Fiona Brinkman
@fionabrinkman.bsky.social
Microbe-loving bioinformatics and genomics professor aiming to better control infectious diseases, and support health, in a sustainable way. Also a Mum.
I can’t recommend this IMPACTT microbiome research meeting enough, so note the July 15th abstract deadline. Fantastic meeting. Amazing location. @SydneyMorgan is also one of the best meeting organizers I know. Plus 19 prizes for students/postdocs for this meeting size is also pretty good odds. :)
Fun fact: #HavingIMPACTT2025 is taking place during larch season! Larch trees are a deciduous conifer, and in the fall the larches around Canmore will turn golden and make for some spectacular viewing. You won't want to forget your hiking boots for this #microbiome #conference!
July 11, 2025 at 4:45 AM
I can’t recommend this IMPACTT microbiome research meeting enough, so note the July 15th abstract deadline. Fantastic meeting. Amazing location. @SydneyMorgan is also one of the best meeting organizers I know. Plus 19 prizes for students/postdocs for this meeting size is also pretty good odds. :)
So humbly honoured to have this recognition. But as we all of know, it really does take a village. This is a tribute to many. It’s important we look wholistically at what enables research innovation.
I also invite you to think of all those who support you and be so grateful for them all - as I am.
I also invite you to think of all those who support you and be so grateful for them all - as I am.
Congratulations to our Platform 5 Co-Lead @fionabrinkman.bsky.social on receiving the 2025 @genomebc.bsky.social Award for Scientific Excellence from Life Sciences British Columbia! Learn more about Life Sciences BC and see all the awards and recipients here: lifesciencesbc.ca/lsbc-news/li...
July 11, 2025 at 4:42 AM
So humbly honoured to have this recognition. But as we all of know, it really does take a village. This is a tribute to many. It’s important we look wholistically at what enables research innovation.
I also invite you to think of all those who support you and be so grateful for them all - as I am.
I also invite you to think of all those who support you and be so grateful for them all - as I am.
In part by request, we are moving www.pseudomonas.com and other web-based resources back to being hosted in Canada. This distracts from moving forward with development/updates/research, but we're honouring user needs. Thank you @glwinsor.bsky.social and SFU Research Computing for tireless efforts!
June 6, 2025 at 7:46 AM
In part by request, we are moving www.pseudomonas.com and other web-based resources back to being hosted in Canada. This distracts from moving forward with development/updates/research, but we're honouring user needs. Thank you @glwinsor.bsky.social and SFU Research Computing for tireless efforts!
@reactome.org - a leading, carefully curated, human-focused biological pathway database - has made impressive changes. This includes to their new chat bot, with still a focus on quality (have to mention quality is still a focus if anything involving LLMs is noted 😊). Worth checking out.
Let's recap last weeks #ReactomeSAB 2025 (scientific advisory board) meeting!
This year, our international #Reactome team was hosted by the OICR in Toronto, where we had the opportunity to tell our external advisors about our work and gather feedback.
This year, our international #Reactome team was hosted by the OICR in Toronto, where we had the opportunity to tell our external advisors about our work and gather feedback.
May 31, 2025 at 5:15 PM
@reactome.org - a leading, carefully curated, human-focused biological pathway database - has made impressive changes. This includes to their new chat bot, with still a focus on quality (have to mention quality is still a focus if anything involving LLMs is noted 😊). Worth checking out.
What’s really cool is that thanks to @xkcd.com I’m now further thinking about how Exceptionally Weird phage-mediated bacterial virulence is, and how it evolved. Art stimulating science.
(With thanks to @makemydna.bsky.social for earlier chats and @iddux.bsky.social for encouraging this)
(With thanks to @makemydna.bsky.social for earlier chats and @iddux.bsky.social for encouraging this)
Discovering cool science in the replies of the xkcd comic:
Hmmm... Just realizing:
Eukaryotic viruses are normal. They evolved to infect their host.
Archaea are normal too.
It’s bacteria, and their phages, that are WEIRD - with phages and other mobile elements evolving genes that help infect the host of their host.
Eukaryotic viruses are normal. They evolved to infect their host.
Archaea are normal too.
It’s bacteria, and their phages, that are WEIRD - with phages and other mobile elements evolving genes that help infect the host of their host.
May 31, 2025 at 4:44 PM
What’s really cool is that thanks to @xkcd.com I’m now further thinking about how Exceptionally Weird phage-mediated bacterial virulence is, and how it evolved. Art stimulating science.
(With thanks to @makemydna.bsky.social for earlier chats and @iddux.bsky.social for encouraging this)
(With thanks to @makemydna.bsky.social for earlier chats and @iddux.bsky.social for encouraging this)
Great to see the inspiring Margaret Dayhoff getting profiled: www.nature.com/articles/s43...
I also smiled at her (appropriately) being google's response to the question asked by people "who is the father of bioinformatics" 😊
I also smiled at her (appropriately) being google's response to the question asked by people "who is the father of bioinformatics" 😊
March 13, 2025 at 3:32 AM
Great to see the inspiring Margaret Dayhoff getting profiled: www.nature.com/articles/s43...
I also smiled at her (appropriately) being google's response to the question asked by people "who is the father of bioinformatics" 😊
I also smiled at her (appropriately) being google's response to the question asked by people "who is the father of bioinformatics" 😊
Music streaming services like Spotify wonderfully have albums, but older album *sides* are lost. The sides were part of the experience. R.E.M. side names are so fun. Bauhaus "Press the eject and give me the tape out of it" line is the end of an album. Wiki documents sides (TY!). Could Spotify?...
March 11, 2025 at 6:54 AM
Music streaming services like Spotify wonderfully have albums, but older album *sides* are lost. The sides were part of the experience. R.E.M. side names are so fun. Bauhaus "Press the eject and give me the tape out of it" line is the end of an album. Wiki documents sides (TY!). Could Spotify?...
Re the #NIH downtimes (including #NCBI #genbank #pubmed etc) See tldr.nettime.org/@ww/11408997...
"Someone is doing networking... Badly..."
Really feel for all those dealing with this
(from NIH IT, to global users).
In general, the decimation of so much critical infrastructure is hard to fathom.
"Someone is doing networking... Badly..."
Really feel for all those dealing with this
(from NIH IT, to global users).
In general, the decimation of so much critical infrastructure is hard to fathom.
ww (@[email protected])
Attached: 2 images
So, three nameservers out of seven for the pubmed.ncbi.nlm.nih.gov are broken. If you try to look at the web site, you stand a 3/7 chance of encountering something that is broken.
...
tldr.nettime.org
March 2, 2025 at 10:03 AM
Re the #NIH downtimes (including #NCBI #genbank #pubmed etc) See tldr.nettime.org/@ww/11408997...
"Someone is doing networking... Badly..."
Really feel for all those dealing with this
(from NIH IT, to global users).
In general, the decimation of so much critical infrastructure is hard to fathom.
"Someone is doing networking... Badly..."
Really feel for all those dealing with this
(from NIH IT, to global users).
In general, the decimation of so much critical infrastructure is hard to fathom.
Re DNA sequence DBs: While sequence is shared across #INSDC databases #ENA #Genbank #DDBJ, the presentation and granularity of annotations/metadata can differ notably, with diff. benefits, impacting searches and downstream analyses. All INSDC databases must be maintained - annotations are important
February 22, 2025 at 9:00 PM
A brief thread of a personal illustration of the benefits of science, antibiotics, and vaccines over this past century:
- I discovered in my twenties that I had an aunt I didn’t know had existed. They had died young, in the 1930’s, of meningitis at age 2 (no antibiotics/vaccines at the time)
- I discovered in my twenties that I had an aunt I didn’t know had existed. They had died young, in the 1930’s, of meningitis at age 2 (no antibiotics/vaccines at the time)
February 22, 2025 at 8:26 PM
A brief thread of a personal illustration of the benefits of science, antibiotics, and vaccines over this past century:
- I discovered in my twenties that I had an aunt I didn’t know had existed. They had died young, in the 1930’s, of meningitis at age 2 (no antibiotics/vaccines at the time)
- I discovered in my twenties that I had an aunt I didn’t know had existed. They had died young, in the 1930’s, of meningitis at age 2 (no antibiotics/vaccines at the time)
Anyone know more re this “ #Starling removal ” to address a flu #H5N1 concern? Are they removing a whole flock? Culling migratory wild birds will have other impacts. I encourage tackling more the root of the problem, knowing it’s challenging (but I need more info) www.cidrap.umn.edu/avian-influe...
Avian flu strikes more Nevada dairy herds, leading to starling removal
www.cidrap.umn.edu
February 9, 2025 at 7:12 PM
Anyone know more re this “ #Starling removal ” to address a flu #H5N1 concern? Are they removing a whole flock? Culling migratory wild birds will have other impacts. I encourage tackling more the root of the problem, knowing it’s challenging (but I need more info) www.cidrap.umn.edu/avian-influe...
Funniest email I've received re @pseudomonas.com in over 20 yrs of hosting this DB:
"Hello There, Would you be open to get pseudomona com for 500 usd? I noticed that you're the owner of pseudomonas, the plural version, so I believe this could be of interest to you too."
"Hello There, Would you be open to get pseudomona com for 500 usd? I noticed that you're the owner of pseudomonas, the plural version, so I believe this could be of interest to you too."
February 9, 2025 at 6:46 PM
Funniest email I've received re @pseudomonas.com in over 20 yrs of hosting this DB:
"Hello There, Would you be open to get pseudomona com for 500 usd? I noticed that you're the owner of pseudomonas, the plural version, so I believe this could be of interest to you too."
"Hello There, Would you be open to get pseudomona com for 500 usd? I noticed that you're the owner of pseudomonas, the plural version, so I believe this could be of interest to you too."
Grateful for @glwinsor.bsky.social and his tireless efforts to maintain this Pseudomonas.com resource for this WHO priority pathogen for over two decades! We encourage any feedback - still accepting responses... bsky.app/profile/pseu...
Are you a #Pseudomonas researcher? Please take our survey and help shape the direction and priority of future pseudomonas.com database development: forms.gle/gTPT6ruf3mqb...
#microsky #idsky
#microsky #idsky
The Pseudomonas Genome Database - Genome annotation and comparative genome analysis
pseudomonas.com
February 2, 2025 at 9:01 PM
Grateful for @glwinsor.bsky.social and his tireless efforts to maintain this Pseudomonas.com resource for this WHO priority pathogen for over two decades! We encourage any feedback - still accepting responses... bsky.app/profile/pseu...
Check out this soap made by my fantastic #SFU colleague @minisciencegirl.bsky.social. She said she was not happy with her streak plating, 😂 but I think it’s awesome. #microsky #IDsky #microbiology #sciart
December 8, 2024 at 6:26 PM
Check out this soap made by my fantastic #SFU colleague @minisciencegirl.bsky.social. She said she was not happy with her streak plating, 😂 but I think it’s awesome. #microsky #IDsky #microbiology #sciart
I discovered this outhouse I walk by in the day on a trail near SFU has a motion-activated floodlight at night - even though the outhouse is always LOCKED at DUSK. Why??!
December 8, 2024 at 6:20 PM
I discovered this outhouse I walk by in the day on a trail near SFU has a motion-activated floodlight at night - even though the outhouse is always LOCKED at DUSK. Why??!
This is really niche, but @makemydna.bsky.social from our group made this wee app “SMDP: SARS-CoV-2 Mutation Distribution Profiler” tinyurl.com/smdpapp so #SARSCoV2 #variant #trackers can quickly check unusual #Lineages (mutation distributions likely due to mulnupiravir use, chronic infection etc?)
November 28, 2024 at 8:35 AM
This is really niche, but @makemydna.bsky.social from our group made this wee app “SMDP: SARS-CoV-2 Mutation Distribution Profiler” tinyurl.com/smdpapp so #SARSCoV2 #variant #trackers can quickly check unusual #Lineages (mutation distributions likely due to mulnupiravir use, chronic infection etc?)
Reposted by Fiona Brinkman
Eight years later, I revisit the tree of life. “Future trees may need to distinguish not only between cultured and uncultured lineages, but between extant and extinct”
rdcu.be/dPNpB
rdcu.be/dPNpB
The ever-changing tree of life
Nature Microbiology - The tree of life is a galvanizing image, anchoring biological diversity within a common framework. From a new view in 2016, the tree has continued to grow, and with it, our...
rdcu.be
August 2, 2024 at 8:40 PM
Eight years later, I revisit the tree of life. “Future trees may need to distinguish not only between cultured and uncultured lineages, but between extant and extinct”
rdcu.be/dPNpB
rdcu.be/dPNpB
Science is amazing - we are always learning.
Learned this week that some bacteria (Corynebacterium matruchotii) can divide into as many as 14 cells at once, and some wolves may aid pollination? There's so much we still don't know. tinyurl.com/3wtvp6xd tinyurl.com/5n74b353
Learned this week that some bacteria (Corynebacterium matruchotii) can divide into as many as 14 cells at once, and some wolves may aid pollination? There's so much we still don't know. tinyurl.com/3wtvp6xd tinyurl.com/5n74b353
November 24, 2024 at 11:37 PM
Science is amazing - we are always learning.
Learned this week that some bacteria (Corynebacterium matruchotii) can divide into as many as 14 cells at once, and some wolves may aid pollination? There's so much we still don't know. tinyurl.com/3wtvp6xd tinyurl.com/5n74b353
Learned this week that some bacteria (Corynebacterium matruchotii) can divide into as many as 14 cells at once, and some wolves may aid pollination? There's so much we still don't know. tinyurl.com/3wtvp6xd tinyurl.com/5n74b353
Love that this study of microbiome transmission and social interactions involves communities with low antimicrobial (antibiotic) use. Would be great to compare with communities more impacted by such drugs, to appreciate antibiotic impact.
bsky.app/profile/fbeg...
bsky.app/profile/fbeg...
Excited to share our last work on microbiome transmission and social interactions published on Nature!
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
Gut microbiome strain-sharing within isolated village social networks - Nature
An investigation into the relationship between network structure and gut microbiome composition among people living in 18 isolated Honduras villages reveals that strain-sharing can be mediated by...
www.nature.com
November 23, 2024 at 8:15 PM
Love that this study of microbiome transmission and social interactions involves communities with low antimicrobial (antibiotic) use. Would be great to compare with communities more impacted by such drugs, to appreciate antibiotic impact.
bsky.app/profile/fbeg...
bsky.app/profile/fbeg...
Reposted by Fiona Brinkman
I spoke to the CBC Radio about a large measles outbreak in New Brunswick - article link below. I cannot stress enough how serious an infection measles is - recycling an op-ed I wrote on the topic(see link on my webpage for explainer video).
www.cbc.ca/news/canada/...
www.bowdish.ca/lab/2024/03/...
www.cbc.ca/news/canada/...
www.bowdish.ca/lab/2024/03/...
November 22, 2024 at 9:44 PM
I spoke to the CBC Radio about a large measles outbreak in New Brunswick - article link below. I cannot stress enough how serious an infection measles is - recycling an op-ed I wrote on the topic(see link on my webpage for explainer video).
www.cbc.ca/news/canada/...
www.bowdish.ca/lab/2024/03/...
www.cbc.ca/news/canada/...
www.bowdish.ca/lab/2024/03/...
So when I messaged a lab member about the Dev version of one of our database resources, my device kept autocorrecting Dev to Dave. So we've decided just to call it Dave.
November 23, 2024 at 7:57 PM
So when I messaged a lab member about the Dev version of one of our database resources, my device kept autocorrecting Dev to Dave. So we've decided just to call it Dave.
California reporting a possible bird flu case in a child. Mild upper respiratory symptoms and "also positive for respiratory viruses." "No known contact with an infected animal", but "investigating a possible exposure to wild birds."
Family tested negative.
www.cdph.ca.gov/Programs/OPA...
Family tested negative.
www.cdph.ca.gov/Programs/OPA...
California Department of Public Health
www.cdph.ca.gov
November 20, 2024 at 5:36 AM
California reporting a possible bird flu case in a child. Mild upper respiratory symptoms and "also positive for respiratory viruses." "No known contact with an infected animal", but "investigating a possible exposure to wild birds."
Family tested negative.
www.cdph.ca.gov/Programs/OPA...
Family tested negative.
www.cdph.ca.gov/Programs/OPA...
At this key time, I encourage you to add your name to this letter campaign, affirming the critical importance of sustaining the world’s biodata resources.
globalbiodata.org/open-letter-...
globalbiodata.org/open-letter-...
OPEN LETTER CAMPAIGN - Global Biodata Coalition
Careers at the Global Biodata Coalition.
globalbiodata.org
November 19, 2024 at 7:19 AM
At this key time, I encourage you to add your name to this letter campaign, affirming the critical importance of sustaining the world’s biodata resources.
globalbiodata.org/open-letter-...
globalbiodata.org/open-letter-...
After the 1st ever report of #H5N1 in Hawaii last week (notable thanks to wastewater surveillance for initial detection), it turns out there’s an infected flock on Oahu. Hope this can get controlled, as Hawaiian wildlife were so beautifully protected before. health.hawaii.gov/docd/disease...
Avian Influenza | Disease Outbreak Control Division
health.hawaii.gov
November 18, 2024 at 2:07 AM
After the 1st ever report of #H5N1 in Hawaii last week (notable thanks to wastewater surveillance for initial detection), it turns out there’s an infected flock on Oahu. Hope this can get controlled, as Hawaiian wildlife were so beautifully protected before. health.hawaii.gov/docd/disease...
Flu note: These mutations showing up in this first-in-Canada Influenza H5N1 case in a teen are indeed not good news, and this is a great analysis, but note that to date there has been no evidence of onward transmission from this case to others. Still, monitoring is key. bsky.app/profile/scot...
The preliminary sequence from the H5N1 human case in British Columbia has been posted and it is not good news. The virus potentially has a quasispecies at HA residue 226 (H3 numbering). This is bad news because we know that mutations at residue 226 can increase binding to human receptors. 1/
November 17, 2024 at 4:13 AM
Flu note: These mutations showing up in this first-in-Canada Influenza H5N1 case in a teen are indeed not good news, and this is a great analysis, but note that to date there has been no evidence of onward transmission from this case to others. Still, monitoring is key. bsky.app/profile/scot...