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Finlay Maguire

@finlaym.bsky.social
1.6K followers 562 following 54 posts

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)

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Reposted by Finlay Maguire
The Narwhal @thenarwhal.ca · 15/01/2026
Damien 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...
thenarwhal.ca
Underfunding threatens Canada’s wildlife disease response | The Narwhal
As bird flu and chronic wasting disease spread, experts say Canada’s wildlife disease monitoring network needs more resources to respond
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Finlay Maguire @finlaym.bsky.social · 14/01/2026
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...
bioinformatics.ca
Postdoctoral Fellow in the Evolution of Wildlife-associated Coronaviridae - Bioinformatics.ca
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Nextstrain @nextstrain.org · 06/11/2025
On 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
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Finlay Maguire @finlaym.bsky.social · 14/09/2025
The associated slogan of "where infinite ambition meets global impact" being mostly evocative of futility ("where an unstoppable force meets an immovable object") also contributes to this feeling.
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Finlay Maguire @finlaym.bsky.social · 14/09/2025
Probably should have seen this coming when they expensively redesigned the logo to detach the head from the rest of the body.
New vs old Dalhousie logo
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Finlay Maguire @finlaym.bsky.social · 14/09/2025
The associated slogan of "where infinite ambition meets global impact" being mostly evocative of futility ("where an unstoppable force meets an immovable object") also contributes to this feeling.
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Finlay Maguire @finlaym.bsky.social · 14/09/2025
Probably should have seen this coming when they expensively redesigned the logo to detach the head from the rest of the body.
New vs old Dalhousie logo
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Finlay Maguire @finlaym.bsky.social · 29/08/2025
"My mantra is transparency, fairness and equity" nothing more transparent, fair, and equitable than unilaterally locking out faculty and refusing to negotiate.
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Reposted by Finlay Maguire
Dalhousie Lettuce @keepdalstrong.bsky.social · 26/08/2025
Six 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.
The Dal "Labour Relations" page indicating that the "latest news" and "latest updates" were all August 20 when they locked out DFA members.
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Finlay Maguire @finlaym.bsky.social · 26/08/2025
"The lockout comes after 83 per cent of DFA members voted to reject the school’s latest contract offer." - I think you'll find it actually came before CTV... Bit disappointed at the publicly non-partisan stance from the DSU president.
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Andrew Roger @andrewjroger.bsky.social · 25/08/2025
I 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.
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Jason Haslam @jasonhaslam.ca · 20/08/2025
Here’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.
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Finlay Maguire @finlaym.bsky.social · 01/04/2025
It may not be worth much right now but this campaign still holds true.
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Torsten Seemann @torstenseemann.bsky.social · 04/03/2025
🦘✂️ 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...
forms.gle
Snippy: Microbial Variant Calling Community Survey
Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...
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Reposted by Finlay Maguire
Pathoplexus @pathoplexus.org · 27/08/2024
📢 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
pathoplexus.org
Pathoplexus| Home
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
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Finlay Maguire @finlaym.bsky.social · 31/10/2023
Francis 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.
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Finlay Maguire @finlaym.bsky.social · 31/10/2023
Final talk in our harmonizing pathogen data collection from Zetty Jamaluddin (UKM) on hAMRonized (github.com/pha4ge/hAMRo...) AMRfinderplus analysis via Google Colab zenodo.org/record/6438173 with recent extensions for batch and microreact Viz. Used in Malaysia with global workshop participants!
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Finlay Maguire @finlaym.bsky.social · 31/10/2023
Patiyan Anderson (MDU-PHL) on AusPathoGen umbrella with data management and Viz via AusTrakka (www.cdgn.org.au/austrakka). Need to optimise data collection to inform surveillance. Core+pathogen specific data driven by end-goal analyses (aiding buy-in and actually having actionable data).
cdgn.org.au
AusTrakka — CDGN
The development of the AusTrakka platform was developed in response to key reports to the Office of Health Protection, Australian Government Department of Health, on public health genomics in Austra...
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Finlay Maguire @finlaym.bsky.social · 31/10/2023
Jillian Paull (Broad) on PHA4GE's wastewater contextual data specification. Making sure investment in WW capacity is not wasted by bad data. Machine readability, interoperability to other specs, reuse of terms from pubmed.ncbi.nlm.nih.gov/35169842/, & input from HIC/LMIC folks across disciplines.
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Finlay Maguire @finlaym.bsky.social · 31/10/2023
Bryan Wee (Roslin) on contextual data for Uganda One Health AMR digital-one-health.github.io w/ red, yellow, green tags for sensitivity and harmonisation of data from ag, env, & clinic. Multidisciplinary data meeting to inform metadata specification (w/ PHA4GE recs) before pilot E. coli seq project.
digital-one-health.github.io
DOH - Home
Digital One Health - University of Edinburgh.
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Finlay Maguire @finlaym.bsky.social · 31/10/2023
Gerald Mboowa (AfricaCDC): 10 genomics centers for excellence coming w/ ACEGID/SANBI/KRISP bioinf support. 2019-2023: only 7 countries with WGS to only 7 without. ONT&Ill diversify the risk of reagent access issues. Federated African Pathogen Data Sharing & Archive to try and solve data challenges.
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Finlay Maguire @finlaym.bsky.social · 31/10/2023
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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Finlay Maguire @finlaym.bsky.social · 31/10/2023
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!
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Finlay Maguire @finlaym.bsky.social · 31/10/2023
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
nature.com
Ten recommendations for supporting open pathogen genomic analysis in public health - Nature Medicine
To support progress in genomic epidemiology, a transparent, user-friendly approach is required.
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Finlay Maguire @finlaym.bsky.social · 30/10/2023
Vincent 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/...)
github.com
GitHub - oschwengers/bakta: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids - GitHub - oschwengers/bakta: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
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Finlay Maguire @finlaym.bsky.social · 30/10/2023
Lightning talks: Hiba Aribi on new RNA analysis tool github.com/omicscodeath.... Nouhaila En najih: SC2 phylotools comparison. Thibaut Cherif: Guinea's One Health AMR. Emma Griffiths: PHA4GE's data standard registry (includes incorporating non-PHA4GE data standards). Lam-Kwong: Hong Kong SC2 db
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Reposted by Finlay Maguire
Duncan MacCannell @drm.bsky.social · 30/10/2023
Alan Christoffels kicks off the first PHA4GE conference in beautiful Stellenbosch, with a wonderful opening keynote from Anita Ghansah #PHA4GEcon
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Finlay Maguire @finlaym.bsky.social · 30/10/2023
Katrina Kalantar (CZID) on their cloud metagenomics workflows characterising the taxonomy, AMR (w/ RGI), & consensus sequences (github.com/chanzuckerbe...). Takeaways: Inference of abundance and significance (v water control), RNA more sensitive than DNA, Sneathia as possible undernoticed pathogen.
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Finlay Maguire @finlaym.bsky.social · 30/10/2023
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).
ncbi.nlm.nih.gov
Datasets
Django project gdh-data-hub
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Finlay Maguire @finlaym.bsky.social · 30/10/2023
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
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Finlay Maguire @finlaym.bsky.social · 30/10/2023
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.
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Adam L @adam-lg.bsky.social · 25/09/2023
"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...
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Alisa Bokulich @alisabokulich.bsky.social · 25/09/2023
For @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...
docs.google.com
BlueSky for Scientists
BlueSky for Scientists Authors: Steve Haroz and Mark Rubin URL: http://blueskyscience.steveharoz.com Features you may miss from Twitter or Mastodon As BlueSky is in beta, some features are not implem...
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Finlay Maguire @finlaym.bsky.social · 15/09/2023
Now Jillian Paull (Broad) on the PHA4GE wastewater contextual metadata scheme: robust but flexible pathogen agnostic metadata collection for sequencing based wastewater surveillance with mapping to other standards (SRA, PHES-ODM, global WW surveillance project).
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Finlay Maguire @finlaym.bsky.social · 15/09/2023
Our daily dose of @pvanheus.bsky.social w/ an overview of wastewater sequencing infrastructure: use workflow langs, manage software deps (containers), standardise input (samplesheet). Data sharing and reporting are custom chaos (stovepipe problem) despite some consolidation on analysis wf/infra
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Finlay Maguire @finlaym.bsky.social · 15/09/2023
Onto Rozita Dara (Guelph) on human centric data & tech governance. Interoperability (legal, operationally, semantic, & technical) vital for agridata. Trust issues with farms so stakeholder engagement is vital in AIV initiatives. Automatic language analysis of data agreements to help transparency.
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Finlay Maguire @finlaym.bsky.social · 15/09/2023
Final #GMI13 day, Academic-Government Teams starts with Ben Howden (MDU) on the Australian Pathogen Genomics Program: need AusTrakka (used differently for research & PH surveillance), accreditation, multidisciplinarity, formal implementation/eval. Wins not always papers & change not always popular!
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Finlay Maguire @finlaym.bsky.social · 15/09/2023
Kristy Horan (MDU) on their ISO accreditation w/ AMR gene+Salmonella DST as example. Focus on entire process and key to credible actionable results. Very geno-pheno dependent, additional curation/wrapped AMRFinderPlus, modified repeat/repro lab model to bfx and explored limit of detection (>40x)
nature.com
An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance -...
The implementation of genomics for identification and surveillance of antimicrobial resistance (AMR) in clinical laboratories remains challenging. Here, Sherry et al. present a bioinformatics platform...
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Finlay Maguire @finlaym.bsky.social · 15/09/2023
Aitana Neves (ELIXIR/SIB) building on www.microbiologyresearch.org/content/jour... as an extension of ELIXIR-CONVERGE (elixir-europe.org/about-us/how...). Plans to develop Global Pathogen Data Network using standardised connected local data platforms a la ENA data hubs (under review with NIH)
microbiologyresearch.org
The Swiss Pathogen Surveillance Platform – towards a nation-wide One Health data exchange platform...
The Swiss Pathogen Surveillance Platform (SPSP) is a shared secure surveillance platform between human and veterinary medicine, to also include environmental and foodborne isolates. It enables rapid a...
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Finlay Maguire @finlaym.bsky.social · 14/09/2023
Errol Strain (FDA) update on ISO23418:2022 (WGS for Foodborne Bacteria): Avoiding serial wheel invention. Work making standard more specific, nuances of defining clonality, collecting protocols, bfx resources, & standard data sets. "Global consensus": long and painful but a worthwhile outcome!
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Finlay Maguire @finlaym.bsky.social · 14/09/2023
In "International Initiatives in Microbial Genomics Data Sharing and Standardization" we have Alan Christoffels stunt- @pvanheus.bsky.social giving an overview of numerous previous and in-current work from PHA4GE's 237 globally distributed members. Check out pha4ge.org & github.com/pha4ge !
pha4ge.org
PHA4GE - Genomic Epidemiology
PHA4GE is a global coalition actively working to establish consensus standards in Public Health Bioinformatics.
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Finlay Maguire @finlaym.bsky.social · 14/09/2023
Heather Carleton (CDC) on PulseNet International and the Global AMR Laboratory and Response Network www.cdc.gov/drugresistan.... PNI going since 2001 with >80 countries, recently published survey of WGS needs/barriers www.liebertpub.com/doi/full/10.... & seeking to revitalise PN Africa w/ Africa CDC
cdc.gov
About CDC’s Antibiotic Resistance Lab Networks
CDC’s Global AR Lab & Response Network fights #AntibioticResistance around the world.
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Finlay Maguire @finlaym.bsky.social · 14/09/2023
Ghassan Matar (AUB, Lebanon) on regional Salmonella surveillance www.liebertpub.com/doi/full/10...., Cholera outbreak w/ paired AST, and XDR A. baumanii sequencing built on regional and global collabs via PulseNet and Subregional WHO EMRO training.
liebertpub.com
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Finlay Maguire @finlaym.bsky.social · 14/09/2023
Joint LMIC/HIC Projects: Sima Tokajian (LAU, Lebanon) & Andrew Page (Theiagen & ex-Quadram) established genomic SC2 surveillance in Lebanon (bmcmedgenomics.biomedcentral.com/articles/10....) which helped track Alpha www.ncbi.nlm.nih.gov/pmc/articles... and characterise ORF3a mutations
bmcmedgenomics.biomedcentral.com
Genomic surveillance of SARS-CoV-2 in COVID-19 vaccinated healthcare workers in Lebanon - BMC Medica...
Background The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifi...
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Finlay Maguire @finlaym.bsky.social · 14/09/2023
Facilitating Ethical Microbial Data Sharing with Innovative Tools with Nicki Tiffin (SANBI): Be more effective and equitable w/ benefit sharing framework gh.bmj.com/content/7/2/..., PHA4GE Genomics Data Sharing Accord, Microbial Genomics License Builder (CC-esque license logos), & ADBEx MOU Builder.
gh.bmj.com
A framework for the promotion of ethical benefit sharing in health research
There is an increasing recognition of the importance of including benefit sharing in research programmes in order to ensure equitable and just distribution of the benefits arising from research. Whils...
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Finlay Maguire @finlaym.bsky.social · 14/09/2023
Asia/Asia-Pacific Surveillance round table: Orapan Sripichai (NIH Thailand), Yu-ping Hong (CDC Taiwan), Agnettah Olorosa (RITM Philippines), Mohd Ali (IMR Malaysia) & Angela Cornelius (IESR NZ). CDC, PulseNet, MDU driver feasibility studies and Terra.bio drove expanded capacity w/ training+resources
terra.bio
Home - Terra.Bio
Focus on your science. Access data, run analysis tools, and collaborate in Terra.Bio a scalable platform for biomedical research.
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Finlay Maguire @finlaym.bsky.social · 14/09/2023
Jillian Waruk (FNHS MB) - health is often science of measuring deficit. In MB during C19 pandemic: no FN data reported without express OK of FNHS and messaging was entirely FN. Resulted in community-based NPI within FNs. Ownership=power to control how evidence is presented and context is always key.
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