Posts Tagged ‘jclub’

Invitation: Group Presentation by TXL //=NEXT-in-list, LAB-ATTEND! – … @ Fri Jan 14, 2022 12pm – 1:30pm (EST) (all)

March 6, 2022

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

Updated invitation: Group Presentation by SP //=NEXT-in-list, LAB-ATTEND! – g… @ Fri Feb 4, 2022 10:30am – 12pm (EST) (all)

March 1, 2022

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)

The power of genetic diversity in genome-wide association studies of lipids | Nature

January 10, 2022

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

Using deep learning to model the hierarchical structure and function of a cell | Nature Methods

September 18, 2021

https://www.nature.com/articles/nmeth.4627

interpretable deep learning model

Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression | Bioinformatics | Oxford Academic

May 3, 2021

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

ADORA1 Gene – GeneCards | AA1R Protein | AA1R Antibody

October 12, 2019

https://www.genecards.org/cgi-bin/carddisp.pl?gene=ADORA1

Journal Club by JG

July 27, 2018

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 and functional characterization of the genetic basis of autism spectrum disorder | Nature Neuroscience

July 27, 2018

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

Today: Jason Moore, Computational Biology and Bioinformatics speaker, 6-6-18 in BML Auditorium at 4 pm

June 7, 2018

https://linkstream2.gerstein.info/tag/talk20180606/
https://twitter.com/MarkGerstein/status/1004566413036617728

Papers for Journal Club

June 7, 2018

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