Syed Muhammad Ali Shirazi

Syed Muhammad Ali Shirazi

BS Biosciences Graduate

COMSATS University Islamabad, Pakistan

Open to Master's positions & research collaborations

As a Biosciences graduate with a strong foundation in genomics, I am deeply interested in the intersection of biological data and computational power. My focus lies in bioinformatics and computational biology, specifically using data driven approaches to uncover the genetic mechanisms behind complex diseases.

Professional Philosophy

I believe that advances in genomics and data analysis will play a key role in bridging the gap between research and clinical application, enabling more precise and personalized approaches to healthcare. Looking ahead, I plan to pursue graduate studies in bioinformatics or computational biology, with the long-term goal of contributing to research that improves our understanding of complex biological systems and human disease.

Background

About Me

I am a Biosciences graduate from COMSATS University Islamabad with a growing focus on bioinformatics and computational biology. My academic journey began with hands-on experience in molecular biology techniques such as DNA extraction and PCR, and gradually evolved toward applying computational approaches to biological data.

My undergraduate research explored the genetic basis of gallstone disease, with a particular focus on the ATP8B1 gene. This work strengthened my understanding of genetic variation and its role in disease, while also reinforcing my interest in using data-driven methods to study complex biological systems. I am especially interested in how modern computational tools, including artificial intelligence, can support research in genomics and molecular biology.

I have also gained experience in genome assembly and annotation, including working with viral genomes such as SARS-CoV-2. This involved assembling sequences using k-mer-based approaches and identifying protein-coding regions through annotation pipelines. I am currently preparing to pursue a Master’s degree, with the goal of further developing my research skills and contributing to the understanding of genetic and genomic data.

Currently

📖 Reading: Bioinformatics Algorithms – Compeau & Pevzner

🎓 Learning: Digital Healthcare Informatics and AI (Coursera)

🔬 Working on: Python and R for data analysis and bioinformatics

Academic Focus

Research Interests

🧬 Genomics & Molecular Biology

Exploring genetic variation and molecular mechanisms underlying human diseases, with an interest in integrating experimental and computational approaches to understand biological function.

📊 Biological Data Analysis

Applying statistical and computational methods to analyze biological and clinical datasets, with a focus on extracting meaningful patterns and supporting data-driven research.

💊 Computational Biology & Translational Research

Utilizing computational tools to investigate biological systems and contribute to the identification of potential therapeutic targets and disease mechanisms.

🤖 AI & Quantitative Methods in Life Sciences

Interested in applying machine learning and quantitative approaches to biological data for improved prediction, classification, and understanding of complex biological processes.

Expertise

Skills & Expertise

🧬

Bioinformatics

Genome assembly (SPAdes, QUAST), sequence alignment (BLAST, MUSCLE, ViralMSA), phylogenetics (FastTree, LSD2, Taxonium), genome annotation (Prokka), pathway analysis (BioCyc, EcoCyc, MetaCyc), primer design validation

💻

Programming

Python (BioPython, pandas, matplotlib), R (basic data analysis, ggplot2), Galaxy platform, command-line tools (bash).

🔬

Wet Lab

PCR (including TETRA-ARMS), DNA extraction (phenol-chloroform), gel electrophoresis, primer design (Primer3), genotyping, Sanger sequencing sample preparation, spectrophotometry, sterile technique.

🤖

Soft Skills

Effective Communication, Adaptability, Social Responsibility, Strategic Thinking

Roles

Current Positions

B.Sc. Graduate – Biosciences

COMSATS University Islamabad

2022 – 2026

Independent Researcher – Bioinformatics & Computational Genomics

Self-directed Research

2025 – Present

Master's Applicant – Bioinformatics, Clinical informatics, Computational biology

Upcoming · Target Fall 2026

In preparation

Talks

Collegiate Presentations

Genetic Determinants of Gallstone Disease: Focus on ATP8B1 Variants in the Pakistani Population

Syed Muhammad Ali Shirazi

Undergraduate Research, COMSATS University Islamabad · 2025

Oral presentation of final year thesis findings to department faculty and students.

Slides

The Relationship Between Physical Activity and Mental Health Among Students

Syed Muhammad Ali Shirazi

Statistical Methods in Biology · COMSATS University Islamabad · December 2024

Statistical analysis examining correlations between physical activity levels and mental health outcomes (stress, anxiety, depression) in students. Used regression analysis, correlation coefficients, and ANOVA to identify significant positive relationships between exercise frequency and improved mental well-being.

View

More presentations expected as research progresses.

Academic Events

Conferences & Seminars Attended

🧬

Second International Symposium on One Health | Pakistan

Participant · Volunteer

oct 2025 · Comsats University Islamabad

Certificate
🎤

Combatting Illegal Wildlife Trade In Pakistan | Endangered Species Day 2025

COMSATS University Islamabad – Management and Organization

2025 · Islamabad, Pakistan

Certificate

Projects

Portfolio

🦠

SARS-CoV-2 Genomic Analysis Pipeline

From Assembly to Drug Target Discovery

Comprehensive end-to-end bioinformatics pipeline analyzing real SARS-CoV-2 pandemic data. Assembled complete viral genome (29,903 bp), performed functional annotation identifying 11 major ORFs, traced evolutionary origins through phylogenetic analysis, and identified guanylate kinase as a potential antiviral drug target. Self-directed learning project demonstrating transition from wet-lab to computational biology.

Key Analyses:
  • Genome Assembly: SPAdes de novo assembly from raw Illumina reads (N50: 29,903 bp)
  • Genome Annotation: Prokka functional annotation, PCR primer design for diagnostics
  • Evolutionary Analysis: Multiple sequence alignment, natural origin confirmation
  • Phylogenetic Dating: Molecular clock analysis, tMRCA estimation (Oct-Nov 2019)
  • Drug Target Discovery: Metabolic pathway analysis, therapeutic target identification
Genome Assembly Phylogenetics BLAST Galaxy Drug Discovery

🎓 Learning Context: This project was completed as part of the Applied Bioinformatics Specialization (UC San Diego, Coursera) to develop computational biology skills beyond my wet-lab molecular biology background.

🧬

Assessment of the role of ATP8B1 Gene in Gallstone in Pakistani Population

My final year project involved investigating the genetic variants of the ATP8B1 gene and their association with gallstone disease within the Pakistani population. By conducting a case-control study, I aimed to identify specific mutations that might predispose individuals to cholestatic liver conditions and gallstone formation. The research focused on understanding how alterations in this p-type ATPase transporter affect bile acid secretion and lipid homeostasis. This study provides a foundational genetic profile that can assist in the early diagnosis and personalized management of gallbladder disorders. The project successfully bridged the gap between clinical observation and molecular genetic validation.

Key Analyses:
  • Variant Identification: Conducted a comprehensive screening of the ATP8B1 gene to identify pathogenic and benign variants relevant to the local population.
  • Association Study: Performed statistical analysis to determine the correlation between specific genetic markers and the prevalence of gallstone disease.
  • Functional Prediction: Utilized bioinformatics tools to predict the impact of identified non-synonymous mutations on the protein's structural integrity and function.
  • Case-Control Comparison: Analyzed genetic data from patients and healthy controls to pinpoint statistically significant risk factors.
  • Population Specificity: Focused specifically on the Pakistani population to account for regional genetic diversity and unique hereditary patterns.
DNA Extraction PCR Gel Electrophoresis Sequence Alignment Chi-square Testing

🎓 Learning Context: This research was conducted as my Final Year Project (FYP) during the 8th semester of my Bachelors in Biosciences at COMSATS University Islamabad. The project was based in the Transitional Genomics Lab and was supervised by Dr. Nasir Masood and Dr. Muhammad Ajmal.

Curriculum Vitae

CV

Download Full CV (PDF)

Last updated: March 2026

Education

2022 – 2026

B.Sc. Biosciences

COMSATS University Islamabad, Pakistan

Key undergraduate courses:

Molecular Biology Genetics Biochemistry Epidemiology Bioinformatics Cell Biology Immunology Biostatistics Biotechnology Essential Techniques in Microbiology Introduction to Computer Programming Virology Evolution BioEthics
2019 – 2021

F.Sc. Pre-Medical

Joint Staff Public School and College, Rawalpindi, Pakistan

Subjects:

Biology Chemistry Physics English Urdu History Islamic Studies

Undergraduate Research

jan 2026

Assessment of the Role of ATP8B1 Gene in Gallstone Disease in the Pakistani Population

Supervisors: Dr. Muhammad Ajmal, Dr. Nasir Masood

Conducted genome sequence analysis and variant interpretation to investigate the genetic contribution of ATP8B1 to gallstone disease.

Certificates

🎓

Applied Bioinformatics Specialization | University of California San Diego

Coursera · 2026

Verify PDF
🎓

Python for Genomic Data Science | Johns Hopkins University

Coursera · 2026

Verify PDF
🎓

Introduction to Clinical Data | Stanford University

Coursera · 2026

Verify PDF
🎓

Introduction to Healthcare | Stanford University

Coursera · 2026

Verify PDF
🎓

Introduction to Genomic Technologies | Johns Hopkins University

Coursera · 2026

Verify PDF

Writing

Blog Posts

March 2026 Career Development

My Journey into Bioinformatics

How I transitioned from pipetting and PCR to Genome Assembly and phylogenetics. Lessons learned from my first computational biology project analyzing SARS-CoV-2 genomes.

Read more →
March 2026 Bioinformatics

Assembling a Pandemic: My First Genome Assembly

Walking through the process of reconstructing the complete SARS-CoV-2 genome from millions of short DNA reads using SPAdes and Galaxy. Understanding N50, de Bruijn graphs, and why assembly is like solving a massive jigsaw puzzle.

Read more →
March 2026 Tutorial

Tools I Learned: A Bioinformatics Toolkit for Viral Genomics

A beginner's guide to the essential bioinformatics tools for viral genome analysis: SPAdes, QUAST, Prokka, MUSCLE, FastTree, and more. What each does and when to use them.

Read more →

Memberships

Affiliations

BIOME – The Biosciences Society - Member

COMSATS University Islamabad

2024 – 2025

Participated in departmental activities, event management and organization.

ISCB - Student Member

International Society for Computational Biology (ISCB)

2026 – Present · Membership ID: 46230

Member of Global community for computational biologists and bioinformaticians advancing scientific understanding through computation.

Active Volunteer | Non-Profit Outreach

sarreraah

2023 – Present

Actively involved in community service initiatives focused on providing essential resources and financial support to underprivileged populations.

Beyond the Lab

Other Interests

📚

Reading

Avid reader of philosophy and poetry with a curiosity for palmistry and human behavior.

🏃

Sports

I stay active through hiking, cricket, and ice skating. I also have a great deal of affection for animals, especially dogs and cats.

♟️

Strategy

I am always up for a strategic game of cards, which I find to be an excellent exercise in focus and probability.

🤝

Impact

Beyond the lab, I am a co-founder of the clothing brand Naadan and am actively involved in non-profit work to support the poor and needy in my community.

Questions

FAQ

Are you open to research collaborations?
Yes! I am actively looking for collaborations in bioinformatics, computational genomics, and AI-driven biological research. Feel free to reach out via email or LinkedIn.
Are you currently applying for Master's programs?
Yes. I am preparing applications for Master's programs in Bioinformatics and Computational Biology for Fall 2026 intake.
What bioinformatics skills did you gain from your SARS-CoV-2 project?
I gained hands-on experience with genome assembly (SPAdes, QUAST), functional annotation (Prokka), sequence alignment (BLAST, MUSCLE), phylogenetics (FastTree, LSD2), pathway analysis (BioCyc), and data visualization. More importantly, I learned to think computationally about biological problems and integrate multiple analysis types into comprehensive workflows.
What unique advantage do you bring to a research team?
My primary advantage is that I have experience in both wet-lab techniques and bioinformatics tools. While many researchers specialize in only one area, I can perform the physical DNA extraction and PCR in the lab, and then transition immediately to the computational side to handle genome assembly and clinical data analysis. This "hybrid" expertise allows me to troubleshoot experimental errors more effectively because I understand the biological context of the data I am processing.

Academic Referees

References

The following individuals have agreed to provide references. Please contact them directly or reach out to me first and I will provide the Reference Letters.

Dr. Muhammad Ajmal

Thesis Supervisor

COMSATS University Islamabad – Dept. of Biosciences

muhammad.ajmal@comsats.edu.pk

Dr. Nasir Masood

Co-Supervisor

COMSATS University Islamabad – Dept. of Biosciences

nasir.masood@comsats.edu.pk

Dr. Faraz Arshad Malik

Associate Professor

COMSATS University Islamabad – Dept. of Biosciences

famalik@comsats.edu.pk

Get in Touch

Contact

Email

shirazi6503@gmail.com

Location

Islamabad, Pakistan

Affiliation

COMSATS University Islamabad

Send me a message below.

Or email me directly at shirazi6503@gmail.com