Marta Ferreira
PhD Student
Experience
PhD Student
University of Porto / i3S
- Developing the project "Multi-tool integration for comprehensive characterization and validation of genomic and transcriptomic data" (expected Nov 2025)
- Focus on automated pipelines for WGS and RNAseq data, integrating multiple variant callers to improve genomic analysis accuracy
Research Fellow
University of Minho / i3S
- Contributed to EU-funded projects (GenomePT, MISTiC), supporting development of computational workflows for high-throughput sequencing data analysis
Research Technician
i3S – Institute for Research and Innovation in Health
- Developed and optimized bioinformatics pipelines within the national GenomePT project, supporting cancer genomics and rare disease research
Professional Internship
Instituto de Medicina Molecular (IMM)
- Performed RNAseq and NET-seq data analyses using multiple bioinformatics tools
Curricular Internship
Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA)
- Analyzed whole-genome sequencing data from food- and waterborne pathogens for public health surveillance studies
Summary
Marta Ferreira, MSc is a PhD candidate in Bioinformatics in Health at the University of Porto / i3S, with over seven years of research experience in genomics, transcriptomics, and bioinformatics tool development. Her work focuses on designing and implementing automated pipelines for whole-genome sequencing (WGS) and RNAseq data, integrating multiple variant callers to improve accuracy and reproducibility. She has contributed to several national and European research projects in cancer genomics, rare diseases, and precision medicine, including SOLVE-RD, LEGOH, MISTiC, and GenomePT.
Marta is proficient in Python, R, and UNIX/Shell scripting, with additional experience NGS analysis tools, and multi-omics data integration, and currently extends her expertise in Nextflow and SQL. She has co-authored 13 peer-reviewed publications in international journals such as Gut, Brain Communications, and Gastric Cancer. In addition to her research, she actively teaches and mentors students, and has organized multiple workshops and PhD training sessions on bioinformatics and omics data analysis.
Her strengths include technical innovation, analytical problem-solving, and collaborative research across computational and experimental teams, making her a versatile and motivated bioinformatician with a strong commitment to scientific excellence.
Skills
Programming And Technical Skills
- Proficient In Python, R, And Unix/shell Scripting For Bioinformatics And Data Analysis.
- Experience With Next-generation Sequencing (Ngs) Analysis Tools, Including Fastqc, Bowtie, Bwa, Samtools, Picard, Tophat, Kallisto, Htseq, Lumpy, Delly, Gridss, And Spades.
- Hands-on Experience Managing Computational Workflows On Hpc Clusters And Ubuntu-based Servers.
- Skilled In Developing And Automating Bioinformatics Pipelines; Currently Extending Expertise To Nextflow.
- Familiar With Version Control Systems (Git/github) And Database Resources Such As Genome Browser, Tcga, Gtex, Ensembl, And Bioportal.
- Basic Knowledge Of Sql And Data Visualization With Tableau.
- Additional Experience With Matlab, C Programming, And Process Analysis Tools (Simnon, Simca).
- Proficient In Standard Office And Documentation Software (Excel, Word, Powerpoint).
Interpersonal And Professional Skills
- Excellent Written And Oral Communication Skills.
- Strong Organizational Abilities, Adaptability, And Problem-solving Capacity.
- Effective Time Management And Goal-oriented Work Ethic.
- Experience In Teaching And Mentoring Students In Bioinformatics.
- Driving License: B1, B.
Languages
Education
Faculty of Sciences, University of Porto / i3S
PhD in Bioinformatics in Health (Doctoral Program in Computer Science) · Bioinformatics in Health (Doctoral Program in Computer Science) · Porto, Portugal
Faculty of Pharmacy and Instituto Superior Técnico, University of Lisbon
Master’s Degree in Pharmaceutical Engineering · Pharmaceutical Engineering · Lisbon, Portugal · 17/20
University of Trás-os-Montes and Alto Douro
Bachelor’s Degree in Biomedical Engineering · Biomedical Engineering · Vila Real, Portugal · 14/20
Certifications & licenses
Driving License: B1, B
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