Geneticist turned Bioinformatician; Big Data Wrangler; Textbook Author; ICYMI: Views are my own RT are not endorsements
Joined December 2007
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Marc Perry @mdperry.bsky.social retweeted
1) Like every year, I am offering my course 'Emerging and re-emerging viral threats' at BOKU University (tinyurl.com/bdzmhc7b) and Medical University of Vienna (tinyurl.com/4de6bm93).
16.11. 10-13:00
20.11. 9-16:00
23.11. 12:30-14:30
24.11. 12:30-17:30
25.11. 12:30-17:30
Marc Perry @mdperry.bsky.social retweeted
I am reviewing 60 pages of hallucinated mostly math produced by Chat GPT 5.6 for a research project. It took me 4 hours of prompting to produced at most 2 pages of correct results. Should have typed the LaTex myself @alexpotato @greg_travis @sunstarsys
Marc Perry @mdperry.bsky.social retweeted
Large upload from Ontario yesterday, providing striking revelations about the evolution of PJ.2.1.
First, there is yet another hugely divergent branch of PJ.2.
This isn't one variant: it's four.
More & more, this resembles the emergence of BA.1/2/3. What is happening? 1/11
Marc Perry @mdperry.bsky.social retweeted
I wasn’t going to bring this up but my HS junior prom date just died at 46 of colon cancer. I don’t need well wishes. Send those to her family.
Another woman I know has been diagnosed with Hodgkin’s lymphoma.
Another with breast cancer.
Another with lung cancer
…Since the onset of the pandemic.
I know cancer happens. Trust me. I get it. I’ve worked with cancer survivors. There’s a cancer center in town. In different places I’ve been when the topic of cancer would come up sometimes people would say, “there’s something in the water.”
Anecdotes are anecdotes.
And trends are trends.
Some pathogens that cause or accelerate cancer are airborne.
And some you inhaled yesterday.
Lay off the SARS-CoV-2 folks. It’s the “something in the air” ending life a wee bit earlier than usual.
Study: More than 2 million new cancer cases caused by infections in 2024
A dozen infectious pathogens contribute to cancer. Finding ways to prevent them could help millions avoid a cancer diagnosis.
Read more: bit.ly/4rOiPYE
ALT Two women embrace. One wears a pink scarf on her head
Marc Perry @mdperry.bsky.social retweeted
Anthropic used really expensive software to find something humans had already hypothesized & still didn’t demonstrate anything biologically significant.
Love AI for bio but the gaps are experimental & they didn’t do the experiments to fill them. As usual, claims are premature.
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Marc Perry @mdperry.bsky.social retweeted
Every week I get a metagenomic readout of the most elevated viruses from wastewater collected the week before (44 sites).
COVID was on the list today for the first time since last winter, along with D68 and a bunch of rhinoviruses.
Marc Perry @mdperry.bsky.social retweeted
"It is foolish to think that you have to read all the books you buy... There are things in life that we need to always have plenty of supplies, even if we will only use a small portion."
I feel seen!
Umberto Eco, who owned 50,000 books, had this to say about home libraries:
“It is foolish to think that you have to read all the books you buy, as it is foolish to criticize those who buy more books than they will ever be able to read. It would be like saying that you should use all the cutlery or glasses or screwdrivers or drill bits you bought before buying new ones.
“There are things in life that we need to always have plenty of supplies, even if we will only use a small portion.
“If, for example, we consider books as medicine, we understand that it is good to have many at home rather than a few: when you want to feel better, then you go to the ‘medicine closet’ and choose a book. Not a random one, but the right book for that moment. That’s why you should always have a nutrition choice!
“Those who buy only one book, read only that one and then get rid of it. They simply apply the consumer mentality to books, that is, they consider them a consumer product, a good. Those who love books know that a book is anything but a commodity.”
Marc Perry @mdperry.bsky.social retweeted
As Fede Gueli points out, @SolidEvidence's wastewater variant dashboard makes it clear that PJ.2.1 is the fastest-growing lineage in the US. I've inserted arrows pointing to some of the PJ.2.1 mutations. The farther above the dotted diagonal line, the faster the growth. 1/6
Marc Perry @mdperry.bsky.social retweeted
I was on @CNN yesterday and told @OmarJimenez something that may still be a surprise to many people:
Bad actors will use AI tools to build dangerous biological weapons
It is already happening
This is not a risk. This is a certainty.
Marc Perry @mdperry.bsky.social retweeted
The Weekly Challenge - 391 #Perl #RakuLang
Task 1: Array Median
Task 2: Arrange Box
theweeklychallenge.org/blog/…
Marc Perry @mdperry.bsky.social retweeted
Sarcopenia, the age-related loss of muscle mass and strength, carries an increased risk of morbidity and mortality. It can, in part, be prevented by lifestyle factors, especially exercise. But there's no approved treatment. Here's a new optimistic review that this is about to change @NatRevDrugDisc
nature.com/articles/s41573-0…
Marc Perry @mdperry.bsky.social retweeted
Ok, since this will affect the address in my credit cards and bills can we think about the impact?
Marc Perry @mdperry.bsky.social retweeted
One interesting result here is that only 52 of 255 qualifying insertions ≥9 nucleotides match the viral genome (either Wuhan, BA.2, or BA.2.86), and the nucleotide composition of those genome-originating insertions are very different from the others.
1/8
If anyone's interested, the main results for my SARS-CoV-2 insertion analysis can be found here, along with the Julia code I wrote for the purpose.
Will do more analysis later, but will probably focus on something else for a while.
github.com/ryhisner/SARS2_in…
Marc Perry @mdperry.bsky.social retweeted
I'm giving a public outreach talk about the human cell atlas project in Toronto Oct.1 eventbrite.ca/e/inside-baseb…
Marc Perry @mdperry.bsky.social retweeted
Excited to share a public beta of Seurat 5.6, implementing major improvements for speed/memory/scalability of the core workflow, especially for large datasets.
Try it out! Installation instructions at: github.com/satijalab/seurat/…
Marc Perry @mdperry.bsky.social retweeted
On August 25, 1991, the Linux kernel was given to the world as a FOSS gift by a young Linus Torvalds. He is the real hero who released the Linux kernel 35 years ago for all of us, paired with GNU as userland tools, GCC C/C++, and more. The rest is history. Long live Linux!!!
Marc Perry @mdperry.bsky.social retweeted
I find it remarkable that this #tardigrade generates such gigantic oocytes relative to its body size & that they squeeze these eggs out of their bodies. Maybe like a #kiwi bird. @SocDevBio bit.ly/4bwQK0N
Marc Perry @mdperry.bsky.social retweeted
BA.3.2 is such a creeper. Here are the wastewater detections from roughly the last month. It's still mostly in the Northeast.
I hope this data source doesn't go away, but I'm afraid it probably will.
