Mohammed Ahmed Hassan

Current position:

I am a bioinformatician who holds a PhD in bioinformatics along with a background in molecular genetics, a BSc, and a MD. I am currently working on some projects with Professor Abd El-Nasser Khattab at National Research Center - Egypt, Director of the Biotechnology Research Institute's Genetics and Cytology Department.

Research Interesting and experience:

I am so interested in applying eDNA plus bioinformatics to the ecology in general but I am so fascinated to utilize the bioinformatics methods and computational tools to microbial communities in marine.

In my current position, I am a researcher and bioinformatician (minor specialist metagenome and genome big data analysis) who holds a PhD in genetic engineering and bioinformatics in combination with a background in molecular genetics, a BSc and a MD, working with Professor Abd El-Nasser Khattab at the National Research Center - Egypt on some projects related to marine microbiology, Professor Abd El-Nasser Khattab is the Director of the Genetics & Cytology Department at the Biotechnology Research Institute.

I am so fascinated by the bioluminescent field and two years ago I decided to apply for a master degree of biological engineering at Siberian Federal University under the supervision of Prof. Dr. Valentina A. Kratasyuk, Professor, Head, Department of Biophysics, Siberian Federal University but for some personal issues I returned again.

I am preparing a bioluminescence unit to detect the low level of heavy metal in the environment and effect of nanoparticles on the environment and making biomeasure for the glow that emitted via the bioluminescent bacteria using the Glow-Max system of Promega - USA.

After returning to Egypt I triggered myself by searching for a new host in our Egyptian environment on the Red Sea Coast. I brought some squid individuals and with a cooperation with Dr. Nasser we succeeded in isolating strains from two regions of the squid (Ink sack and Eye).

Then we made a pure single colony from the plates and we sent a liquid culture to a genomic service lab to have the WGS of the bioluminescent strain utilizing Nanopore sequencing. I used my bioinformatics experience to assemble and polishing the genome then annotate the genome but through the Bandage tool I detected two circular genomes (First node = 4,992,825 bp and Second node = 3,256,386 bp).

1. Shewanella 2024
https://www.ncbi.nlm.nih.gov/nuccore/AP031461
2. Psychrobacter 2024
https://www.ncbi.nlm.nih.gov/nuccore/AP031495.1

I have strong experience in generating command lines to build a metabarcoding pipeline analysis (Bashes) using different tools and linux command lines (Usearch - Vsearch - Classification tool kraken - Assigning taxonomy - abundance analysis using DADA2 whole pipeline and QIIME 2 whole pipeline, whether long reads or short reads).

Solid experience in bacterial genome assembly and annotation (short - long, reads), comparative genome , finding similar genome, phylogenomic tree and synteny gene detection.

I am so interested in analyzing the mtDNA and cpDNA of plants and finding the genetic markers inside the whole genome of plant organelle in PhD I programmed a tool named RFRE tool-(https://sourceforge.net/projects/rfret/) to find the LTR markers and SSR markers in the date palm trees in our desert utilizing the regular expression language.

The tool is programmed by visual basic language and regular expression language.

I have a solid experience in data processing for the DNA barcoding genes and annotation of the processed data to submit the information to BOLD database or to DDBJ or NCBI.

I have experience in analyzing the DNA barcoding genes of desert plant (Egyptian olive cultivars)and building phylogenetic tree by using different tree construction algorithms.

International advanced training course in Bioinformatics:
Genomic prediction and selection in plant breeding, international centre for advanced mediterranean agronomic studies, Mediterranean agronomic institute of Zaragoza, Spain 40 hrs,16-28 January 2016.

Applications of bioinformatics in plant breeding, international centre for advanced Mediterranean agronomic studies, Mediterranean agronomic institute of Zaragoza, Spain 36 hrs, 18-22 January 2014.

My goal is to grow my publication portfolio and advance my career in bioinformatics applications to ecology.

• 2012, 2018, PhD, Bioinformatics, Databases, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Egypt
• 2006, 2011, MSc, Genetics, Agriculture College, Cairo University, Egypt
• 1994, 1998, BSc, Genetics, Ain Shams University, Egypt

• Sharaf, Abdoallah, et al. "Establishing African genomics and bioinformatics programs through annual regional workshops." Nature Genetics (2024): 1-10.
• Said, Eglal M., and M. E. Hassan, DNA barcodes in Egyptian olive cultivars (Olea europaea L.) using the rbcL and matK coding sequences, Journal of Crop Science and Biotechnology, https://doi.org/10.1007/s12892-022-00189-7, https://link.springer.com/article/10.1007/s12892-022-00189-7
• Hassan, M.A.E.#, Hasan, M.E., Finding a Tandem Repeats Motifs in the Completed Genomes of Human Coronavirus (hku1) Which is Identified as a Hotspot Region for the Viruses Recombination by Using Regular Expression Language, Preprints 2019, 10.20944/preprints201910.0249.v1, https://www.preprints.org/manuscript/201910.0249/v1
• Mohamed A. Ezz, Genetic Monitoring and Molecular Phylogeny for Cymothoid Isopod Invasion in Egyptian Lake Qarun Fishes by Using adopted taxonomic marker (COI), bioRxiv 614578, https://doi.org/10.1101/614578, https://www.biorxiv.org/content/10.1101/614578v3.full
• Mohamed A. Ezz#, Amal Mahmoud, Fawzy A. El-Feky, Alaa A. Hemeida, Searching and Analyzing for a Different Lengths of Microsatellite Repeats in the Completed Genome of Phoenix dactylifera Chloroplast, by Using Regular Expression Builder-Language, International Journal of Science and Research (IJSR), 6, 8, August, 2017, 1296 - 1301, International Journal of Science and Research (IJSR), https://www.ijsr.net/archive/v6i8/ART20174522.pdf
• Mohamed A. Ezz#, Mona I. Salah, and Abdullah I. Ammoura, Detection and Protein Modeling for Consensus Region of hsp70 Gene Family in Egyptian Arundo donax, Journal of Life Sciences, 8, 7, July, 2014, 593-602, David Publishing Company, http://www.davidpublisher.org/Public/uploads/Contribute/55272bb0b3042.pdf
• MAI S. MABROUK#, Mohamed A. Ezz, Hslc_Fuge: High Speed and Low Cost Laboratory Centrifuge For Genomic DNA Purification, Journal of Mechanics in Medicine and Biology, 12, 5, December, 2012, 1240026 (12 pages), Worldscientific, https://www.worldscientific.com/doi/pdf/10.1142/S021951941240026X
• Mohamed A. Ezz#, Mohamed H. Soliman, Abd Alkader Y. Gamal El-Din, Aly Z.E. Abdelsalam, Molecular Studies on Heat Shock Gene (HSP70) Using ClustalW Alignment Analysis, Journal of Life Sciences, 6, 4, October, 2010, 593-602, David Publishing Company, http://www.davidpublisher.org/Public/uploads/Contribute/557e72c078e92.pdf

• Genomic prediction and selection in plant breeding, Mediterranean agronomic institute of Zaragoza, Spain, 40, 01/16/2016, 01/28/2016
• Applications of bioinformatics in plant breeding, Mediterranean agronomic institute of Zaragoza, Spain, 36, 01/18/2014, 01/22/2014

• Bioinformatics Methods I, UNIVERSITY OF TORONTO'S, 06/03/2014
• Bioinformatics Methods II, UNIVERSITY OF TORONTO'S, 09/04/2014
• Bioinformatics Certificate Distance Learning: Advanced Bioinformatics Course, Biotech Learning Institute, San Jose, CA, USA, 2008
• Beginner Bioinformatics Course, Biotech Learning Institute, San Jose, CA, USA, 2005

Symposium power of viruses, 05/16/2018, Croatia, Retrieving a Tandem Repeats Motif in the Completed Genomes of Human Coronavirus (Hku1) Which Identified as a HotSpot Region for the Virus Recombination by Using Regular Expression Language

• DNA isolation
• RNA isolation
• SDS-PAGE
• Degenerate PCR protocol
• Long PCR protocol
• RT/PCR
• Real time PCR
• DNA / RNA isolation protocols
• Cloning protocols
• Molecular taxonomy
• Real time PCR experiment
• Microbial ecology and molecular diagnostics

A. I'm very interested in using my programming skills in solving biological problems. I programmed a mini tool to find the SSR and LTR sequences in the organelle genomes and viruses genome RFRE, ( https://sourceforge.net/projects/rfre) .

B. I design a workflow to analyze the metabarcoding genes for NGS data paired end to produce Merging pair-end reads, quality filtering, de-noise, OTU curation, and taxonomic assignment utilizing https://github.com/ezzbioinf/Marine-environmental-DNA-metabarcoding-data-analyses-practical-11-13-October-2023 

C. I have experience in utilizing bioinformatics tools, utilizing different programming languages (Bioperl- Biopython Data analysis and scripting text files- OOP language object oriented programming language and event driven programming language- RegEX regular expression language - Excel programming - Accesses programming) and database normalization and construction from 0NF level to BCNF level. 

D. I have Bioinformatics skills in different areas, pipelines in RNA-seq analysis and de novo assembly.

 E. Metagenomic analysis using QIIME 2 and Submitting processed reads to (MG-RAST) pipeline.

 F. Metagenomic assembly utilizing metaspades. 

G. Metabarcoding pipeline by using R packages DADA2. 

H. Metagenomic 16S rDNA and Metagenomic WGS by using R packages. I. Merging pair-end reads, quality filtering, de-noise, OTU curation, and taxonomic assignment utilizing USEARCH algorithm and UBLASTsearch algorithm.

Bioinformatics experience and eDNA/Metabarcoding analysis long reads:

J. Making an Assembly and de novo assembly (short reads and long reads) using different pipeline tools, Mapping and Visualization for high-throughput data, comparison across species and synteny analysis). 

K. Genome assembly for long reads which comes out from nanopore , MinION Data utilizing MEGAHIT.

 L. Genomic selection pipeline analysis and visualizing SNPs by Flapjack-graphical genotype visualization tool. 

M. Comparative genomics by using CoGe server to identify the synteny gene. 

N. I am familiar with Aligning genomes (multiple genome alignment) with Mauve tool, The CoGe Comparative Genomics Platform to define synteny genes and YASS genomic similarity search tool.

O. Discover the barcode gap utilizing ASAP (Assemble Species by Automatic Partitioning). 

P. I am familiar with NGS pipelines of Data analysis NGS analysis (Quality control for NGS raw data (FASTQ), DNA and RNA-seq NGS read alignment, Variant Calling). 

Q. Visualizing SNPs by Flapjack-graphical genotype visualization. R. Multiple genome alignment (GENOMES) by using the MAUVE tool.

Genomic Analysis :
A. NGS analysis (Quality control for NGS raw data (FASTQ), DNA and RNA-seq NGS read alignment, Variant Calling, Making an Assembly and de novo assembly (short reads and long reads) using different pipeline tools, Mapping and Visualization for high-throughput data, comparison across species and synteny analysis).
B. Visualizing SNPs by Flapjack-graphical genotype visualization.
C. Metagenomic analysis and Metabarcoding using QIIME 2 and Submitting processed reads to (MG-RAST) pipeline
D. Metabarcoding using 12s barcode gene to make biodiversity assessment for fish stock.
E. Metabarcoding analysis using R packages and DADA2 and Excel macros.
F. Metabarcoding analysis utilizing Usearch and Vsearch from OTU to downstream analysis (Alpha and Beta
Diversity).
G. Utilizing Kraken2 and Krona tools in assigning taxonomy and taxonomy visualization.
H. Metabarcoding pipeline analysis for long reads assembly of raw data produced by Nanopore Oxford.
I. Bacterial genome assembly and data annotations - mtDNA assembly and cpDNA assembly using Flye - Canu - Spades - Megahit.
J.Comparative genomics by using CoGe server to identify the synteny gene.
K.I am familiar with Aligning genomes (multiple genome alignment) with Mauve tool, The CoGe Comparative Genomics Platform to define synteny genes and YASS genomic similarity search tool.
L.Multiple genome alignment (GENOMES) by using the MAUVE tool.

Computer skills :

A. (Descriptive Analysis, Comparative Analysis, Experimental Design, GLM Modules) by using SPSS and Excel.

B. LINUX, command lines and shell scripts, Bioperl and Python programming language in genomic data analysis and visualization.

C. System analysis and Database Normalization (0NF to BCNF). 

D. Oracle for PC’s (RDBMS, SQL, SQL*PLUS). E. MS-Visual Basic 6.0.

Phylogenetic tree analysis:

A. Data preparation. 

B. Phylogenetic inference based on distance methods.

 C. Phylogenetic inference using maximum likelihood methods.

 D. Phylogeny inference based on parsimony and other methods.

 E. Estimating selection pressures on alignments of coding sequences (dn/ds).

 F. Testing topology. 

G. Bootstrapping analysis to produce a confidence tree. 

H. Using the suitable Substitution model to construct the phylogenetic tree.

 I. Choose the corrected algorithm to construct the phylogenetic tree and change the option of clustalw algorithm to optimize the tree topology.

Molecular Biology skills:

A. Experience in lab techniques (DNA isolation, RNA isolation from different sources , Bacterial cells, Plant tissue, cell culture, fishes,Blood)

 B. SDS-PAGE, 

C. Degenerate PCR protocol 

D. Long PCR protocol 

E. RT/PCR, Real time PCR, ΔΔcT Calculation for comparative genomic expression).

 F. DNA / RNA isolation protocols 

G. Cloning protocols H. Molecular taxonomy by using DNA barcoding gene and Insilco pipeline analysis to construct phylogenetic tree. I. Real time PCR experiment by using SYBR green dye and Calculating the ΔΔCt value. J. Microbial ecology and molecular diagnostics.

• Haggag S. Zein, PhD, Postdoctoral Fellow, Immunology, Biochemistry, and Microbiology, Ottawa University, Medical School, Ottawa, Canada, haggagsalah@gmail.com, scholar.google.com/citations?user=djUFxucAAAAJ&hl=en
• Dr. Abd El-Nasser Khattab, Professor of Microbial Genetics & Biotechnology, Genetics & Cytology Department, Biotechnology Research Institute, National Research Centre, 33 El Bohouth St., El Dokki, P.O. 12622, Giza, Egypt, +2 01098719984, +202 33370931, khattababdelnasser69@yahoo.com
• Prof. Dr. Hattem M. El-Shabrawi, Plant Biotechnology Dept., National Research Center (NRC), El-Behouth St., Dokki, Giza ,12622, Egypt, +202 333 224 08, +201 115425742, +201 000714793, +202 333 709 31

2019 PhD is Verified International Academic Qualifications Issued by World Education Services (WES), https://wes.credly.com/member-badges/20370073.

2024 PhD is Verified International Qualifications Recognition Statement (NZQA), NZQA Application Number: 092897