Hoffman Lab: Meet the team

The Hoffman Lab at the Princess Margaret Cancer Centre and the University of Toronto develops machine learning techniques to better understand chromatin biology. These models and algorithms transform high-dimensional functional genomics data into interpretable patterns and lead to new biological insight. A key focus of the lab is to train a new generation of computational biologists.

Principal Investigator

Dr. Michael Hoffman

Michael Hoffman creates predictive computational models to understand interactions between genome, epigenome, and phenotype in human cancers. He implemented the genome annotation method Segway, which simplifies interpretation of large multivariate genomic datasets, and was a linchpin of the NIH ENCODE Project analysis. He is a principal investigator at Princess Margaret Cancer Centre and Assistant Professor in the Departments of Medical Biophysics and Computer Science, University of Toronto. He was named a CIHR New Investigator and has received several awards for his academic work, including the NIH K99/R00 Pathway to Independence Award, and the Ontario Early Researcher Award. Michael enjoys kickball (or "soccer baseball" as it is called in Canada), agritourism, the Marvel Cinematic Universe, and making ice cream (favorite flavor: maple walnut).

Postdoctoral Researchers

Dr. Samantha L Wilson

Sam is a postdoctoral fellow studying DNA methylation signatures in cell-free DNA. She is interested in using machine learning approaches to develop predictive models in the context of both pregnancy (cell-free placental DNA; pre-term birth) and cancer (circulating tumour DNA). Sam completed her B.Sc Honours in Genetics at The University of Western Ontario in 2012 (and refuses to call it Western University), and her PhD in Medical Genetics at The University of British Columbia in 2017. Her PhD dissertation focused on DNA methylation profiles of placentas from pregnancies complicated by preeclampsia (a maternal hypertensive disorder) and intrauterine growth restriction (poor fetal growth). Sam is currently funded by the CIHR fellowship and previously funded by the Molly Towell Perinatal Research Foundation and the Princess Margaret Postdoctoral Fellowship of Excellence. While not in the lab, Sam enjoys hiking, spending time with her Corgi, Franki, and cooking yummy things.

Dr. Linh Huynh

Linh is a postdoctoral fellow studying the three-dimensional organization of mammalian genomes. He is also interested in integrating multi-omic data to study gene regulation. Linh obtained his B.E. in computer science and engineering at Ho Chi Minh City University of Technology in 2008, and his PhD in computer science at UC Davis in 2016.

Graduate Students

  • Coby Viner

  • PhD Student in Computer Science
Coby is broadly interested in the intersection of algorithms and computational genomics. He previously worked on analyzing transcription factor binding sites with Shannon information theory and developed Veridical, a method to computationally validate mRNA splicing mutations. Since then, he has worked on modelling the effects of DNA modifications, like methylation, on transcription factor binding. He is currently developing new graph-based methods for integrating DNA accessibility and methylation data. Coby currently holds an NSERC Canada Graduate Scholarship (CGS-D) and previously held a CGS-M. He has also won best oral presentation awards at various conferences. Outside of the lab he enjoys going skiing, playing squash, and trying various Chinese teas.

Mickaël Mendez

Mickaël develops machine learning techniques to integrate the diversity of publicly available next generation RNA sequencing data and characterize cell type specific transcriptional patterns.

Staff

Eric Roberts

  • Technical Analyst
Eric Roberts is a Technical Analyst at the University Health Network for the Princess Margaret Cancer Centre. He is the lead developer in the Hoffman Lab for tools used by researchers in areas of semi-automated genome annotation (Segway) and efficient genomic data storage (Genomedata). Previously Eric has worked on building control systems for sensory deprivation tanks using microcontrollers, game development for the PlayStation Vita and PlayStation 3, and safety-critical video drivers for embedded systems. Eric is always interested in learning and applying new computational methods to epigenomic datasets and has a wide range of programming interests including functional programming, distributed systems, and embedded systems.

Natalia Mukhina

  • Lab Administrator
Natalia provides administrative support to Dr. Michael Hoffman and the Hoffman’s Lab. She obtained her MA in Health Studies at Queen’s University (Canada), with a specialization in Health Communications and Cancer Studies. Natalia is a member of the Association of Health Care Journalists and is interested in creating engaging content about cancer - a complex, sensitive, and often challenging topic to discuss. She runs a blog - "Research News" - for the Breast Cancer Society of Canada.

Visiting Scientists

Summer Students

Leo Li

Leo is a second year Engineering Science student at University of Toronto, currently working as a summer student on developing a pipeline for CUT&RUN analysis. Leo is interested in the intersection of engineering and biology, hopping to extend this interest further in his education. Outside of the lab he enjoys game development, reading books, and playing piano.

Annie Lu

Annie is a second-year student at the University of Toronto studying data science and computer science. Her work in the lab focuses on integrating chromatin long-range interactions to improve gene set enrichment analysis. Annie has been awarded the Lester B. Pearson International Scholarship and the Samuel Beatty Scholarship. Her interests outside the lab include writing, jogging, collecting postcards, and translating articles for the Chinese edition of Scientific American.

Esther Yoo

Esther is a summer student studying Engineering Science at the University of Toronto. She is interested in both molecular genomics and computational biology, and is excited to further pursue her interests throughout her undergraduate career. Esther is currently working on developing an epigenetic clock based on methylation signatures in cell-free DNA to investigate human aging and cancer methylomes. In her spare time, she loves listening to music, reading books, and drinking bubble tea with her friends.

Lab Mascot

Rosalind Franklin the Corgi

  • Best pupper
Rosalind Franklin the Corgi goes by the name Franki. Franki contributes support and smiles to the lab, and is a pupfessional scientific advocate. She is passionate about open-access scientific research, trying to make her namesake proud. Franki is interested in investigating the elasticity properties of chew toys and gene therapy approaches to make her zooms more speedy. She is actively perfecting her fist bump and rollover techniques. In her free time, she enjoys all treats, long walks, the cottage and digging in the sand.

Lab Alumni