Posts Tagged ‘singlecell’

host-viral infection maps from sc-rna seq with a computational framework

June 2, 2020

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

https://www.sciencedirect.com/science/article/pii/S0092867420305687

host-viral infection maps from sc-rna seq with a computational framework

June 2, 2020

https://www.sciencedirect.com/science/article/pii/S0092867420305687

Single cell estimation from bulk data

April 12, 2020

Accurate estimation of cell composition in bulk expression through robust integration of single-cell information

Brandon Jew, Marcus Alvarez, Elior Rahmani, Zong Miao, Arthur Ko, Jae Hoon Sul, Kirsi H. Pietiläinen, Päivi Pajukanta, Eran Halperin doi:

https://doi.org/10.1101/669911

Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq

November 2, 2019

https://www.biorxiv.org/content/10.1101/762773v1

New cell type analysis in human cortex

October 26, 2019

Published: 21 August 2019

Conserved cell types with divergent features in human versus mouse cortex

Rebecca D. Hodge, Trygve E. Bakken, Jeremy A. Miller, Kimberly A. Smith, Eliza R. Barkan, Lucas T. Graybuck, Jennie L. Close, Brian Long, Nelson Johansen, Osnat Penn, Zizhen Yao, Jeroen Eggermont, Thomas Höllt, Boaz P. Levi, Soraya I. Shehata, Brian Aevermann, Allison Beller, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Charles Cobbs, Rachel Dalley, Nick Dee, Song-Lin Ding, Richard G. Ellenbogen, Olivia Fong, Emma Garren, Jeff Goldy, Ryder P. Gwinn, Daniel Hirschstein, C. Dirk Keene, Mohamed Keshk, Andrew L. Ko, Kanan Lathia, Ahmed Mahfouz, Zoe Maltzer, Medea McGraw, Thuc Nghi Nguyen, Julie Nyhus, Jeffrey G. Ojemann, Aaron Oldre, Sheana Parry, Shannon Reynolds, Christine Rimorin, Nadiya V. Shapovalova, Saroja
Somasundaram, Aaron Szafer, Elliot R. Thomsen, Michael Tieu, Gerald Quon, Richard H. Scheuermann, Rafael Yuste, Susan M. Sunkin, Boudewijn Lelieveldt, David Feng, Lydia Ng, Amy Bernard, Michael Hawrylycz, John W. Phillips, Bosiljka Tasic, Hongkui Zeng, Allan R. Jones, Christof Koch & Ed S. Lein

https://www.nature.com/articles/s41586-019-1506-7

Single Cell Resource for Mouse

August 2, 2019

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Tabula Muris is a compendium of single cell transcriptome data from the model organism Mus musculus, containing nearly 100,000 cells from 20 organs and tissues. The data allow for direct and controlled comparison of gene expression in cell types shared between tissues, such as immune cells from distinct anatomical locations. They also allow for a comparison of two distinct technical approaches: “}}

https://tabula-muris.ds.czbiohub.org/

Single-cell genomics of autism

May 18, 2019

https://science.sciencemag.org/content/364/6441/685

Human Cell Atlas Method Development Community timeline

April 6, 2019

https://www.protocols.io/groups/hca

UMAPs

March 2, 2019

A lineage-resolved molecular atlas of C elegans embryogenesis at #singlecell resolution, w/ @JIsaacMurray, @JunhyongKim, @ColeTrapnell & B Waterston https://www.BiorXiv.org/content/10.1101/565549v1 Compares the known cell lineage of the worm to trees based on UMAP cell-type clusters. Remarkable agreement

https://twitter.com/MarkGerstein/status/1101927645145645056

A single-cell molecular map of mouse gastrulation and early organogenesis | Nature

February 28, 2019

https://www.nature.com/articles/s41586-019-0933-9