Neural 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
Liked 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)
https://www.nature.com/articles/s41586-021-04064-3
some focus on its main method
MR-MEGA
https://academic.oup.com/hmg/article/26/18/3639/3976569
https://www.nature.com/articles/nmeth.4627
interpretable deep learning model
Nice analysis integrating bulk & single-cell data, to get at inter-individual differences in the expression of genes in specific
cell types https://academic.OUP.com/bioinformaticsformatics/article/36/3/782/5545976
Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression
https://academic.oup.com/bioinformatics/article/36/3/782/5545976
TWAS of 229k women identifies new candidate susceptibility genes for breast cancer https://www.Nature.com/articles/s41588-018-0132-x Metascan approach. Derive model for imputing transcriptome from #GTEx & validate against TCGA. Application to BCAC.
Genome-wide prediction & functional characterization of the genetic basis of autism spectrum disorder, by @OlgaTroyanskaya lab
https://www.Nature.com/articles/nn.4353 Intersected candidate #ASD genes w/ #BrainSpan gene expression to find a pre-natal signal for the disease
Alternative evolutionary histories in the sequence space of an ancient protein https://www.Nature.com/articles/nature23902 Great viz of different potential but not necessarily realized evolutionary trajectories. Quite relevant for molecular #evolution & #pseudogenes
linkstream2 microblog 