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 aims to gain valuable insights into patient priorities and communication needs—an experience that will inform and strengthen our future research and outreach.
We are proud of Bushra and everyone who contributed to these important initiatives
From left to right: Mohamed, Binh, Yubing and Bushra at CIBC Run For the Cure, London, Oct 2025
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! I am excited to finally share some of the highlights and celebrate the incredible work happening across our group.
Major Publications & Preprints
We are thrilled to announce that two major manuscripts from our lab have made it to preprint and publication this year!
Noor Rizvi (MSc) led a comprehensive study on the mutational landscape of pure ductal carcinoma in situ and its association with prognosis and treatment response. This work, first posted as a medRxiv preprint, is now published in Breast Cancer Research—a huge milestone for Noor and the team! Read the paper here.
Mohamed Meawad (PhD) spearheaded a deep learning project uncovering functional archetypes in the adult human gut microbiome, revealing new insights into interindividual variability and disease signals. This study, initially shared on bioRxiv, has now been accepted in Microbiome—congratulations, Mohamed! Check it out here.
If you’re curious for a quick overview, Vanessa recently presented a summary of these results at the Microbiome Virtual International Forum.
Our collaborative spirit continues to thrive, too. Together with Mike Hallett at Western and the Sunnybrook team, we contributed to a new manuscript on generative and integrative modeling for transcriptomics using FFPE material. This work strengthens our ongoing efforts to profile in-situ breast cancer tissues and identify biomarkers to guide treatment.
[Read the paper here.]https://lab-dumeaux.science/papers/preffect_biorxiv2025)
We are also truly excited for a brand-new partnership with talented MD/PhD student Shengjie Ying and the Anthony Nichols lab at LHSC. This collaboration has already resulted in two impactful publications in The Laryngoscope on transcriptomic predictors and treatment outcomes in idiopathic subglottic stenosis Check out the papers. Kudos to Shengjie and all collaborators for these important contributions!
Awards & Achievements
We are so proud of our trainees’ accomplishments:
Noor received both a TBCRU scholarship (Breast Cancer Canada) and an Ontario Graduate Scholarship (OGS) before graduating in June 2025. We wish her all the best in her next chapter!
Mohamed was also awarded an OGS-M and has officially transferred into our PhD program—excited to see where his research leads next.
Talks & Outreach
Vanessa was pleased to be invited to speak at Memorial Sloan Kettering Cancer Center in New York, sharing insights on tumor genomics and systemic immunity for personalized breast cancer management. Many thanks to Quaid Morris for the invitation and warm welcome!
She was also honored to deliver a plenary talk at CanFunNet (virtual), presenting on the characterization of transcriptional programs supporting drug tolerance in Candida albicans. This work highlights how heterogeneous transcriptional responses enable fungal survival under drug pressure, with implications for overcoming antifungal resistance.
Binh Tran (MSc) continues to break new ground in single-cell profiling of microbial communities. Early results are shedding light on the molecular programs supporting para-resistance in Candida albicans, in collaboration with Dr. Xie at Stanford.
We are also delighted to welcome two new MSc students this fall:
Yubing Xia, recipient of a TBCRU award
will investigate immune responses to aggressive breast cancer subtypes (HER2-positive and triple-negative) during treatment.
Looking Ahead: 24th Systems Biology Workshop
Our 24th Systems Biology Workshop is set for February 6–13, 2026. This year, we’ll bring together 40–50 researchers to explore the organization and dynamics of biological systems across scales—from cellular processes and tissue ecosystems with specific focus on:
Cellular and tissue ecosystem dynamics, including the tumor microenvironment
Complex networks across marine, terrestrial, microbial systems, and human disease
The workshop is unique in its cross-disciplinary focus, uniting molecular biologists, microbiome specialists, computational biologists, and environmental scientists. We cannot wait to see the new ideas and collaborations that will emerge!
Thank you all for making this such an exciting place to do science. Here’s to more discoveries, milestones, and shared successes in the months ahead!
First, we developed novel generative modeling approaches to address the unique challenges of working with FFPE material, enabling more reliable transcriptomic analyses from these challenging samples (Mucaki et al., bioRxiv 2025).
Second, we have 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).
We’ve used deep learning to uncover functional archetypes in the adult human gut #microbiome, shedding light on interindividual variability microbiome stability, and disease associations.
Check out the bluesky thread below for a deep dive into the results and please repost to spread the word!
Big congratulations to first author Mohamed Meawad and awesome milestone for the Dumeaux lab - congratulations to all co-authors!
This year 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 this year cover domains such as the microbiome of the human gut/oral/respiratory/urogenital in the context of health and disease; clinical metagenomics; of animals in relation to food production systems; the microbiome and diet; fungal viruses; approaches for identifying new microbes. The meeting will also discuss high-throughput systems level approaches for studying microbes including genetic screens, single-cell bacterial/fungal profiling, microfluidic sample handling, improved CRISPR/CasX modification toolkits, synthetic biology along with core biostatistical computational approaches including generative modeling in microscopy, sample decomposition and compositional data (CODA) analyses.
…and it’s been another fantastic year (though we missed our NIH and a few other US colleagues). 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! 🚀
Ray MSc defense, Summer 2024, London, ON
We extend our gratitude to the examiners, Drs. Veronica Guariglia Oropeza, Nathalie Berube, and Paul Walton, for their time, effort, and insightful contributions. A special thank you to Dr. Katherine Willmore for chairing the defense. We also appreciate the ongoing support from Drs. Patrick Lajoie, Silvia Penuela, Jeremy Burton, and Greg Gloor, in their roles as committee members over the years.
Presentations & ConferencesVanessa 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. It was a wonderful opportunity to engage with the talented graduate students and faculty there. Thank you again for the invitation!
She will also present a flash talk at the Having IMPACTT 4: Advancing Microbiome Research Symposium, discussing our research investigating the functionality of microbiomes with novel computational and single-cell profiling approaches.
Awards, Grants, and Scholarships
We are grateful for the support from the Natural Sciences and Engineering Research Council of Canada for funding our lab’s research on developing novel computational and genomic approaches for the characterization of host-adapted microbial communities.
Future Events
Don’t miss the upcoming Oncology Research & Education Day on Thursday, June 13. Co-chaired by Drs. Lohmann and Dumeaux, the event will feature over 100 posters, 8 trainee oral presentations, 5 faculty presentations, and a plenary talk by Dr. Charles Gawad from Stanford, who will present his research on “Dissecting Tissue Genomes at Single-Cell Resolution.” It promises to be an inspiring and informative day for all attendees.
Welcoming New Trainees
We are delighted to welcome two MITACS summer interns to our lab. Karen Ribeiro, a medical student from Brazil, and Rohan Sonthalia, a bachelor’s student in technology, computer science, and engineering from India, will be joining us for the summer. We look forward to their contributions and to supporting their development.
Happy October! As many of you are aware, October marks Breast Cancer Awareness Month. Every year, the Translational Breast Cancer Research Unit actively participates in various activities, championing the cause of breast cancer research and raising essential funds.
This year holds special significance for me as it’s my first year as a team member. If you’d like to back our mission and support my inaugural year with the team, please consider donating through this link. Every contribution will directly benefit the TBCRU Traineeship Program, helping nurture the next generation of research talents. Learn more about this year recipients’ research here
Thank you in advance for your generosity and participation!
The 22nd Systems Biology workshop on Computational Paradigms in Molecular Biology Revisited at McGill University’s Bellairs Research Station in Holetown (Barbados) is coming up.
The past decade has witnessed the rapid development of new computational techniques and paradigms in computational biology. These approaches emerged from the machine learning, probabilistic modeling, statistical inference and artificial intelligence communities and have been further refined within the context of a broad range of applications in molecular biology.
This meeting brings together researchers who have expertise with generative modeling and deep learning across a range of different applications including structural biology, drug repositioning and discovery, generative models for single cell analyses, metagenomics, and molecular imaging. Many of our invitees are also committed to the development of computational devices with clinical utility. Such endpoints also raise important ethical and socioeconomic considerations that also must be addressed for AI-related tools to be fully incorporated into modern molecular biology and clinical applications.
April 2023 marks the first year of the Dumeaux lab at Western.🎉
Ray and honor thesis student Teddy have made significant progress in advancing our microbial single-cell RNA profiling platform. Emily’s efforts led to the successful analysis of our initial DNA profiles from in-situ cancer tumors. We are also proud of our collaboration with 3rd-year Computational Biochemistry students — Mohamed, Joshua Jackson, and Alice — on their BIOCHEM-3383F project.
A sincere thank you to Eliseos John Mucaki for representing our research at the 2022 & 2023 London Oncology Research and Education Day.
🌞 This summer was exciting. Mohamed received Western’s DUROP Summer Research Award, and we were pleased to welcome Akshay, who was awarded the MITACS Globalink Internship Award.
Mohamed and Alice have continued their journey with us, focusing on their honor thesis, and we are excited to have Rishi from Microbiology and Immunology onboard. Rishi will continue Akshay’s work in developing our microbial single-cell platform, aiming to characterize the effect of acetate-based treatment on the microbiome (in collaboration with J Burton).
Lastly, our gratitude extends to The Cancer Research Society/CIHR-Institute of Cancer Research and Western’s Collaborative Research Seed Grant. Their support is instrumental to our ongoing research into systemic immune markers for high-risk breast cancer patients. We have also launched the SysNeoBC study with our clinical collaborators at St Jo (Kalan Lynn, Dr. Brackstone, Dr Parsyan). We are grateful for the support of Lakni, an undergraduate work-study student, and Evelyn and Arad, two undergraduate volunteers in the lab this year. Thank you!
The 21st Systems Biology workshop on Cells in Space at McGill University’s Bellairs Research Station in Holetown (Barbados) will bring together researchers interested in exploring cells in their context. Recent advances have reinforced the importance of understanding where cells are localized in tissues to further characterize their similarity and differences (cell types) and shed light on their interactions, communication and functionality.
The invitees collectively champion the development and/or application of EXPERIMENTAL approaches to identify the physical location of cells based on sequencing or imaging methods, and COMPUTATIONAL models to analyze cellular information and/or predict its location.
We are excited to extend discussions to how a wide variety of external factors and stressors, such as space travel, the exposure to microgravity and space radiation, the synergistic effect of microbiomes, infection processes, tumor microenvironments, etc., influence or alter cellular expression and epigenetics programs.
The lab is (re)opening in April 2022 at Western University, London, Ontario (Canada). As we embark in this new journey, we have several undergraduate, graduate and postgraduate positions available for individual interested in health data science and single-cell molecular technologies.
My collaborators and I have a posdoctoral position open related to a project in cancer genomics and informatics, specifically breast ductal in situ carcinoma (DCIS).
The project is led by a multidisciplinary team comprised of Prof Michael Hallett at Concordia (Montreal), Dr E Rakovitch at Sunnybrook Hospital (Toronto), myself and collaborators at the OICR (Toronto), UBC (Vancouver) and MD Anderson (Texas), providing an excellent training environment. This is a CIHR funded project and involves the analysis of a large collection of profiles of DCIS tumors towards specific clinical end-points.
We really need someone here who has a solid background in statistics and data science, preferably with previous experience in the genomics and bioinformatics arenas.
The position would be co-superivsed by Prof Hallett and myself. We are happy to work with you to provide a sufficient level of understanding with respect to the underlying biology and clinical aspects of the project.
Ideal candidates will have:
Ph.D. in biostatistics, computational biology, data science, epidemiology, or related disciplines
expertise in manipulation, analysis, and visualization of high-throughput genomics data
programming experience using R and/or Python.
Duration: 1 year (but with potential for longer)
Salary: 60K / year + benefits
Location: Canada (Montreal or remotely within the country)
All of our groups are extremely diverse and happy to assist you get settled both in life and research. Montreal has a very good standard of living, is culturally diverse and is an active research hub with four universitie and two research hospital systems. Canada has an excellent social system with affordable child care and parental leave. We are more than happy to accomodate any special needs or requirements including those related to covid-19. If there are any private or personnal issues that raise concerns about Canada, Montreal or our groups, we would be happy to direct you to related support groups or trained personnal for those issues.
Please send a CV to vanessa.dumeaux@concordia.ca or michael.hallett@concordia.ca.
Please ensure that you describe your previous academic training, research experience or other items you deem relevant to this position.
This year 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. Therefore, the workshop also seeks to bring investigators interested in the advancement of such techniques to better exploit the unique biological features of these organisms.
…and it was another fantastic year. Thanks to the 2020 participants!
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 of the Concordia’s PERFORM Centre and has approval from the Comité central d’éthique de la recherche du ministre de la Santé et des Services Sociaux.
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 a NSERC Undergraduate Student Research Award to work on this project.
Finally we would 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 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.
Looking forward to attending the Systems Genetics of Cancer Workshop in Portland, Oregon, to discuss the latest research in cancer evolution and much more.
