Michael Steffen Kobor
Michael Steffen Kobor

Michael Steffen Kobor, PhD

Investigator, BC Children's Hospital

Dr. Michael S. Kobor is a Professor in the Department of Medical Genetics at the University of British Columbia (UBC). Dr. Kobor has received many distinctions, including a Tier 1 Canada Research Chair in  Social Epigenetics, the Sunny Hill BC Leadership Chair in Child Development, and an appointment as Fellow of the Canadian Institute for Advanced Research (CIFAR) Child and Brain Development Program. A champion for translational research, he serves as the Lead for the “Healthy Starts” Theme at BC Children’s Hospital. Dr. Kobor's own research is focused on illuminating the mechanisms by which early life environments get “under the skin” to affect health and behaviour across the lifespan.

Paola Arguello Pascualli

Graduate Student 

My academic formation started in Mexico where I am from, studying a BSc in Genomic Sciences at the National Autonomous University of Mexico (UNAM). During my undergrad I had the opportunity to explore different research areas and fell in love with epigenetics. Currently, I am a graduate student in Medical Genetics co-supervised by the Kobor and Dennis labs at UBC. There is a tremendous gap in genetic information for non-european populations, leaving a large proportion of the world behind in the personalized genomic medicine revolution. My research focuses on understanding the role of genetic admixture in biomedical predictors and how can we use that knowledge to help bridge the gap in information for underrepresented populations.

As a mexican student I hate to perpetuate stereotypes but I do love dancing and tequila. Even though I'm probably the worst dancer you'll ever known.

Maria Aristizabal, PhD

Postdoctoral Fellow

I have a PhD from the University of British Columbia, during which I used yeast to carry out mechanistic work into the role of the RNA Polymerase II (RNAPII) enzyme in general and gene-specific transcription. Overall, my work showed an unexpected role for RNAPII in the repression of genes, including retrotransposons.

In my postdoctoral work, I am leveraging the yeast and fruit fly model systems to uncover mechanisms of transcription and chromatin regulation and their contributions to experience-dependent plasticity. For this work, I received independent research funding from the Jacobs Foundation as well as postdoctoral fellowships from the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canadian Institute for Advanced Research (CIFAR) Child and Brain Development program.

Rebecca Asiimwe

Bioinformatician

I have a Bachelor of Science degree in Information Technology, a Master of Science degree in Information Technology, and recently completed my Master of Science degree in Bioinformatics at the University of British Columbia. I am interested in leveraging the power of bioinformatics in understanding the etiology of complex diseases and the potentially actionable molecular events that could provide insights into better treatment options for patients. Prior to joining the Kobor Lab, I worked at the BC Cancer Research Centre as a Graduate Research Assistant in the Shah Lab for Computational Cancer Biology where I conducted novel research to stratify triple negative breast cancers into distinct genomic subgroups based on mutation signatures, genome-wide individual somatic variants (SNVs, CNAs, SVs and INDELs) and clinical outcomes - using a database-driven whole genome profiling approach.

As a Bioinformatician and data analyst in the Kobor Lab, I work closely with colleagues and with local, national, and international collaborators to lead, manage and contribute to existing projects through performing statistical and bioinformatics analyses of high-throughput epigenomics and genotyping data. Such projects are designed to understand the causes and consequences of variation in epigenetic marks across human populations. I also work with the Bioinformatics team to build tools and pipelines to analyze and manage the complexity of our large datasets. I am also responsible for providing guidance and mentorship to students in the lab.

Outside the lab, I love reading, cooking and baking, singing, meeting up with friends and travelling to new places.

Parmida Atashzay

Research Assistant

I completed my undergraduate studies at Simon Fraser University (SFU), majoring in Molecular Biology and Biochemistry. I also pursued a certificate in Genomics and Bioinformatics from SFU. I have been volunteering and working in the medical research field for over 7 years. My recent research projects were at Dr. William Davidson's Lab, on the TEAD3 and Vgll3 protein interaction in Atlantic Salmon to determine the maturity of a fish. Also, Dr. Tim Audas's Lab which is on stress-specific DNA elements that drive the expression of the rINGS RNAs in Alzheimer's disease. I am now working closely with David and Julie and our research team to assess DNA methylation and gene expression patterns in human cells while assisting with planning and designing experiments, analyzing and compiling data, and preparing study reports. Recently, I have been in charge of the DNA extraction projects (blood, blood spots, buccal and saliva).

In my free time, I like to go out with friends, go for a walk and watch movies!

Sanjit Bains

Undergraduate Research Assistant

I recently graduated from UBC with a BSc in Biochemistry. During my undergraduate degree, I completed a directed studies project in the Kobor Lab focused on investigating how chronic stress contributes to Parkinson’s disease risk through genome-wide DNA methylation. My interest in the gene-environment interactions contributing to neurodegeneration has led me to analyze the broader epigenomic changes associated with chronic stress in Parkinson’s model mice with the support of a GSAT Summer Scholarship. 

In my spare time, I love to bake, do Pilates, read, and spend time with friends and family!

Helena Biasibetti Brendler 

Graduate Student

I am originally from Brazil where I received my BSc in Biomedical Science at the Universidade Federal do Rio Grande do Sul. I completed a Masters in Biochemistry at the same University where I researched neurometabolic diseases. My interests in the interaction between stress environment and epigenetic machinery led to my in progress dissertation work at UBC under the supervision of Dr. Michael Kobor. My current PhD project focuses on integrating different epigenetic marks in response to a stress environment in vitro to better understand the causality of epigenetic changes. In pursuit of this project, I am supported by UBC’s International Doctoral Fellowship.

Hilary Brewis

Graduate Student

I have a BSc in Biology from Dalhousie University with a focus in molecular evolution and ecology. My current research focuses on H2A.Z, an evolutionary conserved histone variant that modifies chromatin dynamics and is required for a wide variety of cellular functions. In particular, I am using budding yeast as a model organism to inspect how H2A.Z regulation is driven by its unique amino acid sequence, histone chaperones, and the ATP-dependent chromatin remodeler SWR1-C. 
When I'm not in the lab, you can find me playing soccer, hiking, camping, or binge-watching nerdy TV shows. 

Awards:
Canada Graduate Scholarship – Masters (2017)
Gradate Support Initiative Award (2016)

Josh Brown

Graduate Student

I have a BSc in Biology from the University of Winnipeg, and I am currently a PhD candidate in Medical Genetics at UBC. I study the DNA damage response, using budding yeast as a model organism. My focus is on a scaffolding protein, Rtt107, which carries out multiple functions in the DNA damage response. I examine how Rtt107 carries out these functions by acting in its various complexes, and seek to identify new Rtt107 functions.

Yen Chan

Graduate Student

I completed my undergraduate studies at Western University in London Ontario with a degree in Genetics and am currently pursuing a Master’s in Medical Genetics in the Kobor Lab. My current project is focused on understanding the pathophysiology of Metabolic Syndrome in the context of DNA methylation in whole blood samples of an aging Costa Rican cohort. Metabolic Syndrome is a public health concern that can be attributed to both genetic and environmental factors. As such, DNA methylation and epigenetics can provide a unique, intersectional lens to understand the biology underlying Metabolic Syndrome.

While not at the lab, I enjoy hiking and kayaking around Vancouver and enjoying a beer at one of the city’s many breweries. 

Kristy Dever

Graduate Student

I have a BSc in Biology from UBC with my coursework focusing on physiology and genetics. This lead me to pursue a MSc in Medical Genetics in the Kobor Lab. Using yeast as a model organism, my research focuses on transcription regulation. More specifically, my project aims to identify broader roles for the RNA Polymerase II phosphatase, Fcp1, in this process, and the cell. 

Outside the lab, I enjoy hiking, skiing, reading, running, and spending time with my friends and family.

Joe Dong

Graduate Student

I am a biostatistician with more than six years of experience in analyzing and interpreting omics data. I specialize in using high dimensional genomic, epigenomic, and clinical data to derive various population-based tests.

I hold a Bachelor of Biotechnology from Huazhong Agriculture University in Wuhan, China and I completed my Masters in Human Biology at Fudan University and Computational Chemistry at Southern Methodist University. I enjoy eating, hiking, travelling and reading books!

Hannah-Ruth Engelbrecht

Graduate Student 

I am a South African student who made the leap across the hemispheres to begin my PhD at UBC. I completed my undergraduate training in Human Physiology, and Genetics, and then decided to pursue an MSc(Med) in Human Genetics, specialising in bipolar disorder, all at the University of Cape Town. My current work focuses on perturbations to human health across the lifespan, and the impact of such disturbances on DNA methylation. One goal is to determine whether biomarkers of healthy aging and longevity can be identified at the DNA methylation level.

Beyond the lab, I enjoy hiking, baking, dancing, reading, and writing. I'm also looking forward to indulging in my new passion for snow and cold weather!

Tanya Erb

Research Manager

I manage the administration of the various research activities taking place in the lab. I particularly enjoy supporting the many exciting, multidisciplinary collaborations we have with partners from all over the world. In my spare time, I like spending time with family and friends over a good meal and a new board game, hitting the gym together in the wee hours of the morning, and taking in our beautiful city while cruising the seawall.

Maggie Fu

Graduate Student

I have a BSc in Biochemistry from UBC. Currently, I am a Masters student in the Kobor Lab and my research focuses on the relationship between maternal nutrition and child developmental outcomes. Using statistical models, I analyze DNA methylation data to explore the biology underlying the DOHaD (Developmental Origins of Health and Disease) hypothesis. I am also developing statistical tools in optimizing microarray data analysis. I enjoy coding and its usage in identifying patterns too complicated to be directly observed by the human mind.

My hobbies include snowboarding, listening to music, playing board games, and traveling!

Nicole Gladish

Graduate Student

My background involves broad training from molecular biology techniques to bioinformatics. I received an Advanced Diploma from St. Lawrence College in Biotechnology, completed a BSc. in Biology from UBC, and am currently completing my PhD in Medical Genetics at UBC.

My thesis investigates the impact of early life adversity, such as low socioeconomic status and abuse, and how DNA methylation associates with these experiences to help understand why these individuals are predisposed to later life pro-inflammatory adverse health outcomes such as cardiovascular disease, type II diabetes and cancer.

Outside the lab, I enjoy spending time with my husband and two small children, exploring our new neighbourhood on Burnaby Mountain, and reading whenever I get the chance.

Kendrix Kek

Bioinformatician

I graduated from the University of British Columbia with a BSc in Biology and a minor in English Literature. During my undergraduate studies, I developed an interest in microbiome research and undertook a position at Dr. Laura Parfrey’s lab for two years. In those two years, I have managed to develop some useful bioinformatics skills and completed a thesis project at the lab where I sought to understand the role of a prevalent symbiont, Blastocystis in the gut microbiota. At Kobor Lab, I am hoping to leverage the power of bioinformatics to understand interplay between the socio-economic environment of the study cohort and the genetic/epigenetic mechanisms that drive the development of various diseases.

Outside of work, I enjoy going to the movies and watching TV series at home. On the rare occasions when we have sunny days, I partake in some sports including running and tennis.

Alyssa Kirlin

Graduate Student

Prior to coming to UBC, I received a BSc and a MSc in Biochemistry from Queen’s University. My research focuses on characterizing the functions of YEATS family proteins in yeast and understanding the role these proteins play in chromatin modifying complexes. I am very interested in science communication and science policy.

Outside of the lab, I enjoy baking, board games, and softball.

Awards:
NSERC Post-Graduate Scholarship (2016)
UBC Four Year Fellowship (2015)

Chaini Konwar, PhD

Bioinformatician

I have a PhD in Medical Genetics from the University of British Columbia. My thesis work largely involved understanding molecular variation in placenta associated with inflammation in preterm births. Briefly, I compared molecular marks such as DNA methylation, miRNA, and SNP profiles in placentas from preterm deliveries with and without inflammation. My dissertation laid the groundwork for development of placental-derived biomarkers that could be detected in maternal blood when the inflammation is present.

Currently, as a bioinformatician in the Kobor Lab I work on a myriad of research projects mainly focused on understanding molecular variation in multiple tissues across human populations. Using computational tools in the R programming environment I analyze high dimensional epigenetic, genetic and expression data to understand the impact of early life experiences, with a special focus on social environmental influences on overall child development and adult health outcomes. I am also working closely with our bioinformatics team (Rebecca and Joanne) to ensure data integrity and devise methods for optimal large-scale genomic data management. In addition, I provide mentorship to computation biology trainees, research personnel, and graduate students, and interact with collaborators on a regular basis.

Aside from my computer, I am particularly passionate about cooking, eating, traveling and learning about different cultures!

David Lin, PhD

Research Associate

I have a MSc in Neuroscience from McGill (neuroprotective functions of the normal prion protein) and a PhD in Medical Genetics from UBC (discovery of ABHD17 proteins as novel protein depalmitoylation enzymes). Together with Julie, I lead the array team, coordinating with local and international collaborators to design and conduct human DNA methylation and genotyping array studies. I also carry out DNA methylation analyses mainly using RStudio. I am heavily involved in the tech development side of things in the lab, having adapted the RRBS technique in the lab to examine DNAm in animal models. I am currently optimizing ATAC-Seq as a method of interrogating chromatin states to add an additional layer to our lab's epigenetic studies.

During my spare time, I am an avid video gamer. I enjoy travelling and trying out new foods and beers, and wines (especially Gewürstraminers).

Julie MacIsaac, PhD

Lab Manager and Research Associate

I am involved in many aspects of lab operations. My main job, however, together with David and our other technicians, is to keep the array pipeline running smoothly. We run thousands of DNA methylation and genotyping arrays yearly for collaborators all around the world and in Canada. I have a BSc in Cell and Molecular Biology from Colorado State University and a MSc (focused on multifactorial neural tube defects) and PhD (focused on genetic imprinting) in Medical Genetics from the University of British Columbia.

When I am not in the lab I enjoy playing basketball, traveling, and spending time with my family.

Sarah Merrill, PhD

Postdoctoral Fellow

I am a neuropsychologist using social epigenetics to understand the effects of early environment on biology. I received my undergraduate degree in Neuroscience and Psychology from Wellesley College. I received my Masters and PhD from Cornell University in Developmental Psychology with Dr. Cindy Hazan, Dr. Ritch Savin-Williams, and Dr. Richard Depue. My doctoral work focused on the timing and quality of the neurobiological changes that occur during attachment formation. My current postdoctoral research in the Kobor Lab expands upon my knowledge of attachment and early care environment to investigate how these experiences affect DNA methylation and how these effects persist and interact with other early environmental factors. The purpose of my research is to expand our understanding of social relationships and their interconnective, long-lasting effects on behavior, development, neurobiology, and epigenetics. My hope is that this research will inform policies that affect these important early life experiences for the better. 

Sarah Moore, PhD

Postdoctoral Fellow

I received my BS in psychology at the University of Maryland where I researched child attachment and evolutionary genetics. My interests in the interaction between early social environment and genetic sensitivities led to my dissertation work at Cornell University, and I am currently expanding my bioinformatics tool kit in my postdoctoral position in the Kobor Lab. My current postdoctoral work focuses on integrating multi omics data to uncover the idiosyncratic pathways in which social experiences become biologically engrained. In pursuit of this work, I received the BCCHR Scholars of Excellence and Banting Postdoctoral fellowships.

Sharlin Patel

Research Assistant

I have my Masters in Medical Biotechnology from SP University in India. I did my research project from Gujarat Cancer Research Institute on derivative chromosome 9 deletion in Chronic Myeloid Leukemia patients with a focus on interpretation of atypical D-FISH pattern. Currently I work closely with Julie and David to conduct DNA methylation and genotyping arrays for collaborators globally as well as in Canada. With some assistance from the bioinformatics team in Kobor lab, I am  also enhancing my R coding skills to preprocess and analyze DNA methylation datasets (with an emphasis in social environment variables). Specifically, I am interested in investigating the impact of middle childhood peer relations on the epigenetic profiles of adolescents.

Apart from my work, I enjoy painting specially oil and acrylics, travelling and spending
time with my family.

Samantha Schaffner

Graduate Student

I have a BSc in Biology (Honours, Co-op; Cell and Developmental Biology specialization) from UBC. My research focuses on epigenetic contributions to Parkinson’s disease susceptibility and progression. Specifically, I specialize in genome-wide DNA methylation analysis of human cohorts, mice, and tissue culture systems. In addition, I study epigenetic regulation of the developing brain. 

In my free time, I love to cook new recipes and explore the mountains by hiking and skiing!

Awards:
CIHR Doctoral Research Award (2019)
Four Year Doctoral Fellowship (2018)
Canada Graduate Scholarship – Masters (2017)
Faculty of Medicine Graduate Award (2016)

Oscar Urtatiz, PhD

Research Assistant

I have a Masters in Human Genetics from the University of Los Andes (Colombia) where I researched a genetic condition called albinism characterized by the lack of pigmentation. My interests in pigment cells led to me pursue a PhD in Medical Genetics at the University of British Columbia, working on melanoma. Now, I am supporting David and Julie to conduct thousands of human DNA methylation and genotyping arrays for collaborators all around the world and in Canada.


Outside the lab, I enjoy going hiking, cycling and grabbing coffee on Main St. while reading a book.

Joanne Whitehead, PhD

Bioinformatician

After earning a BSc in Microbiology from the University of Victoria, I completed a PhD in Developmental Biology at Uppsala University in Sweden, focused on the epigenetic regulation of imprinted genes in development and cancer, particularly the role of the chromatin-binding protein CTCF. During my postdoctoral work with a biophysics team at the Curie Institute in Paris, funded by a Marie Curie Fellowship, I initiated studies of the role of mechanical strains in tumourigenesis in a mouse colon cancer model. Later I returned to UVic and started working in bioinformatics in a salmon genomics lab. Now I am excited to be returning to the field of epigenomics, and turning my attention to bioinformatics with respect to human health, nutrition and early life exposures.

When not working, you will find me volunteering with various Early Music organizations in Victoria and on Salt Spring Island, and spending time with my wonderful family!

Alumni

We are very proud of the continuing success of all former Kobor Lab members!

Current positions are up to date to the best of our knowledge. If you have updated information, please let us know!

 

Former Postdoctoral Fellows

Timothy Bredy, PhD, Associate Professor, Queensland Brain Institute, Brisbane, Australia (First position after leaving the Kobor Lab: Assistant Professor, University of California Irvine, CA, USA)

Rachel Clifford, PhD, Senior Research Fellow, University of Nottingham, Nottingham, UK (First position after leaving the Kobor Lab: Research Fellow, University of Nottingham, UK)

Anke Hüls, Assistant Professor of Epidemiology & Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA. PhD, Postdoctoral Research Fellow, Emory University, Atlanta, GA, USA

Meaghan Jones, PhD, Assistant Professor, University of Manitoba, Winnipeg, MB

Linda Lee, PhD, Biochemist/Cell Biologist, University of Calgary, Calgary, AB (First position after leaving the Kobor Lab: Research Associate, University of Calgary, AB)

Eric Thibodeau, PhD: Postdoctoral Fellow, University of Minnesota, MN, USA

 

Former Graduate Students

Evan Gatev, PhD (Bioinformatics), PhD (Finance) at Yale, Associate Professor, Simon Fraser University, Burnaby, BC

Aline Gaub, MSc, (University of Konstanz), PhD Student, Max Planck Institute for Immunology and Epigenetics, Freiburg, Germany

Sarah Goodman, PhD, Postdoctoral Fellow, University of Toronto, ON

Sumaiya Islam, PhD, Variant Scientist, Tempus, Inc., Chicago, IL, USA

Ruiwei Jiang, MSc, Research Scientist, Amazon, Vancouver, BC (First position after leaving the Kobor Lab: Data Analyst, Boeing Canada, Richmond, BC)

Grace Leung, PhD, Research Scientist, AbCellera, Vancouver, BC (First position after leaving the Kobor Lab: Postdoctoral Fellow, Novartis Institutes for Biomedical Research, Cambridge, MA, USA)

Nancy Lévesque, PhD, Exploration Scientist, Canadian Space Agency, Montreal, QC (First position after leaving the Kobor Lab: Postdoctoral Fellow, McGill University, Montreal, QC)

Phoebe Lu, PhD, Research Manager, Office of Research Services, University of British Columbia, Vancouver, BC.

Alexandre Lussier, PhD, Postdoctoral Fellow, Harvard Medical School, Boston, MA, USA (First position after leaving the Kobor Lab: Postdoctoral Fellow, Cornell University, Ithaca, NY, USA)

Lisa McEwen, PhD, Clinical Data Consultant, Vancouver Island Health Authority, Victoria, BC & Adjunct Assistant Professor, University of Victoria, Victoria, BC

Thorsten Schmidt, MSc, (University of Tübingen), Global Portfolio and Strategy Manager, Roche Diagnostics, Basel, Switzerland

Julia Schulze-Hentrich, PhD, Junior Group Leader, Neuroepigenomics, University of Tübingen, Tübingen, Germany

Katarzyna Stepien, MSc, MA Candidate in Counselling Psychology, Yorkville University. 

Christopher Taplin, MSc, Medical Resident, University of Ottawa (First position after leaving the Kobor Lab: Medical Student, University of British Columbia, Vancouver, BC)

Aaron Nikita Verheyden, MSc, (Martin-Luther-Universität Halle), PhD Student, Goethe University Frankfurt, Germany

Alice Wang, PhD, Medical Student, University of Calgary, Calgary, AB (First position after leaving the Kobor Lab: Postdoctoral Fellow, University of Calgary, Calgary, AB)

 

Former Staff

Rachel Edgar, Pre-Doctoral Fellow, European Bioinformatics Institute | EMBL-EBI, Cambridge, UK

Cath Ennis, PhD, Scientific Communications Consultant

Anthony Fejes, Head of Bioinformatics, SolveBio, Oakland, CA, USA (First position after leaving the Kobor Lab: Senior Director of Bioinformatics, Omicia, Oakland, CA, USA)

Alexandra Fok, Genetic Counselor, Genome Sciences Centre, Vancouver, BC

Sonja Horte, Product Manager, Digital Supercluster and Strategic Partnerships, LifeLabs Medical Laboratory Services, Vancouver, BC (First position after leaving the Kobor Lab: Laboratory Manager, Centre for Blood Research, University of British Columbia, Vancouver, BC)

Lucia Lam, Bioinformatician, Rancho BioSciences, Toronto, ON (First position after leaving the Kobor Lab: Bioinformatician, GenomeDX Biosciences, Vancouver, BC)

Sarah M Mah, Graduate Student, McGill University, Montreal, QC

Alexander Morin, MSC, Graduate Student, University of British Columbia, Vancouver, BC

    Sarah Neumann, Marketing Business Development Consultant, Contextual Genomics, Vancouver, BC (First position after leaving the Kobor Lab: Marketing Associate, GenomeDX Biosciences, Vancouver, BC)

    Katia Ramadori, Clinical Genetics Technology student, British Columbia Institute of Technology, Vancouver, BC

     

    Former Undergraduate Students

    Alessandra Albertini

    Neeku Amanat

    Muhamed Amirie

    Hossein Amirjamshidi

    Maria Aristizabal

    Sanjit Bains

    Derek Bogdanoff

    Jenny Chen

    Kristy Dever

    Michael Doyle

    Joseliya Embuscado

    Alysa Gutierrez

    Amy Ho

    Jessica Ho

    Atiya Jaffar

    Nicole Janusz

    Analisa Jia

    Pareesa Kassam

    Jayme Kim

    Jeongin Kim

    Lara Lampe

    Anson Law

    Junoh Lee

    Grace Leung

    Phoebe Lu

    Lisa McEwen

    Quinn McVeigh

    Taylor Morrison

    Lindy Moxham

    Viola Ng

    Stevens Qiu

    Mary Shen

    Irina Stier

    Leyla Tabanfar

    Michael Tjong

    Erik Venalainen

    Alice Wang

    Evan Wang

    Jessica Wang

    Maya Willms

    Rebecka Wombacher

    Calvin Wong

    Ziqing Ye

    Xinyuan You

    Steven Zhao

    Test

    Test Test

    Motivation: High-dimensional DNA methylation (DNAm) array coverage, while sparse in the context of the entire DNA methylome, still constitutes a very large number of CpG probes. The ensuing multiple-test corrections affect the statistical power to detect associations, likely contributing to prevalent limited reproducibility. Array probes measuring proximal CpG sites often have correlated levels of DNAm that may not only be biologically meaningful but also imply statistical dependence and redundancy. New methods that account for such correlations between adjacent probes may enable improved specificity, discovery and interpretation of statistical associations in DNAm array data.