Archive for the 'SciLit' Category
Mutation bias reflects natural selection in Arabidopsis thaliana | Nature
April 14, 2022https://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
Life’s Preference for Symmetry Is Like ‘A New Law of Nature’ – The New York Times
April 14, 2022Interesting paper. Nevertheless, natural designs are still less symmetric than engineered ones. (I think!) Any thoughts on why?
https://www.pnas.org/doi/10.1073/pnas.2113883119
Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution
https://www.nytimes.com/2022/03/24/science/symmetry-biology-evolution.html
Biologically informed deep neural network for prostate cancer discovery | Nature
April 12, 2022https://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 complete sequence of a human genome
April 10, 2022https://www.science.org/doi/10.1126/science.abj6987
Congratulations. Looking forward to mapping trillions of reads against CHM13!
Identification of cell types from single cell data using stable clustering | Scientific Reports
March 27, 2022Invitation: Group Presentation by TXL //=NEXT-in-list, LAB-ATTEND! – … @ Fri Jan 14, 2022 12pm – 1:30pm (EST) (all)
March 6, 2022Neural Distance Embeddings for Biological Sequences
Gabriele Corso, Rex Ying, Michal Pándy, Petar Veličković, Jure Leskovec, Pietro Liò
abs: https://arxiv.org/abs/2109.09740
github: https://github.com/gcorso/NeuroSE
https://arxiv.org/pdf/2109.09740.pdf
https://proceedings.neurips.cc/paper/2021/file/9a1de01f893e0d2551ecbb7ce4dc963e-Paper.pdf
Updated invitation: Group Presentation by SP //=NEXT-in-list, LAB-ATTEND! – g… @ Fri Feb 4, 2022 10:30am – 12pm (EST) (all)
March 1, 2022Liked the extensive scATAC-seq analysis. We discussed this in a journal club.
https://www.nature.com/articles/s41586-021-03209-8
Single-cell epigenomics reveals mechanisms of human cortical development
Ryan S. Ziffra, Chang N. Kim, Jayden M. Ross, Amy Wilfert, Tychele N. Turner, Maximilian Haeussler, Alex M. Casella, Pawel F. Przytycki, Kathleen C. Keough, David Shin, Derek Bogdanoff, Anat Kreimer, Katherine S. Pollard, Seth A. Ament, Evan E. Eichler, Nadav Ahituv & Tomasz J. Nowakowski
Nature volume 598, pages 205–213 (2021)
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