Our Team

Dr. Michael Brudno, Scientific Director

Michael was raised in a family of mathematicians and programmers who gave him puzzles to solve since kindergarten. After receiving his BA in Computer Science, he proceeded with the completion of his PhD at Stanford University in California where he worked on algorithms for whole genome alignments. His contributions include co-authoring over 60 peer reviewed research papers, developing approaches for comparison of genomic sequences, teaching at the University of Toronto, and working at the Hospital for Sick Children where he is the Director of the Centre for Computational Medicine. Michael’s research interest is the development of computational methods for the analysis of clinical and genomic datasets, and the analysis of High Throughput Sequencing data. Aside from Science, his other passions include playing soccer, hiking, skiing, and spending time with his family.

Curriculum Vitae

Dr. Marta Girdea, Software Development Manager

Dr. Girdea has both industrial software development and scientific expertise. She was a Postdoctoral fellow in the Department of Computer Science at the University of Toronto and the Centre for Computational Medicine at the Hospital for Sick Children. As part of her PhD at Université Lille 1 & INRIA Lille – Nord Europe Research Centre in France, she researched new methods for biological sequence alignment. At the CCM, she oversees the technical development, with a strong focus on PhenoTips® and PhenomeCentral.

Amanda Silva, Project Coordinator

Amanda graduated with a BScH from University of Toronto majoring in Human Biology, double minoring in Mathematics and Sociology.  Prior to joining the Centre for Computational Medicine, Amanda worked at Sunnybrook Research Institute in the neurology department where the main research focus was dementia. In her spare time Amanda enjoys listening to country music, going to concerts and watching American Football.

Dong Hu, Sr. Systems Analyst

Dong was hired as a Sr. system analyst and his responsibilities include managing and supporting CCM HPF environment.

In his previous jobs, he had been working for Radhat, Rogers and IBM as Unix systems admin supporting computer and storage systems.

He got his B.Sc on computer science software from NanJing University in China.

Andrew Maksymowsky, Systems Administrator

Andrew is a Computer Engineering student from the University of Toronto currently on his PEY at the Hospital for Sick Children. He is working as a system administrator on the HPF team managing and supporting the CCM HPF environment. Outside of work he is a member of the University of Toronto’s Blue Sky Solar Racing team and enjoys his weekends canoing, kayaking and practicing violin.

Dr. Arun Ramani, Bioinformatics Team Lead

Arun’s curious nature to understand how and why things work has propelled him to a career in research. He holds a PhD in Cellular and Molecular Biology, and joined the CCM team in 2014 to apply his skills in biology with computation and statistics. He is currently developing bioinformatic pipelines to tackle large data sets to gain biological insights. He spends most of his spare time with his family and hanging out with his young son. One of his favourite pastimes is cycling, especially long bike rides exploring the country. His other pleasures include books, music, food and cooking.

Dr. Andrei Turinsky, Sr. Research Associate

Andrei is a mathematician and computer scientist who is happy to apply his skills in medical research. His main interest is to search for patterns in genetic disease data by using various statistical and computational methods. He has many years of experience in data analysis and bioinformatics, and has managed several large-scale, multi-team research projects. His typical tasks involve developing computational software, writing research papers, collaborating with other biomedical teams, supervising students, and teaching. Andrei holds a PhD in Mathematical Computer Science and his Erdős number is 4. His top pursuits outside SickKids are outdoor activities, working as a medical first responder, and watching too many indie movies.

Dr. Yue Jiang, Research Associate

Yue has been a big fan of computer science since college. He spent two years in the research lab at the University of Toronto as a visiting PhD student where he worked on indel detection algorithm development. This is where his interest peaked for the bioinformatics and computer science field. After he completed his PhD from Harbin Institute of Technology in China, he was invited to do post-graduate research work at SickKids. He now works on the analysis of DNA sequencing and RNA sequencing data of cancer genome under Dr. Brudno’s supervision. Yue is a computer games enthusiast, and he plays basketball, ping-pong and swims to keep fit.

Justin Foong, Sr. Bioinformatician

Justin received his masters in computer science from the University of Toronto. He is currently a bioinformatician at the Hospital for Sick Children. He is interested in computational analysis methods and their application to clinical and genomic datasets.

Dorin Manase, Bioinformatician

Dorin graduated with a BSc in computer science and cells and systems biology from the University of Toronto. Keen on pursuing a career at the intersection of both majors, he joined SickKids as a Bioinformatician in training in 2012. After a few years of research experience in genetics and genomics, he recently moved to the Center for Computational Medicine with a desire to further his computational skills. On his own time, Dorin enjoys playing soccer and helps coach at the University of Toronto.

Dr. Sam Khalouei, Bioinformatician

Sam received his Hon.BSc. from the University of Toronto in Computer Science and Human Biology and his MSc. from the University of Ottawa in bioinformatics. He then moved back to the University of Toronto to complete his PhD studies. During postdoctoral fellowship,  Sam carried out next generation sequencing library preparation and also implemented a bioinformatics pipeline. He joined the CCM team in July 2016 and has been involved in different tasks such as optimization of bioinformatics pipelines and analysis of genetic variation data. In his spare time Sam enjoys reading, drawing and painting.

Dr. Sergey Naumenko, Research Associate

Sergey received B.Sc and M.Sc in Computer Science from Kharkiv National University of Radio and Electronics (Kharkiv, Ukraine). Then he joined the sector of nonlinear dynamics in Keldysh Institute of Applied Mathematics (Moscow, Russia), where he studied self-reproducing cellular automata, DNA computing, models of the evolution of early life and the origin of genetic code. In KIAM Sergey also taught a course on Biology Inspired Computing.
Sergey worked on PhD project and defended PhD thesis in the joint laboratory of Evolutionary Genomics (Moscow State University, Russia) and Molecular Evolution (Institute for Information Transmission problems of Russian Academy of Sciences, Moscow, Russa) lead by Alexey Kondrashov and Georgii Bazykin http://evolgenomicsen.fbb.msu.ru/. He studied patterns of molecular evolution of protein-coding genes in mammals and insects (epistasis, homoplasy in phylogenetic trees), and inferred the phylogeny of lake Baikal Gammarid species flock using de-novo assembled transcriptomes. Also Sergey was involved in system administration of HPC for NGS data processing in the lab.
During several years Sergey taught Linux Administration and Parallel programming courses in D.Mendeleyev University of Chemical Technology of Russia (Moscow, Russia), and co-organized ACM-style programming contests for students.
At CCM Sergey is helping clinical researches to investigate molecular causes of rare diseases using WES, WGS, and RNA-seq data analyses: he produces annotated small variant reports for genome and exome analysts in Care4Rare project using WES and WGS data; calls and annotates structural variants using WGS data; performs expression outlier, aberrant splicing, small variant analyses using RNA-seq data. Sergey is specializing in using bcbio (https://bcbio-nextgen.readthedocs.io/en/latest/) sequencing analysis toolkit.
Publications: https://scholar.google.ca/citations?user=SeL177gAAAAJ&hl=en, github:https://github.com/naumenko-sa, twitter: https://twitter.com/SergeyNaumenko6

Ian Stedman, Fellow in Artificial Intelligence Law and Ethics

After completing his LL.B. at the University of Alberta and M.A. in Philosophy at York University, Ian was called to the Ontario Bar where he practiced law in both the private and public sectors.  He then returned to academia and earned an LLM from the University of Toronto before undertaking his doctoral studies at Osgoode Hall Law School.  Ian’s research interests focus on ethics, governance and regulation as they relate to various issues of public interest.  As a rare disease patient and advocate, Ian is particularly interested in exploring the legal, ethical and policy barriers affecting the use of big data and machine learning in health care settings.

Orion Buske, Postdoctoral Fellow

Orion is a PhD student at UofT and SickKids. After working on the ENCODE project at the University of Washington, he traded rain for snow and moved to Toronto. Here, he focused on patient matchmaking and genome analysis for rare diseases. He manages the PhenomeCentral research portal and leads the technical development of the Matchmaker Exchange. His other joys include teaching, entrepreneurship, and Darwinian gardening (cacti seem to do well).

Nicole Sultanum, Graduate Student

Nicole Sultanum is a PhD student at the University of Toronto, focusing on the disciplines of Human-Computer Interaction, Computer Graphics and Data Visualization, and their applications to Medicine and clinical practices. Her research interests include designing visual systems through novel user interfaces, and understanding how people interact and reason with them. In the past, she has explored a wide range of other application domains, spanning education, serious games, art design, and oil & gas. She holds a MSc in Computer Science from the University of Calgary, and prior to her PhD studies she was a full-time researcher at IBM Research Brazil.

Jixuan Wang, Graduate Student

Jixuan is a PhD student at the University of Toronto. He is interested in machine learning and human computer interaction, and especially their applications in medical and clinical practices. Now he is working on building mobile user interfaces to capture structured phenotypic data from clinical encounters. Before coming to Toronto in 2016, he completed a master degree in China working on the annotation of long non-coding RNA and detection of copy number variation by analyzing high-throughput sequencing data. He is a big fan of basketball and works out regularly.