assay. Amphotericin B, Am...