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
Archive for the 'SciLit' Category
UMAPs
March 2, 2019A single-cell molecular map of mouse gastrulation and early organogenesis | Nature
February 28, 2019The single-cell transcriptional landscape of mammalian organogenesis
February 28, 2019Using single-cell combinatorial indexing, we profiled the
transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment.
Small research teams ‘disrupt’ science more radically than large ones
February 28, 2019QT:[[”
“The authors describe and validate a citation-based index of ‘disruptiveness’ that has previously been proposed for patents6. The intuition behind the index is straightforward: when the papers that cite a given article also reference a substantial proportion of that article’s references, then the article can be seen as consolidating its scientific domain. When the converse is true — that is, when future citations to the article do not also acknowledge the article’s own intellectual forebears — the article can be seen as disrupting its domain.
The disruptiveness index reflects a characteristic of the article’s underlying content that is clearly distinguishable from impact as conventionally captured by overall citation counts. For instance, the index finds that papers that directly contribute to Nobel prizes tend to exhibit high levels of disruptiveness, whereas, at the other extreme, review articles tend to consolidate their fields.”
“]]
bioarxiv paper on Golden State Killer
February 2, 2019The effects of death and post-mortem cold ischemia on human tissue transcriptomes | Nature Communications
February 2, 2019Changes in gene activity may one day reveal…time of death
https://www.ScienceMag.org/news/2018/02/changes-gene-activity-may-one-day-reveal-time-death-crime-victims Discusses paper by @RodericGuigo (“Effects of death & post-mortem cold ischemia on….#transcriptomes,”
https://www.Nature.com/articles/s41467-017-02772-x). Obvious forensic interest but maybe a #privacy angle as well
Changes in gene activity may one day reveal the time of death for crime victims
Artificial intelligence turns brain activity into speech
January 23, 2019Human genome-wide measurement of drug-responsive regulatory activity | Nature Communications
January 23, 2019https://www.nature.com/articles/s41467-018-07607-x
Whole-genome STARR-seq
Human genome-wide measurement of drug-responsive regulatory activity Graham D. Johnson, Alejandro Barrera, Ian C. McDowell, Anthony M. D’Ippolito, William H. Majoros, Christopher M. Vockley, Xingyan Wang, Andrew S. Allen & Timothy E. Reddy
Nature Communications volume 9, Article number: 5317 (2018)
Accurate classification of BRCA1 variants with saturation genome editing. – PubMed – NCBI
January 23, 2019https://www.ncbi.nlm.nih.gov/pubmed/30209399
Nature. 2018 Oct;562(7726):217-222. doi: 10.1038/s41586-018-0461-z. Epub 2018 Sep 12.
Accurate classification of BRCA1 variants with saturation genome editing. Findlay GM1, Daza RM1, Martin B1, Zhang MD1, Leith AP1, Gasperini M1, Janizek JD1, Huang X1, Starita LM2,3, Shendure J4,5,6.
linkstream2 microblog 