Anna Goldenberg

Anna Goldenberg

Appointment

  • Fellow
  • Child & Brain Development

Institution

  • University of Toronto
  • Hospital for Sick Children
Genetics and Genome Biology
Department of Computer Science

Country

  • Canada

Education

PhD (Machine Learning), Carnegie Mellon University
MSc (Knowledge Discovery & Data Mining), Carnegie Mellon University
BEng (Engineering Mathematics and Computer Science), University of Louisville

About

Anna Goldenberg develops machine learning methods that combine diverse sets of biological and phenotypic measurements to refine the understanding of complex human diseases, identify the best treatments and individual patient outcomes, and guide decisions to improve the quality of life for patients.

Her data integration method – Similarity Network Fusion (SNF) – was the first to integrate patient data (omics, imaging, etc.) using patient networks. It improved survival outcome predictions in five different cancers.

More than two-thirds of mental health issues have their onset during childhood or adolescence. Identifying children who are at risk for mental illness later in life, and predicting the type of illness, is not easy. There are no blood or genetic ‘tests’; instead, psychiatrists and other health professionals use an individual’s personal and family clinical history to note persistent symptoms and make a diagnosis. Goldenberg believes that by modelling and combining trajectories of social-emotional and neurocognitive measures over time, and using genome-wide genetic and DNA methylation data, it is possible to identify clinically relevant subtypes of childhood and adolescent development and also the corresponding biomarkers that predict traits underlying psychiatric disorders.

The easy-to-use computational tools developed to ascertain longitudinal subtypes and their associated biomarkers will be made available to the larger research community. The findings of Goldenberg and her team will implicate both short- and long-term predictors and biological contributors of psychopathology, helping to unravel the complex relationship between genomics and social-emotional development. Hopefully, these findings will also generate candidate biological targets for novel treatments.

Awards

Department of Computer Science Award for exceptional mentoring and outstanding commitment to graduate student recruitment, University of Toronto, 2016
Early Researcher Award from the Ministry of Research and Innovation, 2016
Best poster presentation award at the Young Investigator Meeting, organized by the CIHR Institute of Cancer Research, 2013
MITACS Theory and Applications award, 2010

Relevant Publications

Corre, C. et al. “Sex specific regulation of weight and puberty by Lin28/let7 axis.” Journal of Endocrinology 228, no. 3 (2016): 179–91.
Rampasek, L., and A. Goldenberg. “TensorFlow: Biology’s Gateway to Deep Learning?” Cell systems 2, no. 1 (2016): 1214.
Saria, S., and A. Goldenberg. “Subtyping: What it is and its role in precision medicine.” IEEE Intelligent Systems Magazine 30, no.4 (2015): 7075.
Colak, R. et al. “JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis.” Bioinformatics 32, no. 2 (2015): 201–10.
Wang, B. et al. “Similarity network fusion for aggregating data types on genomic scale.” Nature Methods 11, no. 3 (2014): 3377.

Mezlini, A. et al. “Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA to gene networks using regularized regression.” PloS One 8, no. 10 (2013): E73168.
Goldenberg, A. et al. “Unsupervised detection of genes of influence in lung cancer using biological networks.” Bioinformatics 27, no. 22 (2011): 316672.

Connect

Goldenberg Lab