Dr. Pilib Ó Broin

Lecturer in Bioinformatics (Biomedical Genomics)
Programme Director, MSc in Biomedical Genomics & MSc in Computational Genomics

Research interests

  • Functional genomics & clinical bioinformatics
  • Machine learning, data fusion and visualisation

Research overview

My research group is primarily interested in the development and application of statistical/machine learning methods in different biological contexts. Examples include:

1. Risk stratification in transplant patients

Current projects include the development of a PSO-optimsed ensemble classifier to provide better predictions of graft survival in kidney transplant patients. This work is focused on sub-clinical detection of antibody-mediated rejection (AMR), a leading cause of graft failure, and is being carried out in collaboration with the kidney transplant program at the Albert Einstein College of Medicine in New York.

2. Cancer Genomics

Current projects include: i) Understanding the role of the bone marrow microenvironment in AML progression and drug resistance, and ii) the development of graph-based machine learning methods to help elucidate the role of circRNAs in prostate cancer drug response. This work is being carried out in collaboration with colleagues here at NUIG as well as at St James’s hospital/TCD.

(Zhang et al. npj Precision Onc, 2017)

3. Neuroscience

This work stems from my affiliation with NICOG – the Centre for Neuroimaging and Cognitive Genomics. Current projects include: i) the development of novel machine learning methods for polygenic risk scoring in genome-wide association studies related to schizophrenia/cognitive function, and ii) the use of convolutional neural networks (CNNs) to identify image-derived phenotypes in MRI scans of bipolar disorder patients for improved intepretability in GWAS studies.

Selected publications

  1. Pilib Ó Broin * , Michael V Beckert*, Tomohisa Takahashi*, Takeshi Izumi, Kenny Ye, Gina Kang, Patricia Pouso, Mackenzie Topolski, Jose L Pena, Noboru Hiroi. Computational analysis of neonatal mouse ultrasonic vocalization. Curr Prot. Mouse Biology. 8(2),e46 (2019) * denotes equal contribution
  2. Michelle Lubetzky, Nicole Hayde, Pilib Ó Broin, Maria Ajaimy, Yi Bao, Omar Mohammed, Daniel Schwartz, James Pullman, Enver Akalin. ‘Molecular signatures and clinical outcomes of transplant glomerulopathy stratified by microvascular inflammation and donorspecific antibody’. Clinical Transplantation e13469 (2018)
  3. Deanna Acosta, Susmita Bagchi, Pilib Ó Broin, Silvia E. Racedo, Bernice Morrow, Rani Sellers, John Greally, Aaron Golden, Eran Andrechek, Teresa Wood, and Cristina Montagna. Transcriptome profiling supports LPA receptor activity in enriched mammary epithelial cell populations during postnatal develop- ment. Sci. Rep. 6:35810 (2017).
  4. Anjali Gupta, Pilib Ó Broin, Yi Bao, James Pullman, Layla Kamal1, Maria Ajaimy, Michelle Lubetzky, Adriana Colovai, Daniel Schwartz, Graciela de Boccardo, Aaron Golden, and Enver Akalin. ‘Clinical and molecular significance of microvascular inflammation in transplant kidney biopsies’. Kidney Int. 89(1): 217-225 (2016)
  5. Tomohisa Takahashi * , Shota Okabe * , Pilib Ó Broin * , Akira Nishi, Kenny Ye, Michael Beckert, Takeshi Izumi, Hiroaki Machida, Gina Kang, Jose L. Pena, Aaron Golden, Takefumi Kikusui, Noboru Hiroi. ‘Struc- ture and function of neonatal social communication in a genetic mouse model of autism spectrum disorders’. Mol. Psych. 21(9):1208 (2016) * denotes equal contribution
  6. Behnam Nabet, Pilib Ó Broin, Jaime M. Reyes, Kevin Shieh, Charles Y. Lin, Christine M. Will, Relja Popovic, Teresa Ezponda, James E. Bradner, Aaron A. Golden, and Jonathan D. Licht. ‘Deregulation of the Ras-Erk signaling axis modulates the enhancer landscape’. Cell reports 12(8):1300-1313 (2015)
  7. Irwin J. Kurland*, Pilib Ó Broin* , Aaron Golden* , Fan Meng, Gang Su, Laibin Liu, Robert P. Mohney, Shilpa Kulkarni, and Chandan Guha. ‘Integrative metabolic signatures for hepatic radiation injury’. PLoS One. 10(6), e0124795 (2015)
  8. Pilib Ó Broin, Terry Smith, and Aaron Golden. ‘Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach’. BMC Bioinformatics. 16(1):22 (2015)
  9. Pilib Ó Broin, Bhavapriya Vaitheesvaran, Subhrajit Saha, Kirsten Hartil, Emily I. Chen, Devorah Goldman, William Harv Fleming, Irwin J. Kurland, Chandan Guha, and Aaron Golden. ‘Intestinal Microbiota Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury’. Int. J. Radiat. Oncol. Biol. Phys.  91(2):360-367 (2015)
  10. Nicole Hayde, Pilib Ó Broin, Yi Bao, Graciela de Boccardo, Michelle Lubetzky, Maria Ajaimy, James Pullman, Adriana Colovai, Aaron Golden, and Enver Akalin. ‘Increased intragraft rejection–associated gene transcripts in patients with donor-specific antibodies and normal biopsies’. Kidney Int. 86(3):600-9 (2014)