Reimand Lab July 2017
Current Lab members
|Jüri Reimand – principal investigator
I am an investigator of informatics and biocomputing at the Ontario Institute of Cancer Research. I also have a faculty appointment of assistant professor at the University of Toronto with the department of Medical Biophysics. I completed my PhD in computer science at the University of Tartu in Estonia in 2010 and my postdoctoral training at the Donnelly Centre of the University of Toronto during 2011-2015. I joined the OICR in summer of 2015 and started my lab shortly after. I am interested in computational biology and cancer research, in particular integrative and network-driven approaches to interpret genomic information and advance our understanding of cancer biology and treatment.
|Diala Abd-Rabbo – postdoctoral fellow
I received my PhD and Master’s degree in Bioinformatics at the department of biochimie et médecine moléculaire at Université de Montréal. During my PhD, I have focused my research on a long-standing interest determining the structural and functional principles of phosphorylation signaling networks using integrative analysis of multi-omics data and working in the budding yeast S. cerevisiae as a model. For my Master’s degree in Bioinformatics, I was able to identify the first molecular signature associated with French Canadian BRCA1/2 mutations in primary cultures in morphologically normal ovarian epithelium cells and tumor ovarian cells using Affymetrix HuFL microarrays. My current research interest is in identifying cancer driver genes and identifying the rewiring events of biological networks in aggressive cancer with poor clinical output and understanding the effect of these events on network function.
|Karina Isaev – graduate student @karini925
I am a master’s student with the Department of Medical Biophysics at the University of Toronto. I am interested in elucidating the functions of long non-coding RNAs (lncRNAs) which are emerging as potential regulators of important processes in cancer. Currently there are over 19,000 annotated lncRNA genes where only a small subset has been functionally described. Using integrative pan-cancer data from projects such as PCAWG and TCGA, I would like to identify key pathways that lncRNAs are implicated in in order to predict their functions.
|Helen Zhu – graduate student
I am a graduate student in Medical Biophysics at U of T.
|Oliver Ocsenas – graduate student
I am a master’s student working on applying deep learning to omics datasets for predicting clinical characteristics of patients.
|Xiao Wang – undergraduate research student
I am a 4th year undergraduate student at the University of Toronto in the program of bioinformatics and human genetics. I am working on a 4th year research project (BCB430) relates to lncRNA (Long non-coding RNA) with multiple tumor types.
|Dike Aduluso – co-op student
I am an undergraduate student in Nanotechnology Engineering at the University of Waterloo.
|Marta Paczkowska – junior bioinformatician
I have just received my master’s degree in Bioinformatics and Systems Biology at the University of Warsaw (Poland). During my studies I had the opportunity to gain knowledge in the fields of computer science and molecular biology. My major interest lies in cancer research. Currently I am working on modelling protein-peptide interactions and pathway analysis.
|Miles Mee – bioinformatician
I recently received my master’s degree in bioinformatics from the University of Guelph. My areas of interest are in healthcare research and web development. Currently, I am investigating how distal enhancer interaction data can contribute to modeling patient survival.
|Tina Huang – research assistant
I am a recent H.B.Sc graduate from the University of Toronto with a specialist in pharmacology. My research interests lie in the use of computational biology approaches for cancer research, particularly in the domain of pharmacogenomics. My current project involves analyzing somatic mutations in cancer genomes for potential kinase rewiring events.
|Nardnisa Sintupisut – research technician
I am a research technician with hands-on experience in large-scale data integration in cancer genomics and regulatory network reconstruction in human carcinoma cell lines. I completed my B.Sc. in Genetics from Kasetsart University and achieved M.Sc. in Bioinformatics from King’s Mongkut of Technology Thonburi, Thailand. After graduation, I worked as a research assistant at the Institute of Biological Chemistry and the Institute of Statistical Science, Academia Sinica, Taiwan. As project responsibilities, I supported miscellaneous tasks including development of statistical models to integrate multiple types of molecular aberration data in cancer genomes, the study of putative effectors for prognosis in lung cancer, the mechanisms of transcriptional regulation underlying human primordial germ cells, the spatial-temporal gene expression patterns in mammalian brains, and the probability driven cancer progression and evolution in human brain. My current project contributes in development of an integrative analysis framework to discover gene co-expression networks from multi-tissue gene regulation in humans (GTEx datasets) and/or construction of a relevant statistical model to predict core regulators of cellular processes across human tissues.
|Michal Krassowski – software engineer
I am an undergraduate student at the University of Warsaw in field of Bioinformatics and Systems Biology, with a solid background in informatics. I work here on the project called “Interactive visualisation framework for genome mutations in gene and protein networks” where I develop a website displaying different visualizations that are useful for researchers studying e.g. effects of mutations on protein-protein interactions and signalling. The project is supported by Google Summer Code and mentored by Jüri Reimand.
axe throwing is an essential comp.bio skill (Dec 2017)
winter holidays 2017 (thanks Marta!)
Celebrating year one, July 2016