Finlay Maguire
@finlaym.bsky.social
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 Maguire
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
November 6, 2025 at 9:46 PM
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
Reposted by Finlay Maguire
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.
September 14, 2025 at 2:05 PM
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.
Reposted by Finlay Maguire
Probably should have seen this coming when they expensively redesigned the logo to detach the head from the rest of the body.
September 14, 2025 at 1:37 PM
Probably should have seen this coming when they expensively redesigned the logo to detach the head from the rest of the body.
Reposted by Finlay Maguire
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.
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.
August 26, 2025 at 2:02 PM
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.
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 Maguire
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.
August 25, 2025 at 12:09 PM
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.
Reposted by Finlay Maguire
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.
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.
August 20, 2025 at 12:13 AM
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.
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
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
Early innate immune response and evolution of a SARS-CoV-2 furin cleavage site inactive variant in bat cells
Baid et al. show that insectivorous E. fuscus bat cells have evolved an advantageous
early innate immune response to SARS-CoV-2 infection relative to human cells. Additionally,
they extend molecular e...
www.cell.com
July 2, 2025 at 4:06 AM
🚨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
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 Maguire
WildEpi 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
@smubareka.bsky.social @finlaym.bsky.social
March 14, 2025 at 3:33 PM
WildEpi 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
@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...
forms.gle/YJP6WQjsk8KK...
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...
forms.gle
March 4, 2025 at 9:04 AM
🦘✂️ 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/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
Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing.
1/14
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.
Pathoplexus.org
August 27, 2024 at 3:45 PM
📢 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
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
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.
www.nature.com
October 31, 2023 at 7:34 AM
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
Reposted by Finlay Maguire
Alan Christoffels kicks off the first PHA4GE conference in beautiful Stellenbosch, with a wonderful opening keynote from Anita Ghansah #PHA4GEcon
October 30, 2023 at 8:02 AM
Alan Christoffels kicks off the first PHA4GE conference in beautiful Stellenbosch, with a wonderful opening keynote from Anita Ghansah #PHA4GEcon
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.
October 30, 2023 at 11:30 AM
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.
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...
If you use Stan, JAGS, PyMC, NumPyro, etc, you might be interested.
www.stat.columbia.edu/~gelman/rese...
September 25, 2023 at 3:01 AM
"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...
If you use Stan, JAGS, PyMC, NumPyro, etc, you might be interested.
www.stat.columbia.edu/~gelman/rese...
Reposted by Finlay Maguire
Monitoring fruit bat colonies could provide early warning for Nipah outbreaks.
www.nature.com/articles/d44...
www.nature.com/articles/d44...
Monitoring fruit bat colonies could provide early warning for Nipah outbreaks
Seed collectors routinely handle bat-eaten fruits and nuts making them potential pathways for spillover of the virus Seed collectors routinely handle bat-eaten fruits and nuts making them potential pa...
www.nature.com
September 25, 2023 at 2:52 PM
Monitoring fruit bat colonies could provide early warning for Nipah outbreaks.
www.nature.com/articles/d44...
www.nature.com/articles/d44...
Reposted by Finlay Maguire
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/document/d/1...
And a running list of Science-Related Feeds on Bsky as they get created
docs.google.com/spreadsheets...
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...
docs.google.com
September 25, 2023 at 1:54 PM
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/document/d/1...
And a running list of Science-Related Feeds on Bsky as they get created
docs.google.com/spreadsheets...
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!
September 15, 2023 at 4:32 PM
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!
Day 2 #GMI13 starts with Indigenous Data Governance Principles and Data Sharing Experiences. Taylor Morriseau (FNHS MB) explains centrality of OCAP principles (fnigc.ca/ocap-training/), specific FN benefits+principles (not pan-indigenous), free+prior informed consent. Emphasises Inclusion != Equity
The First Nations Principles of OCAP® - The First Nations Information Governance Centre
fnigc.ca
September 14, 2023 at 4:40 PM
Day 2 #GMI13 starts with Indigenous Data Governance Principles and Data Sharing Experiences. Taylor Morriseau (FNHS MB) explains centrality of OCAP principles (fnigc.ca/ocap-training/), specific FN benefits+principles (not pan-indigenous), free+prior informed consent. Emphasises Inclusion != Equity
Conference organiser Emma Griffiths kicking us off with a great introduction to the purpose of #GMI13 and the (still) open and growing challenges in global microbial genomics data sharing and harmonisation.
September 13, 2023 at 4:23 PM
Conference organiser Emma Griffiths kicking us off with a great introduction to the purpose of #GMI13 and the (still) open and growing challenges in global microbial genomics data sharing and harmonisation.
Woke up from a dream this morning: I was taking a statistics exam on a moving bus and it was proctored by a colleague dancing while wearing VR goggles.
First day of the academic year is going well.
First day of the academic year is going well.
September 5, 2023 at 7:25 PM
Woke up from a dream this morning: I was taking a statistics exam on a moving bus and it was proctored by a colleague dancing while wearing VR goggles.
First day of the academic year is going well.
First day of the academic year is going well.