milestone · 01
MBA · Marketing
AAMBFS
Business Strategy
Bioinformatics Scientist · Educator
End-to-End Bioinformatics
by Ahmed Mokhtar
Cancer genomics, single-cell and spatial transcriptomics, and reproducible NGS pipelines — built in R and Python. MSc candidate at Cairo University and a freelance bioinformatics instructor with six-plus years training researchers across the field.
- Experience
- 7+ years
- Mentees
- 1000+
- Followers
- 1.6k+
Built on the tools researchers trust
BioconductorNextflowSeuratScanpyGATKAWSDockerSnakemakeCell RangerPyTorchBioconductorNextflowSeuratScanpyGATKAWSDockerSnakemakeCell RangerPyTorch
7+
Years in bioinformatics
500+
Researchers trained
30+
Pipelines shipped
About
Translating omics data into decisions
Ahmed Mokhtar Ramzy Salem
Bioinformatics Scientist · Educator
Available for new collaborations
Bioinformatics scientist with a biotechnology background, focused on cancer genomics and transcriptomics. MSc candidate at Cairo University, postgraduate-diploma trained at Suez Canal University. Six-plus years teaching bioinformatics — from NGS foundations to single-cell and spatial transcriptomics — and shipping reproducible analysis pipelines for independent research.
Single-Cell RNA-seq
Spatial Transcriptomics
Cancer Genomics
TCR Repertoire
Bulk RNA-Seq / DESeq2
Multi-Omics Integration
ML in Genomics
Reproducible Pipelines
Teaching & Mentorship
Education
A multi-disciplinary trajectory
From wet-lab biotechnology to genomics, statistics, and business — a deliberate stack built across six programs.
- milestone · 02in progress
MSc Candidate · Genetics & Bioinformatics
Faculty of Agriculture · Cairo UniversityGenetics Department - milestone · 03in progress
MicroMasters · Statistics & Data Science
MITxComputational Statistics - milestone · 04
Postgraduate Diploma · Bioinformatics
Suez Canal UniversitySystems Biology · NGS - milestone · 05
Diploma · Data Analysis
Arab Academy for Science, Technology & Maritime TransportAnalytics - milestone · 06
Diploma · Data Science
Epsilon InstituteML · Python
Services
Production-grade bioinformatics, end to end
From experimental design to scalable cloud delivery — pick a service or compose a full omics program.
RNA-Seq Analysis
Bulk transcriptomics with DESeq2/edgeR, QC, alignment and pathway enrichment.
STARSalmonDESeq2
Delivery · 2–3 weeksRequest
Single-Cell Sequencing
10x Chromium, Seurat & Scanpy workflows, integration and trajectory analysis.
SeuratScanpyHarmony
Delivery · 3–4 weeksRequest
Spatial Transcriptomics
Visium / Xenium / MERFISH analysis, niche detection, cell–cell interaction.
SquidpySpaceRanger
Delivery · 3–5 weeksRequest
Comparative Genomics
Orthology, synteny, evolutionary models across species and strains.
OrthoFinderMAFFT
Delivery · 2–4 weeksRequest
Metagenomics Pipelines
Shotgun & 16S microbiome analysis with taxonomic and functional profiling.
QIIME2Kraken2
Delivery · 2–4 weeksRequest
GWAS & Population Genetics
QC, imputation, association testing and polygenic risk scoring.
PLINK2REGENIE
Delivery · 3–5 weeksRequest
NeuroBioinformatics
Neuronal vulnerability mapping, multi-omics integration and single-cell brain atlases for neurodegeneration research.
scRNA-seqMulti-omics
Delivery · 4–8 weeksRequest
Bioinformatics DevOps
Reproducible Nextflow / Snakemake stacks with CI/CD and containers.
NextflowDocker
Delivery · 2–3 weeksRequest
Scientific Consulting
Study design, statistical strategy and reviewer-ready interpretation.
RPython
Delivery · From 1 weekRequest
Custom Pipeline Development
End-to-end omics pipelines tailored to your data and infrastructure.
NextflowWDL
Delivery · 3–6 weeksRequest
Cloud Deployment for Omics
AWS / GCP / Azure HPC, batch, S3, Terraform and cost optimization.
AWSTerraform
Delivery · 2–4 weeksRequest
Training & Workshops
Hands-on workshops on NGS, scRNA-seq, R/Python and reproducibility.
LiveCohort
Delivery · 1–4 weeksRequest
Projects
Selected research & pipelines
Case Studies
From problem to result
Three deep-dives across plant genomics, cancer single-cell biology and immuno-oncology — each shown as the actual problem, the method, and the measurable outcome.
Plant Genomics · Deep Learning
Dual-branch autoencoder for Brassica napus trait prediction
- Problem
- Allotetraploid canola hides subgenome-specific signal that flat GBLUP and standard GWAS routinely miss, capping genomic prediction accuracy.
- Method
- Trained a 1.07M-parameter dual-branch deep autoencoder on 1,007 globally diverse accessions, enforcing A/C subgenome separation by architecture. Latent fusion + gradient-based feature importance recover causal loci without phenotype supervision.
- Result
- Recovered BnaA09FLC2 and BnaC05FAE1 unsupervised. Delivered 1.89× QTL enrichment, 4.61× GWAS concordance, and up to +90.8% genomic-prediction gain over GRM-GBLUP across five agronomic traits.
PyTorchGWASGBLUPPython
Publications
Peer-reviewed research
Original research in comparative genomics and cancer immunogenomics — from population-scale SNP architecture to TCR-β repertoire dynamics under checkpoint blockade.
2 publications · open to collaboration
- paper01AcceptedJournal of Scientific Research in Science
Comparative Genomics Analysis of Some Brassica napus Accessions
Comparative GenomicsSNPBrassica napus - paper02Under reviewJournal of Scientific Research in Science
Multi-Dimensional TCR-β Repertoire Characterization in Anti-PD-1-Treated Non-Small Cell Lung Cancer: Development and Multi-Cohort Validation of the Composite Immune Reprogramming Score (CIRS)
TCR-βNSCLCImmuno-oncologyAnti-PD-1Biomarker
Courses · in partnership with BioScience
Browse on BioScienceLearn bioinformatics, production-style
Two formats — short Courses (8–9 weeks) for focused topics, and long-term Schools (4–5 months) for end-to-end mastery. All delivered through BioScience.
Schools · long-term, 4–5 months
Flagship
School
BeginnerAdvanced
NGS & Single-Cell RNA-Seq Data Analysis School
Duration
5 Months
Pace
4h / week
Rating
4.9
School
BeginnerAdvanced
Bioinformatics for CRISPR-Cas Systems School
Duration
4–5 Months
Pace
4h / week
Rating
4.9
School
BeginnerAdvanced
Cancer Informatics School
Duration
5 Months
Pace
4h / week
Rating
4.9
School
BeginnerAdvanced
Metagenomics & Metatranscriptomics Data Analysis School
Duration
4–5 Months
Pace
4h / week
Rating
4.8
New
School
BeginnerAdvanced
Bulk TCR Repertoire & Single-Cell TCR Data Analysis School
Duration
4–5 Months
Pace
4h / week
Rating
4.9
New
School
Advanced · Prereq: scRNA-Seq
Machine Learning for Single-Cell RNA-Seq School
Duration
4–5 Months
Pace
4h / week
Rating
4.9
School
BeginnerAdvanced
Whole Genome Seq Data Analysis School
Duration
5 Months
Pace
4h / week
Rating
4.9
School
BeginnerAdvanced
Whole Exome Seq Data Analysis School
Duration
5 Months
Pace
4h / week
Rating
4.9
New
School
BeginnerAdvanced
Neuroscience Multi-Omics Data Analysis School
Duration
5 Months
Pace
4h / week
Rating
4.9
Courses · focused, 8–9 weeks
New
Course
BeginnerIntermediate
Biostatistics Using R Language
Duration
8 Weeks
Pace
4h / week
Rating
4.9
Course
BeginnerIntermediate
Data Analysis Using R Language
Duration
8 Weeks
Pace
4h / week
Rating
4.9
Bestseller
Course
Intermediate
RNA-Seq Analysis from Scratch
Duration
8 Weeks
Pace
4h / week
Rating
4.9
Course
Advanced
Single-Cell RNA-Seq with Scanpy & Seurat
Duration
9 Weeks
Pace
4h / week
Rating
4.9
New
Course
Advanced
Cancer Bioinformatics in Practice
Duration
8 Weeks
Pace
4h / week
Rating
4.8
Course
Course
Course
Course
Intermediate
Metagenomics: From Reads to Insights
Duration
8 Weeks
Pace
4h / week
Rating
4.7
New
Course
Advanced
Structural Variants & Long-Reads
Duration
8 Weeks
Pace
4h / week
Rating
4.8
Insights
All articles →Scientific writing
Precision Medicine May 24, 2026
Digital Twins in Biology: Building Virtual Humans with Bioinformatics
Virtual computational replicas of organs, tissues and entire patients — how multi-omics, AI and systems biology are building biological digital twins for precision medicine.
#Digital Twins#Precision Medicine#AI#Systems Biology
AI in Biology May 24, 2026
AI-Powered Multi-Omics Integration: The New Era of Precision Medicine
How AI is unifying genomics, transcriptomics, proteomics, spatial and single-cell layers into clinically actionable molecular profiles — and what it means for the future of personalized medicine.
#Multi-Omics#AI#Precision Medicine#Spatial
Spatial Biology May 24, 2026
Spatial Transcriptomics: Mapping Biology in 3D
Preserving the spatial coordinates of gene expression is reshaping cancer research, neuroscience and clinical diagnostics — and AI is unlocking 3D molecular atlases at organ scale.
#Spatial#Transcriptomics#3D Biology#Cancer
Gene Editing May 24, 2026
CRISPR Bioinformatics and AI: The Computational Revolution Behind Gene Editing
Guide RNA design, off-target prediction, single-cell CRISPR screens, base/prime editing and generative Cas engineering — how AI and bioinformatics power modern gene editing.
#CRISPR#AI#Gene Editing#Single-Cell
AI in Biology May 24, 2026
Large Language Models in Bioinformatics: Beyond Chatbots
LLMs are learning the language of biology — DNA, proteins, pathways and literature — powering protein design, omics interpretation and generative biology.
#LLMs#AI#Protein Design#Generative Biology
NGS Tutorials May 4, 2026
Designing a production scRNA-seq pipeline with Nextflow
How to architect a reproducible single-cell pipeline that scales from a laptop to AWS Batch without rewriting code.
#scRNA-seq#Nextflow#AWS
AI in Biology Apr 22, 2026
Foundation models in biology: what actually works
A pragmatic look at scGPT, Evo, Geneformer and ESM-3, and when classical methods still win.
#AI#scRNA-seq#Genomics
Computational Biology Apr 8, 2026
Cancer multi-omics integration with MOFA2 in practice
Step-by-step walkthrough integrating expression, methylation and mutations into latent factors with biological interpretation.
#Cancer#MOFA2#R
Testimonials
What collaborators & mentees say
1000+ mentees and researchers trained across Egypt, Tunisia, Nigeria, the UAE, Italy, Germany and more.
CUCairo UniversitySCUSuez Canal UniversityHUHeliopolis UniversityADUAbu Dhabi UniversityACUAhram Canadian UniversityBBioScienceMMITx
“Ahmed rebuilt our entire RNA-seq stack on AWS in three weeks. Reproducible, traceable, and 40% cheaper than what we had.”
Dr. Lina Haddad
Head of Genomics
“Working with Ahmed on our spatial transcriptomics atlas elevated the entire paper. Reviewers specifically praised the methods.”
Prof. Yusuf Kaya
Principal Investigator
“His scRNA-seq course is the clearest, most production-minded I've taken. My PhD timeline literally shifted because of it.”
Marco Esposito
PhD Candidate · Computational Biology
“You may not remember me — 3 years ago I reached out about getting into bioinformatics and did a one-to-one mentoring session with you. You built me a clear roadmap, I followed every step, and alhamdulillah I'm now doing my PhD in Germany. I got accepted for the PhD scholarship because of the advice and the path you laid out. Thank you, truly.”
Former Mentee
PhD Candidate · Germany
“I've taken similar courses in Germany on R and Bash, and after every one I felt the material was too hard to digest. Honestly, with Ahmed it became much easier — step by step, gradually, and his teaching style is excellent. Mashallah.”
Dr. Asmaa
Researcher
“I'm taking the Immunogenetics & Informatics course with Dr. Ahmed Mokhtar — the immunology content, the data work, and the Bash scripting are all very good. The lectures are advanced, he's honest with the information, and he follows up step-by-step on every project we build.”
Dr. Asmaa
Faculty of Pharmacy
“مع حضرتك د. جاكلين، الصراحة كنت عايزة أشكر جداً بشمهندس أحمد مختار، والصراحة هو شاطر جداً وممتاز، وكان من أفضل المواقع اللي اشتغلت مع بيوساينس فيها.”
Dr. Jacqueline
Freelance Project · Client Feedback
“The mentoring session was so beneficial. Your clear communication, personalized advice, and industry insights were invaluable. The course recommendations and practical tips have put me on the right path.”
Dina Mostafa
Mentee
“Thank you Dr. Ahmed for the insightful session. Your detailed explanations significantly clarified my understanding and dispelled any confusion I had. I truly appreciate the time and effort you dedicated.”
Malak Abdelfattah
Mentee
“Thank you very much for sparing time to share an insight towards advancing my career in the field of biomedical science.”
Adedara Joshua
Researcher · Nigeria
“The mentoring session was really good. I learned a lot about the global bioinformatics market and what is most in demand. I'll work with your advice and share the results.”
Houda Boulaares
Researcher · Tunisia
FAQ
Frequently asked questions
Everything you might want to know before reaching out.
Cancer genomics, single-cell and spatial transcriptomics, multi-omics integration, and reproducible NGS pipelines. I work with academic labs, biotech startups, and clinical teams.
Yes — I'm a freelance bioinformatics instructor with 6+ years of teaching experience. Workshops, one-on-one mentoring, and structured cohort-based courses.
R and Python primarily, with Bioconductor, Seurat, Scanpy, Nextflow, Snakemake, Docker, and AWS/HPC for orchestration and scale.
Most projects start with a free 30-minute consultation, followed by a scoped proposal. I support both fixed-scope deliverables and ongoing retainers.
Cairo, Egypt — working with collaborators worldwide. Async-first, with overlap for live working sessions.
Contact
Let's build something measurable
Bring your dataset, study, or platform idea. Initial scoping calls are free and end with a concrete plan.