• We congratulate Mac Reeves, Madelyn Wong, Jonathan Li and Kevin Fong for completion of their undergraduate theses.

• Congratulations to Vaibhav Gupta for successfully completing his Ph.D. qualifying exam.

• After a lot of hard work, we have managed to get the first of the data science servers up and running at Western. These servers are our work horse, offering significant CPU, GPU and storage for the life-science related data scientists at Western.

• With Eileen Rakovitch and her team at Sunnybrook we recently legally protected our approach for identifying breast DCIS patients who would not benefit radiation therapy, and we are continuing to expand our projects. In fact,we recently completed our first sample profiling with the Akoya PhenoCycler assay!

• We are continuing our collaborative work with Judy Berman’s lab, Lucy Xie and Rebecca Shapira related to Candida albicans.

• Our team remains highly focused on our combinatorial intervention sequencing (COIN-seq) assay with our first data and manuscripts to appear this year in 2024.

• Our Barbados 2024 - Computational Paradigms in Molecular Biology Revisited workshop was nice. The meeting had a great mix of laboratory and computational scientists of different types. Next year, our intended topic is along the lines of “the analysis challegnes of small but many organisms”, a phrase that is supposed to cover metagenomics of fungi, bacteria and viruses.

• We welcome Mac Reeves to our team. In the context of his undergraduate thesis, Mac is applying the Akoya spatial imaging system to DCIS samples.

• Madelyn Wong is also joining us for her undergraduate thesis. She is working with the Combinatorial Intervention (COIN)-seq team to explore regulators of early events in EMT in early breast carcinoma.

• Jonathan Li joins us from the Department of Computer Science and the Ivey School of Business. Jonathan is modifying the FCOS detection algorithm to enable it to better address issues related to microscopy of Candida albicans.

• Our manuscript that identifies and explores the phenotypic heterogeneity in Candida albicans fungal populations was accepted to eLife (in press)

• We developed new versions of Candescence to identify strains of Candida albicans that have differential survival capacity when grown with mouse macrophages. This collaboration with Leah Cowen’s lab at the University of Toronto was recently accepted to nBio.

• We received a CIHR project grant in the Spring 2023 competition with E. Rakovitch at Sunnybrook Hospital in Toronto. This grant will allow us to continue our effort to idenify signatures of DCIS patients who will or will not benefit from radiotherapy.

• Thanks to the CFI, a group of bio-data scientists at Western have received funding to build a substantial and secure computing infrastructure to drive our research.

• The next Bellairs Systems Biology meeting (February 2024) is focused on computational methods in biology.

– We welcome Vaibhav Gupta to the lab as a PhD candidate working on high-throughput perturbation techniques.

– The lab also welcomes undergraduate Maddy Trim (Honours thesis in Cancer Biology), Michael Tran (Medical Bioinformatics thesis), Remi Sampaleanu (Biochemistry Honours thesis), and Rajan Leung.

– Our 21st Systems Biology meeting at Bellairs is shaping up The topic this year is Cells in Space.

– I am excited to be teaching BIOCHEMISTRY/PATHOLOGY 4450A The genetic basis of human cancer this term.

– Our first Candescence manuscript appeared in Microbiology Spectrum!

– Some grants and papers submitted, some reviews back and some new papers to come soon.

– We welcome Thomas Qu to the lab as an MSc candidate working on high-throughput perturbation techniques.

– We also welcome summer research assistants Lauren Chalykoff and Eric Chalykoff who are assisting with breast cancer lab and informatics projects.

– A thank you to Eliseos John Mucaki for presenting our work at the the 2022 London Oncology Research and Education Day.

– Both Vanessa Dumeaux and I joined the Department of Oncology at Western, and the Centre for Translational Cancer Research.

– We have started organizing the 21st Systems Biology meeting at Bellairs. The topic this year is Cells in Space.

– I am excited to teach BIOCHEMISTRY/PATHOLOGY 4450A “The genetic basis of human cancer” this fall.

– Our first Candescence manuscript was accepted to Microbiology Spectrum! Appearing soon.

I started in April at the University of Western Ontario as the Western chair in Bioinformatics within the Department of Biochemistry. I’m happy to be here for many reasons, not the least of which is that my wife Vanessa Dumeaux finally found a position and can lead her own lab. Really though, she’s been doing that for the last decade - without funding and without a salary and mostly without students … with three kids … four if you count me.

In fact, the Schulich of Medicine and Denistry has hired quite a few Data Scientists in the past year. We each have specific expertise in different types of biology or diseases, different -omic technologies and different quantitative techniques. We all share the philosophy of modern data science: to maintain a sustained dialogue with large datasets by fluently exploiting computational and statistical tools as our primary means of exploring biological systems.

• Here is how I see things. You have bioinformatics which is largely about building databases, portals and information management systems. You have computational biology which is largely about building new types of analytic approaches for problems in the life sciences using computation and statistics. You have biostatistics which is about applying and developing statistical and modelling approaches to classify, predict and measure different types of events. Machine learning seeps into all aspects of this triumvariate.

• Data scientistists in the biomedical domain are people who apply and develop these tools to explore biological datasets - this whole “data to knowledge” thing. That’s very much different than being either a bioinformatician, computational biology or biostatistician per se. Data scientists need not only apply and develop these tools, but also look carefully at the output and combine that with their knowledge of biological systems to develop sound hypotheses and mature, physiologically relevant models.

• Several of us (Vanessa and I included) have both wet and dry components to our lab, making the environment truly inter-disciplinary and a great place for trainees to carry out their reearch. We also have some nice equipment (both computers and lab stuff)!

• There are many open positions at all levels.Here are the links to these groups that have different foci (see the Figure above).

– Tallulah Andrews, Biochemistry
– Christina Castellani, Pathology and Laboraty Medicine
– Vanessa Dumeaux, Anatomy & Cell Biology
– Greg Gloor, Biochemistry
– Jennifer Guthrie, Microbiology and Immunology
– Mike Hallett, Biochemistry
– Art Poon, Pathology and Laboratory Medicine
– Parisa Shooshtari, Pathology and Laboratory Medicine\

• We are preparing to open our lab at Western in April, 2022.

• There are several open positions.

• This includes MSc and PhD positions in both lab and computational projects.

• There are also postdoc and research assocate positions available primaril in the context of breast cancer.

• We are always open to undergraduates interested in rotations and/or summer internships.

Please see the lab and project descriptions as a first step. There is information for applying in join below.

• I haven’t updated the lab site in the past year. The pandemic flew by in a storm of pure, constant work it seems.Several things occurred.

• We are looking for a postdoc or research assistant for a breast cancer genomics/informatics project related to ductal carcinoma in situ. There is many opporunities to develop deep learning based approaches or for more traditional biostatistical analyses.

• The 2021 Bellairs workshop entitled Encoding and Decoding Function in the Genome was cancelled due to covid-19. We are picking up where we left off for the 2022 workhop here.

• Mike Hallett recently presented Candescence at the Candida and Candiasis 2021 meeting. A version of the talk can be found here

• The manuscript and deep learning software for Candescence was recently released.

• Aki Kiribakis successfully defended his MSc thesis. December.

• Vanessa Dumeaux and I accepted positions at Western University in London, Ontario.

• Our meeting this year includes approximately 50 researchers who each have a unique “non-model” model system, or are using well-established model systems in new ways. This year has a particularly broad range of topics including models for marine systems, cancer, development and evolution. Emerging Model Systems. January

• WTF? March

• In response to covid-19, several of my students and colleagues at Concordia Department of Biology prepared this primer into the literature of covid-19 for our students. Hopefully it assists you with exploring the disease. A primer into the covid-19 literature.

• As announced by Concordia, courses will remain in an on-line format this fall. In repsonse to these covid-19-related measures, we have optmized the deliver of our bioinformatics course for this format. You can read more about it here BIOL 480/510/630 Bioinformatics: Data Science for Biology. We have also modernized the structure the course to follow closer the excellent on-line resource R for Data Science In essence, we will work within the tidyverse to better advance students visualization and data analysis skills.

• It was a great pleasure to speak at the first Canadian Fungal Network meeting Twitter: @CanFunNet. A lot of great talks. Mike spoke about drug tolerance in Candida albicans. The talk is available here. Van spoke about a deep learning-based tool to recognize Candida albicans morphologies.

• Shawn Simpson successfully completed his MSc where he analyzed the microbiome of the Barbadian coral reef. The manuscript is currently available from the bioRxiv

• With Vincent Martin, Malcolm Whiteway and Agropur, we received funding from Genome Canada/Genome Quebec for a syntheic biology application entitled Bioprocess Development for Lactose Valorisation.

• Several members of the lab with Vanessa Dumeaux created a not-for-profit cooperative entitled SCIEL. The mandate of SCIEL is to bring deep learning-based single cell approaches to market.

• Samira Massahi successfully defended her MSc thesis.

• We’d like to congratulation our long-time collaborator and provider of deep insight, Vanessa Dumeaux, for receiving two start-up grants. Our lab is proud to be collaborating on a PERFORM project entitled microbe-2-brain that explores correlations between the gut microbiome, the systemic response, and brain patterns of over-weight individuals undergoing an exercise intervention.

• The second project is a Team Startup/Accelarator grant that will build a high-resolution map of cancer immunity in HER2+ breast cancer patients.

• We would also like to congratulate Vicky Brunet who recently was awarded an NSERC USRA. She will be joining our lab this summer to work on projects related to the human gut microbiome. April

• Lastly, we would like to congratulate Mathieu Harb, a new master’s student in our lab, who received a scholarship from the NSERC CREATE Synthetic Biology program for two years. April

• Esko Ukkonen visited Concordia and gave a seminar. April

• Congratulations to Sanny Khurdia for his successful application for a graduate scholarship at the PERFORM centre at Concordia. This will allow Sanny to explore single cell approaches in the context of the human gut microbiome, complementing a project led by our long time collaborator Vanessa Dumeaux. Thank you also to PERFORM and the work of the evaluation committee! May

• My application to Concordia for permission to search for a Tier II Canada Research Chair in Cellular Systems Design was successful. (This eventually led to the hiring of Elena Kuzmin in the Department of Biology.) May

• Our introduction to bioinformatics, biological data science and computational biology has been shifted from the winter to fall terms. It will start in September 2019. Course Web Page. June

• Opened our a very tiny wet-lab for (human tumor) sample preparation, droplet-isolation techniques and some DIY genomics.

• Mike gives a talk at the PERFORM centre Feb. 20.

• Tacos, sushi and the end of the world. An event to celebrate the end of BIOL 480 and the glory of our future AI over-lords. We watched Elon Musk’s documentary “Do you trust this computer?”. GE 100 at high noon. (April)

• Mike will be at the AACR Annual Meeting, Chicago (April, 15-17)

• Vanessa gives a talk at the CR-CHUM, Montreal (March, 14).

• Vanessa visits and gives a talk at Radboud University Medical Center Tumor Immunology, Nijmegen, April 19.

• Mike will teach a revamped Bioinformatics course in Winter 2018.

• Vanessa participates in the Systems Genetics of Cancer workshop, Portland (Jun 11-13)

• Mike attended the IRIC Symposium on Machine Learning Biological Systems. A nice two day even organized by Sebastien Lemieux, Sylvie Mader , Mike Tyers, Lea Harrington and Brian Wilhelm. Many nice talks about how ML is being used in clincal and basic research settings.

• Mike attended RECOMB Comparative Genomics is an annual meeting that brings together algorithmic oriented researchers interested in comparative genomics, genome evolution and related areas. October.

• With David Walsh (Concordia), we are organizing The Reef Microbiome workshop in Barbados, Jan 26-Feb 2 of 2019.

• Vanessa presents a poster and short talk at the 10th Annual Canadian Cancer Immunotherapy Consortium, Montreal, Dec, 13-15

• Mike participates in BIRS-CMO Workshop on Challenges and Synergies in the Analysis of Large-Scale Population-Based Biomedical Data, Oaxaca, Mexico, Nov 26 - Dec 1.

• Vanessa attends Rendez-vous Genome Quebec, Montreal, Dec,5

• Vanessa starts her new position at the PERFORM Center Nov 2017.

• Vanessa presents a poster at Cell Symposium on Human Immunity, Banff, Oct 22

• Vanessa attends the 4th Annual PERFORM Centre Research Conference, May 19

• Mike gives a talk at the Department of Biochemistry, Concordia University.

• Sadiq Saleh successfully completed his Ph.D. defense.

• Vanessa visits Genomic Health, Redwood City, CA, Feb 20-22.

• Our workshop organized with T. Sorlie (Norway) Cancer and the Immune System, Barbados, Jan 20-27

• Moved to Concordia Loyola in the Dept. of Biology

• Vanessa gives a talk at the Molecular Interception of Disease Symposium, Qatar, Nov 5-6

• Bjorn Fjukstad, UiT the Arctic University of Norway, visits the lab, Aug 01 - Feb 01

• Summer students: Jason Da Silva Castanheira, Kaylee Novack, Elizabeth Levitis

• Shawn Beaulieu, Msc student, starts in the lab, May 01

• Ilaria Kolobova, Caroline Labelle, and Karla Felix Navarro visit the lab, Jan-May

• Sadiq Saleh presents his senior seminar at McGill, March 2

• Mike gives a talk at the University of Toronto, Feb 25

• Vanessa gives a talk at the Genetic Networks workshop, Barbados, Jan 25

• Mike gives a talk at Concordia University, Jan 5

• Organize with B. Andrews (UoT) Genetic Networks workshop Barbados, Jan 22-29

• Mike gives a talk at the Canadian Cancer Research Conference, Montreal, Nov 8-10

• Vanessa presents a poster at the Canadian Cancer Research Conference, Montreal, Nov 10

• Sadiq Saleh presents a poster at the Canadian Cancer Research Conference, Montreal, Nov 9

• Vanessa participates in workshop on Systems Genetics of Cancer, Cambridge, Sep 20-23

• Vanessa visits MAP5 Paris, Sep 17-20

• Eric defends his PhD thesis, Montreal, June 30

• Systems Biology Symposium: Personalized medicine of Cancer, Montreal, May 28

• Bjorn Fjukstad UiT the Arctic University of Norway, visits the lab, Feb 17 -March 2