André Salgado is a PhD student in Computer Science and Engineering at Instituto Superior Técnico (IST), conducting research at the Gulbenkian Institute for Molecular Medicine (GIMM) and INESC-ID. His doctoral work focuses on applying genomic language models (gLMs) to biomarker discovery, using colorectal cancer (CRC) as a case study. In his first PhD year, he developed a reproducible pipeline for shotgun metagenomic data processing, now used across GIMM initiatives—including the Microbiome in Health & Disease Translational Lab, the Advanced Breast Cancer Translational Lab, and the EU-funded ENDOTARGET project (Horizon Europe). He completed PhD coursework in research methodologies with top grades. His final project in the “Research Topics” course (18/20) evolved into a comparative study on taxonomic profilers for CRC biomarker discovery, now being finalized as a 15-page publication. This laid the foundation for his current focus on gLM-based alternatives to traditional pipelines. During this period, André also taught a 3-month Software Engineering course at IST, delivering weekly 3-hour practical classes to third-year undergraduates. He received a global teaching rating of 8.56/10, highlighting strong communication and mentorship skills. André is an active member of the BIOMICS Twinning Project (HORIZON-WIDERA-2023-ACCESS-02,grant number:101159926), a collaboration between GIMM, EMBL-EBI (UK), CRG (Spain), and ETH Zurich (Switzerland). Through BIOMICS, he receives advanced training in biomedical data science and benefits from an international community of computational researchers. In 2024, he received the DMM Conference Travel Grant from The Company of Biologists, a prestigious award supporting early-career researchers in disease-related research. With this support, he presented a poster at the Cold Spring Harbor Laboratory (CSHL) Microbiome Meeting in New York—one of the world’s leading microbiome conferences. His poster summarized first-year PhD research, including pipeline development and initial CRC microbiome analyses. Currently, André is completing a three-month research visit (March–June 2025) at the University of Cambridge, hosted by Dr. Alexandre Almeida in the Microbiome Function and Diversity group. This collaboration was instrumental for benchmarking traditional ML Pipelines for CRC prediction, and his continued guidance remains valuable for the remainder of the PhD. Previously, André earned a Master’s in Computer Science and Engineering at IST and joined the Health and Medical Data Analytics (HMDA) program. As part of this program, he attended a summer school in France and a semester abroad at UPM (Spain), taking courses in Big Data, Machine Learning, Complex Data in Health, and Data Visualization. His thesis on circular DNA alignment earned a perfect score (20/20), was presented at ISBRA 2023, and published in the proceedings. He also placed 4th internationally in the EIT Health Innovation Challenge with a digital health solution—Portugal’s top result. His academic path began with a Bachelor’s in Computer Science and Engineering at the University of Beira Interior, where he earned a 19/20 in his final project course, conducting research on software reliability. Early experiences include a summer internship at GLINTT, contributing to a healthcare-focused project, and a highly impactful internship at SAP Portugal, where he developed an internal tool that has since been adopted across SAP.