News & updates.

On April 29, four trainees from the lab presented at London Health Research Day, the annual Schulich-wide graduate research showcase.

• Yubing Xia — selected talk: Systemic B-cell Immune States Associate with Response to Neoadjuvant Therapy in HER2-Positive Breast Cancer
• Binh Tran — poster: Novel Transcriptional Profiling Approach to Study Para-Resistance in Candida albicans
• Mohamed Meawad — poster: Delineating Functional Patterns in Global Gut Microbiomes
• Bushra Kabbani — poster: Systemic–Tumour Immune Response to Neoadjuvant Chemo-Immunotherapy in Triple-Negative Breast Cancer

Welcome to Shreya Parmar, joining us this summer as a Canadian Organization for Undergraduate Health Research (COUHR) trainee. Shreya will work with Binh on novel genomics approaches to functionally profile complex microbial communities.

On May 26, members of the lab joined Breast Cancer Canada's Megabike Day, where 29 riders take to the streets on a giant 30-foot bike to raise critical funds for breast cancer research and care. Funds raised locally support the Translational Breast Cancer Research Unit at Western — including our own work on systemic immunity in breast cancer.

On May 26, we welcomed Dr. Paula Gordon, breast radiologist and Clinical Professor of Radiology at UBC, as a virtual speaker for Oncology Grand Rounds. Her talk, Breast Cancer Update: The basics, early detection, and the important role of breast density, covered the modifiable and non-modifiable risks of breast cancer, the case for early detection, and what's available to women in Ontario.

Dr. Gordon was a pioneer in breast ultrasound and is widely recognized for her advocacy work that has changed how women with dense breasts are screened in the USA, Canada, the UK, and beyond. She volunteers as Medical Advisor to DenseBreastsCanada.ca and DenseBreast-Info.org, and is an Officer of the Order of Canada.

Many thanks to our patient partner for suggesting Dr. Gordon as a speaker; exactly the kind of bridge between research and lived experience we hope to build more of.

This year's Systems Biology workshop at McGill University's Bellairs Research Station in Holetown (Barbados) explored the fundamental organization and dynamics of biological systems across multiple scales. The invitees covered domains such as the gut microbiome and cancer tissues.

We discussed high-throughput systems level approaches including metabolic network modeling, high-resolution imaging and spatial/single-cell profiling.

A big thank you to the 2026 participants and co-organizers!

Kudos to Bushra and the team for spearheading the Canadian Cancer Society volunteering and community outreach!

Our group recently participated in the CIBC Run for the Cure and attended the CCS Choosing Hope Symposium (RIOT, Western University). RIOT offers a unique opportunity to bridge the gap between academia and individuals impacted by cancer. By engaging with patients and survivors, our team gains valuable insights into patient priorities and communication needs.

We are proud of Bushra and everyone who contributed to these important initiatives.

It has been a whirlwind year in the lab — so much so that regular updates have fallen by the wayside as our team grows and our projects multiply!

Noor Rizvi (MSc) led a comprehensive study on the mutational landscape of pure DCIS, now published in Breast Cancer Research. Mohamed Meawad (PhD) uncovered functional archetypes in the gut microbiome, now accepted in Microbiome.

Noor received both a TBCRU scholarship and an OGS before graduating in June 2025. Mohamed was awarded an OGS and has transferred into the PhD program.

Vanessa spoke at Memorial Sloan Kettering Cancer Center and delivered a plenary at CanFunNet.

Welcome to Bushra Kabbani and Yubing Xia (TBCRU award recipient), who will investigate immune responses to aggressive breast cancer subtypes.

Two new preprints this week! Big congratulations to first authors Eliseos J. Mucaki and Noor Rizvi, and collaborators Mike Hallett and Eileen Rakovitch.

First, we developed PREFFECT — novel generative modeling approaches to address the unique challenges of working with FFPE material (Mucaki et al., bioRxiv 2025).

Second, we characterized the DNA mutational landscape of DCIS, identifying specific mutated genes associated with early recurrence, particularly in the context of radiotherapy (Rizvi et al., medRxiv 2025).

Excited to share our latest work, now on bioRxiv! We used deep learning to uncover functional archetypes in the adult human gut microbiome, shedding light on interindividual variability, microbiome stability, and disease associations.

Analyzing 9,838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes: Archetype 1 enriched in sugar metabolism; Archetype 2 dominated by fatty acid metabolism; Archetype 3 defined by amino acid and nitrogen metabolism.

Functional archetypes emerged as potential confounders in disease-associated microbial signatures, including type-2 diabetes, colorectal cancer, and IBD.

Big congratulations to first author Mohamed Meawad and all co-authors!

This year's Systems Biology workshop at McGill University's Bellairs Research Station in Holetown (Barbados) brings together researchers to discuss challenges associated with the profiling and analyses of metagenomic microbial communities (bacterial, fungal and viral).

The invitees cover domains such as the microbiome of the human gut/oral/respiratory/urogenital in the context of health and disease; clinical metagenomics; fungal viruses; and single-cell bacterial/fungal profiling.

A big thank you to the 2025 participants!

We are thrilled to celebrate Ray's successful writing and defense of her MSc thesis titled "Functional Profiling of the Gut Microbiome from Bulk to Single-cell: A Pilot Study on Exercise-Induced Effects." Ray holds a special place in our lab as the first student to join us, paving the way for future research endeavors.

Having you in the lab has been a fantastic experience. The groundwork you have laid will serve as a robust foundation for Binh, future students, and the lab as a whole. Thank you for your dedication and congratulations on this significant achievement!

We extend our gratitude to the examiners, Drs. Veronica Guariglia Oropeza, Nathalie Berube, and Paul Walton, for their time and insightful contributions.

Vanessa gave a talk titled "From Genes to Microbes: Multidimensional Approaches for Predicting Breast Cancer Therapy Responses" as part of the Stanford Cancer Biology Seminar Series.

She also presented a flash talk at the Having IMPACTT 4: Advancing Microbiome Research Symposium. Mohamed and Ray attended the London Health Research Day, each presenting a poster.

We are grateful for NSERC support for our research on computational and genomic approaches for the characterization of host-adapted microbial communities.

Congratulations to Mohamed, who received an MSc Vector Scholarship in Artificial Intelligence. Ray received an ACB travel award to attend the Having IMPACTT 4 symposium.

Welcome to MITACS summer interns Karen Ribeiro (medical student from Brazil) and Rohan Sonthalia (computer science & engineering, India).

Congratulations to Ray (Qianrui Wang), Noor Rizvi, and Aybars Nazlica for their poster presentations at the Anatomy and Cell Biology Research Day.

Great job everyone! Looking forward to what this year brings!

October marks Breast Cancer Awareness Month. Every year, the Translational Breast Cancer Research Unit (TBCRU) actively participates in various activities, championing breast cancer research and raising essential funds.

This year holds special significance as it's Noor's first year as a team member. Every contribution will directly benefit the TBCRU Traineeship Program, helping nurture the next generation of research talents.

The 22nd Systems Biology workshop on Computational Paradigms in Molecular Biology Revisited at McGill University's Bellairs Research Station is coming up (February 2-9, 2024).

This meeting brings together researchers with expertise in generative modeling and deep learning across applications including structural biology, drug repositioning, generative models for single-cell analyses, metagenomics, and molecular imaging.

Many invitees are committed to the development of computational devices with clinical utility, raising important ethical and socioeconomic considerations.

April 2023 marks the first year of the Dumeaux Lab at Western.

Ray and Teddy advanced our microbial single-cell RNA profiling platform. Emily led successful analysis of initial DNA profiles from in-situ cancer tumors. Mohamed, Joshua Jackson, and Alice collaborated on their BIOCHEM-3383F project.

This summer: Mohamed received Western's DUROP Summer Research Award and we welcomed Akshay (MITACS Globalink). This fall: Dalwinder (post-doc), Aybars (PhD), and Noor (MSc) join us — congratulations to Aybars and Noor for the TBCRU fellowship.

We also launched the SysNeoBC study with our clinical collaborators at St Jo (Kalan Lynn, Dr. Brackstone, Dr. Parsyan).

The 21st Systems Biology workshop on Cells in Space at McGill University's Bellairs Research Station will bring together researchers interested in exploring cells in their context.

The invitees champion EXPERIMENTAL approaches to identify the physical location of cells based on sequencing or imaging methods, and COMPUTATIONAL models to analyze cellular information and predict location.

We are excited to extend discussions to how external factors and stressors, such as space travel, microgravity, microbiomes, infection processes, and tumor microenvironments, influence cellular expression and epigenetics programs.

Vanessa Dumeaux joins Western University as an Assistant Professor in the Department of Anatomy & Cell Biology at the Schulich School of Medicine & Dentistry.

She is also a Member of the Center for Translational Cancer Research and an Affiliate Assistant Professor in the Department of Oncology.

We are excited to build the Dumeaux Lab at Western and look forward to recruiting talented MSc and PhD students!

Embedded below: introduction-to-transcriptomics lecture slides.

Looking forward to speaking at the 7th Canadian Conference on Epigenetics on November 2–5, 2021 in Estérel, Québec. Hope to see you there in person, and otherwise on Zoom.

Code release for the analyses of matched microbiome–MRI data before and after an exercise intervention. See the microbiome2brain code repository on the software page.

Looking forward to hearing about all the fascinating links between the microbiome and human health at the Having IMPACTT microbiome symposium.

Check out our poster and connect to chat about the gut–brain axis.

Embedded below: introduction-to-deep-learning lecture slides.

My collaborators and I have a postdoctoral position open related to a project in cancer genomics and informatics, specifically breast ductal carcinoma in situ (DCIS).

The project is led by a multidisciplinary team comprising Prof. Michael Hallett (Concordia, Montreal), Dr. E. Rakovitch (Sunnybrook Hospital, Toronto), myself, and collaborators at OICR (Toronto), UBC (Vancouver), and MD Anderson (Texas). This is a CIHR-funded project involving the analysis of a large collection of DCIS tumor profiles toward specific clinical end-points.

We need someone with a solid background in statistics and data science, preferably with previous experience in genomics and bioinformatics. The position would be co-supervised by Prof. Hallett and myself; we are happy to work with you to provide sufficient grounding in the underlying biology and clinical aspects of the project.

• PhD in biostatistics, computational biology, data science, epidemiology, or related disciplines
• Expertise in manipulation, analysis, and visualization of high-throughput genomics data
• Programming experience in R and/or Python

Duration: 1 year (with potential for longer). Salary: $60K/year + benefits. Location: Canada (Montréal or remotely within the country).

All of our groups are extremely diverse and happy to assist you in getting settled both in life and in research. Please send a CV to vanessa.dumeaux@concordia.ca or michael.hallett@concordia.ca, describing your previous academic training, research experience, and other items you deem relevant to this position.

This year's Systems Biology workshop at McGill University's Bellairs Research Station in Holetown (Barbados) brings together researchers interested in the development of new model organisms.

The emergence of many new "non-model" model systems is at least in part due to recent advancements in gene editing technologies, cellular imaging, and single-cell genomics. The workshop also seeks to bring together investigators interested in advancing such techniques to better exploit the unique biological features of these organisms.

…and it was another fantastic year. Thanks to the 2020 participants!

Vicky presents at Concordia's Undergraduate Research Showcase. Thank you for the fantastic work this summer on the microbiome2brain project!

Vanessa is now an Affiliate Professor in the Biology Department at Concordia University. Looking forward to continuing fruitful collaborations with members of the Department and welcoming students to conduct interdisciplinary research in genomics and human health.

This study is being conducted by Vanessa Dumeaux, PhD at Concordia's PERFORM Centre, with approval from the Comité central d'éthique de la recherche du ministre de la Santé et des Services Sociaux.

This free event is complemented by three days of professional development activities and methodology workshops.

We are grateful to the PERFORM Centre for their support of our new microbiome2brain project, exploring changes in the gut microbiome and brain activity associated with an exercise training intervention. We would also like to congratulate Vicky Brunet, who was awarded an NSERC Undergraduate Student Research Award to work on this project.

We would also like to thank Concordia University for their support of our Team Startup grant that will build a high-resolution map of cancer immunity in HER2+ breast cancer patients.

This year's Systems Biology workshop at McGill University's Bellairs Research Station in Holetown (Barbados) brings together a broad group of researchers with expertise in developing single-cell genomics or massively parallel reporter assays, or computational approaches associated with these technologies.

Collectively, participants have experience in a variety of contexts — from exploring microbial and tumor microenvironments, to epigenetic and transcriptional regulation.

Great line-up of speakers at the IRIC 2018 Annual Symposium. See you there!

The 5th annual Canadian Conference on Epigenetics will be held in Estérel, Québec.

Congrats to Bjørn for the release of "Reproducible Data Analysis Pipelines for Precision Medicine" on bioRxiv. Code is available at github.com/uit-bdps/walrus.

Looking forward to attending the Systems Genetics of Cancer Workshop in Portland, Oregon, to discuss the latest research in cancer evolution and much more.