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Alberto J Martin, PhD

Principal Investigator

Network Biology Lab

Alberto J. Martín is a biologist and computational scientist whose career bridges biology, computer science, and artificial intelligence. He obtained his BSc in Biology from Universidad Autónoma de Madrid, and a Master’s in Bioinformatics and Computational Biology at Universidad Complutense de Madrid. In 2009, he completed his PhD in Computer Science at University College Dublin, specializing in protein structure prediction and machine learning. He then pursued postdoctoral research at the University of Padua (Italy), focusing on graph-based representations of biological systems and their applications to protein stability and functional annotation.

In 2013, he moved to Chile to join Fundación Ciencia & Vida as a postdoctoral researcher. He later became Assistant Professor at Universidad Mayor (2017–2022), where he contributed to curriculum development in data science and genomics. Since 2022, he has been Associate Professor at the School of Engineering, Universidad San Sebastián, and Associate Researcher at Fundación Ciencia & Vida, where he leads the Network Biology Lab. Since January 2025, he also serves as Acting Director of the PhD Program in Computational Biology.

His research focuses on computational methods for the inference and comparison of biological networks, with applications to gene regulation, microbiome dynamics, and complex diseases. He has authored over 50 peer-reviewed publications and actively promotes international collaborations at the intersection of computational biology, machine learning, and high-performance computing.

Grants

Group leader in CYTED Network “RIABIA-pro - Red Iberoamericana de Prospectiva en Inteligencia Artificial para Biociencias y Biotecnologı́a” [526RT0199] (2026 - 2029). Scientist in Fondecyt Regular [1260214], 4 years research project (April 2026 to April 2030) “Adenosine A2A Receptor on Dendritic Cells: A Critical Checkpoint for T Cell Exhaustion and Cancer Immunotherapy”. Scientist in FONDECYT Exploración project [13250023], 4 years research project (November 2025 to October 2029) “Impact of GABA-Producing Bacterial Consortia in Neuroprotection: Unraveling Mechanisms and Predictive Modeling of the Gut-Brain Axis and Neurodegenerative Diseases”. Scientist in FONDECYT Exploración [13240042], 4 years research project (November 2024 to October 2028) “Collective Mind: from computational modeling to computational sociology. Unveiling the Role of Self and Situational Awareness in Agent-Based Systems”. Scientist in Fondecyt Regular [1230764], 4 years research project (April 2023 to April 2027) “MODEL-GUIDED ANALYSIS OF MICROBIAL INTERACTIONS LEADING TO COLONIZATION RESISTANCE AND DYSBIOSIS IN THE GUT MICROBIOTA”. Scientist in Fondecyt Regular [1231629], 4 years research project (April 2023 to April 2027) “Deciphering the molecular crosstalk between tumor microbiota, CD8+ T cell and tumor cells in the tumor microenvironment in lung adenocarcinoma”. Scientist in Fondecyt Regular [1220196], 4 years research project (April 2022 to April 2026).“Not too much, not too little, just right: the unexpected role of adenosine in the antitumor immune response”. Scientist in Anillo 2021 “Modeling of Epigenetic Gene Regulatory Networks in sweet cherry floral buds in response to differential seasonal climate conditions” [ACT210007] 3 years project. Scientist in Fondequip Mayor “Renovación Infraestructura del Laboratorio Nacional de Supercomputacion” [EQY210001] (2021). Group leader in CYTED Network: “RED IBEROAMERICANA DE INTELIGENCIA ARTIFICIAL PARA BIG BIODATA (RIABIO)” [521RT0118] (2021-2024). Scientist in Proyecto Apoyo a Formación de Redes Internacionales de CONICYT 2018 [REDES180138] (2019-2021) “Discovery of neuroprotective bacterial metabolites and their mechanism of action in C. elegans”. Scientist in Proyecto Estrategico 2018 CYTED [919PTE0588] (2019-2022). “DESARROLLO DE CONSORCIOS BACTERIANOS PARA EL TRATAMIENTO DE ENFERMEDADES NEURODEGENERATIVAS”. Scientist in Fondecyt Regular [1190074], 4 years research project (April 2019 to April 2023). “IDENTIFICATION OF CROSS-FEEDING INTERACTIONS IN THE GUT MICROBIOME FOR DESIGNING MICROBIAL COMMUNITIES”. Principal Investigator Fondecyt Regular [1181089] 4 years research project (April 2018 to April 2022)“Development of Computational Methods for the Determination of Causal-Condition Specific Gene Regulatory Networks”. Principal Investigator Fondecyt Iniciacion [11140342] 3 years research project (November 2014 to November 2017)“From gene expression data to dynamic simulation of gene regulatory networks: development of inference methods based on local motifs and their biological applications”.

Collaborations

Selected Publications

Featured Publications presents a curated selection of the researcher’s most significant scientific contributions, reflecting their expertise, findings, and the broader impact of their work in advancing knowledge within their field.

Bioinformatics Advances
scExplorer: A Comprehensive Web Server for Single-Cell RNA Sequencing Data Analysis
PLOS Neglected Tropical Diseases
Comparative and systems analyses of Leishmania spp. non-coding RNAs through developmental stages
Briefings in Bioinformatics
Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states
Microbiology Spectrum
Using metabolic networks to predict cross-feeding and competition interactions between microorganisms.
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