Dr. Ahmed Shaheen, MD

A Research Journey: From Clinical Practice to Computational Innovation

Clinical & Computational Neuroscience

My Research Story

Bridging clinical understanding with scientific discovery.

From foundational wet-lab science...

...to leading large-scale international collaborations...

...to building the future of AI-driven medical research.

Phase 1: Foundational Experience

From Wet Lab to Clinical Data

  • Hands-on experience in animal modeling, stereotactic surgery, and cell culture techniques.
  • Worked as a Clinical Research Assistant in Rheumatology and Neuropsychiatry.
  • Gained crucial understanding of experimental design, clinical study protocols, and patient data.

The Computational Pivot

The COVID-19 lockdown became a catalyst for growth.

I immersed myself in the world of data science, machine learning, and programming, recognizing it as the future of medical discovery.

Phase 2: Mastering Computational & Data Science

  • Research Fellowship in applying ML/DL to neuroimaging (MRI) and electrophysiological (EEG/MEG) data.
  • Expertise in complex data analysis, biostatistics and computational methods.
  • Developed and published open-source R packages for clinical database extraction and analysis.

Milestone: The Long COVID Study

My first major project ~ 3 year.

  • Initiated and led multicentric international collaborations.
  • Coordinated 100+ researchers across 20 countries, studying over 2,400 patients.
  • Developed a deep learning model and deployed a public ML-powered risk calculator.

View the Long COVID Risk Predictor

Phase 3: Leadership & AI-Driven Innovation

  • Leading the **Shaheen Clinic Research Group** and serving in leadership roles in global consortia.
  • Developing novel LLM-based frameworks to **automate systematic reviews** and clinical trial analysis.
  • Building practical tools: Deep Learning MRI segmentation tools, BioMedical Pathway Engine, and R/Python packages.

Scaling Knowledge: Shaheen Clinic LLC

A U.S. Company to Empower Researchers Globally

To formalize and expand my commitment to education, I founded Shaheen Clinic LLC.

  • Provides advanced training in medical research and data science.
  • Develops and distributes practical tools for data analysis.
  • Offers expert research consultations for academics and institutions.

Visit Shaheen Clinic LLC

Key Research Highlights

A selection of publications showcasing my multidisciplinary journey.

(Press down for examples)

First Author & Project Coordination: Large-Scale Deep Learning Study

Deep learning analysis of long COVID and vaccine impact... development of a risk calculator in a multicentric study

  • My Role: First Author & Project Coordination.
  • Skills Demonstrated: Research leadership, multicentric study coordination, deep learning model development, and creating a clinical risk calculator.
  • Publication: Frontiers in Public Health

Cutting-Edge AI: LLMs for Automated Research

Application of a general LLM-based classification system to retrieve information about oncological trials

  • My Role: Co-author.
  • Skills Demonstrated: Large Language Model (LLM) framework development, Natural Language Processing (NLP), and automated text classification for research.
  • Publication: medRxiv (Preprint)

Advanced Meta-Analysis in Neuroscience

Non-Invasive Brain Stimulation Improves Word Retrieval Deficits in Parkinson's Disease: A Meta Analysis of Clinical Trials

  • My Role: Co-author, managing study conduct, the statistical analysis and methodology.
  • Skills Demonstrated: Systematic review, advanced meta-analysis, and research in neurodegenerative diseases (Parkinson's).
  • Publication: Preprint / In Submission

Domain Expertise: Molecular Neuroscience

MicroRNAs regulation in Parkinson's disease, and their potential role as diagnostic and therapeutic targets

  • My Role: Co-author, contributed to writing and review.
  • Skills Demonstrated: Deep domain knowledge in the molecular pathogenesis of neurodegeneration and comprehensive scientific writing.
  • Publication: npj Parkinson's Disease

Foundational Preclinical Research

Effects of environmental enrichment on the behavioural consequences of early-life stress in rats

  • My Role: Co-author on this foundational study during my undergraduate years.
  • Skills Demonstrated: Animal modeling (rats), behavioral experiments, and preclinical research design from the ground up.
  • Publication: Bulletin of the Egyptian Society of Physiological Sciences

A Multidisciplinary Skillset

Foundational Science

  • Animal Modeling (Rodents)
  • Stereotactic Surgery
  • Behavioral Experiments
  • Molecular Biology (Western Blot)
  • Cell Culture

Computational & AI

  • ML/DL Development
  • LLM Implementation
  • Advanced Biostatistics
  • EEG/MEG Time-Series Analysis
  • Software & Package Dev (R/Python)

Leadership & Entrepreneurship

  • Founder & CEO, Shaheen Clinic LLC
  • Research Leadership & Management
  • Large-Scale Collaboration
  • Scientific Writing & Editing
  • Teaching & Mentorship

Full Portfolio & Publications

My work is documented across 60+ publications (H-index 14), open-source code repositories, and academic profiles.

I believe in open science and making tools accessible to the research community.

The Next Chapter

I am actively seeking opportunities to apply my multidisciplinary skills to impactful questions in clinical and neuroscience research, aiming to become a physician-scientist and entrepreneur who leads at the intersection of medicine and technology.

Email: ahmeds1999haheen@gmail.com

LinkedIn • X (Twitter) • YouTube

Thank you.