Maor Knafo

GitHub - maorkn/CRISPR_HUNTER: scripts for genric crispr desgin scripts for genric crispr desgin. Contribute to maorkn/CRISPR_HUNTER development by creating an account on GitHub.

This is the pipeline I've built and use to find crispr targets on weird organisms, if anyone is looking for one:
github.com/maorkn/CRISP...

Memories all the way down. — Maor Knafo - System Biology Could memories be an emergent cellular property ? The 60s were a weird time, and no one was weirder than a group of scientists studying the transfer of memories via cannibalism in flatworms. Flatworm...

The 60s were a weird time, and no one was weirder than a group of scientists studying the transfer of memories via cannibalism in flatworms.

A new blog post in praise of cellular learning!

www.maorknafo.com/reducible-be...

Laplace and All His Demons. — Maor Knafo - System Biology The evening deepened. The games were played, the food was eaten, and the events moved along their planned course, drawn by invisible threads, traveling along hewn tracks. Noah rubbed his eyes sleepil...

Wrote a short story
www.maorknafo.com/reducible-be...

This is an image that has haunted me since I was a child because it captures something truly inherent to the human experience. We can get used to anything. A new blog post about habituation—it's been a while, needed to get un-used to a few things. maorknafo.com/reducible-beau…🧪

Waddington's landscape contamination in the lab today!
🍄📷🧪

As always, my unbelievably talented partner
@ShiraHoland
had the punishing job of integrating all of this information into the beautiful figures you see here. Hope you like it! biorxiv.org/content/10.1... 13/13
🧪🍄

This paper has been a long time coming and required a lot of thought and work by everyone in the
@ZivReichLab, especially @rutikapon.bsky.social @reinatnevo
@SRezenman
and Ivgeni Tsigalnitski. 12/13

Stress seldom encountered does not require such a network and its costly upkeep, so strategies such as #bethedging are sufficient and could be refined upon recurring exposures. 11/13

We think then that #creativity in response or stress-induced variability could arise when cells have a robust, redundant network of responses, allowing multiple adaptive avenues to be explored and explored. 10/13

Our hypothetical model of what is going on is quite counterintuitive. NaCl, as it is a very exotic stress, has a minimal proteomic response attributed to it, while pH is an integral part of the yeast way of life. 9/13

A similar picture was conveyed. pH stress, which elicits a high proteomic response, also has high diversity after the onset of stress. In contrast, NaCl stress has minimal variability in proteomic response and maintains the same level of diversity under stress. 8/13

We wanted to probe this phenomenon deeper, so we utilized our #gUMIBEAR barcoding and tracking method to see the population's lineage dynamics at high temporal resolution. 7/13

We saw something quite striking. Not all stresses are the same. For the same morality level, #ShannonEntropy behaved differently, indicating that some stresses, not others, induced the population variability. 6/13

But rather multimodal distributions, exemplifying what we think are multi-state phenotypes. We used #ShannonEntropy to portray these populations accurately and plotted them against the stress in various insult levels. 5/13

Once we had multiple stresses measured on our newly constructed library, we noticed something interesting. Distributions were not what you would expect from noisy populations when stress was administered, 4/13

Stress is not a binomial phenomenon, i.e., it's not only an on-or-off thing but a much more nuanced experience. Testing multiple levels of each perturbation, ranging from mild to lethal, allows us to describe the relationship between the magnitude of stress and variability. 3/13

Many works have described the function of #noise and its relationship to #stress, but we wanted to quantify this relationship in a way that has yet to be widely measured. This required many levels of stressful perturbations. 2/13

A new #preprint! Variability is strange, right? Especially when it arises in the background of an identical genetic background. Why would cells, having the same machinery, regulation, and environment, behave differently? Why would there be #noise? 1/13 rb.gy/45y36m

Right???

Terrarium going a bit crazy these past weeks. Constantly changing. 🍄📷

ganoderma sp fungi growing on a dead tree stump.

ganoderma sp.? 🧪🍄📷
"What an organism feeds upon is negative entropy. Or, to put it less paradoxically, the essential thing in metabolism is that the organism succeeds in freeing itself from all the entropy it cannot help producing while alive"

Erwin Schrödinger, What is Life?

Guys, guys, am I just seeing things or is this a budding yeast cell???
Great song BTW 🧪🍄

It's about how a cell (yeast), when faced with an unresolved stress, can utilize something similar to reinforcement learning to repurpose old, redundant functions for new stress-alleviating ones. ☺️

Mine is kinda long... But beautiful.

Starting to look like autumn (finally). False parasol? 🧪🍄

The Art of Destruction (and the destruction of art). — Maor Knafo - System Biology One night in 2001, William Basinski sat on the rooftop of his apartment building in New York. I can only assume he was pretty tired. He had spent the whole night working on a project and was resting...

The Art of Destruction (and the destruction of art).
www.maorknafo.com/reducible-be...

This village has a secret that almost everybody knows. — Maor Knafo - System Biology And suddenly, the sound of a horn. The horn hadn't been in years. Maybe ever, but everyone intuitively knew its purpose. They were to stop whatever they were doing and march to the village center to...

This village has a secret that almost everybody knows.
www.maorknafo.com/reducible-be...

🧪🧪New blog post!
How (and why) do organisms optimize tasks, and why are they flat about it? The use of Mutual Information in Pareto fronts and slimy aliens.🌌👾📊
maorknafo.com/reducible-beau…
In the comments, I'll link to the previous posts, which I think are helpful (and cool😆).

I sometimes think about hiding an Amazon gift card in there just to see if someone, anyone, reads them for real.

Still new to this :-) #microbiome