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Aedin Culhane

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Aedin Culhane

Prof.

 https://orcid.org/0000-0002-1395-9734

Accepting PhD Students

PhD projects

Cancer Genomics, Single Cell Biology, Genomics, Bioinformatics, Multi 'Omics, Bioconductor, Digital Pathology, Real world evidence, AI and data analytics,

1996 …2026

Research activity per year

Personal profile

Biography

Aedín Culhane is Director of the Limerick Digital Cancer Research Centre and is Professor of Biomedical Sciences (Cancer Genomics) in the UL School of Medicine. She is also ELIXIR-Ireland head of node and co-lead of the eHealth-Hub for cancer.
 
She is a computational oncologist with expertise in multi-omics data integration, statistical genomics, clinical bioinformatics and genomics in oncology.  She has over 20 years experience in cancer genomics, of which over 15 years were in the Dana-Farber Cancer Institute and Harvard TH Chan School of Public Health in Boston, USA.
 
Her research focuses on algorithm development and integrating cancer real world and molecular data to understand tumour development, progression, drug response and resistance. She has developed multiple algorithms that extend matrix factorization for multi modal data integration. These are published as open source software packages in R/Bioconductor. Since returning to Ireland in 2021, accessible data is a focus of the lab research, this includes preparedness for the European Health Data Space (EHDS) and Life science data space, data standards, interoperability and software best pratice. Getting these right will provide the foundation to catalyze a revolution in cancer data integrative analysis and understanding in cancer.
 
She is a leader in the Bioconductor  a global open source, open development software in R for genomics and an advocate for open source science. Connect with UL's Bioconductor leaders; Dr Maria Doyle  and Dr. Nicholas Cooley
 
She is co-lead and PI of the all-island eHealth- Hub for Cancer funded under the HEA North-South program in partnership with Prof Mark Lawler, Queens University Belfast.  Together with Catherine O Mahoney, they lead OHDSI-Ireland, the national node of OHDSI in Ireland.  They host monthly webinar, register/learn more on the eHealth-Hub for Cancer Website.
 
She is a member of the Ireland 1+ million genome (1+ MG) program and is delivering the technical aspects of the Genomic Data Infrastructure with her team that will be an important step toward realising 1+MG and European federated genomics to advance our understanding of health and disease.
 
She is head of node of ELIXIR-Ireland. ELIXIR Ireland is the Irish node of ELIXIR, the European infrastructure for life science data. We connect researchers, data resources, and computational tools to advance biological research.
 
She is national lead on CANDLE, National Cancer Data Node (NCDN) Developers, building NCDN that align with and deliver EHDS for cancer research. She is also leading genomics and imaging data standards in the EU Joint Action Precision Cancer Medicine
 
Links to projects and programs we lead are below. Here are linked to personal pages;

Research Interests

Cancer Computational Genomics and; Digital Health Director of the Limerick Digital Cancer Center Lead the all-island eHealth-Hub for Cancer Member, All-Ireland Cancer Institute Steering Group Open Science: Bioconductor, ELIXIR, OHDSI
  • Single Cell Genomics methods for the Human Cell Atlas Program
  • Spatial Biology Methods development for the National Spatial Profiling Platform
  • Cancer genomics, clinical cancer research, translational oncology
  • Latent Space and Matrix Factorisation and Cancer Genomics algorithm development
  • Immune-Oncology, Tumor Microenvironment
  • European 1+ Million Genomes Program GDI
  • Real world evidence
Specialties: Bioconductor, R, bioinformatics, genomics, multivariate analysis, multi-omics, biostatistician, transcriptomics, proteomics, epigenomics, computational biology, mathematical oncology, tumor microenvironment, tumor immunology, neuro-immunology, kidney cancer, breast cancer, ovarian cancer, electronic health records, data harmonisation, genomics, real world data, real world evidence, data standards, open science, FAIR data

Teaching Interests

I teach 6-week, intensive 9 credit microcredentials that are open to everyone, students and staff in UL, as well as professional or students wishing to upskill in real world data reserach and readiness for the European Health Data Space secondary data use. These courses are available through skillnet Ireland which provide substantial tutiion discount to eligible students.

Micro-credentials also known as MicroCreds are short, university accredited, assessed and enterprise powered qualifications that can be undertaken at different EU universities and stacked to create a personalized certificate, diploma or masters degree.

BM6053: Introduction to Real World Data in Cancer Clinical Research 

The purpose of this module is to upskill professionals who interact, manage, curate or analyse cancer electronic health data and/or are engaged in cancer real world evidence research. Real-world data describes health data, collected outside of randomised controlled trials typically as part of routine clinical practice. If analysed appropriately, real world data can generate real-world evidence, which can offer insights into disease and the benefits and risks of therapeutic interventions as observed in a real-life environment. This module describes the types of data in a cancer patient’s electronic health record and their secondary use in research

BM6063: Data Analytics for Cancer Real World Data Research  

The purpose of this module is to provide practical experience and upskill data scientists and health informatics professionals who manage, curate or analyse cancer electronic health data and/or are engaged in cancer real world evidence research. The module will provide students with an understanding of the research challenges posed by traditional siloed healthcare data, and how standardisation of data can facilitate sharing and federated data analysis. This module will provide practical experience in transforming health data to widely used international data standards to facilitate of large-scale, federated data analytics research. It will prepare participants for real-world data research. By working with real-world cancer data and developing software and data science skills, participants will be able to contribute to the growing efforts in federated data sharing and secondary analysis of health data.

 

More - coming soon ;-).

Connect on linkedin and tell me what you would like .. 

 

Related documents

Education/Academic qualification

PhD, Cloning and Characterisation of Interleukin-18 in rat brain, University of Manchester

External positions

ELIXIR Head of Node, ELIXIR

1 Jul 2025 → …

Lead, eHealth-Hub For Cancer

2022 → 2027

Senior Research Scientist, Dana-Farber Cancer Institute

2017 → 2021

Senior Research Scientist, Harvard T.H. Chan School of Public Health

2017 → 2021

Research Scientist, Dana-Farber Cancer Institute

2011 → 2017

Research Scientist, Harvard T.H. Chan School of Public Health

2011 → 2017

Instructor (Adjunct), Brandeis University

2008 → 2010

Research Associate, Dana-Farber Cancer Institute

2005 → 2011

Research Associate, Harvard University

2005 → 2011

Postdoctoral Fellow, University College Dublin

2003 → 2005

Postdoctoral Researcher, University College Cork

2001 → 2003

Computational Biology Support and Training Officer, Biotechnology and Biological Sciences Research Council

1999 → 2001

Keywords

  • RC0254 Neoplasms. Tumors. Oncology (including Cancer)
  • Clinical Informatics
  • Data Standards
  • European Health Data Space
  • National cancer data node
  • QA76 Computer software
  • Bioinformatics
  • Computational Biology
  • AI
  • ML
  • software quality
  • R
  • Bioconductor
  • QR180 Immunology
  • Tumor Microenviroment
  • Neuro-Immune
  • CAR T-cells
  • NK Cells
  • QH426 Genetics
  • Genomics
  • Multi 'omics
  • Epidemiology
  • Real World Data
  • QH301 Biology
  • Oncology
  • Early Onset Cancer
  • Colorectal Cancer
  • Cancer
  • HA Statistics
  • Biostatistics
  • Data Science
  • Data Analytics
  • Tensor Matrix Factorization
  • Multi Modal Data Integration
  • Tensor

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  1. SDG 3 - Good Health and Well-being
    SDG 3 Good Health and Well-being
  2. SDG 4 - Quality Education
    SDG 4 Quality Education
  3. SDG 10 - Reduced Inequalities
    SDG 10 Reduced Inequalities

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  • Convergence of machine learning and genomics for precision oncology

    Reardon, B., Culhane, A. C. & Van Allen, E. M., Mar 2026, In: Nature Reviews Cancer. 26, 3, p. 217-229 13 p.

    Research output: Contribution to journal › Review article › peer-review

  • The 1+Million Genomes Minimal Dataset for Cancer

    Riba, M., Sala, C., Culhane, A. C., Flobak, Å., Patocs, A., Boye, K., Plevova, K., Pospíšilová, Š., Gandolfi, G., Morelli, M. J., Bucci, G., Edsjö, A., Lassen, U., Al-Shahrour, F., Lopez-Bigas, N., Hovland, R., Cuppen, E., Valencia, A., Poirel, H. A. & Rosenquist, R. & 7 others, Scollen, S., Arenas Marquez, J., Belien, J., De Nicolo, A., De Maria, R., Torrents, D. & Tonon, G., May 2024, In: Nature Genetics. 56, 5, p. 733-736 4 p.

    Research output: Contribution to journal › Comment/debate

  • Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data

    Hsu, L. L. & Culhane, A. C., Dec 2023, In: Scientific Reports. 13, 1, 1197.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • Genome-scale screens identify factors regulating tumor cell responses to natural killer cells

    Sheffer, M., Lowry, E., Beelen, N., Borah, M., Amara, S. N. A., Mader, C. C., Roth, J. A., Tsherniak, A., Freeman, S. S., Dashevsky, O., Gandolfi, S., Bender, S., Bryan, J. G., Zhu, C., Wang, L., Tariq, I., Kamath, G. M., Simoes, R. D. M., Dhimolea, E. & Yu, C. & 11 others, Hu, Y., Dufva, O., Giannakis, M., Syrgkanis, V., Fraenkel, E., Golub, T., Romee, R., Mustjoki, S., Culhane, A. C., Wieten, L. & Mitsiades, C. S., Aug 2021, In: Nature Genetics. 53, 8, p. 1196-1206 11 p.

    Research output: Contribution to journal › Article › peer-review

  • An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence

    Dhimolea, E., de Matos Simoes, R., Kansara, D., Al'Khafaji, A., Bouyssou, J., Weng, X., Sharma, S., Raja, J., Awate, P., Shirasaki, R., Tang, H., Glassner, B. J., Liu, Z., Gao, D., Bryan, J., Bender, S., Roth, J., Scheffer, M., Jeselsohn, R. & Gray, N. S. & 11 others, Georgakoudi, I., Vazquez, F., Tsherniak, A., Chen, Y., Welm, A., Duy, C., Melnick, A., Bartholdy, B., Brown, M., Culhane, A. C. & Mitsiades, C. S., 8 Feb 2021, In: Cancer Cell. 39, 2, p. 240-256.e11

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • 6 Membership of council
  • 5 Membership of committee
  • 1 Membership of board
View all 12 activities