A gene sequence-to-expression machine learning model achieves improved accuracy by incorporating information about potential long-range interactions.
Yang Young Lu and William Staford Noble
Archive for the 'SciLit' Category
A wider field of view to predict expression | Nature Methods
November 10, 2021The triumphs and limitations of computational methods for scRNA-seq | Nature Methods
November 10, 2021Liked this @KharchenkoLab review – in particular, the descriptions of the various low-dimensional approximations & the simple motivation for these using PCA. Also, found the step-by-step workflow in the text & figures helpful.
Note also the reference to expression entropy for determining the direction in trajectories.
Review Article
Published: 21 June 2021
The triumphs and limitations of computational methods for scRNA-seq
Peter V. Kharchenko
Nature Methods volume 18, pages723–732 (2021)
Anatomical structures, cell types and biomarkers of the Human Reference Atlas
November 10, 2021Anatomical structures, cell types and biomarkers of the Human Reference Atlas https://www.nature.com/articles/s41556-021-00788-6.pdf
cell type specific brain eQTL paper preprint
November 3, 2021UK Biobank 450k Whole Exome release coming soon on the Research Analysis Platform
November 2, 2021Article
Published: 18 October 2021
Exome sequencing and analysis of 454,787 UK Biobank participants
Joshua D. Backman, Alexander H. Li, Anthony Marcketta, Dylan Sun, Joelle Mbatchou, Michael D. Kessler, Christian Benner, Daren Liu, Adam E. Locke, Suganthi Balasubramanian, Ashish Yadav, Nilanjana Banerjee, Christopher Gillies, Amy Damask, Simon Liu, Xiaodong Bai, Alicia Hawes, Evan Maxwell, Lauren Gurski, Kyoko Watanabe, Jack A. Kosmicki, Veera Rajagopal, Jason Mighty, Regeneron Genetics Center, DiscovEHR, Marcus Jones, Lyndon Mitnaul, Eli Stahl, Giovanni Coppola, Eric Jorgenson, Lukas Habegger, William J. Salerno, Alan R. Shuldiner, Luca A. Lotta, John D. Overton, Michael N. Cantor, Jeffrey G. Reid, George Yancopoulos, Hyun M. Kang, Jonathan Marchini, Aris Baras, Gonçalo R. Abecasis & Manuel A. Ferreira -Show fewer authors
Nature (2021)
https://www.nature.com/articles/s41586-021-04103-z
seems to be an incredible data set – 450K exomes!
graph genome applied in Rice pan-genome
October 17, 2021Cell
2021 Jun 24;184(13):3542-3558.e16. doi: 10.1016/j.cell.2021.04.046. Epub 2021 May 28.
Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
https://www.sciencedirect.com/science/article/abs/pii/S009286742100581X
motif discovery on personal genomes
October 9, 2021Navigating the new era of assisted suicide and execution drugs | Journal of Law and the Biosciences | Oxford Academic
October 2, 2021https://academic.oup.com/jlb/article/4/2/424/4265564
QT:{{”
Meanwhile, the standard PAS protocol in the USA involves the prescription of a lethal dose of a barbiturate, typically
pentobarbital or secobarbital, to be consumed by the patient in liquid form. Often, the dose is mixed with juice, in what is often called a ‘potion’, to combat the bitter taste of the drugs. The patient is legally required to drink the potion by themselves, to ensure the decision remains autonomous. Physicians are free to prescribe, off-label, any drug they deem fit for these lethal purposes, under protection from prosecution. Only three lethal medications
(secobarbital, pentobarbital, and phenobarbital) have been used, according to state statistics, aside from anti-nausea and anti-anxiety medications to combat side effects.5 In the Netherlands and Belgium, physicians typically rely on sodium thiopental and pancuronium bromide when euthanizing patients at their behest.13
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Oral delivery of systemic monoclonal antibodies, peptides and small molecules using gastric auto-injectors | Nature Biotechnology
September 25, 2021https://www.nature.com/articles/s41587-021-01024-0
An easily swallowed capsule injects drugs straight into the gut https://www.nature.com/articles/d41586-021-02443-4
linkstream2 microblog 