Jose A Caparros-Martin, PhD
Data analysis · Genomics · Reproducible research
Data analysis · Genomics · Reproducible research
This site summarizes my work across biology, biotechnology, and data science, including my training, experience, publications, and projects.
I hold a degree in Biology and a PhD in Biotechnology. My early research focused on molecular genetics, where I contributed to identifying genes associated with rare human developmental disorders, with an emphasis on research that can translate into clinical and societal benefit.
After moving to Australia, I helped establish the Human Microbiome Collaboration Centre at Curtin University. There, I worked on microbiome profiling as a marker of disease and its potential for earlier detection, monitoring, and prevention in chronic conditions.
More recently, my work has increasingly leaned into computational approaches. I am especially focused on bioinformatics and applied machine learning, including language models and multi-agent systems, to extract insight from complex biological data and improve biomedical research workflows.
Outside of work, I spend time with my family and enjoy astronomy, fossil collecting, and exploring Western Australia.
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This project explores traditional machine learning (ML) and large language models (LLMs) to classify sentences by suicide risk using a labeled dataset from Kaggle, aiming to detect language patterns associated with suicidal ideation.
Repo: GitHub Repo
Pilot study evaluating whether early-life nasal microbiota from healthy infants predicts wheezing in the first year of life.
Preprint: MedRxiv link
Repo: AERIAL microbiota
In this project, we investigated the molecular pathways underlying the gut–lung axis in chronic lung diseases to identify potential therapeutic targets. We identified gut microbiota–derived metabolites that modulate lung inflammation and immune responses in cystic fibrosis and other chronic lung diseases. We published multiple papers and presented these findings at international conferences. Below are examples of our work in this area.
Bile acids and early inflammation in CF lung disease - findings from the COMBAT CF cohort: Caparros-Martin et al. Microbiome (2023)
Bile acids and airway microbiota remodeling in COPD: Caparros-Martin et al. BMJ Open Resp Res (2024)
In this project, We studied how activation of liver nuclear receptors can reshape the gut microbiota and influence downstream physiology, including metabolic outcomes. Because these receptors are commonly triggered by drugs, diet-derived compounds, and other xenobiotics, this host-driven modulation of the microbiota has direct implications for human health and therapeutic responses.
Nuclear receptor–gut microbiota interactions in response to statin therapy: Caparros-Martin et al. Microbiome (2017)
During my postdoctoral training in molecular genetics, I led projects to identify causative genes and define disease mechanisms across rare human disorders, with a focus on skeletal dysplasias (including short-rib polydactyly syndromes and osteogenesis imperfecta). I also contributed to studies in congenital multiminicore myopathy and Neu-Laxova syndrome. In parallel, I investigated how the Ellis–van Creveld (EVC/EVC2) complex functions in primary cilia to mediate Hedgehog signalling. Below are examples of our work in this area.
The role of the EVC/EVC2 complex in Hedgehog signaling and skeletal development: Caparros-Martin et al. Human Molecular Genetics (2013)
Identification and molecular characterization of BMP1 mutations in osteogenesis imperfecta: Martinez-Glez et al. Human Mutation (2012)