Carl de Boer, PhD, PLEng
Carl is the founding member of the lab. He did his PhD in the lab of Tim Hughes at the University of Toronto, and a post-doc at the Broad Institute in Aviv Regev’s group. He is currently an Assistant Professor in the School of Biomedical Engineering at UBC. You can reach Carl here.
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Cassandra Jensen, PhD
Cassandra is a Research Associate in the de Boer lab. Her project involves engineering synthetic chromosomes to improve models of gene regulation and to study mechanisms of de novo gene birth. Cassandra previously worked as a Senior Scientist at Boreal Genomics (Natera), and was a Postdoctoral Researcher in the Boer lab before that.
Postdoctoral Researchers
Dogancan Ozturan
I earned my PhD in Biomedical Sciences and Engineering from Koç University under the supervision of Dr. Nathan A. Lack in 2022. After a brief postdoctoral fellowship at Vancouver Prostate Centre, I joined de Boer lab in September 2023. My main focus is the high throughput characterization of gene regulation, transcription factor biology and technology development.
Emmanuel Cazottes
Understanding how gene expression is regulated by distal enhancer is crucial for decoding human health and disease. In the de Boer lab, I am developing an innovative high-throughput technology to measure enhancer regulatory activity across diverse cellular contexts, including cancer and stem cells. By leveraging artificial intelligence to analyze this comprehensive dataset, I aim to uncover the underlying principles governing enhancer function and their impact on human disease.
Before joining the de Boer lab, I obtained my PhD from the lab of Claire Rougeulle, Université Paris Cité in France, where I worked on the evolution of X Chromosome Inactivation and gene regulation in primates.
Beyond the bench, I engage actively in science communication through events such as the Pint of Science Festival, European Researchers’ Night and the national French Science Festival. Emmanuel.cazottes@ubc.ca | X/Twitter | Bsky
Graduate Students
Ishika Luthra
Ishika is a PhD student in Bioinformatics. She graduated from Simon Fraser University with a Bachelors of Applied Science in Biomedical Engineering in 2018. She is currently working on using CNN models to predict cell type specific motifs using single cell ATAC sequencing data. Her interests include yoga, baking and hiking.
Syed Asfar Lathif Salaudeen
Asfar is pursuing his PhD in Genome Science and Technology at UBC. He received his B.Tech degree in Biotechnology in 2020 at Crescent University, Chennai, India. Besides being a huge biology enthusiast, he is also interested and curious in expanding his knowledge in Programming and Statistics, which drove him to join our team! He is also highly passionate about teaching and communicating science. In his leisure time, Asfar loves to make tea and enjoy having a good cup for any excuse! When not learning something new or indulging in his love for tea, he likes to spend time watching Netflix and walking along shores.
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Omar Tariq
Omar is a PhD student at the School of Biomedical Engineering. He graduated in 2020 from the University of Ottawa with a degree in Biomedical Science where he developed an interest in computational biology research. He is investigating how mutations in cancer-associated Transcription Factors affect their function.
Abdul Muntakim Rafi (Rafi)
Abdul Muntakim Rafi is a Ph.D. candidate in Biomedical Engineering. He completed his Bachelor’s degree in Electrical and Electronic Engineering at Bangladesh University of Engineering & Technology and later pursued his Master’s in Electrical and Computer Engineering at University of Windsor.
Rafi’s research concentrates on employing machine learning to design cis-regulatory models, develop methods to interpret them, and explore ways to enhance their performance, contributing to a quantitative comprehension of cis-regulatory logic. He has expertise in various programming languages and machine learning libraries, publications in top-tier ML conferences, and experience of working as a machine learning engineer in software companies and startups. Rafi has successfully supervised undergraduate students in the lab and is always on the lookout for motivated undergrads/high schoolers to join his research endeavors.
Nick Mateyko
Nick is pursuing a MSc in Genome Science and Technology at UBC. He obtained his BSc in Biochemistry at the University of Victoria, where he worked on the structural biology of bacterial enzymes. He was drawn to the de Boer lab by his interest in synthetic biology and machine learning and a desire to understand eukaryotic gene regulation. In his spare time, he enjoys cooking, running, and trying to climb as many mountains as he can around Vancouver.
Will Cheney
I’m a PhD student at University of British Columbia studying biomedical engineering. My interests lie in adapting and engineering proteins for therapeutic or practical use. I’ve previously built opioid biosensors by engineering Human receptor proteins and am currently working on understanding human transcription factor binding sites. A key challenge is massive sample space of possible DNA and protein sequences. To overcome this, I’m using synthetic biology to generate enormous datasets and training machine learning models to learn how transcription factors function.
Madison Chapel
Madison is a masters student in the bioinformatics program. Before joining the de Boer lab, she completed her BSc in microbiology at the University of Manitoba and her BSc in computer science at University of the People. Madison is interested in exploring the underlying complexity of gene regulatory networks, and wants to focus on understanding how this complexity evolves. She plans to use her time in the de Boer lab to advance her understanding of machine learning. Outside of the lab, she spends her time cooking, sewing, and exploring Vancouver’s beaches and parks.
endeavors are anchored in two domains: 1) Blackboard-to-Lab: Leveraging theoretical, computational, and algorithmic advancements to solve problems in the omics space; 2) Lab-to-Clinic: Collaborating with clinicians to solve real-world problems via synthetic data generation and machine learning.
JJ Hum
JJ is pursuing a MSc in Genome Science and Technology at UBC. After graduating from the UBC-BCIT Honours Bachelors of Biotechnology program in 2020, JJ worked at BC Centre for Disease Control and Boreal Genomics. In the de Boer lab, JJ is currently working on developing a magnetic cell sorter for high-throughput gene regulation assays. Outside of research, JJ enjoys knitting and playing various musical instruments.
Kenyon Alexander
Kenyon is an MSc student in Genome Science and Technology at UBC. He received his bachelors in Computational Molecular Biology from Brown University in Providence, Rhode Island, where he also studied music. For the last few years, Kenyon was a client success manager at a B2B software startup, working with significant brands in the consumer packaged goods industry to improve their retail businesses. Kenyon is delighted to be returning to his biotechnology roots in the de Boer lab, and is particularly interested in synthetic biology and machine learning. In his spare time, Kenyon enjoys singing, playing guitar and fiddle, running, and spending time with friends and family.
Staff
Sambina Islam Aninta
Sambina Islam Aninta is currently a Research Technician in the de Boer lab. She completed her undergraduate in Combined Honours in Computer Science and Biology in UBC. Previously, Sambina worked at BC GSC and Amgen researching on drug development as well as did her thesis at SBME on ML applications in COPD. She is currently interested in studying the application of ML in gene regulation and ultimately contribute to understanding autoimmune disease pathway.
Outside of research, she loves running, exploring new restaurants and traveling to new cities.
Satyam Priyadarshi
Satyam Priyadarshi is a Research Technician in Carl de Boer’s lab at UBC, with an academic background in Physics and Astronomy. During his undergraduate studies, he focused on the synthesis of quantum materials at the Quantum Matter Institute and worked on the search for dark photons with the Belle II research group at UBC. After graduating, Satyam transitioned into bioinformatics at the Beaty Biodiversity Research Centre, where he analyzed gene expression patterns in the Genome Evolution Lab. Currently, he is working to standardize the evaluation of genomic models across various datasets.
In addition to his research, he serves as an advisor to the UBC Astronomy Club, leading outreach initiatives. Outside the lab, he enjoys hiking, playing badminton and tennis, swimming, exploring new restaurants and cafés, and travelling.
Eric Yan
Eric is a research technician working on a joint project between the de Boer and Shakiba labs as well as United Therapeutics to study how stem cells can be turned into lung cells. His background in precision antisense therapy for Duchenne muscular dystrophy fostered his interest in translational research and precision medicine, which led him to his current work at UBC. Outside working hours, Eric can often be found practicing Brazilian jiu-jitsu, playing guitar, or exploring the city.
Daniella Liao
Daniella is currently a lab technician in the de Boer Lab. She completed her undergraduate studies majoring in Biochemistry at UBC. She previously worked at Zymeworks Inc. researching antibody-drug conjugates. In the de Boer lab, Daniella is focusing on developing an induced pluripotent stem cell library containing different synthetic regulatory DNA sequences. Outside the lab, she enjoys exploring new restaurants in Metro Vancouver and travelling.
Manaswi Yendluri
Manaswi is an Administrative Assistant in the de Boer lab and helps with supporting daily operations. She graduated from UBC with a degree in Psychology in 2023. In her free time, she enjoys travelling, music, and hiking.
Undergraduate Students
Justin Qian
Justin is an undergraduate Engineering Physics student at UBC with research interests broadly in machine learning, physics, and biology. As a co-op student, he is working with Rafi to implement active learning approaches to more effectively train the lab’s cis-regulatory models with. In his free time, he likes biking, reading, and travelling.
Alumni
Postdoctoral Researchers
Najmeh Nikpour, PhD
While completing my PhD in Molecular and Biochemical Parasitology at the Institute of Parasitology (McGill University) I became interested in understanding strategies involve in gene regulation of Eukaryotes. Her project used novel quantitative models to gather cell-type specific gene regulatory programs via large-scale decoding of regulatory sequences in hESCs.
Graduate Students
Hadis Kamali Dehghan
Hadis obtained her master’s degree in the Genome Science and Technology Program. Her previous work included Biomedical Engineering, including designing scaffolds for regenerative medicine. Her thesis project aimed to find drugs to treat gene regulation changes in diseases.
Undergraduate Students
Phoenix Jin
Phoenix is pursuing an Honours BSc degree in Biotechnology at UBC-BCIT, with a keen interest in genomics and cell biology. As a co-op student and as part of the 2024 SBME Synergy studentship program, she worked with Dogancan to identify genomic regions suitable for transgene integration to tackle transgene silencing. In her free time, she enjoys traveling, hiking, and music.
Björn Holst
Björn is an undergraduate Computer Science student pursuing a BSc degree at UBC. Björn’s research interests revolve around machine learning in STEM – with a focus on genetics, human movement, and robotics. For the 2023 SBME Summer Studentship program, Björn worked with Rafi to investigate data-driven methods of improving cis-regulatory model performance. In his free time, Björn loves volleyball and poetry.
Hudson Nock
Hudson is pursuing a bachelor’s degree in engineering physics at UBC. He has a strong interest in machine learning and mathematics which drew him towards a coop position in the de Boer lab. In the spring of 2023, Hudson worked with Rafi towards interpreting neural networks that were trained to predict DNA expression levels.
Emilia Chen
Emilia completed her BSc in Microbiology & Immunology and Computer Science at the University of British Columbia. She did Directed Studies followed by a SBME/GSAT Summer Studentship in the de Boer lab. Emilia enjoys integrating multidisciplinary approaches in problem-solving. Emilia worked with Ishika and Najmeh on investigating the grammatical rules in regulatory elements. Outside of research, Emilia loves exploring the great outdoors and good food.
Yimin Wang
Yimin was a co-op student from BCIT who worked with Omar and Asfar on target capture approaches for enriching for specific genomic sequences.
Chris-Andra McIntosh
Chris-Andra investigated regulation of the TNFAIP3 gene as part of the CBR-SBME Undergraduate Research Program in the Summer of 2020.