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Fiona Brinkman @fionabrinkman.bsky.social · Jul 11

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. :)

IMPACTT Microbiome @impactt-microbiome.bsky.social · Jul 11

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!

Having IMPACTT 5: Advancing Microbiome Research. Sept 22-24, 2025. Canmore, Canada.

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Fiona Brinkman @fionabrinkman.bsky.social · Jul 11

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.

IMPACTT Microbiome @impactt-microbiome.bsky.social · Jul 10

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...

Life Sciences British Columbia: In the News. 2025 Genome British Columbia Award for Scientific Excellence. Dr. Fiona Brinkman.

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Fiona Brinkman @fionabrinkman.bsky.social · Jun 6

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!

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Fiona Brinkman @fionabrinkman.bsky.social · May 31

@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.

thenancyli.bsky.social @thenancyli.bsky.social · May 20

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.

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Fiona Brinkman @fionabrinkman.bsky.social · May 31

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)

Ricardo D. Righetto @lifeonthewedge.bsky.social · May 31

Discovering cool science in the replies of the xkcd comic:

Fiona Brinkman @fionabrinkman.bsky.social · May 31

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.

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Fiona Brinkman @fionabrinkman.bsky.social · May 31

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.

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Fiona Brinkman @fionabrinkman.bsky.social · May 31

Basically: Bacterial virulence appears to be a complex arrangement, with phages evolving genes that facilitated infection of the eukayotic host of their bacterial host. Evolving to infect not just your host, but actually the-host-of-your-host is non-trivial. Likely not easily duplicated in archaea.

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Fiona Brinkman @fionabrinkman.bsky.social · May 31

Indeed, we found the lack of archaeal pathogens so fascinating, we wrote a paper on it! Mutually-exclusive phage/virus populations infecting Bacteria and Archaea, and association of "offensive" bacterial virulence factors with phage/mobile elements, may be key. pmc.ncbi.nlm.nih.gov/articles/PMC...

The proportional lack of archaeal pathogens: Do viruses/phages hold the key?

Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. We hypothesize that the scarcity of di...

pmc.ncbi.nlm.nih.gov

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Fiona Brinkman @fionabrinkman.bsky.social · Mar 13

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" 😊

People ask "who is the father of bioinformatics?" and google's response is Margaret Dayhoff.

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Fiona Brinkman @fionabrinkman.bsky.social · Mar 11

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?...

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Fiona Brinkman @fionabrinkman.bsky.social · Mar 11

Interesting. No alarm bells, but still Erin Gill @makemydna.bsky.social checked this saltation using her SMDP app eringill.shinyapps.io/covid_mutati... finding it most fits the mutation distribution of a chronic infection. Chronic infections are still a source of novelty (cc @sarperotto.bsky.social)

This BA.3 saltation best fits a chronic infection mutation distribution - approximately 10^6 times more likely than the global Omicron distribution in the SMDP app.

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Fiona Brinkman @fionabrinkman.bsky.social · Mar 2

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.

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

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 22

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

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 22

I appreciate how scary it can be for young parents to give their baby vaccines - they hear so much about reactions. But as vaccination rates go down its becoming more and more important to vaccinate to protect your child.

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 22

- Imagine, given this history of meningitis impacts, how meaningful it was when my kids got the H. influenzae vaccine in the 2000s. No meningitis.

Very grateful for the science that led to this vaccine. So many kids (including in our family) are enjoying their lives now with no meningitis impacts

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 22

- My aunt's age 2 death was meaningful since in the 60’s I had meningitis (bacterial, likely H. influenzae) at age 2 - but survived thanks to antibiotics

- BUT a colleague’s son in the 80’s had such meningitis. Due to growing antibiotic resistance they had treatment failure: became deaf in one ear

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 22

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)

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 9

I should clarify that I’m referring to microbial sequence data here! Human genome data is a whole other kettle of fish

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 9

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

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 9

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."

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 9

Indeed NCBI is getting hammered due to all the download requests (likely due to concerns about POTUS Exec Order data deletion potential). A reminder that the @ebi.embl.org www.ebi.ac.uk/ena/browser/... has a daily sync of data. It’s not exactly the same, so maintaining both resources is important.

ENA Browser

www.ebi.ac.uk

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Fiona Brinkman @fionabrinkman.bsky.social · Feb 2

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...

Pseudomonas Genome Database @pseudomonas.com · Feb 1

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

The Pseudomonas Genome Database - Genome annotation and comparative genome analysis

pseudomonas.com

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Fiona Brinkman @fionabrinkman.bsky.social · Dec 10

Also the cautionary note that I'll encourage them to handle Gram-positive with a membrane, like Mycobacteria, and avoid forcing predictions into "secreted" under certain scenarios. Forcing predictions, versus enabling a category of "unknown" can mislead and really drive down precision...

Fiona Brinkman @fionabrinkman.bsky.social · Dec 10

Thanks for this! I'm contacting the authors as we're funded to improve PSORTb (finally - with 3D data!) & perhaps we can collaborate! Am I going batty though, or did they compare against PSORTb gutted with no SCL-BLAST module?? Hardly a comparison? Note they force predictions. Will check it out...

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Fiona Brinkman @fionabrinkman.bsky.social · Dec 8

Love that you are noting this built environment impact on infectious disease spread (i.e. rats not crossing busy roads!) but I'm afraid the DOI link to your paper in this thread isn't working??

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