RNA-Seq Analysis
Bulk transcriptomics with DESeq2/edgeR, QC, alignment and pathway enrichment.
STARSalmonDESeq2
Delivery · 2–3 weeksRequest
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
- 100s
- 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
Services
Production-grade bioinformatics, end to end
From experimental design to scalable cloud delivery — pick a service or compose a full omics program.
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
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 say
“The session was incredibly beneficial. You answered all my questions about the Bioinformatics field roadmap and provided me with significant help.”
Nagham Mohamed
1:1 Mentoring Session
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.