Finlay Maguire
Ast Prof CS+Epi at Dalhousie/Pathogenomics Bioinformatics Lead at Shared Hospital Lab (Sunnybrook): infectious disease genomic epidemiology (AMR/SC2/Zoonoses) & socially-focused collab data science (he/him)
- Reposted by Finlay MaguireDamien Joly, the chief executive officer of the Canadian Wildlife Health Cooperative, is warning a lack of funding for wildlife disease monitoring is undermining Canada’s ability to detect and respond to emerging threats to biodiversity, agriculture and human health. thenarwhal.ca/wildlife-dis...
- Come join my group as a postdoc on a fun wildepi.ca project looking at the evolution of endemic alpha- and betacoronaviruses in Canadian wildlife. Computational work will inform concurrent experimental work in the @banerjeelab.ca and @smubareka.bsky.social groups! bioinformatics.ca/jobs/postdoc...
- Reposted by Finlay MaguireOn Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
- Reposted by Finlay MaguireSix days. Six days with no news for students or locked out faculty, counsellors, and librarians. Six days with no news for other staff, community partners, or research collaborators at other univs. Six days of the senior admin doing nothing. 15 days since the admin was at the bargaining table.
- Reposted by Finlay MaguireI gave a symposium talk at the European Society for Evolutionary Biology 2025 (#eseb2025) meeting last week and this was my title slide showcasing how I was speaking as an independent scientist because @dalhousieu.bsky.social @dalhousie.bsky.social has locked us out.
- Reposted by Finlay MaguireHere’s where we stand: My union moved on salary and was willing to talk: Dal mgmnt was not interested My union offered to find ways to save money: Mgmnt said no. My union wanted to work together to build new child care: Mgmnt didn’t care. Let’s #KeepDalStrong, we said. No, they replied.
- Reposted by Finlay Maguire🚨Second study from the lab. @CellReports SARS-CoV- and SARS-CoV-2-like viruses are found in insectivorous bats, but the antiviral responses in these bats remain less studied. Here we show how bat cells respond to SARS-CoV-2 and shed light on virus entry. www.cell.com/cell-reports... #LZCI
- Reposted by Finlay MaguireWildEpi was well represented at the One Health - AMR and Zoonosis meeting in Calgary. Dr. Samira Mubareka and Dr. Finlay Maguire. @smubareka.bsky.social @finlaym.bsky.social
- Reposted by Finlay Maguire🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again! forms.gle/YJP6WQjsk8KK...
- Reposted by Finlay Maguire📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬 Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing. 1/14
- Day 2 of #pha4gecon: Sarah Hersey (Head of WHO IPSN) chairing resource limited infra for pathobioinf. First Joel Sevinsky, building on www.nature.com/articles/s41... Terra+theaigen wfs FISMA/FedRAMP compliant example. Cloud costs 1-2% of consumables. New Theaigen Global Health Initiative non-profit
- Kim Ng (SSI) on IT challenges scaling infrastructure and new MicrobeSeq initiative microbeseqen.ssi.dk/about-microb... federating regional and SSI HPC based on IRIDA, microreact, galaxy, nextflow, ansible, git, and PHA4GE/elixir standards/recommendations. Key message: don't reinvent the wheel!
- Abebe Negeri (Ethiopian Public Health Institute) new Pathogen Genomics Core Facility est. 2021, largely SC2 so far but plans for HIV, TB, polio, AMR, IPAC etc. Integration of multiple programs key for sustainability and making most of a core. Need for full time staff and well-defined career paths!
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View full threadFrancis Chikuse on Africa PGI mammoth priority pathogens prioritisation process. Process driven through 4 expert groups: Malaria, AMR (chaired by Iruka Okeke), foodborne diseases, vaccine preventable diseases. Priority AMR projects: Neonatal sepsis, invasive salmonella typhi, one health.
- A great sets of talks on QA to kick off #pha4gecon sessions: Josephina Campos (IPSN), Karen Osman (UKHSA), Constantina Laou (UKHSA@AfricaCDC), and Sarah Mwangi (AfricaCDC) about the challenges of external quality assurance programs for pathogen genomics at a national, regional, and global level.
- First up in Computational Tools for Pathogen Surveillance we have Jen Guthrie highlighting the undersampling and sequencing of non-tuberculosis mycobacterium, needs for genepi doi.org/10.1111/nyas... and a new abscessus workflow incorporating improved pangenome phylogenetics: github.com/waglecn/mabs
- Ilene Mizrachi (SRA head at NCBI) on the many excellent resources on NCBI e.g., datasets www.ncbi.nlm.nih.gov/datasets/, contamination screening suite, and >1.6m pathogen analyzed in NCBI pathogens with >1000 FDA regulatory actions, and NCBI virus (e.g., www.biorxiv.org/content/10.1... and VADR).
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View full threadVincent Rennie and Annelies van Rie on MAGMA Automated mapping of transmission hotspots, treatment recommendations, and phylogenetic cluster selection: www.medrxiv.org/content/10.1..., @oschwengers.bsky.social on Bakta's recent updates and gene name harmonisation efforts (github.com/oschwengers/...)
- Reposted by Finlay MaguireAlan Christoffels kicks off the first PHA4GE conference in beautiful Stellenbosch, with a wonderful opening keynote from Anita Ghansah #PHA4GEcon
- Reposted by Finlay Maguire"Past, Present, and Future of Software for Bayesian Inference" - An interesting overview of what, exactly, building software to do Bayesian inference means If you use Stan, JAGS, PyMC, NumPyro, etc, you might be interested. www.stat.columbia.edu/~gelman/rese...
- Reposted by Finlay MaguireMonitoring fruit bat colonies could provide early warning for Nipah outbreaks. www.nature.com/articles/d44...
- Reposted by Finlay MaguireFor @mblscience.bsky.social & other science recent arrivals, here is a much more comprehensive intro to Bsky doc by @markrubin.bsky.social that might be helpful: docs.google.com/document/d/1... And a running list of Science-Related Feeds on Bsky as they get created docs.google.com/spreadsheets...
