Interview: Meet the Researcher Noor Rizvi

Thank you to our collaborators especially E. Rakovitch (Sunnybrook) and M. Hallett (Western) for their leadership on the Ontario DCIS Project.

We are grateful for the support from funding sources incl. CIHR, Breast Cancer Canada, and the Ontario Graduate Scholarship Program.

Special thanks to the patients, advocates, and donors — your contributions make this work possible. It truly takes a village!

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, 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 & Conferences 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. 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.

Mohamed and Ray recently attended the London Health Research Day, where they each presented a poster showcasing their latest research findings.

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.

Congratulations to Mohamed, who has been awarded an MSc Vector Scholarship in Artificial Intelligence. This prestigious scholarship recognizes his outstanding research contributions and potential in the field.

Ray received an ACB travel award to attend the Having IMPACTT 4: Advancing Microbiome Research Symposium in Canmore, Alberta. We are proud of her achievements and look forward to her continued success.

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.

Congratulations to Ray, Noor, and Aybars for their poster presentations introducing their research at the Anatomy and Cell Biology Research Day

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

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.

🍂 As the new semester starts, we are happy to welcome new talents to our team: Dalwinder (post-doc), Aybars (PhD), and Noor (MSc). 🌟 Further, congratulations to Aybars and Noor for securing the Translational Breast Cancer Research Unit fellowship, backed by Breast Cancer Canada.

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.

If you are interested in joining our research, please check our current training and career opportunities.</p>

Looking forward to speak at the 7th Canadian Conference on Epigenetics on Nov 2-5 2021 in Estérel, QC.

Early bird registration deadline is on Sep, 3. Visit the conference website for more info.

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:

microbiome2brain code repository

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!

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!

Vicky presents at Concordia’s Undergraduate Research Showcase. Thank you for the fantastic work done 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 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.

Program

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

Register Now for PCRC 2019

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.

See you there!

The 5th annual Canadian Conference on Epigenetics to be held in Estérel, Quebec.

Congrats to Bjorn for the release of Reproducible Data Analysis Pipelines for Precision Medicine. on biorxiv. Code 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.

This is my new academic website, based off Trevor Bedford’s, Sohrab Shah’s and Michael Hallett’s website template.