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Reposted by Tim Read

Robert Petit @rpetit3.bsky.social · 3d

Seems I'm not good at Bactopia v4 progress updates!

Since my last update:
- Nextflow v25+ compatible
- Converted to nf-test
- nf-bactopia plugin released

If you are interesting in testing (very much appreciated!), I now have a dev build available here: github.com/bactopia/bac...

Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia

Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...

github.com

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Tim Read @timothyread.bsky.social · 7d

This is the sort of routine task that you would hope LMMs could do for you but it always seems that they can't

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Graham Usher @bishopnorwich.bsky.social · 8d

This was a powerful speech by Pope Leo which built on Pope Francis’ teaching legacy.
He criticised those who “have chosen to deride the increasingly evident signs of climate change, to ridicule those who speak of global warming”.
It was a privilege to be in the room. www.bbc.co.uk/news/article...

Pope Leo hits out at critics of global warming

In his first major statement on climate change, the pontiff criticises those who minimise climate change.

www.bbc.co.uk

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Reposted by Tim Read

BK. Titanji @boghuma.bsky.social · 10d

It’s #MythBustingMonday.
Today’s myth: “Multiple vaccines at once will overload a child’s immune system.”
This idea is popular with anti-vaccine groups and also POTUS. But immunology, decades of research, and real-world data all say the same thing: it’s false. 🧵

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Adam Rutherford @adamrutherford.bsky.social · 15d

Phenomenal. In my 10 year update of A Brief History, I make the point that in the first edition, not one disease had been successfully treated using gene therapy. Today that number is at least 7.

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Tim Read @timothyread.bsky.social · 19d

Good luck with your new adventure!

Jodi Lindsay @jodi-lindsay.bsky.social · 19d

After nearly 27 years, this is my last week at St George’s Hospital Medical School/St George’s, University of London/City St George’s University of London. I’ve met and worked with many amazing colleagues, particularly during my time as Director of Cross Cutting Research Themes and ..

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Reposted by Tim Read

Dave Jones @cleanpowerdave.bsky.social · 22d

I had to triplecheck this because I didn't believe it...

All of the world's discovered reserves of fossil fuels = the same energy as just 5 days of sunlight hitting the Earth🤯

Solar power is basically unlimited🤷‍♂️

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Reposted by Tim Read

Kayla Stoy @kaylastoy.bsky.social · 29d

Proud of the work in this new preprint from my postdoctoral research.

We used experimental evolution of mutualistically cross-feeding yeast to test how generalized interactions alter benefit evolution and opportunities for coevolution.

www.biorxiv.org/content/10.1....

Partner fidelity and coevolution: Useful but not required for rapidly increased mutualistic benefits

Evolutionary theory predicts that specialization between mutualistic partners is beneficial, limiting conflict and increasing the opportunity to evolve cooperative benefits through sustained reciproca...

www.biorxiv.org

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Tim Read @timothyread.bsky.social · 29d

Delighted to see the first version of our new ELife paper. A collaboration with Levi Morran, we show how an intact antibiotic resistance gene (mecA) changes the course of S. aureus evolution on a new host. Kudos to Michelle Su and Kim Hoang for making this happen.

elifesciences.org/reviewed-pre...

Host and antibiotic jointly select for greater virulence in Staphylococcus aureus

elifesciences.org

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Reposted by Tim Read

Ghouly Hoye 🇨🇦 👻 @hollyhoye.bsky.social · Sep 8

“Well I don’t like that study because it doesn't give me the result I want’

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Tim Read @timothyread.bsky.social · Sep 7

People reacting to the news that BLAST now outputs CSV files?

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Reposted by Tim Read

Peter Gleick @petergleick.bsky.social · Sep 6

During the day yesterday in California, >75%of all electricity was produced by renewable #energy, including solar.
After the sun went down, half of all electricity STILL came from renewables, including wind batteries, hydro, geothermal, etc.

The graph from the California independent system operator showing the mix of electricity produced yesterday generated from imports, exports, wind, nuclear, fossil fuels and lots of solar and batteries.

Tweet from the Department of Energy saying wind and solar energy is essentially worthless when it's dark outside and the wind is not blowing. Basically showing the DOE doesn't understand energy.

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Reposted by Tim Read

Antonio Camargo @apcamargo.bsky.social · Sep 6

A BLAST update adding support for compressed files and csv output with headers is a Good Friday night surprise!

blast.ncbi.nlm.nih.gov/doc/blast-ne...

2025 BLAST NEWS — BlastNews 0.1.1 documentation

blast.ncbi.nlm.nih.gov

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Reposted by Tim Read

BK. Titanji @boghuma.bsky.social · Sep 5

In under 24h following the newly identified outbreak of #Ebola in the DRC, the virus has been isolated, sequenced and the virus sequence data made publicly available.
virological.org/t/the-16th-e...

The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host

Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

virological.org

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Reposted by Tim Read

Zamin Iqbal @zaminiqbal.bsky.social · Sep 4

Ok this is mad
"...an ant that lays individuals from two distinct species. In this life cycle, females must clone males of another species because they require their sperm to produce the worker caste"

www.nature.com/articles/s41...

One mother for two species via obligate cross-species cloning in ants - Nature

In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

www.nature.com

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Reposted by Tim Read

Giulio Ermanno Pibiri @jermp.bsky.social · Aug 28

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...

AllTheBacteria - all bacterial genomes assembled, available and searchable

The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...

www.biorxiv.org

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Reposted by Tim Read

Joseph D. Ortiz @earthsciinfo.bsky.social · Aug 30

The data shows that the future will be electric & renewable ... 🧪🔌💡☀️💨🌊🔋 The global energy transition is underway. And that is good for #Climate #Environment #PublicHealth #Economics interactive.carbonbrief.org/factcheck/so...

Factcheck: 16 misleading myths about solar

Carbon Brief factchecks 16 of the most common myths about solar power

interactive.carbonbrief.org

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Tim Read @timothyread.bsky.social · Aug 28

Fantastic news - congratulations!

UBC Science @science.ubc.ca · Aug 27

Congratulations to Dr. Kayla King who was awarded the 2025 Francis Crick Medal & Lecture by the Royal Society for contributions to the fields of evolutionary biology & genetics of infectious disease. @zoology.ubc.ca @ubcmicroimmuno.bsky.social @kayla-king.bsky.social @royalsociety.org bit.ly/4lGJrWB

Dr. Kayla King awarded Royal Society’s Francis Crick Medal

Evolutionary biologist Dr. Kayla King has been awarded the 2025 Francis Crick Medal and Lecture by the Royal Society of London for contributions to the fields of evolutionary biology and genetics of i...

bit.ly

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Reposted by Tim Read

Robert Petit @rpetit3.bsky.social · Aug 13

Bactopia update!

Bactopia is now compatible with @nextflow.io v25 syntax and the plugin (github.com/bactopia/nf-...) is converted to the latest structure. I'm hoping to have a development build soon.

If you're interested in testing please let me know here or at github.com/bactopia/bac...

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Reposted by Tim Read

Helen Branswell 🇨🇦 @helenbranswell.bsky.social · Aug 13

The "data" package Secretary Kennedy used to bolster his argument for discontinuing #BARDA funding for #mRNA research doesn't support his argument. @jakescottmd.bsky.social lays it out in a must read for @statnews.com. www.statnews.com/2025/08/13/r...

Kennedy's case against mRNA vaccines collapses under his own evidence

“This isn't scientific disagreement. It's either staggering incompetence or willful misrepresentation,” writes infectious disease physician Jake Scott.

www.statnews.com

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Richard Lenski @relenski.bsky.social · Aug 12

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.

telliamedrevisited.wordpress.com/2025/08/12/s...

STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.

STEPS To It

Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.

telliamedrevisited.wordpress.com

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Reposted by Tim Read

Robert Petit @rpetit3.bsky.social · Aug 6

Howdy! I'm currently writing up version 4 of Bactopia!

Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:

github.com/bactopia/bac...

Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia

Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...

github.com

6 12

Reposted by Tim Read

Audrey John MD PhD @odomjohnlab.bsky.social · Aug 5

To say that "the data show these vaccines fail" in regards to the mRNA plaform is unforgivable.

For those of you that don't remember - this is the data from a SINGLE dose. In December 2020. So good I cried in grateful tears.

Kaplan Meier curve showing efficacy of mRNA vaccine against COVID-19

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Reposted by Tim Read

Brent Toderian @brenttoderian.bsky.social · Jul 30

“Helsinki has not recorded a single traffic fatality in the past 12 months, city and police officials confirmed this week.”

City engineer credits lower speed limits and smart design.

I agree. #Helsinki #VisionZero

Helsinki goes a full year without a traffic death

A city traffic engineer credits the success to lower speed limits and smarter design.

yle.fi

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Saganism @sagan.bsky.social · Jul 29

Carl Sagan explains how the ancient Greeks knew the Earth was round and calculated its circumference over 2,000 years ago.

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