https://www.nature.com/articles/s41586-021-04269-6
https://twitter.com/MarkGerstein/status/1510065060806283269
Interesting paper, relating de novo mutation rate to epigenetic features. Wonder exactly how this connects to the fact that the background mutation rate in cancer genomes depends strongly on epigenetics.
Important genomic regions mutate less often than do other regions https://www.nature.com/articles/d41586-022-00017-6
https://www.nature.com/articles/s41586-021-03922-4
https://twitter.com/SEHanlon/status/1513548800949989377
At #AACR22, @VanAllenLab gives a nice overview of his paper using an interpretable NN model to get insights into determining cancer severity (https://nature.com/articles/s41586-021-03922-4)
Biologically informed deep neural network for prostate cancer discovery
Liked the way he hard-coded specific genes & pathways into the model & looked in detail where the model misclassified specific patients #AACR22 #AACR2022
Also, thought the hard-coding of genes into the model was similar to that in another interpretable AI approach (for brain disease, https://science.org/doi/10.1126/science.aat8464) Could have used the “rank projection trees” from this to highlight important genes #AACR22 #AACR2022
the Kuramoto model of synchronization that could explain tissue level behavior from individual cells. Here is a nice YouTube video that explain this type of physical behavior with the Cornell professor in dynamic systems and chaos Steven Strogatz:
This Price Surge Really Hits New Yorkers Hard – The New York Times
https://www.nytimes.com/2022/03/07/nyregion/new-york-price-surge.html
https://www.theweek.co.uk/news/world-news/russia/955813/why-world-leaders-refuse-give-russia-dna
Thought this story was intriguing in relation to genomic #privacy & how the pandemic has potentially amplified worries about it. It was presaged by an opinion piece we did a decade ago
(https://USAToday.com/story/opinion/tory/opinion/2013/06/27/dov-greenbaum-and-mark-gerstein-on-nsa-and-genetics/2465589)
Valved N95 that I like to wear with a surgical mask on top
https://us.vwr.com/stibo/low_res/std.lang.all/67/42/9356742.jpg
https://www.dropbox.com/s/nxcex66wgw7goo7/VWR-mask-with-valve.product-89201-510.9356742.jpg?dl=0
Shown at
https://us.vwr.com/store/product/4788523/vwr-n95-disposable-respirators but not currently available
Published: 05 January 2022
Decoding gene regulation in the fly brain
Jasper Janssens, Sara Aibar, Ibrahim Ihsan Taskiran, Joy N. Ismail, Alicia Estacio Gomez, Gabriel Aughey, Katina I. Spanier, Florian V. De Rop, Carmen Bravo González-Blas, Marc Dionne, Krista Grimes, Xiao Jiang Quan, Dafni Papasokrati, Gert Hulselmans, Samira Makhzami, Maxime De Waegeneer, Valerie Christiaens, Tony Southall & Stein Aerts Nature (2022)
Nature paper today on Fly brain GRNs, https://doi.org/10.1038/s41586-021-04262-z
Some integrative analyses might be useful…
linkstream2 microblog 
