Bioinformatics & Systems Biology

Joseph
Emmanuel
G. Lopez

Decoding life through mathematics and code.

Molecular Biology and Biotechnology student at the University of the Philippines Diliman. I study how evolutionary and quantitative frameworks illuminate cancer progression and the dynamic systems that govern life.

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About

Biology meets computation

I am a Molecular Biology and Biotechnology student at the University of the Philippines - Diliman with a strong interest in computational biology, particularly in how evolutionary and mathematical modeling can be applied to understand dynamic biological systems.

I am especially drawn to cancer biology and infectious disease as domains where evolutionary frameworks and quantitative approaches can offer insights into disease progression and treatment dynamics.

My computational experience includes building and deploying pipelines, utilizing server infrastructures, and applying tools for genomic, transcriptomic, and evolutionary analysis. I thrive in the process of solving biological questions through mathematical and computational approaches, and I am continually developing my skills across bioinformatics, systems biology, and data analysis.

Outside of research, I am involved in science outreach and community building, with experience in managing alumni relations and tutoring students in STEM, reflecting my belief that science and analysis is only meaningful if it is collaborative and accessible. Aside from the life sciences, I am also interested in utilizing data science for improving systems in healthcare and public policy.

Evolutionary Genomics Cancer Biology Infectious Disease Systems Biology Bioinformatics Transcriptomics Mathematical Modeling Data Science Public Health Science Outreach

Institution

University of the Philippines Diliman
BS Molecular Biology and Biotechnology

Research Focus

Treatment-driven selection in breast cancer; transcriptomic time-series analysis; evolutionary dynamics in disease

Location

Quezon City, Philippines

Contact

jglopez2@up.edu.ph
(+63) 995-008-8123

Experience

Research & Work

Sep 2024 – Present
Evolutionary Genomics & Systems Biology Lab
UP Diliman

Undergraduate Thesis Student

Advisor: Dr. Isaiah Paolo Lee, PhD

  • Analyzing treatment-driven selection across breast cancer stages in Filipino patients through transcriptomic time-series analysis.
  • Developed an end-to-end Bash pipeline for processing and cleaning high-throughput biological datasets, focusing on variant calling and analysis.
  • Created advanced data visualizations in RStudio translating statistical metrics into interpretable insights for senior stakeholders.
  • Optimized large-scale workloads on HPC clusters using Slurm, resolving computational bottlenecks to improve pipeline stability and speed.
  • Benchmarked computational tools via literature reviews to select best-suited algorithms for analysis.
Jul 2024 – Aug 2024
Philippine Genome Center
Core Facility for Bioinformatics

Bioinformatics Intern

  • Developed and deployed a Galaxy Docker build on internal servers to standardize bioinformatics workflows for end-users.
  • Designed and implemented genome assembly workflows to streamline analysis of genomic data.
  • Used Slurm, Bash scripting, and Git for server resource management and code repository maintenance.
  • Diagnosed and resolved configuration errors during Galaxy implementation on internal servers.
Feb 2023 – Jul 2024
Regenerative Biology Laboratory
UP Diliman

Research Intern

Advisor: Michael Velarde, PhD

  • Performed wet-lab protocols including bacterial culture in a microbiology setting.
  • Applied bioinformatics tools to analyze sequences and construct phylogenetic trees.
  • Generated informative heatmaps for gene expression data and performed network analyses in RStudio.
University of the Philippines Association of Biology Majors
Vice President for Alumni Relations August 2024 – July 2025
Alumni Relations Committee Member September 2023 – July 2024, August 2025 – Present
  • Served as the primary liaison for alumni relations, managing communication channels and implementing strategies that sustained their connection and support for the organization.
  • Spearheaded the logistical planning and execution for Career Talks with 50 attendees, ensuring smooth operations and maximizing alumni and student participation.
  • Led fundraising efforts that successfully secured ₱150,000 to host an improv show to improve alumni engagement with the organization.
  • Improved and maintained an alumni database to streamline communication and engagement efforts, facilitating targeted outreach of over 900 alumni.
University of the Philippines Data Science Society
Philippine Junior Data Science Convention Externals Manager July 2024 – July 2025
Vice Director for Mentorships February 2026 – Present
  • Cultivated partnerships with organizations including GlobalCo, DICT, and DOTr for the Philippine Junior Data Science Convention.
  • Collaborated with internal committees to align external partnerships with promotional efforts.
  • Developed the final financial report for stakeholders.
  • Coordinate external partnerships and stakeholder engagements to deliver workshops that foster skill development.
Sep 2021 – Present
Independent

STEM Tutor

  • Provided pro bono tutoring in Mathematics and Science to 6 students.
  • Designed tailored learning resources to reinforce classroom learning and address specific challenges.
  • Employed collaborative tutoring approaches to foster student understanding and success.
Projects

Selected Work

Python · Machine Learning

Kidney Stone Predictor

A classification application that predicts the presence or absence of kidney stones given urine sample measurements. Gradient Boosting Classification is applied to a set of physicochemical urine features to produce reliable, interpretable predictions.

Scikit-learn Gradient Boosting Classification Python
GitHub → Live Demo →
R · Machine Learning

Breast Tissue Impedance Classifier

An interactive Shiny dashboard that classifies breast tissue types from electrical impedance measurements. Five supervised classifiers are trained, compared, and deployed, with live single-sample prediction and interpretability tools built in.

R Shiny Random Forest SVM Classification
GitHub → Live Demo →
Skills

Technical Toolkit

Languages & Analysis

R / Bioconductor ggplot2 Python NumPy Pandas Scikit-learn Matplotlib Seaborn Bash HTML/CSS JavaScript

Bioinformatics Tools

FastQC Trimmomatic STAR Cufflinks GATK Arriba VarRNA dNdSc ASEP Galaxy

Infrastructure & DevOps

Slurm (HPC) Docker Git / GitHub Conda MobaXterm Linux

Wet Lab

Microbial Isolation Genomic DNA Extraction Plasmid DNA Extraction PCR Bacterial Culture

Analytical Methods

Variant Calling Transcriptomic Analysis Phylogenetic Analysis Gene Expression Network Analysis Statistical Modeling

Soft Skills

Technical Presentations Scientific Writing Project Management Stakeholder Communication Outreach
Publications

Manuscripts

2026

Analyzing treatment-driven selection across breast cancer stages in Filipino patients through transcriptomic time-series analysis

Lopez, J. E. G.

In Preparation
2021

A correlational study on the gross domestic product and GDP per capita of a country and its COVID-19 incidence and mortality rates

Lopez, J. E. G. — doi:10.22541/au.163519367.70608655/v5

Preprint
View Preprint →
Education

Academic Background

Expected July 2026
University of the Philippines Diliman
BS Molecular Biology and Biotechnology
Statistics Differential Equations Linear Algebra Bioinformatics Systems Biology Biotech Enterprise
Graduated May 2022
Ateneo de Manila High School
Senior High School — STEM Strand
Award for Excellence in the STEM Strand
Contact

Let's work together

I am open to research collaborations, internship opportunities, and conversations about computational biology, cancer genomics, and data-driven approaches to public health. Feel free to reach out.

Email jglopez2@up.edu.ph Phone (+63) 995-008-8123 LinkedIn joseph-emmanuel-lopez
Based Quezon City, Philippines