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Pakistan

Bioinformatician | Data Scientist

Profile Summary

I am a PhD-trained bioinformatician with expertise in next-generation sequencing (NGS) analysis, multi-omics data integration, and structural bioinformatics. I specialise in helping researchers and biotech teams extract meaningful biological insights from complex datasets, with a strong focus on RNA-seq, whole-exome/genome sequencing (WES/WGS), and proteomics. My experience includes designing and implementing end-to-end bioinformatics pipelines for variant calling, transcriptomic analysis, and downstream functional interpretation. I have worked extensively with tools such as GATK, Mutect2, and R/Bioconductor, as well as high-performance computing (HPC) environments to handle large-scale datasets efficiently and reproducibly. In addition to genomics, I bring a unique strength in structural and dynamic analysis of proteins. I have conducted molecular dynamics simulations (GROMACS, NAMD) and developed computational approaches to study protein interactions, hydrogen-bond networks, and allosteric mechanisms. This allows me to connect sequence-level variation with structural and functional outcomes—an area of increasing importance in disease research. I have also developed computational tools for automated analysis of experimental data, reflecting my ability to go beyond standard workflows and build tailored solutions for specific research problems. Services I offer: RNA-seq analysis (differential expression, pathway analysis, visualization) WES/WGS variant calling and interpretation Multi-omics data integration and network analysis (e.g., WGCNA) Bioinformatics pipeline development (Python, R, Bash) Protein structure analysis and molecular dynamics simulations Data analysis, visualization, and scientific reporting I am comfortable working independently or as part of collaborative, multidisciplinary teams, and I prioritise clear communication, reproducibility, and timely delivery. If you are looking for a bioinformatics expert who can combine genomics, structural biology, and data science to solve complex biological problems, I would be glad to collaborate.

Subject Matter Expertise

• ★ Bioinformatics
• ★ Gene & Protein Expression Analysis
• ★ Structural Bioinformatics
• ☆ Chemoinformatics
• ☆ Evolutionary Biology
• ☆ Biostatistics
• ☆ Biochemistry
• ☆ Biophysics
• ☆ Systems Biology

Services

• Writing

Writing Technical Writing, Newswriting, Audio Transcription, General Proofreading & Editing, Translation

Work Experience

Lahore University of Management Sciences

- Present

Reseacher

SHAPE Global

October 2025 - Present

Education

PhD (Life Sciences )

Lahore University of Management Sciences

September 2021 - Present

MS Bioinformatics (RCMS (SINES))

National University of Sciences and Technology

July 2017 - October 2020

BS Bioinformatics (Computer Science)

University of Agriculture, Faisalabad

October 2013 - May 2017

Certifications

• Certification details not provided.

Publications

BOOK CHAPTER

Maham Hamid, Safee Ullah Chaudhary, Alessandro Pandini, Shahid M. Khan (2026). Allosteric Network Analysis Toolkit for Single-Domain Phosphoproteins . Methods in Molecular Biology.

PREPRINT

Maham Hamid, Ishrat Jabeen, Safee Ullah Chaudhary, Shahid Khan (2025). Conservation of the hydrogen-bond network in bacterial response regulators .

Maham Hamid, Salman T. Khawaja, Thomas S. Reese, Shahid Khan (2025). An AlphaFold guided model for the evolution of the CaMKII interactome .

Maham Hamid, Uzma Habib, Rehan Zafar Paracha Identification and Computational Analysis of 3D-Structure Of MOCS1 .

JOURNAL ARTICLE

Maham Hamid, Muhammad Farhan Khalid, Shahid Khan, Safee Ullah Chaudhary (2025). PERCEPTRON-XFMS: An Open-Source Web Server for Analysis of X-ray Footprinting with Mass Spectrometry Data . Journal of Molecular Biology.

Hamid, Maham, Abid, Rizwan, Nisar, Haseeb, Chaudhary, Safee Ullah, Sahibzada, Kashif Iqbal, Firdous, Safia, Mudassar, Muhammad, Sadaf, Saima(2024). Association of epilepsy and neurological impairments with homozygous recessive missense mutations found in the genes responsible for ganglioside biosynthesis (ST3GAL5) and calcium voltage-gated channels (CACNA1H)-insights through molecular dynamic simulations. Journal of Biomolecular Structure and Dynamics. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--12. Taylor \& Francis

The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS <head> <META HTTP-EQUIV="Refresh" CONTENT="0;URL=/servlet/useragent"> </head> . International Journal of Molecular Sciences.

Maham Hamid, Muhammad Farhan Khalid, Safee Ullah Chaudhary, Shahid Khan (2022). The Solvation of the <i>E. coli</i> CheY Phosphorylation Site Mapped by XFMS . International Journal of Molecular Sciences.