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Mark Cyril Mercado

@markcyrilmercado

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Bioinformatics researcher building reproducible genomics and RNA-seq pipelines with AI-ready systems.

Philippines

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What I'm looking for

I’m looking for a research role where I can build reproducible genomics pipelines, pair bioinformatics with molecular biology, and apply machine learning to biological phenotyping—while contributing clear documentation, peer mentoring, and impactful scientific outputs.

I’m a molecular biology and bioinformatics researcher currently pursuing an MS Molecular Biology and Biotechnology (in progress) as a GREAT Program Scholar, with a GREAT discipline for reproducible research. I design and execute bioinformatics pipelines for high-throughput sequencing analysis—RNA-seq gene expression, draft whole-genome assembly, ANI-based taxonomic identification, and homology-based functional annotation—using structured research documentation to keep results transparent and reusable.

As lead developer, I’ve built modular open-source pipeline tools like Eggplant_Pipeline and RNA-SeqMAP, and I’m contributing to a DOST-PCAARRD-funded eggplant breeding research project where I help identify and structurally characterize gene families (e.g., SmelDMP, GRF-GIF) for haploid inducer development. I also design in silico CRISPR-Cas gRNA candidates, work on off-target prediction, and apply machine learning to biological phenotyping—bridging wet-lab questions with computational rigor, mentoring, and clear scientific communication.

Experience

Work history, roles, and key accomplishments

Graduate Research Associate

Institute of Plant Breeding, UPLB

Aug 2024 - Jul 2026 (1 year 11 months)

Planned and executed thesis research on eggplant doubled haploid production, including computational and in silico characterization of the SmelDMP gene family to support haploid inducer line development. Improved and generalized a modular SmelDMP bioinformatics pipeline, curated RNA-seq accessions, and conducted early ML training optimization for microspore phenotyping.

ANI Based Taxonomic Identification HMMER BLAST Functional Annotation Phylogenetics CRISPR Cas GRNA Design Machine Learning For Phenotyping Research Data Management

Peer Tutor (Part-time)

UPLB Learning Resource Center (LRC)

Dec 2022 - Jun 2023 (6 months)

Provided one-on-one, paired, and small-group tutorials in Biology and Chemistry as a peer tutor under the SUPSA/PEER tutoring program. Supported administrative and clerical coordination for the university’s tutoring activities.

Chemistry Tutoring Small Group Instruction Administrative Support Student Support

Undergraduate Thesis Student

University of the Philippines Los Baños

Jan 2022 - Jan 2023 (1 year)

Developed and executed a bioinformatics pipeline for Illumina short-read sequencing to draft genome assembly and perform ANI-based taxonomic identification of bacterial isolates. Performed in silico mining and structural characterization of the CGTase gene and protein from whole-genome sequences.

Illumina ANI Based Identification In Silico Gene Mining

Volunteer - Ugnayan ng Pahinungod

UPLB Ugnayan ng Pahinungod

Jan 2017 - Jan 2023 (6 years)

Facilitated psychosocial support and stress-management training for high school students and contributed to community outreach activities. Participated in volunteer events including OpenStreetMap-related annotation work.

Stress Management Community Outreach Volunteer coordination Student Support Training Delivery OpenStreetMap

Education

Degrees, certifications, and relevant coursework

University of the Philippines Los Baños (UPLB)

Master of Science, Molecular Biology and Biotechnology

2024 -

Activities and societies: Minor in Computer Science; GREAT Program Scholar; thesis research in plant breeding and genomics.

MS candidate in Molecular Biology and Biotechnology with a minor in Computer Science under the GREAT Program. Current work includes thesis research on eggplant haploid/doubled haploid line development and related genomics and machine-learning approaches.

University of the Philippines Los Baños (UPLB)

Bachelor of Science, Biology (Cell and Molecular Biology)

2017 - 2023

Grade: Cum Laude

Activities and societies: Undergraduate thesis (2023): draft genome assembly + ANI; in silico mining/characterization of CGTase.

B.S. Biology (Major in Cell and Molecular Biology), graduated cum laude. Completed undergraduate thesis involving Illumina short-read genome assembly, ANI-based taxonomic identification, and in silico mining/structural characterization of the CGTase gene in bacterial isolates.

Pagbilao Academy

High School Diploma, High School

2010 - 2015

Grade: 2nd Honorable Mention

Completed high school education, graduating with 2nd Honorable Mention. Completed a research-focused high school track and academic excellence recognition.